@article {pmid39845798, year = {2024}, author = {He, G and Man, J and Chen, Y and Zhang, X and Wang, X and An, K and Amu, L and Chen, W and Wang, B and Shi, Y and Wang, X and Wei, S}, title = {Identification of Salvia miltiorrhiza germplasm resources based on metabolomics and DNA barcoding.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1518906}, pmid = {39845798}, issn = {1663-9812}, abstract = {INTRODUCTION: Salvia miltiorrhiza radix et rhizoma (Danshen) is a crucial medicinal material for treating cardiovascular and cerebrovascular diseases. However, the presence of adulterants and intraspecific variability poses challenges to its clinical safety.<br><br>METHODS: This study collected samples of S. miltiorrhiza from various regions and commonly encountered adulterants. The composition differences of S. miltiorrhiza radix and its adulterants were analyzed by fingerprint and broad-target metabolomics. Chloroplast genome was used to distinguish intra-genus species and DNA barcoding was used to identify germplasm sources.<br><br>RESULTS: The fingerprinting analysis proved that there is no chemical composition consistency between S. miltiorrhiza radix and its adulterants. Broad-targeted metabolomics can distinguish S. miltiorrhiza radix from Salvia yunnanensis radix, Dipsacus asperoides radix, and Arctium lappa radix. Additionally, comparative chloroplast genome analysis indicated that atpF and rps4-trnT-UGU were the potential DNA barcodes for S. miltiorrhiza. 259 samples from 13 provinces and 21 origins were amplified and sequenced, resulting in the identification of 62 haplotypes. The unique haplotypes found in Shanxi Luoyang, Shandong Qingdao and other places can be used as molecular geographic markers for the identification of the germplasm source of S. miltiorrhiza.<br><br>DISCUSSION: This study systematically differentiates S. miltiorrhiza from its adulterants and highlights the potential of unique haplotypes as markers for sourcing. The findings provide strong scientific evidence for the clinical safety of S. miltiorrhiza, emphasizing the importance of proper cultivation, selection, and breeding of varieties.}, }
@article {pmid39845644, year = {2025}, author = {Yu, Z and Qi, Y and Wei, Y and Zhuang, G and Li, Y and Wang, B and Akbar, S and Xu, Y and Hua, X and Xu, Q and Deng, Z and Zhang, J and Huang, Y and Yu, F and Zhou, J}, title = {A cost-effective oligo-based barcode system for chromosome identification in longan and lychee.}, journal = {Horticulture research}, volume = {12}, number = {1}, pages = {uhae278}, pmid = {39845644}, issn = {2662-6810}, abstract = {Oligonucleotide (Oligo)-based fluorescence in situ hybridization (FISH) represents a highly effective methodology for identifying plant chromosomes. Longan is a commercially significant fruit species, yet lacking basic chromosomal markers has hindered its cytogenetic research. In this study, we developed a cost-effective oligo-based system for distinguishing chromosomes of longan (Dimocarpus longan Lour., 2n = 2x = 30). For this system, each synthesized oligo contained two chromosome-specific sequences that spanned a distance of over 200 kb, and a PCR-based flexible amplification method coupled with nested primers was used for probe labeling. The use of these oligo-based barcodes enabled the marking of 36 chromosomal regions, which allowed for the unambiguous distinction of all 15 chromosomes in both longan and lychee (Litchi chinensis Sonn., 2n = 2x = 30) species. Based on the identification of individual chromosomes, we constructed karyotypes and detected genome assembly errors involving the 35S ribosomal RNA gene (35S rDNA) in longan and lychee. Developing oligo-based barcodes offers considerable promise for advancing cytogenetic research in longan, lychee, and their related species. Furthermore, this cost-effective synthesis system can be referred to the development of new oligo libraries among other species.}, }
@article {pmid39845497, year = {2025}, author = {Lee, DJ and Kim, J and Euo, SS and Lee, JS and Lee, H and Roh, SJ}, title = {A new species of the genus Oiketicoides Heylaerts, 1885 (Lepidoptera, Psychidae) from Korea with its natural parasitoid enemy.}, journal = {ZooKeys}, volume = {1223}, number = {}, pages = {311-317}, pmid = {39845497}, issn = {1313-2989}, abstract = {Oiketicoidesgohadoensis Roh &amp; Lee, sp. nov. is described as new to science. The morphology of male adult, including genitalia, is described, and DNA barcodes for precise identification of the species are provided. A parasitoid, Neophryxepsychidis Townsend, 1916 (Diptera, Tachinidae) of O.gohadoensis is also reported for the first time in Korea, together with its DNA barcode sequence.}, }
@article {pmid39843438, year = {2025}, author = {Lin, C and Liu, C and Chen, L and Cheng, H and Ashfaq, M and Hebert, PDN and Gao, Y}, title = {Data on insect biodiversity in a Chinese potato agroecosystem from DNA metabarcoding.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {131}, pmid = {39843438}, issn = {2052-4463}, support = {59-0212-9-001-F//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; }, mesh = {*DNA Barcoding, Taxonomic ; Animals ; *Biodiversity ; *Solanum tuberosum/genetics ; *Insecta/classification/genetics ; China ; East Asian People ; }, abstract = {Potato (Solanum tuberosum) is a staple crop important in global food security. As a leading potato producer, China faces significant challenges from insect pest infestations that compromise yield and quality. However, insect communities within Chinese potato fields remain poorly characterized. This study aimed to explore insect diversity in potato fields in Yunnan Province. From autumn 2021 to summer 2022, five Malaise traps were strategically deployed to capture insect samples. In total, 245 samples were collected over 49 weeks, and DNA metabarcoding was performed on bulk samples. The generated sequences were curated and analyzed using the Barcode of Life Data System and the Multiplex Barcode Research and Visualization Environment. The analysis assigned sequences to 1,688 Barcode Index Numbers (BINs) as species proxies derived from the Global Insecta Library, along with 166 BINs from the China Insecta dataset. This research provides valuable insights for barcoding local biodiversity and developing regional reference libraries and presents a comprehensive dataset of insect biodiversity within potato agroecosystems, encompassing 1,707 BINs linked to known insect taxa.}, }
@article {pmid39838754, year = {2025}, author = {Zhang, D and Zhou, Y and Li, X and Luan, Q}, title = {CRISPR/Cas13a-Enhanced Porous Hydrogel Encapsulated Photonic Barcodes for Multiplexed Detection of Virus.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e2408725}, doi = {10.1002/smll.202408725}, pmid = {39838754}, issn = {1613-6829}, support = {82102511//National Natural Science Foundation of China/ ; 82102181//National Natural Science Foundation of China/ ; BK20210021//National Natural Science Foundation of China/ ; BK20210009//National Natural Science Foundation of China/ ; M2021031//Research Project of&#xa0;Jiangsu Province Health Committee/ ; 2024-LCYJ-MS-15//Medical School of Nanjing University/ ; (YKK23068)//Nanjing Medical Science and Technique Development Foundation YKK23068/ ; }, abstract = {In this study, we present an ultrasensitive and specific multiplexed detection method for SARS-CoV-2 and influenza (Flu) utilizing CRISPR/Cas13a technology combined with a hydrogel-encapsulated photonic crystal (PhC) barcode integrated with hybridization chain reaction (HCR). The barcodes, characterized by core-shell structures, are fabricated through partial replication of periodically ordered hexagonally close-packed silicon dioxide beads. Consequently, the opal hydrogel shell of these barcodes features abundant interconnected pores that provide a substantial surface area for probe immobilization. Furthermore, the inherent structural colors remain stable during detection events due to the robust mechanical strength of the barcode cores. This integration of CRISPR/Cas13a and HCR leverages both the highly specific RNA recognition capabilities and trans-cleavage activity of Cas13a while employing HCR to enhance sensitivity. Upon encountering target RNA, Cas13a cleaves a hairpin probe, thereby initiating subsequent HCR amplification for enhanced detection sensitivity. Our method demonstrates high accuracy and sensitivity in multiplexed detection of SARS-CoV-2, Flu A and Flu B RNA with a limit-of-detection as low as 200 aM. Importantly, this assay also exhibits acceptable accuracy in repeated clinical sample testing. Thus, our platform represents a promising strategy for highly sensitive multiplexed virus detection in clinical.}, }
@article {pmid39837566, year = {2025}, author = {Zhuoma, D and Tingyin, D and Jun, L and Pei, Q and Duoji, C and Feng, D and Fang, D and Yan, Z}, title = {Study on Quality Evaluation of Tibetan Dracocephali tangutici Herba Based on DNA Barcode and HPLC Fingerprinting.}, journal = {Phytochemical analysis : PCA}, volume = {}, number = {}, pages = {}, doi = {10.1002/pca.3503}, pmid = {39837566}, issn = {1099-1565}, support = {XZ202101ZD0024G//Project of Science and Technology Programme of Tibet Autonomous Region/ ; }, abstract = {OBJECTIVES: The quality of 30 batches of the Tibetan Dracocephali tangutici Herba was evaluated using HPLC fingerprinting and DNA sequences.<br><br>METHODS: Botanical identification of 30 batches of D. tangutici herba was conducted using the DNA barcoding approach, specifically analyzing the ITS and rbcL sequences. HPLC fingerprints of Tibetan Dracocephali tangutici Herba were established. The quality of 30 batches of D. tangutici herba was comprehensively evaluated using principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and entropy weighting method (EWM) combined with grey relation analysis (GRA).<br><br>RESULTS: The botanical provenance of all 30 batches of herbs was proven to be Dracocephali tangutici Maxim. using DNA barcoding techniques, namely, ITS sequence and rbcL sequence testing. A total of 17 common peaks were chosen from the HPLC fingerprinting analysis. Among these, three peaks were recognized by comparing them with three reference standards: chlorogenic acid, cryptochlorogenic acid, and salvianolic acid B. The similarity scores of the 30 batches of D. tangutici herba varied between 0.846 and 0.991. The 30 batches of samples were categorized into two groups using PCA. The findings from OPLS-DA indicated that chlorogenic acid and four flavonoids could be the crucial components for evaluating the quality of D. tangutici herba. Additionally, the combined evaluation results of EWM and GRA suggested that the quality of the 30 batches of samples varied significantly.<br><br>CONCLUSION: The results of this study can provide a reference basis for the development of quality standards for D. tangutici herba in Tibet.}, }
@article {pmid39834682, year = {2025}, author = {}, title = {Correction to "Species Identification of Livefood Flightless Fly (Torinido-Shoujoubae) Through DNA Barcoding".}, journal = {Ecology and evolution}, volume = {15}, number = {1}, pages = {e70864}, doi = {10.1002/ece3.70864}, pmid = {39834682}, issn = {2045-7758}, abstract = {[This corrects the article DOI: 10.1002/ece3.11622.].}, }
@article {pmid39842982, year = {2023}, author = {Zaki, ZMM and Kuroda, A and Morimura, N and Hayashi, Y and Hitoshi, S}, title = {Depletion of transit amplifying cells in the adult brain does not affect quiescent neural stem cell pool size.}, journal = {The journal of physiological sciences : JPS}, volume = {73}, number = {1}, pages = {19}, doi = {10.1186/s12576-023-00876-2}, pmid = {39842982}, issn = {1880-6562}, abstract = {Neural stem cells (NSCs) are maintained in the adult mammalian brain throughout the animal's lifespan. NSCs in the subependymal zone infrequently divide and generate transit amplifying cells, which are destined to become olfactory bulb neurons. When transit amplifying cells are depleted, they are replenished by the quiescent NSC pool. However, the cellular basis for this recovery process remains largely unknown. In this study, we traced NSCs and their progeny after transit amplifying cells were eliminated by intraventricular infusion of cytosine β-D-arabinofuranoside. We found that although the number of neurosphere-forming NSCs decreased shortly after the treatment, they were restored to normal levels 3 weeks after the cessation of treatment. More importantly, the depletion of transit amplifying cells did not induce a significant expansion of the NSC pool by symmetric divisions. Our data suggest that the size of the NSC pool is hardly affected by brain damage due to antimitotic drug treatment.}, }
@article {pmid39831564, year = {2025}, author = {Mariz, J and Nawaz, A and Bösch, Y and Wurzbacher, C}, title = {Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14055}, doi = {10.1111/1755-0998.14055}, pmid = {39831564}, issn = {1755-0998}, support = {WU 890/2-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, the number of unknown and undescribed fungi is predicted to exceed the number of known fungal species by far. Despite efforts to uncover these dark fungal taxa, we still face inherent sampling biases and methodological limitations. Here, we present a framework that combines taxonomic knowledge, molecular biology and data processing to explore the fungal biodiversity of enigmatic aquatic fungal lineages. Our work is based on serial screening of environmental fungal cells to approach unknown fungal taxa. Microscopic documentation is followed by DNA analysis of laser micro-dissected cells, coupled with a ribosomal operon barcoding step realised by long-read sequencing, followed by an optional whole genome sequencing step. We tested this approach on a range of aquatic fungal cells mostly belonging to the ecological group of aquatic hyphomycetes derived from environmental samples. From this initial screening, we were able to identify 60 potentially new fungal taxa in the target dataset. By extending this methodology to other fungal lineages associated with different habitats, we expect to increasingly characterise the molecular barcodes of dark fungal taxa in diverse environmental samples. This work offers a promising solution to the challenges posed by unknown and unculturable fungi and holds the potential to be applied to the diverse lineages of undescribed microeukaryotes.}, }
@article {pmid39831278, year = {2025}, author = {Nguyen, AD and Vu, TTT and Nguyen, TT}, title = {Mountainous millipedes in Vietnam. III. Two new dragon millipedes from limestone mountains in northern Vietnam (Polydesmida, Paradoxosomatidae, Hylomus), with an identification key to Vietnamese Hylomus species.}, journal = {ZooKeys}, volume = {1223}, number = {}, pages = {247-262}, pmid = {39831278}, issn = {1313-2989}, abstract = {Two new species of the dragon millipede genus Hylomus Cook &amp; Loomis, 1924 are described from mountainous areas in northern Vietnam, namely Hylomuspiccolo sp. nov. and Hylomusborealis sp. nov. The COI barcodes are provided for these species, and an identification key is presented to all Vietnamese Hylomus species.}, }
@article {pmid39830292, year = {2024}, author = {Crous, PW and Wingfield, MJ and Jurjević, &#x17d; and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, &#xd8; and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ}, title = {Fungal Planet description sheets: 1697-1780.}, journal = {Fungal systematics and evolution}, volume = {14}, number = {}, pages = {325-577}, doi = {10.3114/fuse.2024.14.19}, pmid = {39830292}, issn = {2589-3831}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.}, }
@article {pmid39825896, year = {2025}, author = {Ellisor, D and Gregg, M and Folz, A and Possolo, A}, title = {Robust discrimination between closely related species of salmon based on DNA fragments.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {39825896}, issn = {1618-2650}, abstract = {Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (COI), using ensembles of fragments aligned to genetic barcodes that serve as digital proxies for the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation (NextGen) Sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE (Muscle 5.2) (Edgar in Nat Commun 13:6968, 2022), applied to multiple versions of each fragment perturbed according to the nucleobase identification error probabilities underlying the quality scores. The Damerau-Levenshtein distance was used to determine the genetic barcode of the candidate species that is closest to each aligned, perturbed fragment. The "votes" that the sampled fragments cast for the different candidate species are then pooled and converted into identification probabilities, using weights determined by the entropy of the fragment-specific identification probability distributions. This novel approach to quantify the uncertainty associated with measurements made using NextGen Sequencing can be applied to discriminate closely related species, hence to value-assignment for reference materials supporting determinations of the authenticity of seafood, for example, NIST Reference Materials 8256 and 8257 (Coho salmon) (Ellisor et al., 2021).}, }
@article {pmid39824859, year = {2025}, author = {Holmes, CL and Dailey, KG and Hullahalli, K and Wilcox, AE and Mason, S and Moricz, BS and Unverdorben, LV and Balazs, GI and Waldor, MK and Bachman, MA}, title = {Patterns of Klebsiella pneumoniae bacteremic dissemination from the lung.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {785}, pmid = {39824859}, issn = {2041-1723}, support = {K99A1175481//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI042347//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Klebsiella pneumoniae/pathogenicity/isolation &amp; purification ; *Bacteremia/microbiology ; *Klebsiella Infections/microbiology ; *Lung/microbiology/pathology ; Animals ; Female ; Mice ; Humans ; Mice, Inbred C57BL ; Male ; }, abstract = {Bacteremia, a leading cause of death, generally arises after bacteria establish infection in a particular tissue and transit to secondary sites. Studying dissemination from primary sites by solely measuring bacterial burdens does not capture the movement of individual clones. By barcoding Klebsiella pneumoniae, a leading cause of bacteremia, we track pathogen dissemination following pneumonia. Variability in organ bacterial burdens is attributable to two distinct dissemination patterns distinguished by the degree of similarity between the lung and systemic sites. In metastatic dissemination, lung bacterial clones undergo heterogeneous expansion and the dominant clones spread to secondary organs, leading to greater similarity between sites. In direct dissemination, bacterial clones exit the lungs without clonal expansion, leading to lower burdens in systemic sites and more dissimilarity from the lung. We uncover bacterial and host factors that influence the dynamics of clonal sharing and expansion. Here, our data reveal unexpected heterogeneity in Klebsiella bacteremia dynamics and define a framework for understanding within-host bacterial dissemination.}, }
@article {pmid39823405, year = {2025}, author = {Miller, D and Dziulko, A and Levy, S}, title = {Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0299440}, pmid = {39823405}, issn = {1932-6203}, mesh = {Humans ; *SARS-CoV-2/metabolism ; Protein Interaction Mapping/methods ; Host-Pathogen Interactions ; COVID-19/virology/metabolism ; Protein Interaction Maps ; Viral Proteins/metabolism ; High-Throughput Screening Assays/methods ; HEK293 Cells ; }, abstract = {Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve. Current high-throughput PPI assays have screened entire viral-host PPI networks. However, these studies are time consuming, often require specialized equipment, and are difficult to further scale. Here, we develop methods that make larger-scale viral-host PPI screening more accessible. This approach combines the mDHFR split-tag reporter with the iSeq2 interaction-barcoding system to permit massively-multiplexed PPI quantification by simple pooled engineering of barcoded constructs, integration of these constructs into budding yeast, and fitness measurements by pooled cell competitions and barcode-sequencing. We applied this method to screen for PPIs between SARS-CoV-2 proteins and human proteins, screening in triplicate >180,000 ORF-ORF combinations represented by >1,000,000 barcoded lineages. Our results complement previous screens by identifying 74 putative PPIs, including interactions between ORF7A with the taste receptors TAS2R41 and TAS2R7, and between NSP4 with the transmembrane KDELR2 and KDELR3. We show that this PPI screening method is highly scalable, enabling larger studies aimed at generating a broad understanding of how viral effector proteins converge on cellular targets to effect replication.}, }
@article {pmid39823165, year = {2025}, author = {Ivanova, A and Chalupska, R and Louro, AF and Firth, M and González-King Garibotti, H and Hultin, L and Kohl, F and Lázaro-Ibáñez, E and Lindgren, J and Musa, G and Oude Blenke, E and Silva, AM and Szeponik, L and Taylor, A and Viken, I and Wang, X and Jennbacken, K and Wiseman, J and Dekker, N}, title = {Barcoded Hybrids of Extracellular Vesicles and Lipid Nanoparticles for Multiplexed Analysis of Tissue Distribution.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2407850}, doi = {10.1002/advs.202407850}, pmid = {39823165}, issn = {2198-3844}, support = {825828//European Union's Horizon 2020 Research and Innovation Programme/ ; }, abstract = {Targeted delivery of therapeutic agents is a persistent challenge in modern medicine. Recent efforts in this area have highlighted the utility of extracellular vesicles (EVs) as drug carriers, given that they naturally occur in bloodstream and tissues, and can be loaded with a wide range of therapeutic molecules. However, biodistribution and tissue tropism of EVs remain difficult to study systematically. Here, a multiplexed approach is developed for simultaneous tracking of EVs from various cell lines within a single in vivo experiment. EVs are used from 16 different cell lines, and through controlled fusion with lipid nanoparticles (LNPs) carrying single-stranded DNA barcodes, uniquely barcoded hybrid EV particle (hEV) library is generated. These hEVs are combined for a multiplexed in vivo biodistribution profiling in mice, and discovered that HAP1-derived hEVs demonstrated lung tropism, suggesting that these hEVs may be used for targeted drug delivery into lung tissue. To examine this possibility further, it is shown that HAP1 hEV loaded with Cre mRNA displayed functional delivery to the lungs. Overall, the barcoded hEV technology enables rapid profiling of biodistribution across EV cell sources, which is poised to improve throughput and extent of EV studies, while reducing the number of animals required for research.}, }
@article {pmid39821740, year = {2025}, author = {Dou, HY and Huang, TS and Wu, HC and Hsu, CH and Chen, FJ and Liao, YC}, title = {Targeted sputum sequencing for rapid and broad drug resistance of Mycobacterium tuberculosis.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {39821740}, issn = {1439-0973}, support = {IV-111-PP-23//National Health Research Institutes, Taiwan/ ; PH-112-PP-05//National Health Research Institutes, Taiwan/ ; 110-2314-B-400-038//Ministry of Science and Technology, Taiwan/ ; }, abstract = {PURPOSE: Rapid detection of drug resistance in Mycobacterium tuberculosis (Mtb) from clinical samples facilitates the timely provision of optimal treatment regimens for tuberculosis (TB) patients.<br><br>METHODS: In November, 2023, the WHO released its second catalogue of resistance-conferring mutations in Mtb. Utilizing this information, we developed a single 17-plex PCR assay covering 16 key resistance genes and modified thermo-protection buffer to amplify 30 kbp DNA directly from sputum samples for nanopore sequencing. We implemented our protocol using rapid barcoding for sequencing with both a Flongle and a MinION flow cell.<br><br>RESULTS: The single multiplex PCR assay was successfully validated on clinical sputum samples using the thermo-protection buffer. The protocol was applied to both Flongle and MinION flow cells, analyzing 12 and 40 samples, respectively. Data analysis suggested that optimal performance could be achieved by processing 6 and 12 samples with similar microscope staining scores on these two platforms. This approach facilitated rapid antimicrobial resistance (AMR) predictions directly from sputum on the day of collection or the following day, with a cost of less than $35 per sample. Compared to AMR predictions based on whole-genome sequencing (WGS) using Mykrobe and TBProfiler, our amplicon-based analysis tool, ARapidTb, demonstrated superior resistance detection capabilities. When analyzing publicly available nanopore WGS datasets for 442 isolates, ARapidTb achieved agreement rates of 95.8% and 98.0%, outperforming Mykrobe (89.4% and 98.3%) and TBProfiler (75.6% and 89.8%).<br><br>CONCLUSIONS: Our study significantly reduces the time required for drug resistance detection, enabling quicker initiation of appropriate treatments and potentially improving patient outcomes and TB management.}, }
@article {pmid39821447, year = {2025}, author = {Zhang, C and Li, J and Yan, F and Wang, Z and Zeng, X and Zhang, J}, title = {Comparative analysis of the complete chloroplast genome of seven Wikstroemia taxa (Thymelaeaceae) provides insights into the genome structure and phylogenetic relationships.}, journal = {Planta}, volume = {261}, number = {2}, pages = {40}, pmid = {39821447}, issn = {1432-2048}, support = {2022QB-153//Science Fund for Distinguished Young Scholars of Gansu Province/ ; KYQD2022013//Doctoral Start-up Foundation of Hexi University/ ; 22JR11RG225//the Natural Science Foundation of Gansu Province, China/ ; 202210740073//National College Students Innovation and Entrepreneurship Training Program/ ; 22CX8NA071//the Technology Innovation Guidance Program Project of Gansu Provincial "Research and Popularization of Ecological Planting Techniques for Economic Shrubs Daphne tangutica Maxim. in Qilian Mountains"/ ; No. 32260472//the National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *Genome, Chloroplast/genetics ; Wikstroemia/genetics ; Base Composition/genetics ; RNA, Transfer/genetics ; }, abstract = {New insights into the phylogeny of species in the family Thymelaeaceae and support of the recognition of D. genkwa and D. aurantiaca as species in the genus Wikstroemia are provided. Wikstroemia (Thymelaeaceae) is an economically important genus because some of its species are used in traditional medicine and also contribute to pulp production. The morphological characteristics of Wikstroemia species exhibit continuous natural variation, posing a challenge in accurately distinguishing this genus from its sister genera solely based on morphological traits. Consequently, the classification of, and phylogenetic relationships between, Wikstroemia and its sister genera, as inferred from morphological characteristics, remain contentious. Chloroplast genome information has proven to be a valuable tool in plant phylogeny. Here, we performed a comparative analysis of the chloroplast genomes of 15 species in the genus Wikstroemia, all of which exhibited typical quadripartite structures, with sizes ranging from 150,054 bp to 175,898bp. These genomes encoded 122-143 genes, including 79-95 protein-coding genes, 36-40 tRNA genes, and 8 rRNA genes. The overall GC content displayed minimal variation, ranging from 36.6% to 37.47%. The distributions of SSRs and codon bias exhibited similarities among Wikstroemia species. High variability hotspots were found in 15 intergenic spacers and 5 genes. Phylogenetic analyses consistently grouped all Wikstroemia species into a single clade. Notably, Daphne genkwa and D. aurantiaca were found to be nested within Wikstroemia, rather than being closely related to other Daphne species. Furthermore, phylogenetic analyses suggested that Wikstroemia is paraphyletic relative to Stellera chamaejasme. These findings provide new insights into the phylogeny of Wikstroemia and Daphne within the Thymelaeaceae, contributing to improved species identification and increasing the taxonomic and phylogenetic resolution of Wikstroemia.}, }
@article {pmid39821021, year = {2025}, author = {Merle, C and Fre, S}, title = {Recording Lineage History with Cellular Barcodes in the Mammary Epithelium and in Breast Cancer.}, journal = {Advances in experimental medicine and biology}, volume = {1464}, number = {}, pages = {77-94}, pmid = {39821021}, issn = {0065-2598}, mesh = {*Breast Neoplasms/pathology/genetics/metabolism ; Humans ; *Cell Lineage/genetics ; Female ; Animals ; *Single-Cell Analysis/methods ; Mammary Glands, Human/pathology/cytology/metabolism ; Mammary Glands, Animal/pathology/metabolism/cytology ; Neoplastic Stem Cells/pathology/metabolism ; }, abstract = {Lineage tracing methods have extensively advanced our understanding of physiological cell behaviour in vivo and in situ and have vastly contributed to decipher the phylogeny and cellular hierarchies during normal and tumour development. In recent years, increasingly complex systems have been developed to track thousands of cells within a given tissue or even entire organisms. Cellular barcoding comprises all techniques designed to genetically label single cells with unique DNA sequences or with a combination of fluorescent proteins, in order to trace their history and lineage production in space and time. We distinguish these two types of cellular barcoding as genetic or optical barcodes. Furthermore, transcribed cellular barcodes can integrate the lineage information with single-cell profiling of each barcoded cell. This enables the potential identification of specific markers or signalling pathways defining distinct stem cell states during development, but also signals promoting tumour growth and metastasis or conferring therapy resistance.In this chapter, we describe recent advances in cellular barcoding technologies and outline experimental and computational challenges. We discuss the biological questions that can be addressed using single-cell dynamic lineage tracing, with a focus on the study of cellular hierarchies in the mammary epithelium and in breast cancer.}, }
@article {pmid39820073, year = {2025}, author = {Yeh, YH and Kirschner, R}, title = {Study of endophytic fungi of Ipomoea pes-caprae reveals the superiority of in situ plant conservation over ex situ conservation from a mycological view.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2040}, pmid = {39820073}, issn = {2045-2322}, support = {NSTC 110-2811-B-002-568//National Science and Technology Council/ ; NSTC 111-2811-B-002-092//National Science and Technology Council/ ; NSTC 112-2811-B-002-150//National Science and Technology Council/ ; MOST 108-2621-B-002-007//National Science and Technology Council/ ; 109-2621-B-002-004//National Science and Technology Council/ ; 110-2621-B-002-001-MY2//National Science and Technology Council/ ; }, mesh = {*Ipomoea/microbiology ; *Endophytes/genetics ; *Fungi/genetics/classification/isolation &amp; purification ; *Biodiversity ; Conservation of Natural Resources/methods ; Taiwan ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {In nature conservation, ex situ and in situ conservation strategies are discussed for protecting endangered species of plants and animals. However, the impacts of these strategies on the microbes associated with these species are rarely considered. In our study, we chose the endophytic fungi of the pantropical creeping plant Ipomoea pes-caprae as representative coastal plant in two natural coastal populations and two botanical gardens in Taiwan as collection sites in order to investigate the potential effect of ex situ plantation on the biodiversity of microbes intimately associated with this plant. In a culture-dependent approach, endophytic fungi were isolated under axenic conditions and identified to species, genus, or higher taxonomic ranks with DNA barcodes and morphology. In addition to yielding ca. 800 strains and over 100 morphospecies, a principal component analysis (PCA) of the distribution of the dominant fungal species showed clear differences in the composition of endophytic fungal species depending on the sampling sites. We conclude that the endophytic fungi from the original site are replaced by other species in the ex situ plantations. Due to the limitations of ex situ conservation of microbes and from a mycological and microbial perspective, in situ conservation should outweigh ex situ approaches.}, }
@article {pmid39819888, year = {2025}, author = {Sun, J and Philpott, M and Loi, D and Hoffman, G and Robson, J and Mehta, N and Calcutt, E and Gamble, V and Brown, T and Brown, T and Oppermann, U and Cribbs, AP}, title = {Enhancing single-cell transcriptomics using interposed anchor oligonucleotide sequences.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {67}, pmid = {39819888}, issn = {2399-3642}, support = {MR/V010182/1//RCUK | Medical Research Council (MRC)/ ; }, mesh = {*Single-Cell Analysis/methods ; *Oligonucleotides/genetics ; *Gene Expression Profiling/methods ; Humans ; Transcriptome ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, RNA/methods ; }, abstract = {Single-cell transcriptomics, which utilises barcodes and unique molecular identifiers (UMIs) for polyA+ mRNA capture, is compromised by oligonucleotide synthesis errors. To address this, we modified the oligonucleotide capture design and integrated an interposed anchor between the barcode and the UMI. This design significantly reduces the need to discard reads due to synthesis inaccuracies. Our results demonstrate that this anchor-enhanced design substantially improves gene expression profiles in droplet-based single-cell sequencing analyses.}, }
@article {pmid39819789, year = {2025}, author = {Chaumeau, V and Sawasdichai, S and Min, TZMMM and Kularbkeeree, T and Jaruwan, N and Gloria, N and Lee, NY and Trackoolchengkaew, M and Phanaphadungtham, M and Rongthong, P and Inta, A and Watthanaworawit, W and Nosten, F}, title = {Identification of Southeast Asian Anopheles mosquito species with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a cross-correlation approach.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {8}, pmid = {39819789}, issn = {1756-3305}, support = {220211/WT_/Wellcome Trust/United Kingdom ; OPP1177406//Bill and Melinda Gates Foundation/ ; }, mesh = {*Anopheles/classification/chemistry/genetics ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Animals ; Myanmar ; Southeast Asian People ; }, abstract = {BACKGROUND: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is proposed for mosquito species identification. The absence of public repositories sharing mass spectra and open-source data analysis pipelines for fingerprint matching to mosquito species limits the widespread use of this technology. The objective of this study was to develop a free open-source data analysis pipeline for Anopheles species identification with MALDI-TOF MS.<br><br>METHODS: Anopheles mosquitoes were captured in 33 villages in Karen (Kayin) state in Myanmar. A subset of 403 specimens was selected for inclusion in either the reference or the test panel (270 and 133 specimens, respectively). Three hundred fifty-nine specimens could be identified with DNA barcodes and were assigned to 21 sensu stricto species and five sibling species pairs or complexes. A total of 3584 mass spectra of the head of these specimens identified with DNA barcoding were acquired and the similarity between mass spectra was quantified using a cross-correlation approach adapted from the published literature. A reference mass spectra database was created using all spectra of the PCR-identified specimens assigned to the reference panel. A simulation experiment was carried out by querying the reference database with the spectra of the test panel to evaluate the performance of species identification with MALDI-TOF MS at varying thresholds of the cross-correlation index for the algorithm to output an identification result and with varying numbers of technical replicates for the tested specimens, considering PCR identification results as the reference.<br><br>RESULTS: With one spot and a threshold value of -14 for the cross-correlation index on the log scale, the sensitivity was 0.99 [95% credible interval (CrI): 0.98-1.00], the predictive positive value was 0.99 (95% CrI: 0.98-0.99), and the accuracy was 0.98 (95% CrI: 0.97-0.99). It was not possible to directly estimate the sensitivity and negative predictive value because there was no true negative (i.e., queries of species not referenced in the database) in the assessment.<br><br>CONCLUSIONS: The cross-correlation approach can be used to match mass spectral fingerprints to predefined taxa. MALDI-TOF MS is a valuable tool for rapid, accurate, and affordable identification of Anopheles species.}, }
@article {pmid39816673, year = {2025}, author = {Marquisseau, A and Canale-Tabet, K and Labarthe, E and Pascal, G and Klopp, C and Pornon, A and Escaravage, N and Rudelle, R and Vignal, A and Ouin, A and Ollivier, M and Pichon, M}, title = {Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e137540}, pmid = {39816673}, issn = {1314-2828}, abstract = {BACKGROUND: DNA barcoding and metabarcoding are now powerful tools for studying biodiversity and especially the accurate identification of large sample collections belonging to diverse taxonomic groups. Their success depends largely on the taxonomic resolution of the DNA sequences used as barcodes and on the reliability of the reference databases. For wild bees, the barcode sequences coverage is consistently growing in volume, but some incorrect species annotations need to be cared for. The COI (Cytochrome Oxydase subunit 1) gene, the most used in barcoding/metabarcoding of arthropods, suffers from primer bias and difficulties for covering all wild bee species using the classical Folmer primers.<br><br>NEW INFORMATION: We present here a curated database for a 250 bp mini-barcode region of the 16S rRNA gene, suitable for low-cost metabarcoding wild bees in applications, such as eDNA analysis or for sequencing ancient or degraded DNA. Sequenced specimens were captured in Occitania (south-west of France) and morphologically identified by entomologists, with a total of 530 individuals belonging to 171 species and 19 genera. A customised workflow including distance-tree inferences and a second round of entomologist observations, when necessary, was used for the validation of 348 mini-barcodes covering 148 species. Amongst them, 93 species did not have any 16S reference barcode available before our contribution. This high-quality reference library data are freely available to the scientific community, with the aim of facilitating future large-scale characterisation of wild bee communities in a context of pollinators' decline.}, }
@article {pmid39814875, year = {2025}, author = {Elzain, IA and Idris, AB and Karim, AA and Ahmed, NM and Elzaki, SG and Yılmaz, S and Hassan, MA and Abdalla, HS}, title = {Analysis of DNA cox1 barcoding revealed novel haplotype in Schistosoma haematobium isolated from Western Sudan.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2062}, pmid = {39814875}, issn = {2045-2322}, mesh = {Humans ; Sudan/epidemiology ; *Haplotypes ; Child ; Animals ; *Schistosoma haematobium/genetics/isolation &amp; purification ; Adolescent ; Male ; *Schistosomiasis haematobia/parasitology/epidemiology/genetics ; Cross-Sectional Studies ; Female ; Young Adult ; *DNA Barcoding, Taxonomic/methods ; Child, Preschool ; Phylogeny ; Feces/parasitology ; Cyclooxygenase 1/genetics ; Genetic Variation ; Electron Transport Complex IV/genetics ; }, abstract = {Schistosomiasis poses a significant global health threat, particularly in tropical and subtropical regions like Sudan. Although numerous epidemiological studies have examined schistosomiasis in Sudan, the genetic diversity of Schistosoma haematobium populations, specifically through analysis of the mtcox1 gene, remains unexplored. This study aimed to investigate the risk factors associated with urogenital schistosomiasis among school pupils in El-Fasher, Western Sudan, as well as the mtcox1 genetic diversity of human S. haematobium in this region. A cross-sectional study was conducted among school pupils aged 4 to 19 years. In total, 196 urine samples and 196 fecal samples were collected from participants across schools, health centers, and refugee camps in El-Fasher. Samples were examined using simple centrifugation/sedimentation technique and formol-ether concentration method to detect S. haematobium and S. mansoni eggs, respectively. S. haematobium mtcox1 partial gene was amplified and sequenced by the Sanger technique. A neighbor-joining phylogenetic tree was generated by MEGA software, and a haplotype network was constructed using PopART v.1.7 with the median-joining network method. In this study, S. haematobium was detected in 6.1% (12/196) of the participants while no S. mansoni ova were observed in fecal samples. The infection was more common among those who relied on indirect water supply like tankers (6, 50%). No infection was observed among residents of refugee camps. Only eight samples were PCR-positive, which were successfully sequenced, and included in the genetic diversity analysis. A unique haplotype (Hap_1) with no sequence diversity was found among cox1 sequences from El-Fasher strains. Both El-Fasher S. haematobium haplotype (Hap_1) and Gezira haplotype (Hap_31) fall within the mainland Africa group (group 1). In conclusion, this study identified a novel S. haematobium strain and provides insights into the evolutionary history and phylogeography of S. haematobium in Sudan, particularly in the western region. This genetic data could help in the control and monitoring of urogenital schistosomiasis in this region. For the first time, we utilized the DNA mtcox1 barcoding to investigate S. haematobium haplotypes in Western Sudan.}, }
@article {pmid39814794, year = {2025}, author = {Yassin, S and Elsohafy, SM and El-Hawiet, A and Abdel-Kader, MS and Ghareeb, DA and Darwish, FA and Amer, ME}, title = {Comparative phytochemical and pharmacological analysis of two cultivars of Annona squamosa L. cultivated in Egypt.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {8}, pmid = {39814794}, issn = {2396-8370}, abstract = {This study compared two Annona squamosa L. cultivars, Abdelrazik (Annona A.) and Balady (Annona B.), in terms of their chemical profile, in vitro cytotoxicity against HCT-116 and A549 cell lines, and total acetogenin. In addition, the two cultivars pulp were compared regarding carbohydrates and magnesium ions content and immunomodulating activity. The two cultivars were also differentiated genetically by DNA barcoding using the universal primer matK and the specific primer Annona squamosa matK. The results showed that Annona A. seeds had higher acetogenin content and exhibited more potent cytotoxic activity against the two cell lines. In contrast, Annona B. pulp had higher carbohydrate content and lower magnesium ions content. The splenic lymphocyte proliferation assay revealed that Annona A. pulp extract was slightly more active as an immunostimulant. The specific primer used for DNA barcoding was more effective for species identification, while the universal primer was better for cultivar differentiation. Overall, our findings indicate the potential for using active compounds of Annona squamosa L. cultivars to develop new therapeutic agents for cancer therapy and immune enhancement.}, }
@article {pmid39813480, year = {2025}, author = {Câmara, PEAS and Pellizzari, FM and Lopes, FAC and Amorim, ET and Bones, FLV and Anjos, DA and Carvalho-Silva, M and Convey, P and Rosa, LH}, title = {DNA metabarcoding reveal hidden diversity of periphytic eukaryotes on marine Antarctic macroalgae.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {96}, number = {suppl 2}, pages = {e20240570}, doi = {10.1590/0001-3765202420240570}, pmid = {39813480}, issn = {1678-2690}, mesh = {Antarctic Regions ; *Seaweed/classification/genetics ; *DNA Barcoding, Taxonomic ; *Biodiversity ; Eukaryota/classification/genetics ; }, abstract = {Polar marine macroalgae thrive in extreme conditions, often displaying geographic isolation and high degree of endemism. The "phycosphere" refers to the zone around the algae inhabited by microrganisms. Our study used DNA metabarcoding to survey the eukaryotic communities associated with seven seaweed species obtained at King George Island (South Shetland Islands, maritime Antarctic), including two Rhodophyta, two Chlorophyta and three Phaeophyceae. The ITS2 region was used as a barcode and our analysis yielded 77 eukaryotic ASVs spanning five Kingdoms (Fungi, Metazoa, Chromista, Protozoa, and Viridiplantae) and ten phyla (Ascomycota, Basidiomycota, Cercozoa, Ciliophora, Ochrophyta, Amebozoa, Chlorophyta, Rhodophyta, Bryophyta and Cnidaria). Additionally, we identified 14 potential new occurrence records for Antarctica. Ciliates and green algae were the most species-rich groups. The most abundant assigned associated species was Monostroma angicava (Chrorophyta). Within the macroalgal, the Chlorophyceans Ulothrix sp. hosted the greatest number of taxa, followed by Monostroma hariotii. Our data suggested that Antarctic macroalgae host a rich diversity of associated organisms and the biodiversity associated with the phycosphere remains underestimated.}, }
@article {pmid39813353, year = {2025}, author = {Trende, R and Darling, TL and Gan, T and Wang, D and Boon, ACM}, title = {Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eads2927}, doi = {10.1126/sciadv.ads2927}, pmid = {39813353}, issn = {2375-2548}, mesh = {Animals ; *SARS-CoV-2/physiology/genetics/pathogenicity ; *COVID-19/transmission/virology ; Cricetinae ; *Disease Models, Animal ; Lung/virology ; Humans ; Virus Shedding ; Trachea/virology ; }, abstract = {The transmission bottleneck, defined as the number of viruses shed from one host to infect another, is an important determinant of the rate of virus evolution and the level of immunity required to protect against virus transmission. Despite its importance, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission bottleneck remains poorly characterized. We adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes, infected donor hamsters with this pool, and exposed contact hamsters to paired infected donors, varying the duration and route of exposure. Following exposure, the nasal turbinates, trachea, and lungs were collected and the number of barcodes in each tissue was enumerated. We found that longer and more direct exposures increased the transmission bottleneck and that the upper airway is the primary source of transmitted virus in this model. Together, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission.}, }
@article {pmid39811811, year = {2024}, author = {Duan, HN and Jiang, YZ and Yang, JB and Cai, J and Zhao, JL and Li, L and Yu, XQ}, title = {Skmer approach improves species discrimination in taxonomically problematic genus Schima (Theaceae).}, journal = {Plant diversity}, volume = {46}, number = {6}, pages = {713-722}, pmid = {39811811}, issn = {2468-2659}, abstract = {Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next generation barcodes in plants. However, conserved DNA barcoding markers, including complete plastid genome and nuclear ribosomal DNA (nrDNA) sequences, are inadequate for accurate species identification. Skmer, a recently proposed approach that estimates genetic distances among species based on unassembled genome skims, has been proposed to effectively improve species discrimination rate. In this study, we used Skmer to identify species based on genomic skims of 47 individuals representing 10 out of 13 species of Schima (Theaceae) from China. The unassembled reads identified six species, with a species identification rate of 60%, twice as high as previous efforts that used plastid genomes (27.27%). In addition, Skmer was able to identify Schima species with only 0.5× sequencing depth, as six species were well-supported with unassembled data sizes as small as 0.5 Gb. These findings demonstrate the potential for Skmer approach in species identification, where nuclear genomic data plays a crucial role. For taxonomically difficult taxa such as Schima, which have diverged recently and have low levels of genetic variation, Skmer is a promising alternative to next generation barcodes.}, }
@article {pmid39811021, year = {2025}, author = {Mutafchiev, Y and Roman, Y and Griffiths, K and Kenderov, L and Michalski, ML}, title = {DNA-elucidated life cycle of a highly pathogenic avian nematode: Streptocara incognita (Spirurida: Acuariidae) and its morphological development from infective third-stage larva to adult.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {7}, number = {}, pages = {100238}, pmid = {39811021}, issn = {2667-114X}, abstract = {Streptocara incognita Gibson, 1968 is an acuariid nematode associated with lethal cases of streptocarosis of diverse aquatic birds in North America and Europe. This study reports S. incognita as an agent causing severe and fatal necrosis of the oesophagus and proventriculus of anatids, i.e. Somateria mollissima (L.), Marmaronetta angustirostris (Ménétriés), Tadorna tadorna (L.) and Spatula querquedula (L.), kept in open pens in the Zoological Park, Clères, France. Comparative analysis of 12S rRNA gene sequences revealed that third-stage infective nematode larvae found in the amphipod Gammarus pulex pulex (L.) in the river passing through the pens belong to S. incognita thus elucidating the life cycle of this species. A partial sequence of the cox1 gene was also generated. To complement the brief original description of S. incognita, a detailed morphological description of the adult stages is provided based on light and scanning electron microscopy. Additionally, morphological data on the developing third- and fourth-stage larvae found in the definitive host and third-stage infective nematode larvae found in G. pulex pulex are also provided. This is the first record of an intermediate host of S. incognita. Somateria mollissima, M. angustirostris and S. querquedula are new host records.}, }
@article {pmid39809848, year = {2025}, author = {Kniesz, K and Hoffman, L and Martínez Arbizu, P and Kihara, TC}, title = {High genomic connectivity within Anatoma at hydrothermal vents along the Central and Southeast Indian Ridge.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1971}, pmid = {39809848}, issn = {2045-2322}, mesh = {*Hydrothermal Vents ; Animals ; *Gastropoda/genetics/classification ; India ; Ecosystem ; Phylogeny ; Gene Flow ; DNA Barcoding, Taxonomic ; Genomics/methods ; }, abstract = {Hydrothermal vents are ecosystems inhabited by a highly specialized fauna. To date, more than 30 gastropod species have been recorded from vent fields along the Central and Southeast Indian Ridge and all of them are assumed to be vent-endemic. During the INDEX project, 701 representatives of the genus Anatoma (Mollusca: Vetigastropoda) were sampled from six abyssal hydrothermal vent fields. Traditional morphology and COI barcoding of Hoffman et al. (Eur J Taxon 826:135-162, 2022) were combined with 2b-RAD sequencing to investigate the anatomid community structure and connectivity between the different vent fields. Consequently, 2b-RAD sequencing supported the primary species hypothesis (based on morphology) for 125 individuals of the recently described taxa A. discapex, A. declivis, A. laevapex and A. paucisculpta. We assigned 22 additional specimens to species with 2b-RAD sequencing and updated the community analyses that confirmed the pattern of expanding populations. Population structure and FST values indicated high connectivity along the six sampled vent fields for the three most abundant species. High levels of gene flow are suggested, pointing to high dispersal potential of the target species along the study area. However, low levels of heterozygosity revealed a small gene pool and therefore an increased vulnerability towards environmental change. Our results demonstrate that 2b-RAD sequencing, in combination with other molecular methods, can accurately characterise macrobenthic mollusc communities. Sequencing technology is an essential tool for ongoing monitoring. Furthermore, we highlight that the inferred molecular and ecological patterns provide valuable insights into hydrothermal vent ecosystems, which are crucial for the successful conservation of these ecosystems.}, }
@article {pmid39809825, year = {2025}, author = {Eroğlu, M and Çelik, I and Düşükcan, M and Ünal, EM and Çoban, MZ and Gündüz, F and Keskin, E}, title = {DNA barcoding of invasive Gambusia holbrooki Girard, 1859 and Atherina boyeri Risso, 1810 inhabiting Upper Euphrates River Basin, Türkiye.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1907}, pmid = {39809825}, issn = {2045-2322}, support = {SUF-16.13//F&#x131;rat University Scientific Research Projects Coordination Office/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Introduced Species ; *Rivers ; *Cyprinodontiformes/genetics/classification ; Electron Transport Complex IV/genetics ; Turkey ; Phylogeny ; Lakes ; Biodiversity ; }, abstract = {The main contributor to Türkiye's abundant freshwater fish biodiversity is its geographic location. This fauna consists of endemic, native, and non-native fish species. The introduction of Gambusia holbrooki Girard, 1859 to Lake Amik in the 1920s for the biological control of malaria was the first introduction of nonnative species to Türkiye. Atherina boyeri Risso, 1810 and other nonnative fish species have recently been introduced to Türkiye's freshwaters. In this research, the first records of invasive Gambusia holbrooki (Keban Dam Lake, in Elazığ Province) and Atherina boyeri (Karakaya Dam Lake, in Elazığ Province) are cited from the Upper Euphrates River Basin in the Eastern Anatolia Region of Türkiye. In situ electrofishing equipment was used to gather the specimens. Fish muscle samples were used to extract genomic DNA, which was then used to barcode the mitochondrial cytochrome c oxidase subunit I (COI) gene to identify different species of fish. The identification of invasive fish species using DNA barcoding is an effective technique, as evidenced by the comparison of amplified COI sequences to the BLAST database.}, }
@article {pmid39807677, year = {2025}, author = {Lin, YC and Lee, LR and Tsai, TH and Lin, J and Hsu, YS and Kesavan, M and Lin, YL and Chen, YF and Chen, JT}, title = {A Streamlined Approach to Anticounterfeiting Technologies: Patterned AAO Membranes Based on Photonic Crystal Effects with Tunable Color Shifts and pH Responsiveness.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e2409919}, doi = {10.1002/smll.202409919}, pmid = {39807677}, issn = {1613-6829}, support = {//Center for Emergent Functional Matter Science of National Yang Ming Chiao Tung University/ ; NSTC 112-2628-E-A49-012//National Science and Technology Council/ ; NSTC 113-2628-E-A49-006//National Science and Technology Council/ ; NSTC113-2740-M-007-001//National Science and Technology Council/ ; }, abstract = {Anticounterfeiting technologies have become increasingly crucial due to the growing issue of counterfeit goods, particularly in high-value industries. Traditional methods such as barcodes and holograms are prone to replication, prompting the need for advanced, cost-effective, and efficient solutions. In this work, a practical application of anodic aluminum oxide (AAO) membranes are presented for anticounterfeiting, which addresses the challenges of high production costs and complex fabrication processes. Unlike previous approaches requiring metal coatings for color generation, this method uses commercial aluminum foils to produce colorful AAO membranes without metal layers. Elemental mapping suggests that impurities on the aluminum surface contribute to enhanced reflectivity, aiding photonic crystal formation. A two-step anodization process that creates patterned AAO membranes is further introduced, with the pattern clarity controlled by anodization time. Additionally, a pH-responsive film composed of 2-anilino-6-dibutylaminofluoran (ODB-2) and thermoplastic polyurethane (TPU) is integrated, enabling dynamic color changes under varying pH conditions, further enhancing the anticounterfeiting functionality. This streamlined approach provides a scalable and cost-effective solution for developing versatile AAO membranes for industrial anticounterfeiting applications.}, }
@article {pmid39805772, year = {2024}, author = {Chen, ZY and Hua, ZY and Yuan, Y}, title = {[Establishment and application of chloroplast genome database with the largest number of species in world].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {23}, pages = {6257-6263}, doi = {10.19540/j.cnki.cjcmm.20240909.101}, pmid = {39805772}, issn = {1001-5302}, mesh = {*Genome, Chloroplast ; Databases, Genetic ; Phylogeny ; Microsatellite Repeats/genetics ; Plants/genetics/classification ; }, abstract = {The chloroplast genome is an important tool for studying plant classification, evolution, and the heterologous production of secondary metabolites and protein drugs. With advancements in sequencing technology and reductions in sequencing costs, chloroplast genome data have rapidly accumulated. However, existing chloroplast genome databases suffer from issues such as incomplete data, inadequate management, and inconsistent, inaccurate information, posing significant challenges for the development and utilization of the chloroplast genome. Therefore, it is urgently necessary to establish a database that provides comprehensive and reliable chloroplast genome information. This article provides a brief introduction to the Chloroplast Genome Information Resource(CGIR), the most comprehensive chloroplast genome database globally in terms of species coverage. The database, consisting of five modules, i.e.,(1) genomes,(2) genes,(3) simple sequence repeats(SSRs),(4) DNA barcodes, and(5) DNA signature sequences(DSSs), currently includes 34 923 chloroplast genome assemblies from 16 717 species. Based on the functionalities of these modules, the article systematically summarizes the progress in the application of the database in plant phylogenetic analysis, species identification, and chloroplast genetic engineering. The chloroplast genome database will be continuously updated in the future to provide a solid and reliable data foundation for chloroplast genome research, further promoting studies on traditional Chinese medicine(TCM)identification, resource conservation, and germplasm innovation.}, }
@article {pmid39805757, year = {2024}, author = {Li, XY and Guo, H and Ma, MX and Xu, LW and Huang, YH and Zhang, Y and Yang, CP and He, F and Tian, XX}, title = {[Mini-barcode combined with ITS2 for identification of bulk Artemisiae Scopariae Herba].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {24}, pages = {6685-6691}, doi = {10.19540/j.cnki.cjcmm.20240912.101}, pmid = {39805757}, issn = {1001-5302}, mesh = {*Artemisia/genetics/chemistry/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; }, abstract = {Artemisiae Scoporiae Herba is derived from Artemisia scoparia or A. capillaris. The accurate identification of the herbs, particularly when dealing with bulk samples, is critical for ensuring the quality and efficacy of the medicinal product. This study aimed to establish a comprehensive molecular approach by combining multiple markers for the precise identification of Artemisiae Scoporiae Herba. The ITS2 from A. scoparia, A. capillaris, and other common Artemisia species were retrieved from GenBank. MEGA was used to build a phylogenetic tree with these sequences, and the effectiveness of ITS2 in species identification was assessed. The analysis revealed that while ITS2 could distinguish Artemisiae Scoporiae Herba from other closely related species of Artemisia, it was insufficient to differentiate between A. scoparia and A. capillaris. To address this limitation, the chloroplast genome of A. capillaris was assembled and compared with the published chloroplast genomes of A. scoparia and A. capillaris, on the basis of which a DNA mini-barcode was developed. The rpoA-rps11 region was selected as the target for the development of mini-barcode due to its potential for distinguishing between these two species. Specific primers were designed to differentiate A. scoparia from A. capillaris. The ITS2 sequences and the newly developed mini-barcode were used together for Sanger sequencing to identify individual samples of Artemisiae Scoporiae Herba, while DNA metabarcoding was employed for the identification of bulk samples. The identification results of representative individual samples and bulk samples from different regions consistently confirmed A. capillaris. This study established a method that combined ITS2 and mini-barcode to identify bulk samples of Artemisiae Scoporiae Herba from different regions. This approach overcomes the limitations of morphological and chemical methods, enhancing species identification accuracy and supporting a stable supply of medicinal materials.}, }
@article {pmid39803186, year = {2025}, author = {Yao, J and Zheng, Z and Xu, T and Wang, D and Pu, J and Zhang, Y and Zha, L}, title = {Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of Polygonatum.}, journal = {Ecology and evolution}, volume = {15}, number = {1}, pages = {e70831}, pmid = {39803186}, issn = {2045-7758}, abstract = {The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, have garnered attention of scholars. This study sequenced and analyzed the chloroplast genomes of six species of Polygonatum medicinal plants (P. zanlanscianense, P. kingianum, P. sibiricum, P. cyrtonema, P. filipes, and P. odoratum, respectively) to explore their interspecific relationships. The sequence length (154, 578-155, 807 bp) and genome structure were conserved among the six Polygonatum species, with a typical tetrad structure. Among the 127-131 genes contained in the genomes, 84-85 are protein-coding genes, 37-38 are transfer RNA genes, and 6-8 are ribosomal RNA genes. The genomes contained 64-76 simple sequence repeats (SSRs) and 36-62 long repetitive sequences. Codon bias patterns tended to use codons ending in A/T. In 30 types of codons with RSCU > 1, 93.3% ended in A/T of the six species. Twenty-one highly variable plastid regions were identified in the chloroplast genomes of the six medicinal plants. Furthermore, a phylogenetic analysis encompassing these and 53 other chloroplast genomes of Polygonatum species revealed that P. cyrtonema, P. odoratum, and P. filipes clustered together on one clade, whereas P. kingianum and P. zanlanscianense formed separate clades. Notably, P. sibiricum emerged as a standalone clade, and our phylogenetic tree reinforces the classification of P. sibiricum as forming a monophyly. This study provides a novel basis for intragenus taxonomy and DNA barcoding molecular identification within the genus Polygonatum medicinal plants.}, }
@article {pmid39802739, year = {2025}, author = {Meng, Z and Zheng, Q and Wang, W and Zhu, Y and Li, Y and Dong, F and Luo, W and Zhang, Z and Wang, F and Shen, H and Xie, Q and Li, H}, title = {Oligo-FISH barcode chromosome identification system provides novel insights into the natural chromosome aberrations propensity in the autotetraploid cultivated alfalfa.}, journal = {Horticulture research}, volume = {12}, number = {1}, pages = {uhae266}, pmid = {39802739}, issn = {2662-6810}, abstract = {Alfalfa is one of the most economically valuable forage crops in the world. However, molecular cytogenetic studies in alfalfa lag far behind other cash crops and have reached a bottleneck. Here, we developed a novel chromosome identification system by designing 21 oligo probes in specific regions of each chromosome, which can be used as a barcode to simultaneously distinguish all chromosomes in a cell. Using this system, we revealed the chromosome karyotype features and evolutionary differences among 10 cultivated alfalfa varieties. Interestingly, we also found two chromosomal variation types, i.e. aneuploidy and large chromosomal segment deletions in the seeds of three alfalfa varieties. Variation frequency analysis showed that only 7/173 seeds in those three alfalfa varieties had chromosome aberrations, which indicated that the inheritance and meiosis of alfalfa had evolved to a relatively stable state. Remarkably, 4/7 variation seeds were chromosome 2 aberrations, suggesting that chromosome 2 appears to be more susceptible to natural chromosomal aberrations than other chromosomes during inheritance. DNA sequence variation analysis showed that the difference of presence and absence variations (PAVs) among homologous copies of chromosome 2 was larger than that of the other seven chromosomes. We suggest that such large PAV divergence among homologous copies may provide the physical basis for natural chromosome 2 aberrations propensity. Our study provides a valuable and efficient tool for alfalfa's molecular cytogenetics and sheds new insights into the propensity for natural chromosome aberrations during autopolyploid inheritance.}, }
@article {pmid39801509, year = {2025}, author = {Hao, L and Yu, K and Zhang, F}, title = {Description of five new species from southern China, with note on the type species of Latouchia Pocock, 1901 (Araneae, Halonoproctidae).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e137852}, pmid = {39801509}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Latouchia Pocock, 1901 previously included 25 known species and one subspecies from Asia, 12 species and one subspecies were reported in China.<br><br>NEW INFORMATION: Five new species of Latouchia Pocock, 1901 from southern China are described: L.calcicola sp. nov. (&#x2642;&#x2640;) from Hainan, L.jinyun sp. nov. (&#x2642;&#x2640;) from Chongqing, L.linmufu sp. nov. (&#x2642;&#x2640;) from Hunan, L.wenchuan sp. nov. (&#x2642;) from Sichuan and L.yaoi sp. nov. (&#x2642;&#x2640;) from south part of Shaanxi. DNA barcodes of the new species described herein are provided. The potential error in the previous illustrations of the alleged male of L.fossoria Pocock, 1901 (type species of the genus) is pointed out.}, }
@article {pmid39799216, year = {2025}, author = {Shi, C and Guo, Y and Yao, L and Xu, Y and Zhou, J and Hua, M}, title = {Development of a mitochondrial mini-barcode and its application in metabarcoding for identification of leech in traditional Chinese medicine.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1698}, pmid = {39799216}, issn = {2045-2322}, mesh = {Animals ; *Leeches/genetics ; *DNA Barcoding, Taxonomic/methods ; *Medicine, Chinese Traditional ; RNA, Ribosomal, 16S/genetics ; Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {In Traditional Chinese Medicine (TCM), the medicinal leech is vital for treatments to promote blood circulation and eliminate blood stasis. However, the prevalence of counterfeit leech products in the market undermines the quality and efficacy of these remedies. Traditional DNA barcoding techniques, such as the COI barcode, have been limited in their application due to amplification challenges. This study identified high variability in the 16 S rRNA gene within the mitochondrial genome across five leech species, leading to the development of a novel 219 bp mini-barcode. Compared with the traditional COI barcode, our mini-barcode showed remarkable identification efficiency, classifying 142 out of 147 leech samples from fresh and processed materials. In contrast, the COI barcode could only successfully identify 79 out of the 147 samples. In the case of seven batches of leech decoction pieces, the mini-barcode identified six, whereas the COI barcode only recognized one. Additionally, the mini-barcode effectively discerned five leech species within Chinese patent medicines when combined with metabarcoding technology. These results confirm the mini-barcode's potential as a reliable tool for rapidly and precisely identifying leech species in TCM products.}, }
@article {pmid39795359, year = {2025}, author = {Jiamahate, A and Bozorov, TA and Wang, J and Zhang, J and Zhang, H and Wang, X and Yang, H and Zhang, D}, title = {Insights from DNA Barcodes-Based Phylogenetic Analysis of Medicinal Plants and Estimation of Their Conservation Status: A Case Study in the Tianshan Wild Forest, China.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39795359}, issn = {2223-7747}, support = {Grant No.2021xjkk0500//Third Xinjiang Scientific Expedition Program/ ; 2021-XBQNXZ-015//the West Light Talents Cultivation Program of the Chinese Academy of Sciences/ ; Grant No. 31700289//the National Natural Science Foundation of China/ ; 2022D01A354//the Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; ZDBS-LY-SM009//Key Research Program of Frontier Sciences, Chinese Academy of Sciences/ ; 2022TSYCLJ0049//Leading Talents in Technological Innovation programme/ ; }, abstract = {The Tianshan wild fruit forest region is a vital repository of plant biodiversity, particularly rich in the unique genetic resources of endemic medicinal plants in this ecological niche. However, human activities such as unregulated mining and excessive grazing have led to a significant reduction in the diversity of these medicinal plants. This study represents the first application of DNA barcoding to 101 medicinal plants found in the Tianshan wild fruit forests, using three genetic loci along with morphological identification methods. A phylogenetic analysis was performed to delineate species relationships. The results indicate that the internal transcribed spacer (ITS) region has been identified as the most reliable barcode for species identification across different families, while combining data from multiple gene segments can improve species detection. Moreover, the Analytical Hierarchy Process (AHP) was employed to assess and prioritize the 101 medicinal plants, highlighting 23 species as candidates for urgent conservation efforts in the region. The approaches and insights from this study provide a significant benchmark for DNA barcoding studies on medicinal plants with local significance and establish an evaluative framework for the conservation of biodiversity and the surveillance of genetic resources among medicinal plants in the Tianshan wild fruit forest area.}, }
@article {pmid39794360, year = {2025}, author = {Maulding, ND and Zou, J and Zhou, W and Metcalfe, C and Stuart, JM and Ye, X and Hafner, M}, title = {Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer.}, journal = {NPJ systems biology and applications}, volume = {11}, number = {1}, pages = {5}, pmid = {39794360}, issn = {2056-7189}, mesh = {Humans ; *Breast Neoplasms/genetics/drug therapy ; *Drug Resistance, Neoplasm/genetics ; Female ; Cell Line, Tumor ; Pyridines/pharmacology ; Gene Expression Regulation, Neoplastic/genetics ; Piperazines/pharmacology ; Single-Cell Analysis/methods ; }, abstract = {Understanding transcriptional heterogeneity in cancer cells and its implication for treatment response is critical to identify how resistance occurs and may be targeted. Such heterogeneity can be captured by in vitro studies through clonal barcoding methods. We present TraCSED (Transformer-based modeling of Clonal Selection and Expression Dynamics), a dynamic deep learning approach for modeling clonal selection. Using single-cell gene expression and the fitness of barcoded clones, TraCSED identifies interpretable gene programs and the time points at which they are associated with clonal selection. When applied to cells treated with either giredestrant, a selective estrogen receptor (ER) antagonist and degrader, or palbociclib, a CDK4/6 inhibitor, pathways dynamically associated with resistance are revealed. For example, ER activity is associated with positive selection around day four under palbociclib treatment and this adaptive response can be suppressed by combining the drugs. Yet, in the combination treatment, one clone still emerged. Clustering based on partial least squares regression found that high baseline expression of both SNHG25 and SNCG genes was the primary marker of positive selection to co-treatment and thus potentially associated with innate resistance - an aspect that traditional differential analysis methods missed. In conclusion, TraCSED enables associating features with phenotypes in a time-dependent manner from scRNA-seq data.}, }
@article {pmid39792883, year = {2025}, author = {Park, JW and Park, K and Kwak, IS}, title = {First report of a major management target species, chironomid Paratanytarsus grimmii (Diptera: Chironomidae) larvae, in drinking water treatment plants (DWTPs) in South Korea.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0315390}, doi = {10.1371/journal.pone.0315390}, pmid = {39792883}, issn = {1932-6203}, mesh = {Animals ; *Chironomidae/genetics/classification ; *Larva/genetics ; Republic of Korea ; Drinking Water ; Water Purification ; Phylogeny ; }, abstract = {Ensuring the supply of safe and high-quality drinking water can be compromised by the presence of chironomid larvae in drinking water treatment plants (DWTPs), which may contaminate municipal water systems through freshwater resources. Chironomids are dominant species known for their resilience to a broad range of extreme aquatic environments. This study aimed to identify the morphological characteristics and obtain genetic information of the chironomid Paratanytarsus grimmii found in the water intake source and freshwater resource of DWTPs in Korea, highlighting the potential possibility of a parthenogenetic chironomid outbreak within DWTP networks. The distribution of chironomid larvae at the water intake source site (DY) of the Danyang DWTP and the freshwater resource (ND) of the Nakdong River was investigated. A total of 180 chironomid individuals, encompassing three subfamilies and six species from six 6 genera were identified at the DY site, with Procladius nigriventris being the dominant species. At the ND site, fifty chironomid individuals, encompassing two subfamilies and six species from six genera, were identified, with Cricotopus sylvestris being the dominant species. The morphological characteristics of the head capsule, mentum, mandible, and antennae of six P. grimmii larvae collected from the DY and ND sites were characterized. DNA barcoding and phylogenetic analysis revealed distinct mitochondrial diversities between the P. grimmii larvae from DY and those from ND. These results provide crucial information for the morphological identification and DNA barcoding of the key management target chironomid P. grimmii larvae, which can be used to detect the occurrence of this chironomid species in DWTPs.}, }
@article {pmid39791888, year = {2025}, author = {Manmana, Y and Kinugasa, S and Hiruta, Y and Citterio, D}, title = {Development of a Semiquantitative Barcode Readout Approach for Paper-Based Analytical Devices (PADs) for Enzymatic H2O2 and Glucose Detection.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.4c04113}, pmid = {39791888}, issn = {1520-6882}, abstract = {The integration of barcode technology with smartphones on paper-based analytical devices (PADs) presents a promising approach to bridging manual detection with digital interpretation and data storage. However, previous studies of 1D barcode approaches have been limited to providing only a "yes/no" response for analyte detection. Herein, a method of using barcode readout for semiquantitative signal detection on PADs has been achieved through the integration of barcode technology with a distance-based measurement concept on PADs. To demonstrate the feasibility of this concept, a PAD fabrication strategy incorporating barcodes was explored, using the enzymatic reaction between horseradish peroxidase (HRP), 3,3'-diaminobenzidine (DAB), and H2O2 as a model system. The enzyme-catalyzed polymerization of DAB to polyDAB in the presence of hydrogen peroxide results in the appearance of color observable by the naked eye inside a paperfluidic channel, with the color-changed length depending on the H2O2 concentration. At the same time, the barcode pattern displayed as a result of this distance-based color evolution overlaid with a paper-based barcode layer can be read using a smartphone application. Parameters affecting the signal readout performance were studied. The developed device can be used to detect H2O2 concentrations in the range of 0.25 to 10 mM within 90 min with 79.6% of barcode signals correctly readable. Additionally, results from different smartphone models showed a consistent reading performance (78.4-79.6%). Finally, the quantification of glucose levels in artificial urine samples was demonstrated. This developed PAD signaling strategy offers end-users more simplicity and can be used as a standalone device or in conjunction with other digital devices.}, }
@article {pmid39789982, year = {2025}, author = {Xu, Y and Chan, MTJ and Yang, M and Meng, H and Chen, CH}, title = {Time-resolved single-cell secretion analysis via microfluidics.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4lc00904e}, pmid = {39789982}, issn = {1473-0189}, abstract = {Revealing how individual cells alter their secretions over time is crucial for understanding their responses to environmental changes. Key questions include: When do cells modify their functions and states? What transitions occur? Insights into the kinetic secretion trajectories of various cell types are essential for unraveling complex biological systems. This review highlights seven microfluidic technologies for time-resolved single-cell secretion analysis: 1. Microwell real-time electrical detection: uses microelectrodes for precise, cell-specific, real-time measurement of secreted molecules. 2. Microwell real-time optical detection: employs advanced optical systems for real-time, multiplexed monitoring of cellular secretions. 3. Microvalve real-time optical detection: dynamically analyzes secretions under controlled in situ stimuli, enabling detailed kinetic studies at the single-cell level. 4. Droplet real-time optical detection: provides superior throughput by generating droplets containing single cells and sensors for high-throughput screening. 5. Microwell time-barcoded optical detection: utilizes sequential barcoding techniques to facilitate scalable assays for tracking multiple secretions over time. 6. Microvalve time-barcoded optical detection: incorporates automated time-barcoding via micro-valves for robust and scalable analysis. 7. Microwell time-barcoded sequencing: captures and labels secretions for sequencing, enabling multidimensional analysis, though currently limited to a few time points and extended intervals. This review specifically addresses the challenges of achieving high-resolution timing measurements with short intervals while maintaining scalability for single-cell screening. Future advancements in microfluidic devices, integrating innovative barcoding technologies, advanced imaging technologies, artificial intelligence-powered decoding and analysis, and automations are anticipated to enable highly sensitive, scalable, high-throughput single-cell dynamic analysis. These developments hold great promise for deepening our understanding of biosystems by exploring single-cell timing responses on a larger scale.}, }
@article {pmid39787166, year = {2025}, author = {Guarniero, I and Stancampiano, L and Franch, R and Armaroli, E and Macchioni, F and Negrisolo, E}, title = {Genetic variability and population structure analysis of Protostrongylus oryctolagi (Nematoda: Protostrongylidae) in Lepus europaeus from Central and Northern Italy.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0313998}, pmid = {39787166}, issn = {1932-6203}, mesh = {Animals ; Italy ; *Genetic Variation ; *Haplotypes ; Hares/genetics/parasitology ; Phylogeny ; Genetics, Population ; }, abstract = {Nematodes are abundant and ubiquitous animals which are poorly known at intraspecific level. This work represents the first attempt to fill the gap on basic knowledge of genetic variability and differentiation in Protostrongylus oryctolagi, a nematode parasite of lagomorphs. 68 cox1 sequences were obtained from brown hares collected in five locations in Northern and Central Italy, highlighting the presence of a high amount of genetic variation inside this species. The eleven haplotypes identified (Haplotype diversity equal to 0.702) were split into two lineages: lineage A (comprising six different haplotypes, A1-A6) and lineage B (B1-B5). The mean intra-lineage amount of genetic variation was 0.3%, whereas the inter-lineage percentage of variation was ten-fold higher (3%). These two lineages were non-randomly distributed in the investigated areas. Lineage A showed a preference for Central Italy (Tuscany) even if it was sporadically found also in northern territories (Emilia-Romagna), while B-haplotypes were present exclusively in Emilia-Romagna. The analysis of molecular variance identified two main barriers to gene flow: (i) a strong major one which separate samples of Central Italy (PIA and GR7) from the northern ones (RE1, RE3 and MO1; ΦST = 0.750, P = 0.00); (ii) a secondary faint barrier which separates Pianosa island from Grosseto (ΦST = 0.133, P = 0.00). Any difference was found among northern samples (ΦST = 0.009, P = 0.00). The observed data may be explained by several factors ranging from the parasite's biology (presence of a narrow host spectrum), the final host's behaviour (small home range), the natural dispersion of the host-parasite dyad occurred in past or the recent passive men-mediated migration. Finally, the presence of unconventional shortened amplicons revealed the presence of NUMTs (nuclear copy of mitochondrial genes) in the P. oryctolagi nuclear genome, suggesting caution when using DNA barcode as unique marker for the identification of species belonging to this genus. "In short, if all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable". Nathan Augustus Cobb, from "Nematodes and Their Relationships", 1915.}, }
@article {pmid39781258, year = {2025}, author = {Fernando, MATM and Fu, J and Adamowicz, SJ}, title = {Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation.}, journal = {Ecology and evolution}, volume = {15}, number = {1}, pages = {e70817}, pmid = {39781258}, issn = {2045-7758}, abstract = {Advancements in DNA sequencing technology have facilitated the generation of a vast number of DNA sequences, posing opportunities and challenges for constructing large phylogenetic trees. DNA barcode sequences, particularly COI, represent extensive orthologous sequences suitable for phylogenetic analysis. Phylogenetic placement analysis offers a promising method to integrate COI data into tree-building efforts, yet the impacts of backbone tree completeness and species composition remain under-explored. Using a dataset comprising 27 genes and 4520 species of bony fishes, we assessed the accuracy of phylogenetic inference by "placing" COI sequences onto backbone trees. The backbone tree completeness was varied by subsampling 20%, 40%, 60%, 80%, and 99% of the total species separately, followed by placement of those missing species based on their COI sequences using software packages EPA-ng and APPLES. We also compared the effects of biased, random, and stratified sampling strategies; the latter ensured the representation of all major lineages (Family) of bony fish. Our findings indicate that the placement accuracy is consistently high across all levels of backbone tree completeness, where 70%-78% missing species are correctly placed (by EPA-ng) in the same locations as the reference tree derived from the complete data. High completeness produces slightly high placement accuracy, although in many cases the differences are nonsignificant. For example, at the 99% completeness level with stratified sampling, EPA-ng placed 78% missing species correctly, and when only considering placement with high confidence (LWR > 0.9), the percentage is 87%. Additionally, stratified sampling outperforms random sampling in most cases, and biased sampling has the worst performance. The likelihood-based EPA-ng consistently provide higher accurate placements than the distance-based APPLES. In conclusion, COI-based placement analysis represents a potential route of using the available vast barcoding data for building large phylogenetic trees.}, }
@article {pmid39776788, year = {2024}, author = {Sander, PN and Gillen Miller, JT and Lairson, LL}, title = {Induced cell phenotype activity recording of DNA-tagged ligands.}, journal = {RSC chemical biology}, volume = {}, number = {}, pages = {}, pmid = {39776788}, issn = {2633-0679}, abstract = {Based on their ability to canvas vast genetic or chemical space at low cost and high speed, DNA-encoded libraries (DEL) have served to enable both genomic and small molecule discovery. Current DEL chemical library screening approaches focus primarily on in vitro target-based affinity or activity. Here we describe an approach to record the phenotype-based activity of DNA-encoded small molecules on their cognate barcode in living cells. We transfected chloroalkane-derivatized DNA barcodes carrying photoreleasable small molecules into cells. Following photorelease, bioactive compounds induced expression of a reporter gene cassette containing self-labeling HaloTag protein that becomes covalently modified by encoding barcodes. We demonstrate that we can recover activity information from cells that received active compound following immunoprecipitation-based enrichment. This generalizable approach should enable future strategies that facilitate phenotype-based screens of DNA-encoded chemical libraries in complex cellular or organism level systems.}, }
@article {pmid39775746, year = {2024}, author = {de Freitas, EA and Dos Santos, DB and Moraes Ferreira, CS and Silva-Oliveira, C and Evangelista-Gomes, GF and Veneza, IB}, title = {Integrative use of DNA barcode and morphology reveal high level of diversity in the ornamental fish on the lower Amazon basin.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0316455}, pmid = {39775746}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Electron Transport Complex IV/genetics ; Brazil ; Phylogeny ; Rivers ; Lakes ; Characiformes/genetics/classification ; }, abstract = {The Amazon basin is the world's largest hydrographic basin, in terms of both its total area and its species diversity, with more than 2,700 species of fish. Despite this diversity, the data available on the fish fauna of the Amazon basin are still relatively scant and incomplete, in particular from the streams and floodplain lakes of the lower Amazon, which may contain a large proportion of the still undescribed species of the basin. Many of these species are expected to be of interest to the ornamental fish market. The investigation of the diversity of potential ornamental fish using molecular tools is even more limited. Given this scenario, the present study employed DNA barcoding to investigate the diversity of ornamental fish found in two streams and a floodplain lake of the lower Amazon. The mitochondrially encoded cytochrome c oxidase I (MT-CO1) molecular marker was used to identify the taxa, in combination with morphological keys. A total of 51 ornamental species were identified, representing 13 families and three orders. A majority of the species were found at only one of the sampling points, which indicates that the distribution of the species is influenced by ecological factors. The most speciose order was the Characiformes, followed by the Cichliformes and Siluriformes, while the family with the greatest diversity of species was the Acestrorhamphidae (31.3% of the total number of species), followed by the Cichlidae (27.4%), and the Lebiasinidae (9.8%). One specie was registered in the region of the lower Amazon for the first time, and evidence was found of the possible existence of species not formally described of Aphyocharax, Astyanax, Apareiodon and Hemigrammus.}, }
@article {pmid39774107, year = {2025}, author = {Dufresnes, C and Jablonski, D and Ambu, J and Prasad, VK and Bala Gautam, K and Kamei, RG and Mahony, S and Hofmann, S and Masroor, R and Alard, B and Crottini, A and Edmonds, D and Ohler, A and Jiang, J and Khatiwada, JR and Gupta, SK and Borzée, A and Borkin, LJ and Skorinov, DV and Melnikov, DA and Milto, KD and Konstantinov, EL and Künzel, S and Suchan, T and Arkhipov, DV and Trofimets, AV and Nguyen, TV and Suwannapoom, C and Litvinchuk, SN and Poyarkov, NA}, title = {Speciation and historical invasions of the Asian black-spined toad (Duttaphrynus melanostictus).}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {298}, pmid = {39774107}, issn = {2041-1723}, support = {RFIS 3211101356//National Natural Science Foundation of China (National Science Foundation of China)/ ; SPP1991 VE247/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Bufonidae/genetics/classification ; *Introduced Species ; Phylogeny ; Genetic Speciation ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Madagascar ; Phylogeography ; Asia, Southeastern ; India ; }, abstract = {Animal translocations provide striking examples of the human footprint on biodiversity. Combining continental-wide genomic and DNA-barcoding analyses, we reconstructed the historical biogeography of the Asian black-spined toad (Duttaphrynus melanostictus), a toxic commensal amphibian that currently threatens two biodiversity hotspots through biological invasions (Wallacea and Madagascar). The results emphasize a complex diversification shaped by speciation and mitochondrial introgression that comprises two distinct species. One species (true D. melanostictus) is distributed in the Indian subcontinent and is invasive in Wallacea. The other species, whose nomenclature remains unsettled, diverged from D. melanostictus in the Miocene era (~7 Mya) and diversified across Southeast Asia, from where it was introduced to Madagascar. Remarkably, the Indonesian population of D. melanostictus was recently established from India, which suggests historical, possibly human-assisted dispersal across the Bay of Bengal, reflecting the centuries-old connection between these regions.}, }
@article {pmid39774015, year = {2025}, author = {Appleyard, SA and Ward, RD and Pogonoski, JJ and Graham, A and Last, PR and Deagle, BE and Holmes, B and Gomon, MF and Bray, DJ and Johnson, JW and Hay, AC and Moore, GI and Hammer, MP and Russell, B and Graham, KJ}, title = {Australia's marine fishes DNA barcode reference library for integrated taxonomy, metabarcoding &amp; eDNA research.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {21}, pmid = {39774015}, issn = {2052-4463}, mesh = {*DNA Barcoding, Taxonomic ; Animals ; *Fishes/genetics/classification ; Australia ; *Electron Transport Complex IV/genetics ; Gene Library ; Aquatic Organisms/genetics/classification ; }, abstract = {Over 15 000 species of fishes are found globally in the marine environment and DNA barcodes are used extensively to describe, catalogue, understand and manage this diversity. The dataset outlined here represents a DNA barcode reference library of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) from 9767 voucher specimens (representing at least 2220 species and 288 families) of marine fishes. This publicly available dataset in the Barcode of Life Data System (BOLD) represents 17 years (2005-2022) of barcoding of marine fishes identified from Australian territorial waters. Tissues targeted for sequencing with their matching physical specimens (and extracted DNA), obtained via a multi-agency sampling effort, are mostly maintained and curated by the CSIRO Australian National Fish Collection (ANFC) in Hobart, Australia. Species-level integrated taxonomy (assigned after combined morphological and genetic assessment) has been determined for 91% of the dataset. The library represents the most complete COI barcode reference dataset for marine fishes from Australian waters and is currently utilised for integrated taxonomy, (meta)barcoding and eDNA studies.}, }
@article {pmid39771256, year = {2024}, author = {Fedosov, VE and Pisarenko, OY and Fedorova, AV and Afonina, OM and Ignatova, EA}, title = {On the Cryptic Speciation in the Mosses with East Asia-East North America Disjunction: A Case Study of Two Poorly Understood Mosses from the Southern Extremity of the Russian Far East.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {24}, pages = {}, doi = {10.3390/plants13243558}, pmid = {39771256}, issn = {2223-7747}, support = {23-14-00043//Russian scientific foundation/ ; }, abstract = {A survey of the moss flora of the southernmost part of the Russian Primorsky Territory yielded several intriguing taxa, whose identity is assessed herein based on an integrative morpho-molecular approach. Bellibarbula recurva was previously known in inland Asia only from the Sino-Himalayan region and the new locality is distant from the earlier known ones to ca. 3000 km. Despite the morphological uniformity, Russian specimens are remarkably distinct in sequences of all three obtained DNA markers, approaching an American specimen in the rps4 sequence. Another probable relic, Symblepharis cf. crispifolia, appeared to be fairly common in the southern part of the Primorsky Territory, where low mountains are covered with hard-leaved forests. Russian specimens of Symblepharis cf. crispifolia var. brevipes show significant divergence from S. crispifolia s.str., which also has complex phylogenetic structure, obscuring further taxonomic implications. The description and illustrations of both taxa based on Russian specimens are provided, and the area, where both species occur, is briefly characterized; it includes numerous thermophilous species, which are rare or do not occur northwards. Our case study uncovers the problem of cryptic speciation within species distributed in temperate climate and is considered to represent relics of Arcto-Tertiary flora.}, }
@article {pmid39771168, year = {2024}, author = {Li, X and Jia, H and Liu, D and Zhou, X and Wu, K}, title = {Potential Regional Pollination Services of Spodoptera litura (Lepidoptera: Noctuidae) Migrants as Evidenced by the Identification of Attached Pollen.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {24}, pages = {}, doi = {10.3390/plants13243467}, pmid = {39771168}, issn = {2223-7747}, support = {2023FY100500//Science &amp; Technology Fundamental Resources Investigation Program/ ; }, abstract = {Many species of noctuid moths exhibit long-distance migratory behavior and have an important pollination service function in terrestrial ecosystems. Spodoptera litura (Fabricius) is a globally distributed insect; however, its role in pollination remains underexplored. In this study, the feeding preferences and inter regional pollination of S. litura adults were explored. We conducted pollen analysis on 1253 S. litura migrants captured from 2018 to 2021 on Beihuangcheng Island in the Bohai Strait of China, which is located in the East Asian insect migration path. The results show that an average of 51.1% of S. litura migrants carry plant pollen each year, and the carrying rate shows fluctuations based on sex, year, and season. By combining morphological identification and DNA barcoding, pollen species were identified from 40 species of plants, representing 21 families and 26 genera, mainly from angiosperms of Dicotyledoneae, with Asteraceae, Apocynaceae, and Amaranthaceae being the dominant taxa. The geographical distribution range of Chrysanthemum zawadskii and Adenophora trachelioides and a migration trajectory simulation analysis indicate that S. litura predominantly migrate from Liaoning Province in Northeast China to North China over the Bohai Sea in autumn. These findings indicate the potential pollination activities of S. litura in North China and Northeast China, enriching our understanding of the interaction between S. litura and the plants it pollinates.}, }
@article {pmid39769939, year = {2024}, author = {Wu, Z and Yu, W and Luo, F and Jin, Y and Pan, L and Deng, Q and Wang, Q and Yu, M}, title = {Construction of Heterogeneous Aggregation-Induced Emission Microspheres with Enhanced Multi-Mode Information Encryption.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {24}, pages = {}, doi = {10.3390/molecules29245852}, pmid = {39769939}, issn = {1420-3049}, abstract = {Traditional organic light-emitting materials hinder their anti-counterfeiting application in solid state due to their aggregation-caused quenching effect. A facile and straightforward method was reported to introduce AIE molecules into microspheres and manipulate different reaction parameters to prepare AIE microspheres with different morphologies. In this strategy, fluorescent microspheres with spherical, apple-shaped, and hemoglobin-like types were synthesized. Driven by the photocyclization and oxidation of tetraphenylethene, microspheres can be used as an aqueous fluorescence ink with erasable properties. The fluorescent patterns printed by microsphere ink on paper can be irreversibly erased by prolonged exposure to ultraviolet light (365 nm, 60 mw/cm[2]). Moreover, the multi-morphology microspheres can be further arranged for multiple-information encryption and anti-counterfeiting of barcodes and two-dimensional codes, in which double validation was carried out through fluorescence spectroscopy and laser confocal microscopy. This approach provides a new method for more reliable anti-counterfeiting and information encryption.}, }
@article {pmid39769610, year = {2024}, author = {Ye, C and Tang, X and Yang, F and Zhang, X and Shang, Y and Xia, Y and Wang, Y and Guo, S and Zha, L and Guo, Y and Wen, D}, title = {Rapid and Accurate Detection of Chrysomya megacephala (Diptera: Calliphoridae) Using Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/insects15121008}, pmid = {39769610}, issn = {2075-4450}, support = {No. 82072114//National Natural Science Foundation of China/ ; }, abstract = {Estimating the postmortem interval (PMI) is critical in the field of forensic science, and necrophagous insects play a significant role in this process. Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae) is a common necrophagous insect species, making its rapid and accurate identification essential. However, commonly used molecular biology methods, such as DNA barcode, still have some limitations in identifying necrophagous insects as they are often complex, time-consuming, and reliant on laboratory instruments. Therefore, in this study, we have developed an innovative detection system for the rapid and accurate identification of C. megacephala based on the Cytochrome b gene using recombinase polymerase amplification (RPA) and lateral flow dipstick (LFD) in combination. The developed RPA-LFD detection system achieved complete amplification in just 15 min at 37 °C with good sensitivity and specificity. Only 7.8 × 10[-4] ng or more of target DNA fragments were required, and a positive detection rate of 100% was achieved in 18 C. megacephala samples from actual cases. In addition, the ability of the developed RPA-LFD detection system in combination with rapid DNA extraction methods to enable on-site detection was preliminarily explored. The results suggested that when the RPA-LFD detection system was combined with the grinding ddH2O extraction method (a rapid DNA extraction method), the process from species acquisition to visualization of detection results could be completed in less than 20 min. In conclusion, this innovative RPA-LFD detection system outperforms commonly used molecular biology methods for C. megacephala identification in terms of speed, sensitivity and convenience, making it suitable for direct application at crime scenes, promising to provide important assistance in estimating PMI and expanding the impact of forensic entomological evidence.}, }
@article {pmid39769570, year = {2024}, author = {Han, Y and Achterberg, KV and Chen, X}, title = {DNA Barcodes and Morphology Reveal Two New Species of the Genus Prochas Walkley, 1959 (Ichneumonidae, Campopleginae), from China.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/insects15120968}, pmid = {39769570}, issn = {2075-4450}, support = {31920103005//the Key International Joint Research Program of the Na-325 tional Natural Science Foundation of China/ ; 32070467//the National Natural Science Founda-326 tion of China/ ; 2017YFD0200101//the National Key Research and Development Plan/ ; 2019YFD0300104//the National Key Research and Development Plan/ ; 2018R51004//the Fundamental Research Funds for the Central Universities, the Special Re-328 search Fund for Distinguished Scholars of Zhejiang Province, China/ ; 2023qd31//the Scien-329 tific Research Starting Foundation of Chuzhou University, China/ ; }, abstract = {DNA barcoding is an effective modern tool in taxonomy, evolutionary biology, and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. We combined morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene using the automatic barcode gap discovery (ABGD) to investigate species boundaries. The genus Prochas Walkley (Hymenoptera, Ichneumonidae, Campopleginae) was first reported from China and is new for the Oriental and Eastern Palearctic regions. Using an integrative taxonomy method, two new species P. rugipunctata sp. nov. and P. striata sp. nov. are hereby described and illustrated. A key to the world species and a distribution map are provided.}, }
@article {pmid39769553, year = {2024}, author = {Enguídanos García, A and Galià-Camps, C and Pérez-González, CM and Víquez, D and Mateos, E}, title = {Expanding Soil Invertebrate Knowledge in Panama: The Genus Lepidocyrtus (Collembola, Entomobryidae) in the Parque Natural Metropolitano as a Study Case.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/insects15120951}, pmid = {39769553}, issn = {2075-4450}, support = {2023-GEBI-Panama//European Society of Evolutionary Biology/ ; 2023-Linn&#xe9;Sys-Panama//Linnean Society of London &amp; Systematics Association/ ; Internacionalitzaci&#xf3;UB-Panama//Universitat de Barcelona/ ; 2021SGR689//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; 2021SGR1271//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, abstract = {Panama, located in the heart of the Mesoamerican hotspot, harbors an extraordinary species diversity across the Tree of Life. The Collembola species of the genus Lepidocyrtus play an important role in soil biological processes such as decomposition, being used to monitor soil health and functional parameters. However, the limitation of morphological characters and molecular resources hampers the evaluation of local soil diversity. Here, using 30 Lepidocyrtus specimens collected in the Parque Natural Metropolitano (PNM), we unravel the diversity of this Panamanian protected area through molecular tools and new taxonomic traits. Our phylogenies, in combination with species delimitation analyses, indicate that the PNM harbors an extremely rich community of Lepidocyrtus species, two of them cited in Panama for the first time, and three of them potentially new to science. We highlight that the presence of the dental tubercle and pseudopores on the BP4 region are not monophyletic and, therefore, can be used as supplementary characters to morphologically resolve species complexes. Overall, this study sheds light on the Lepidocyrtus richness of the PNM, which acts as a shelter for Panamanian and the Mesoamerican hotspot species.}, }
@article {pmid39769528, year = {2024}, author = {Chen, H and van Achterberg, C and Li, Y and Liu, Z and Wang, J and Luo, S}, title = {Parasitoids of Insect Pests Feeding on Scaevola taccada (Goodeniaceae) from Yongxing Island in South China Sea.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/insects15120926}, pmid = {39769528}, issn = {2075-4450}, abstract = {Scaevola taccada (Goodeniaceae) is an important evergreen coastal plant on islands in the South China Sea, which shows excellent tolerance for salty and drought conditions. Nevertheless, the growth of S. taccada populations on these islands in the South China Sea has been threatened by a few serious insect pests. However, we know little about the biology of these pests. In this study, we surveyed and identified the parasitoids of two main pests (Herpetogramma submarginale (Swinhoe, 1901) and Ophiomyia scaevolana Shiao and Wu, 1996) of S. taccada communities on Yongxing Island in the South China Sea, with the aim to assess their potential in biological control. Dolichogenidea stantoni (Ashmead, 1904) is a gregarious endoparasitoid of the larva of H. submarginale and contributes an average 48.9% parasitism rate on H. submarginale. Opius biroi, Fischer, 1960 and Euderus albitarsis (Zetterstedt, 1838) are both solitary endoparasitoids of the larva of O. scaevolana, with a respective 5.8% and 64.4% parasitism rate on O. scaevolana. We summarize the species diagnosis, biology, and distribution of the three parasitoid species. The potential of these parasitoids used in biological control is also discussed.}, }
@article {pmid39769523, year = {2024}, author = {Lei, T and Gu, J and Zhao, M and Chen, Y and Song, C and Qi, X}, title = {Seasonal Dynamics of Non-Biting Midges (Diptera: Chironomidae) and Relevant Environmental Factors.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/insects15120921}, pmid = {39769523}, issn = {2075-4450}, support = {32070481//National Natural Science Foundation of China/ ; 32100353//National Natural Science Foundation of China/ ; LY22C040003//Zhejiang Provincial Natural Science Foundation/ ; }, abstract = {The family Chironomidae is speciose and is present in almost all freshwater habitats. Adult non-biting midges emerge from waterbodies and swarm in high numbers, occasionally disrupting people's outdoor activities. In order to understand the seasonal dynamics of species composition, a continuous observation of non-biting midge diversity was performed. Adult non-biting midges were collected using light traps from the autumn of 2022 to the summer of 2023 in an urban wetland park. Species were identified based on morphological characteristics and DNA barcodes. Alpha diversity was evaluated using Margalef, Pielou, and Shannon-Wiener indexes. Beta diversity was evaluated using unconstrained NMDS analysis and constrained CCA. The impacts of environmental factors, including barometric pressure, temperature, relative humidity, and wind speed, on the variation in species composition were estimated in the constrained analyses. A total of 42 species were identified, with 29 species belonging to Chironominae, 9 species belonging to Orthocladiinae, and 4 species belonging to Tanypodinae. The species composition varied across different seasons. Summer sites and autumn sites shared the highest similarity in diversity, and spring sites presented the lowest diversity. The variation was significantly correlated with environmental conditions. The results showed that seasonality is a factor influencing the diversity of adult non-biting midges.}, }
@article {pmid39765491, year = {2024}, author = {Chen, H and Olmi, M and Wang, J and Sun, Q and Luo, S}, title = {DNA Barcoding Reveals Species Diversity and Host Associations of Dryinidae Wasps (Insecta, Hymenoptera): A Case Study from the Xisha Islands in the South China Sea.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {24}, pages = {}, doi = {10.3390/ani14243587}, pmid = {39765491}, issn = {2076-2615}, abstract = {Dryinidae is a cosmopolitan wasp family, with over 1900 species found worldwide [...].}, }
@article {pmid39764454, year = {2024}, author = {Jiang, S and Zhao, G and Ding, Y and Ye, S and Li, Z and You, C and Yin, Y and Guo, X}, title = {Deciphering dengue: novel RNA barcoding segments for enhanced serotype-specific identification and global surveillance of dengue viruses.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1474406}, pmid = {39764454}, issn = {1664-302X}, abstract = {INTRODUCTION: Dengue viruses (DENVs), the causative agents of dengue hemorrhagic fever and dengue shock syndrome, undergo genetic mutations that result in new strains and lead to ongoing global re-infections.<br><br>OBJECTIVES: To address the growing complexity of identifying and tracking biological samples, this study screened RNA barcode segments for the four DENV serotypes, ensuring high specificity and recall rates for DENV identification using segments.<br><br>RESULTS: Through analyzing complete genome sequences of DENVs, we screened eight barcode segments for DENV, DENV-1, DENV-2, DENV-3, and DENV-4 identification. Comparing the screened barcode segments to sequences of known strains and determining the proportion of correctly or incorrectly identified nucleotides, these segments demonstrated an average recall rate at nucleotide level of 91.34% for four DENV serotypes, a specificity of 99.50% at species level within the Flaviviridae family, and a precision rate of 100% for identifying DENVs. For arboviruses, the nucleotide-level specificity was 63.58%. We designed and used the "Barcoding" software to streamline segment design, integrating automated sequence preprocessing, evaluation of barcode segments, and primer design, significantly reducing manual intervention and enhancing overall efficiency. We also established an online database called "Barcodes" for storing and preparing barcode segments.<br><br>CONCLUSION: This work established a standard framework for DENV identification and barcode segment selection, promising significant advancements in the real-time management and control of DENVs, thereby enhancing surveillance capabilities and facilitating targeted interventions in dengue outbreak-prone regions.}, }
@article {pmid39764013, year = {2024}, author = {Comstock, WJ and Navarro, MV and Maybee, DV and Rho, Y and Wagner, M and Wang, Y and Smolka, MB}, title = {Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.12.16.628391}, pmid = {39764013}, issn = {2692-8205}, abstract = {Understanding kinase action requires precise quantitative measurements of their activity in vivo . In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we developed a proteomic kinase activity sensor platform (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a novel versatile system for systematically and spatially probing kinase action in cells.}, }
@article {pmid39763829, year = {2024}, author = {Feng, Y and Chen, D and Applegate, CC and Gonzalez Medina, NY and Kuo, CW and Arogundade, OH and Wright, CL and Xu, F and Drnevich, J and Smith, AM}, title = {Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.12.16.628827}, pmid = {39763829}, issn = {2692-8205}, abstract = {Sample multiplexing is an emerging method in single-cell RNA sequencing (scRNA-seq) that addresses high costs and batch effects. Current multiplexing schemes use DNA labels to barcode cell samples but are limited in their stability and extent of labeling across heterogeneous cell populations. Here, we introduce Nanocoding using lipid nanoparticles (LNPs) for high barcode labeling density in multiplexed scRNA-seq. LNPs reduce dependencies on cell surface labeling mechanisms due to multiple controllable means of cell uptake, amplifying barcode loading 10-100-fold and allowing both protection and efficient release by dissolution. In cultured cell lines and heterogeneous cells from tissue digests, Nanocoding occurs in 40 minutes with stability after sample mixing and requires only commercially available reagents without novel chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples containing lipid-rich debris and heterogeneous cells from adipose tissue of obese rodents show more than 95% labeling with all known subtypes identified. Using Nanocoding, we investigate gene expression changes related to aging in adipose tissue, profiling cells that could not be readily identified with current direct conjugate methods using lipid or antibody conjugates. This ease of generating and tuning these constructs may afford efficient and robust whole-sample multiplexing with minimal sample crosstalk.}, }
@article {pmid39762652, year = {2025}, author = {Hong, SJ and Resnick, SJ and Iketani, S and Cha, JW and Albert, BA and Fazekas, CT and Chang, CW and Liu, H and Dagan, S and Abagyan, MR and Fajtová, P and Culbertson, B and Brace, B and Reddem, ER and Forouhar, F and Glickman, JF and Balkovec, JM and Stockwell, BR and Shapiro, L and O'Donoghue, AJ and Sabo, Y and Freundlich, JS and Ho, DD and Chavez, A}, title = {A multiplex method for rapidly identifying viral protease inhibitors.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {}, pmid = {39762652}, issn = {1744-4292}, support = {1U19AI1711401//HHS | National Institutes of Health (NIH)/ ; 1017195.01//Burroughs Wellcome Fund (BWF)/ ; N/A//jack ma foundation/ ; DGE-2038238//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; }, abstract = {With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor's potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.}, }
@article {pmid39758945, year = {2024}, author = {Senofsky, SR and Zamudio, I and Pan, B and McFadden, CS}, title = {Efficacy of the 28S rDNA barcode in differentiating Caribbean octocorals.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e140454}, pmid = {39758945}, issn = {1314-2828}, abstract = {The ecological landscape of Caribbean reefs is rapidly changing as octocorals fill the void left by declining scleractinian populations. Effective molecular barcodes are necessary to accurately identify these octocorals and monitor this shifting ecosystem. We tested the efficacy of the 28S rDNA as a barcode compared to the most commonly used mtMutS barcode on a collection of octocorals from across the Caribbean. Based on pairwise genetic distance values, 28S appeared to be more effective at differentiating species within the families Plexauridae and Gorgoniidae, while mtMutS was slightly more effective at distinguishing species of Pterogorgiidae. However, the standard 28S rDNA primers did not amplify all species as effectively as mtMutS, especially those belonging to the genus Eunicea. A shorter 28S barcode developed for eDNA applications distinguished species as effectively as the complete 28S barcode.}, }
@article {pmid39758943, year = {2024}, author = {Boóz, B and Kovács, Z and Bartalovics, B and Boda, P and Miliša, M and Pernecker, B and Pařil, P and Rewicz, T and Simon, AB and Csabai, Z and Móra, A}, title = {Chironomids (Diptera) from Central European stream networks: new findings and taxonomic issues.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e136241}, pmid = {39758943}, issn = {1314-2828}, abstract = {BACKGROUND: Chironomidae, with over 7,300 described species, are amongst the most diverse and abundant insect families in freshwater ecosystems worldwide. Chironomids are known for their widespread distribution from various water types. The level of documentation of chironomid fauna varies considerably amongst European countries, with more comprehensive knowledge for Western Europe compared to other regions. Despite the recent extensive sampling effort and the increasing number of available data, the chironomid fauna of Central European countries still remains poorly known.<br><br>NEW INFORMATION: This study contributes to the knowledge of chironomid fauna in three river catchments in Croatia, Hungary and Czechia. A combination of morphological and molecular techniques was employed, with a focus on larvae, although pupae and exuviae were also examined. We found 207 taxa, amongst which 170 were identified to species level. In Croatia, 14 species were recorded for the first time and two species were newly recorded in Czechia. DNA barcoding of 31 specimens resulted in 23 BINs, including eight new ones to BOLD. We provided detailed notes on taxa with taxonomic problems and/or morphological peculiarities. Our results highlight that extensive studies conducted in relatively small areas and a limited range of habitats (only streams in hilly regions) can remarkably contribute to the local and global knowledge on Chironomidae fauna, especially when the taxonomically difficult and often problematic larvae are investigated.}, }
@article {pmid39753672, year = {2025}, author = {Acford-Palmer, H and Andrade, AO and Phelan, JE and Santana, RA and Lopes, SCP and Medeiros, JF and Clark, TG and Araujo, MS and Campino, S}, title = {Application of a targeted amplicon sequencing panel to screen for insecticide resistance mutations in Anopheles darlingi populations from Brazil.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {731}, pmid = {39753672}, issn = {2045-2322}, support = {no. 261868591//British Council, Newton Institutional Links Grant/ ; 304830/2022-4//CNPq productivity grant/ ; BB/X018156/1//UK Research and Innovation/ ; INV-003970/GATES/Bill &amp; Melinda Gates Foundation/United States ; 442653/2019-0//Brazilian Ministry of Health/DECIT/CNPq N&#xb0; 23/2019/ ; CON-80002357//ICEMR/ ; }, abstract = {Large-scale surveillance and informed vector control approaches are urgently needed to ensure that national malaria programs remain effective in reducing transmission and, ultimately, achieving malaria elimination targets. In South America, Anopheles darlingi is the primary malaria vector and is responsible for the majority of Plasmodium species transmission. However, little is known about the molecular markers associated with insecticide resistance in this species. In this study, we developed a low-cost, high throughput amplicon sequencing ("amp-seq") panel, consisting of 11 amplicons targeting genes linked to mosquito species identification (cox-1 and its2) and insecticide resistance (ace-1, GSTe2, vgsc and rdl). When used in tandem with dual-index barcoding of amplicons, this approach permits high numbers of loci and samples to be sequenced in single runs, thereby decreasing costs and increasing efficiency. By screening 200 An. darlingi mosquitoes collected in Brazil, our amp-seq approach identified 10 point mutations leading to amino acid changes in ace-1 (V243I, N294H, S673N, S674N/T) and GSTe2 genes (I114V, D128E, T166I, T179I, and T205A). Overall, our work has demonstrated the utility of amp-seq to provide insights into the genetic diversity of An. darlingi mosquitoes. The amp-seq approach can be applied as a wide-scale insecticide-resistance surveillance technique to better inform vector-control methods.}, }
@article {pmid39752373, year = {2025}, author = {, }, title = {Correction: Mitochondrial DNA barcoding of mosquito species (Diptera: Culicidae) in Thailand.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0317172}, doi = {10.1371/journal.pone.0317172}, pmid = {39752373}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0275090.].}, }
@article {pmid39751771, year = {2024}, author = {Chen, KS and Noureldein, M and Rigan, DM and Hayes, JM and Savelieff, MG and Feldman, EL}, title = {Basic Science and Pathogenesis.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {20 Suppl 1}, number = {}, pages = {e086555}, doi = {10.1002/alz.086555}, pmid = {39751771}, issn = {1552-5279}, mesh = {Animals ; *Interneurons ; Mice ; *Alzheimer Disease/genetics ; Male ; Mice, Transgenic ; Disease Models, Animal ; Transcriptome ; Hippocampus/metabolism ; Parvalbumins/metabolism ; Somatostatin/metabolism/genetics ; }, abstract = {BACKGROUND: Inhibitory interneurons normally regulate neural networks underlying memory and cognition, but are disrupted in Alzheimer's disease. Proper interneuron activity reduces amyloid-beta, whereas hyperexcitability elevates amyloid levels. Still, the underlying pathologic processes mediating interneuron dysfunction remain unknown. Therefore, we employed a spatial transcriptomics approach to map transcriptomic profiles of interneurons in a temporal and spatial manner.<br><br>METHOD: Coronal hemibrain sections from early stage (12 wks) and late stage (30 wks) male mice (5XFAD) underwent fluorescence in situ hybridization to identify interneuron subtypes (parvalbumin-expressing, PV+, or somatostatin-expressing, SST+). Slides were submitted for GeoMx DSP spatial transcriptomics (2 duplicate slides per timepoint, n = 2 5XFAD and n = 2 WT per slide). Regions of interest (ROIs) were defined in hippocampal and cortical regions (Figure 1). UV-liberated barcodes from each ROI, restricted to PV+ or SST+ interneurons, were collected by microcapillary and sequenced by the NanoString Max/Flex nCounter system. Differentially expressed genes (DEGs) were assessed by linear mixed-effect model and the GeoMx analysis suite, and attribution to respective time points, cell type, and anatomic region were sequentially parsed.<br><br>RESULT: In early-stage disease, 1,562 DEGs were uniquely expressed by PV+ interneurons and 2,284 DEGs were uniquely expressed by SST+ interneurons. Similarly, at late-stage disease, 2,790 DEGs were expressed by PV+ interneurons and 2,346 DEGs were uniquely expressed by SST+ interneurons (Figure 2). Focusing on the CA1 region, previously implicated as having a central role in hippocampal dysfunction, interneurons again showed unique alterations. Early-stage PV+ interneurons in CA1 uniquely expressed 310 DEGs, with "metabolic pathways" having the most DEGs (Figure 3). By contrast, early-stage SST+ interneurons in CA1 uniquely expressed 422 DEGs, enriched in pathways canonically linked to "amyotrophic lateral sclerosis" and "Alzheimer disease."<br><br>CONCLUSION: The most significant altered pathways within AD interneurons at the earliest stages of disease included neurodegeneration and metabolism pathways. Zero or few DEGs overlapped across all regions or neuronal subtypes. Thus, interneurons display distinct profiles and transcriptional changes by brain area at early- and late-stage disease. These findings will inform future mechanistic experimentation, and suggest investigation into neural circuit dysfunction in AD will require consideration of anatomic subregion specificity.}, }
@article {pmid39750797, year = {2024}, author = {Perlaza, D and Gil, LL and Cervantes-González, A and Serrano-Requena, S and Tamayo, NV and Sánchez-Aced, &#xc9; and Álvarez-Sánchez, E and Escabias, JA and Muñoz, L and Dolcet, SS and Dols-Icardo, O and Lleo, A and Belbin, O}, title = {Basic Science and Pathogenesis.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {20 Suppl 1}, number = {}, pages = {e090718}, doi = {10.1002/alz.090718}, pmid = {39750797}, issn = {1552-5279}, mesh = {Humans ; *Alzheimer Disease/genetics ; HEK293 Cells ; Genetic Predisposition to Disease ; Polymorphism, Single Nucleotide/genetics ; Linkage Disequilibrium ; Multifactorial Inheritance/genetics ; Synapses/genetics/pathology ; }, abstract = {BACKGROUND: Synaptic degeneration is a primary neuropathological factor associated with cognitive decline in Alzheimer's disease (AD). In 2021, we generated a synaptic Polygenic Risk Score (PRS) that comprised only 8 variants within 6 synaptic genes (APOE, PICALM, BIN1, PTK2B, DLG2 and MINK1) that predicted AD with 72% accuracy in two neuropathological cohorts. This supports the hypothesis that genetic variants that regulate an individual's vulnerability to AD-related synapse degeneration could be used to identify individuals at-risk for AD prior to the appearance of clinical symptoms. The aim of this study was to determine whether the constituent variants of the linkage disequilibrium (LD) blocks represented by the PRS have regulatory activity in vitro.<br><br>METHOD: We cloned an oligonucleotide library of 137 putative regulatory variants each represented by 5 barcodes per allele into pMPRA1 vector. Then we transfected the plasmids into HEK293 cells (n = 5). We extracted DNA and RNA from the cells and sequenced on an Illumina MiSeq. Using the mpra package in R, we normalized the tag counts to a common size of 10 million reads and computed paired log ratios of RNA/DNA counts for each barcode. We used weighted linear models to test for differential activity of the minor versus the major allele of each SNP using the mpralm function, adjusting for multiple testing using the Benjamini-Hochberg method.<br><br>RESULT: We acquired approximately 15 million reads of DNA and RNA from 5 independent experiments. We found that 35 out of the 137 SNPs tested had differential activity between alleles (adj. p <0.05, Figure 1A). Three of the SNPs that showed regulatory activity were included in the PRS (BIN1: rs17014923 and rs35114168; DLG2: rs286043) and the remaining 32 are captured on LD blocks within the synaptic PRS.<br><br>CONCLUSION: All LD captured by the synaptic PRS contain SNPs that impact on regulatory activity, thus supporting a potential mechanism by which changes in the expression of these specific loci that encode synaptic proteins could lead to a modified cumulative risk for AD. Further studies to determine the precise mechanism involved in this regulatory activity at the synapse could guide future therapeutic strategies for AD.}, }
@article {pmid39748949, year = {2024}, author = {Cabrera-Sosa, L and Safarpour, M and Kattenberg, JH and Ramirez, R and Vinetz, JM and Rosanas-Urgell, A and Gamboa, D and Delgado-Ratto, C}, title = {Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1488109}, pmid = {39748949}, issn = {1664-8021}, abstract = {INTRODUCTION: Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control programs. We previously designed AmpliSeq assays for MMS, which include different traits of interest (resistance markers and pfhrp2/3 deletions), and SNP barcodes to provide population genetics estimates of Plasmodium vivax and Plasmodium falciparum parasites in the Peruvian Amazon. The present study compares the genetic resolution of the barcodes in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate population genetics of Amazonian malaria parasites.<br><br>METHODS: We analyzed 51&#xa0;P. vivax and 80&#xa0;P. falciparum samples from three distinct areas in the Loreto region of the Peruvian Amazon: Nueva Jerusal&#xe9;n (NJ), Mazan (MZ), and Santa Emilia (SE). Population genetics estimates and costs were compared using the SNP barcodes (P. vivax: 40 SNPs and P. falciparum: 28 SNPs) and MS panels (P. vivax: 16 MS and P. falciparum: 7 MS).<br><br>RESULTS: The P. vivax genetic diversity (expected heterozygosity, He) trends were similar for both markers: He MS = 0.68-0.78 (p > 0.05) and He SNP = 0.36-0.38 (p > 0.05). P. vivax pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS = 0.04-0.14 and FST-SNP = 0.03-0.12 (pairwise p > 0.05). In addition, P. falciparum genetic diversity trends (He MS = 0-0.48, p < 0.05; He SNP = 0-0.09, p < 0.05) and pairwise FST comparisons (FST-MS = 0.14-0.65, FST-SNP = 0.19-0.61, pairwise p > 0.05) were concordant between both panels. For P. vivax, no geographic clustering was observed with any panel, whereas for P. falciparum, similar population structure clustering was observed with both markers, assigning most parasites from NJ to a distinct subpopulation from MZ and SE. We found significant differences in detecting polyclonal infections: for P. vivax, MS identified a higher proportion of polyclonal infections than SNP (69% vs. 33%, p = 3.3 &#xd7; 10[-5]), while for P. falciparum, SNP and MS detected similar rates (46% vs. 31%, p = 0.21). The AmpliSeq assay had a higher estimated per-sample cost compared to MS ($183 vs. $27-49).<br><br>DISCUSSION: The SNP barcodes in the AmpliSeq assays offered comparable results to MS for investigating population genetics in P. vivax and P. falciparum populations, despite some discrepancies in determining polyclonality. Given both panels have their respective advantages and limitations, the choice between both should be guided by research objectives, costs, and resource availability.}, }
@article {pmid39747844, year = {2025}, author = {Coulombe, P and Tomellini, E and Chagraoui, J and Mayotte, N and Sauvageau, G}, title = {Deciphering the effect of UM171 on human hematopoietic progenitor cell fate through clonal analysis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {195}, pmid = {39747844}, issn = {2041-1723}, support = {PJT-178113//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; FDN-143286//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; HZN-C4R1-1//Stem Cell Network (Le R&#xe9;seau de cellules souches)/ ; }, mesh = {*Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Animals ; *Cell Differentiation ; Mice ; *Mast Cells/cytology/metabolism/drug effects ; Cell Proliferation ; Cell Lineage ; Cell Self Renewal/drug effects ; Hematopoietic Stem Cell Transplantation ; Signal Transduction ; }, abstract = {Ex vivo expansion of hematopoietic stem cells (HSC) requires the maintenance of a stemness state while cells are proliferating. This can be achieved via exposure to UM171 which leads to the degradation of chromatin modifiers and prevents the loss of key epigenetic marks. However, the chromatin landscape varies across populations within the hematopoietic system and the effect of UM171 on self-renewal and differentiation potential of different hematopoietic progenitor cells is less characterized. To address this, we use the CellTag barcoding approach to track the fate of individual stem and progenitor cells during in vitro expansion. We show that, in addition to its HSC self-renewing property, UM171 specifically modulates cell fate of a precursor common to erythroid, megakaryocytic, and mast cells in favor of self-renewal and a mast-bias differentiation trajectory. This differentiation bias can be driven by pro-inflammatory signaling pathways that are activated downstream of UM171 and results in an abundant mast cell population that can be transplanted as part of the graft to populate mice tissues in xenotransplantation studies.}, }
@article {pmid39747602, year = {2025}, author = {Cho, S and Martino, N and Yun, SH}, title = {Half-wave nanolasers and intracellular plasmonic lasing particles.}, journal = {Nature nanotechnology}, volume = {}, number = {}, pages = {}, pmid = {39747602}, issn = {1748-3395}, support = {R01-EB033155//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01-EB034687//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; Fund for Medical Discovery fundamental research fellowship award//Massachusetts General Hospital (MGH)/ ; }, abstract = {The ultimate limit for laser miniaturization would be achieving lasing action in the lowest-order cavity mode within a device volume of ≤(λ/2n)[3], where λ is the free-space wavelength and n is the refractive index. Here we highlight the equivalence of localized surface plasmons and surface plasmon polaritons within resonant systems, introducing nanolasers that oscillate in the lowest-order localized surface plasmon or, equivalently, half-cycle surface plasmon polariton. These diffraction-limited single-mode emitters, ranging in size from 170 to 280 nm, harness strong coupling between gold and InxGa1-xAs1-yPy in the near-infrared (λ = 1,000-1,460 nm), away from the surface plasmon frequency. This configuration supports only the lowest-order dipolar mode within the semiconductor's broad gain bandwidth. A quasi-continuous-level semiconductor laser model explains the lasing dynamics under optical pumping. In addition, we fabricate isolated gold-coated semiconductor discs and demonstrate higher-order lasing within live biological cells. These plasmonic nanolasers hold promise for multi-colour imaging and optical barcoding in cellular applications.}, }
@article {pmid39745647, year = {2025}, author = {Raj, B}, title = {Single-Cell Profiling of Lineages and Cell Types in the Vertebrate Brain.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {299-310}, pmid = {39745647}, issn = {1940-6029}, mesh = {Animals ; *Single-Cell Analysis/methods ; *Brain/cytology/metabolism ; *Zebrafish/genetics ; *CRISPR-Cas Systems ; *Cell Lineage/genetics ; *Gene Editing/methods ; Transcriptome ; Gene Expression Profiling/methods ; }, abstract = {CRISPR-Cas tools have recently been adapted for cell lineage tracing during development. Combined with single-cell RNA sequencing, these methods enable scalable lineage tracing with single-cell resolution. Here, I describe, scGESTALTv2, which combines cumulative CRISPR-Cas9 editing of a lineage barcode array with transcriptional profiling via droplet-based single-cell RNA sequencing (scRNA-seq). The technique is applied in developing zebrafish brains to generate mutations in the barcode array during development. The recorded lineages along with cellular transcriptomes are then extracted via scRNA-seq to define cell relationships among thousands of profiled brain cells and dozens of cell types.}, }
@article {pmid39745646, year = {2025}, author = {Bowling, S and Camargo, FD}, title = {CARLIN: A Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {281-298}, pmid = {39745646}, issn = {1940-6029}, mesh = {Animals ; Mice ; *Cell Lineage/genetics ; *DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Single-Cell Analysis/methods ; CRISPR-Cas Systems ; Gene Editing/methods ; Gene Expression/genetics ; }, abstract = {The CRISPR-activated repair lineage tracing (CARLIN) mouse line uses DNA barcoding to enable high-resolution tracing of cell lineages in vivo (Bowling et al, Cell 181, 1410-1422.e27, 2020). CARLIN mice contain expressed barcodes that allow simultaneous interrogation of lineage and gene expression information from single cells. Furthermore, barcode editing is fully inducible, resulting in cell lineage labeling that can be performed at any time point in development or adulthood. This chapter details the protocols followed for maintaining CARLIN mice, inducing barcoding, and amplifying the CARLIN barcode from DNA, RNA, and single-cell RNA-sequencing libraries for next-generation sequencing.}, }
@article {pmid39745644, year = {2025}, author = {Spanjaard, B and Junker, JP}, title = {LINNAEUS: Simultaneous Single-Cell Lineage Tracing and Cell Type Identification.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {243-263}, pmid = {39745644}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Animals ; Gene Editing/methods ; Gene Expression Profiling/methods ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Humans ; }, abstract = {A key goal of biology is to understand the origin of the many cell types that can be observed during diverse processes such as development, regeneration, and disease. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the origins of cell states and relationships between cells remains challenging. Here we present LINNAEUS (Spanjaard et al, Nat Biotechnol 36:469-473. https://doi.org/10.1038/nbt.4124 , 2018; Hu et al, Nat Genet 54:1227-1237. https://doi.org/10.1038/s41588-022-01129-5 , 2022) (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, LINNAEUS can be used to reconstruct organism-wide single-cell lineage trees. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.}, }
@article {pmid39745643, year = {2025}, author = {Baron, CS and Alemany, A}, title = {Paired Single-Cell Transcriptome and DNA Barcode Detection in Zebrafish Using ScarTrace.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {221-241}, pmid = {39745643}, issn = {1940-6029}, mesh = {Animals ; *Zebrafish/genetics ; *Single-Cell Analysis/methods ; *DNA Barcoding, Taxonomic/methods ; *CRISPR-Cas Systems ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; Embryo, Nonmammalian/metabolism ; }, abstract = {ScarTrace is a CRISPR/Cas9-based genetic lineage tracing method that allows for uniquely barcoding the DNA of single cells at a target GFP sequence during developing zebrafish embryos. Single cells from barcoded adult zebrafish can be isolated from various tissues (e.g., marrow, brain, eyes, fins), and their transcriptome and barcode sequences are captured by single-cell cDNA amplification and genomic DNA nested PCR, respectively. Computationally, cell type and barcode identification permit clone tracing and lineage tree reconstruction of tissues to unravel fate decisions during embryogenesis.}, }
@article {pmid39745641, year = {2025}, author = {Fang, W and Yang, Y and Ji, H and Kalhor, R}, title = {Reconstructing Progenitor State Hierarchy and Dynamics Using Lineage Barcoding Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {177-199}, pmid = {39745641}, issn = {1940-6029}, mesh = {*Cell Lineage/genetics ; *Algorithms ; Animals ; Phylogeny ; Cell Differentiation/genetics ; Stem Cells/cytology/metabolism ; Single-Cell Analysis/methods ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Software ; Humans ; }, abstract = {Measurements of cell phylogeny based on natural or induced mutations, known as lineage barcodes, in conjunction with molecular phenotype have become increasingly feasible for a large number of single cells. In this chapter, we delve into Quantitative Fate Mapping (QFM) and its computational pipeline, which enables the interrogation of the dynamics of progenitor cells and their fate restriction during development. The methods described here include inferring cell phylogeny with the Phylotime model, and reconstructing progenitor state hierarchy, commitment time, population size, and commitment bias with the ICE-FASE algorithm. Evaluation of adequate sampling based on progenitor state coverage statistics is emphasized for interpreting the QFM results. Overall, this chapter describes a general framework for characterizing the dynamics of cell fate changes using lineage barcoding data.}, }
@article {pmid39745638, year = {2025}, author = {Ratz, M and von Berlin, L}, title = {Clonal Tracking in the Mouse Brain with Single-Cell RNA-Seq.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {103-137}, pmid = {39745638}, issn = {1940-6029}, mesh = {Animals ; Mice ; *Single-Cell Analysis/methods ; *Brain/metabolism/cytology/embryology ; RNA-Seq/methods ; Cell Lineage/genetics ; Cell Tracking/methods ; Lentivirus/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Gene Expression Analysis ; }, abstract = {Lineage tracing methods enable the identification of all progeny generated by a single cell. High-throughput lineage tracing in the mammalian brain involves parallel labeling of thousands of progenitor cells with genetic barcodes in vivo followed by single-cell RNA-seq of lineage relations and cell types. Here we describe the generation of barcoded lentivirus, microinjections into the embryonic day 9.5 mouse forebrain, dissociation of 2-week-old mouse brain tissue, single-cell RNA-seq library preparation, and data analysis using a custom software. Compared to traditional methods based on sparse fluorophore labeling of progenitor cells, lineage tracing with genetic barcodes and single-cell RNA-seq has a >100-fold higher throughput while using >10 times fewer mice.}, }
@article {pmid39745637, year = {2025}, author = {Gentile, E and Maynard, A and He, Z and Treutlein, B}, title = {Lineage Recording in Human Brain Organoids with iTracer.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {85-101}, pmid = {39745637}, issn = {1940-6029}, mesh = {Humans ; *Organoids/cytology/metabolism ; *Brain/cytology ; *Induced Pluripotent Stem Cells/cytology/metabolism ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; *CRISPR-Cas Systems ; Transcriptome ; Cell Differentiation ; }, abstract = {Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enables highly resolved descriptions of cell states within these systems; however, approaches are needed to directly determine the lineage relationship between cells. Here we provide a detailed protocol (Fig. 1) for the application of iTracer (He Z, Maynard A, Jain A, et al., Nat Methods 19:90-99, 2022), a recently published lineage recorder that combines reporter barcodes with inducible CRISPR-Cas9 scarring and is compatible with single-cell and spatial transcriptomics. iTracer is used to explore clonality and lineage dynamics during brain organoid development. More broadly, iTracer can be adapted to any iPSC-derived culture system to dissect lineage dynamics during normal or perturbed development.}, }
@article {pmid39745636, year = {2025}, author = {Rodriguez Fraticelli, AE and Sánchez, PS}, title = {Single-Cell Lineage Tracing and Clonal State-Fate Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {65-84}, pmid = {39745636}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Humans ; Cell Differentiation ; Animals ; Clone Cells/cytology ; DNA Barcoding, Taxonomic/methods ; Lentivirus/genetics ; Cell Tracking/methods ; }, abstract = {Lineage tracing has significantly advanced our comprehension in many areas of biology, such as development or immunity, by precisely measuring cellular processes like migration, division, or differentiation across labeled cells and their progeny. Traditional recombinase-based prospective lineage tracing is limited by the need for a priori cell type information and is constrained in the numbers of clones it can simultaneously track. In this sense, clonal lineage tracing with integrated random barcodes offers a robust alternative, enabling researchers to label and track a vast array of cells and their progeny over time. Moreover, clonal lineage tracing can be combined with single-cell omics technologies to study cell states and their maintenance over time. Key steps in these protocols include stable barcode integration, cell division to expand clones, and simultaneous capture of cellular properties with barcode information. Here, we comment on those steps and summarize important parameters to take into account during the design of single-cell lineage tracing experiments. Also, we present the main features for various available lentiviral libraries of expressed barcodes than can be captured alongside the transcriptome of individual cells. We cover other crucial aspects of experimental design, such as the optimization of cellular sampling, library diversity, and the minimization of clonal dropouts. Regarding sequencing data analysis, we provide some tips based on our experience, as well as available computational tools for the assignment of clonal identities and the identification of fate determinants. We finally discuss limitations of current methodologies and use an example step-by-step protocol to illustrate key points during the process. In sum, we provide a roadmap for considering and implementing single-cell lineage tracing studies to comprehensively explore fate determinants and their mechanisms.}, }
@article {pmid39745115, year = {2025}, author = {González-Peña, R and Laredo-Tiscareño, SV and Huerta, H and Hernández-Triana, LM and De Luna-Santillana, EJ and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and García-Rejón, JE and Hidalgo-Martínez, DO and Garza-Hernández, JA}, title = {FIRST STATE AND NATIONAL RECORDS OF CULICOIDES DEBILIPALPIS AND CULICOIDES REEVESI IN CHIHUAHUA, MEXICO.}, journal = {Journal of the American Mosquito Control Association}, volume = {}, number = {}, pages = {}, doi = {10.2987/24-7207}, pmid = {39745115}, issn = {1943-6270}, abstract = {In July 2022, adult female Culicoides were collected from San Buenaventura (54 specimens) and Urique (3 specimens) in Chihuahua, Mexico. Culicoides reevesi and Culicoides debilipalpis were new records for the state, with C. reevesi also being a first for Mexico. The study highlights DNA barcode identification challenges and emphasizes the need for ongoing surveillance along the Mexico-USA border.}, }
@article {pmid39745059, year = {2025}, author = {Huang, Z and Xie, X and Wu, Y and Liu, R and Lv, Y}, title = {Breaking Barcode Limits: Metal Nanoparticle Lego Brick Self-Assembly for High-Throughput Screening.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.4c13706}, pmid = {39745059}, issn = {1520-5126}, abstract = {As precision medicine increasingly reveals the biological diversity among individuals, the demand for higher-throughput screening techniques, particularly suspension array technologies capable of more multiplexing from smaller samples in a single run, is intensifying. However, advancements in the multiplexing capability of current suspension platforms have lagged with limited alleviation, necessitating breakthroughs for innovative solutions that enable larger-scale measurements. Here, we introduce such a breakthrough with a novel mass-cytometric barcode engineering by metal nanoparticle-based "Lego Brick"-like self-assembly for high-throughput barcode design and capacity amplification. The suspension array capacity can be expanded to over 20,500 unique barcodes by flexibly assembling just 10 types of barcoding units (metal nanoparticles) onto the surface of the barcoding center (magnetic spheres) through a universal biotin-streptavidin binding template, significantly enhancing both throughput and versatility. Further multiplexed immunoassay, termed MassMAP, demonstrates high-throughput profiling of cancer biomarkers, highlighting the revolutionary potential of Lego Brick self-assembly in massive cytometric screening for higher-throughput applications.}, }
@article {pmid39742275, year = {2024}, author = {Ado, S and Dong, C and Attaf, N and Moussa, M and Carrier, A and Milpied, P and Navarro, JM}, title = {FB5P-seq-mAbs: monoclonal antibody production from FB5P-seq libraries for integrative single-cell analysis of B cells.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1505971}, doi = {10.3389/fimmu.2024.1505971}, pmid = {39742275}, issn = {1664-3224}, mesh = {Animals ; *Single-Cell Analysis/methods ; *Antibodies, Monoclonal/immunology/genetics ; *B-Lymphocytes/immunology/metabolism ; Mice ; Receptors, Antigen, B-Cell/genetics/immunology ; Gene Library ; Flow Cytometry/methods ; Sequence Analysis, RNA/methods ; Humans ; Transcriptome ; }, abstract = {Parallel analysis of phenotype, transcriptome and antigen receptor sequence in single B cells is a useful method for tracking B cell activation and maturation during immune responses. However, in most cases, the specificity and affinity of the B cell antigen receptor cannot be inferred from its sequence. Antibody cloning and expression from single B cells is then required for functional assays. Here we propose a method that integrates FACS-based 5'-end single-cell RNA sequencing (FB5P-seq) and monoclonal antibody cloning for integrative analysis of single B cells. Starting from a cell suspension, single B cells are FACS-sorted into 96-well plates for reverse transcription, cDNA barcoding and amplification. A fraction of the single-cell cDNA is used for preparing 5'-end RNA-seq libraries that are sequenced for retrieving transcriptome-wide gene expression and paired BCR sequences. The archived cDNA of selected cells of interest is used as input for cloning heavy and light chain variable regions into antibody expression plasmid vectors. The corresponding monoclonal antibodies are produced by transient transfection of a eukaryotic producing cell line and purified for functional assays. We provide detailed step-by-step instructions and describe results obtained on ovalbumin-specific murine germinal center B cells after immunization. Our method is robust, flexible, cost-effective, and applicable to different B cell types and species. We anticipate it will be useful for mapping antigen specificity and affinity of rare B cell subsets characterized by defined gene expression and/or antigen receptor sequence.}, }
@article {pmid39741786, year = {2024}, author = {Haverinen, R and Pototski, A and Mutanen, M and Mikalauskas, D and Yakovlev, RV and Müller, GC and Prozorov, AM and Saldaitis, A}, title = {Integrative review of Xylomoiastrix, X.retinax and X.stangelmaieri (Lepidoptera, Noctuidae, Xyleninae, Apameini).}, journal = {ZooKeys}, volume = {1221}, number = {}, pages = {309-342}, doi = {10.3897/zookeys.1221.132205}, pmid = {39741786}, issn = {1313-2989}, abstract = {The relationship of Xylomoiastrix Mikkola, 1980; Xylomoiaretinax Mikkola, 1998; and Xylomoiastangelmaieri Mikkola, 1998 is reconsidered based on 59 genitalia slides (37 males and 22 females) and 40 barcodes of adults collected from the type localities and areas in-between. Due to lack of stable morphologic differences, apart from the wing coloration of X.retinax, and low genetic distance between the three, they are considered as three subspecies of X.strix: the nominotypical one X.strixstangelmaieri stat. nov. and X.strixretinax stat. nov. Included are photographs of all specimens covering 37 adults, and 28 male and 18 female genitalia, as well as a phylogenetic tree and a map showing collecting localities.}, }
@article {pmid39739757, year = {2024}, author = {Ramaprasad, A and Blackman, MJ}, title = {A scaleable inducible knockout system for studying essential gene function in the malaria parasite.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae1274}, pmid = {39739757}, issn = {1362-4962}, support = {751865//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; //European Society of Clinical Microbiology and Infectious Diseases/ ; 220318/A/20/Z/WT_/Wellcome Trust/United Kingdom ; CC2129/CRUK_/Cancer Research UK/United Kingdom ; CC2129/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The malaria parasite needs nearly half of its genes to propagate normally within red blood cells. Inducible ways to interfere with gene expression like the DiCre-lox system are necessary to study the function of these essential genes. However, existing DiCre-lox strategies are not well-suited to be deployed at scale to study several genes simultaneously. To overcome this, we have developed SHIFTiKO (frameshift-based trackable inducible knockout), a novel scaleable strategy that uses short, easy-to-construct, barcoded repair templates to insert loxP sites around short regions in target genes. Induced DiCre-mediated excision of the flanked region causes a frameshift mutation resulting in genetic ablation of gene function. Dual DNA barcodes inserted into each mutant enables verification of successful modification and induced excision at each locus and collective phenotyping of the mutants, not only across multiple replication cycles to assess growth fitness but also within a single cycle to identify specific phenotypic impairments. As a proof of concept, we have applied SHIFTiKO to screen the functions of malarial rhomboid proteases, successfully identifying their blood stage-specific essentiality. SHIFTiKO thus offers a powerful platform to conduct inducible phenotypic screens to study essential gene function at scale in the malaria parasite.}, }
@article {pmid39739202, year = {2024}, author = {Bard, NW and Davies, TJ and Cronk, QCB}, title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14056}, doi = {10.1111/1755-0998.14056}, pmid = {39739202}, issn = {1755-0998}, support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.}, }
@article {pmid39736908, year = {2024}, author = {Nguyen, QH and Van Nguyen, T and Vi, TTX and Vu, TTT and Nguyen, LTN and Nguyen, YTH and Nguyen, HD and Tu, TQ and Chu, MH}, title = {Dataset on ITS and some chloroplast DNA regions of Boehmeria holosericea Blume in Vietnam.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {111193}, pmid = {39736908}, issn = {2352-3409}, abstract = {Species of the Boehmeria genus have the potential to be natural medicines and have industrial fibre production uses. Many species of this genus are morphologically similar and are difficult to distinguish, especially when their morphology is distorted. This dataset includes sequence information of several DNA regions isolated from the genome of Boehmeria holosericea, namely ITS (from the nuclear genome), matK, trnL-trnF, trnH-psbA, and rpoC1 (from the chloroplast genome) and phylogenetic analysis results based on the isolated sequences. On the phylogenetic tree based on the matK gene sequence, B. holosericea is grouped with B. umbrosa, B. clidemioides, B. spicata, and B. macrophylla with a bootstrap coefficient of 100%. In the phylogenetic tree based on the trnH-psbA spacer region sequences, B. holosericea was grouped with B. clidemioides (a bootstrap coefficient of 96%). In the phylogenetic tree based on the rpoC1 gene sequences, B. holosericea was grouped with B. spicata (a bootstrap coefficient of 100%). In the phylogenetic tree based on the ITS region sequences, B. holosericea was grouped with B. macrophylla (a bootstrap coefficient of 73%), and based on the trnL-trnF spacer region, B. holosericea was grouped with B. pilociuscula (a bootstrap coefficient of 16%). Two genes, matK and rpoC1 and the trnH-psbA region from the chloroplast genome, are potential DNA barcode candidates that could aid in the species identification of B. holosericea. This dataset the first report on the ITS, matK, trnL-trnF, trnH-psbA, and rpoC1 sequences and the phylogeny of B. holosericea.}, }
@article {pmid39732835, year = {2024}, author = {Eastburn, DJ and White, KS and Jayne, ND and Camiolo, S and Montis, G and Ha, S and Watson, KG and Yeakley, JM and McComb, J and Seligmann, B}, title = {High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31285}, pmid = {39732835}, issn = {2045-2322}, support = {R44GM140771/GF/NIH HHS/United States ; R44GM140771/GF/NIH HHS/United States ; R44GM140771/GF/NIH HHS/United States ; R44GM140771/GF/NIH HHS/United States ; }, mesh = {*Single-Cell Analysis/methods ; Animals ; *Brain/metabolism ; *Kidney/metabolism/cytology ; *Lung/metabolism/cytology ; *Gene Expression Profiling/methods ; Mice ; Transcriptome ; Humans ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective and high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial indexing approach, all probes within the same fixed cell receive an identical barcode, enabling the reconstruction of single-cell gene expression profiles across as few as several hundred cells and up to 100,000 + cells per sample. The TempO-LINC approach is easily scalable based on the number of barcodes and rounds of barcoding performed; however, for the experiments reported in this study, the assay utilized over 5.3 million unique barcodes. TempO-LINC offers a robust protocol for fixing and banking cells and displays high-sensitivity gene detection from multiple diverse sample types. We show that TempO-LINC has a multiplet rate of less than 1.1% and a cell capture rate of ~ 50%. Although the assay can accurately profile the whole transcriptome (19,683 human, 21,400 mouse and 21,119 rat genes), it can be targeted to measure only actionable/informative genes and molecular pathways of interest - thereby reducing sequencing requirements. In this study, we applied TempO-LINC to profile the transcriptomes of more than 90,000 cells across multiple species and sample types, including nuclei from mouse lung, kidney and brain tissues. The data demonstrated the ability to identify and annotate more than 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies with high data quality.}, }
@article {pmid39731283, year = {2024}, author = {Nieto-Clavijo, C and Morales, L and Delgado-Aldana, A and Hernández, PC and Torres-Molina, I and Gonzalez-Cuiza, A and Cortés-Muñoz, F and Chaparro-Olaya, J}, title = {Enhanced Blastocystis subtyping from stool samples using semi-nested barcode PCR: validation with an NGS-based approach.}, journal = {BioTechniques}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/07366205.2024.2442835}, pmid = {39731283}, issn = {1940-9818}, abstract = {In 2006, a PCR method was introduced to subtype Blastocystis by Sanger sequencing of an ≈610 bp amplicon of the 18S rRNA gene. This method, known as barcoding-PCR, has become widespread, although the primer pair used can amplify non-Blastocystis sequences, which can result in false positives. Barcoding-PCR is most effective with DNA extracted from Blastocystis cultures, limiting its sensitivity when used directly with stool samples. As a result, barcoding-PCR can sometimes yield negative results for stool samples confirmed as Blastocystis-positive by microscopy. To improve subtyping from stool-derived DNA, we developed a Semi-Nested barcode PCR that amplifies the barcoding region in a second reaction. Our study shows that this Semi-Nested approach outperforms classical barcoding-PCR, detecting Blastocystis more reliably from stool samples with stronger gel signals and no false positives. This was confirmed by near-complete concordance (68/70 samples) with the Santin-PCR coupled to Next-Generation Sequencing (NGS) as reference standard for Blastocystis subtyping. Of particular interest, one amplicon matched the only previous report of ST35, marking this as the second global detection of ST35 and the first in Colombia. Overall, Semi-Nested barcoded PCR offers a more robust and sensitive alternative compared to classical barcoding-PCR for subtyping Blastocystis directly from stool samples.}, }
@article {pmid39730712, year = {2024}, author = {Nurtaza, A and Dyussembekova, D and Islamova, S and Samatova, I and Zhanybekova, Z and Umirzakova, A and Magzumova, G and Muranets, A and Kakimzhanova, A}, title = {In Vitro conservation and genetic diversity analysis of rare species Ribes janczewskii.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31117}, pmid = {39730712}, issn = {2045-2322}, support = {AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; }, mesh = {*Genetic Variation ; Genotype ; Fruit/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Conservation of Natural Resources ; }, abstract = {Ribes janczewskii is a rare and valuable plant known for its resistance to spring frosts, pests, and diseases. It is used in hybridization to develop resistant currant varieties but is on the verge of extinction, listed in Kazakhstan Red Book. This study developed a micropropagation and slow-growth storage protocol for conservation. Genotypes were identified through DNA barcode analysis (rbcL, ITS, and matK) and sequences uploaded to the National Center for Biotechnology Information database. Genetic diversity was assessed using iPBS primers, generating 98 fragments with 88-94% polymorphic bands. Biochemical analysis of fruits showed vitamin C content from 4.64 to 5.61 mg/100 g, vitamin E from 2.26 to 3.16 mg/100 g, vitamin B5 from 3.18 to 4.93 mg/100 g, and quercetin up to 12.5 mg/100 g. Micropropagation stages were optimized with 12% hydrogen peroxide for surface sterilization, achieving up to 73.3% explant viability. Effective hormonal combinations for in vitro culture included WPM with BAP 0.2 mg L[-1] and GA 0.5 mg L[-1], and for propagation, BAP 0.25 mg L[-1], GA 0.5 mg L[-1], and IBA 0.5 mg L[-1]. Mannitol (20 g L[-1]) was used for slow-growth storage, keeping explants viable for 4 months without re-cultivation.}, }
@article {pmid39729996, year = {2024}, author = {Park, J and Cook, S and Lee, D and Choi, J and Yoo, S and Bae, S and Im, HJ and Lee, D and Choi, H}, title = {Generation of super-resolution images from barcode-based spatial transcriptomics by deep image prior.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {100937}, doi = {10.1016/j.crmeth.2024.100937}, pmid = {39729996}, issn = {2667-2375}, abstract = {Spatially resolved transcriptomics (ST) has revolutionized the field of biology by providing a powerful tool for analyzing gene expression in situ. However, current ST methods, particularly barcode-based methods, have limitations in reconstructing high-resolution images from barcodes sparsely distributed in slides. Here, we present SuperST, an algorithm that enables the reconstruction of dense matrices (higher-resolution and non-zero-inflated matrices) from low-resolution ST libraries. SuperST is based on deep image prior, which reconstructs spatial gene expression patterns as image matrices. Compared with previous methods, SuperST generated output images that more closely resembled immunofluorescence images for given gene expression maps. Furthermore, we demonstrated how one can combine images created by SuperST with computer vision algorithms. In this context, we proposed a method for extracting features from the images, which can aid in spatial clustering of genes. By providing a dense matrix for each gene in situ, SuperST can successfully address the resolution and zero-inflation issue.}, }
@article {pmid39729477, year = {2024}, author = {Lee, M and Lee, HY and Kang, JS and Lee, H and Park, KJ and Park, JY and Yang, TJ}, title = {Correction: Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0316742}, doi = {10.1371/journal.pone.0316742}, pmid = {39729477}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0294457.].}, }
@article {pmid39729273, year = {2025}, author = {Randall, E and Keillor, B and Cooke, DEL}, title = {The Use of eDNA Metabarcoding to Detect and Identify Phytophthora in Water Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2892}, number = {}, pages = {117-138}, pmid = {39729273}, issn = {1940-6029}, mesh = {*Phytophthora/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; Water/chemistry ; Water Microbiology ; Metagenomics/methods ; }, abstract = {We describe a protocol to amplify DNA barcodes of known and unknown taxa of Phytophthora and related plant pathogenic oomycetes from a range of environments. The methods focus on sampling pathogen propagules from water using in situ sampling and filtration equipment and buffers that enable efficient storage and DNA extraction for later downstream processing.}, }
@article {pmid39728620, year = {2024}, author = {Husted, AL and Sutton, VR and Presnar, LA and Blackburn, RK and Staton, JL and Borgianini, SA and D'Antonio, EL}, title = {The Multifunctional Catalytic Hemoglobin from Amphitrite ornata: Protocols on Isolation, Taxonomic Identification, Protein Extraction, Purification, and Characterization.}, journal = {Methods and protocols}, volume = {7}, number = {6}, pages = {}, doi = {10.3390/mps7060100}, pmid = {39728620}, issn = {2409-9279}, support = {n/a//Pritchards Island State Funding/ ; 17220-15-39011//University of South Carolina, Office of the Vice President for Research/ ; n/a//University of South Carolina, Office of Undergraduate Research/ ; }, abstract = {The multifunctional catalytic hemoglobin from the terebellid polychaete Amphitrite ornata, also named dehaloperoxidase (AoDHP), utilizes the typical oxygen transport function in addition to four observed activities involved in substrate oxidation. The multifunctional ability of AoDHP is presently a rare observation, and there exists a limitation for how novel dehaloperoxidases can be identified from macrobenthic infauna. In order to discover more infaunal DHP-bearing candidates, we have devised a facilitated method for an accurate taxonomic identification that places visual and molecular taxonomic approaches in parallel. Traditional visual taxonomic species identification by the non-specialist, at least for A. ornata or even for other marine worms, is a very difficult and time-consuming task since a large diversity is present and the method is restricted to adult worm specimens. The work herein aimed to describe a method that simplifies the taxonomic identification of A. ornata in particular through the assessment of its mitochondrial cytochrome c oxidase subunit I gene by employing the DNA barcoding technique. Furthermore, whole-worm specimens of A. ornata were used to extract and purify AoDHP followed by an H2O2-dependent peroxidase activity assay evaluation against substrate 2,4,6-trichlorophenol. AoDHP isoenzyme A was also overexpressed as the recombinant protein in Escherichia coli, and its peroxidase activity parameters were compared to AoDHP from the natural source. The activity assay assessment indicated a tight correlation for all Michaelis-Menten parameters evaluated. We conclude that the method described herein exhibits a streamlined approach to identify the polychaete A. ornata, which can be adopted by the non-specialist, and the full procedure is predicted to facilitate the discovery of novel dehaloperoxidases from other marine invertebrates.}, }
@article {pmid39725934, year = {2024}, author = {Feng, W and Zhang, Z and Zhang, J and Nan, P and Song, Z and Zhang, W and Yang, J and Wang, Y}, title = {Comparative plastomic analysis of cultivated Dioscorea polystachya and its close relatives provides insights on the inter- and intraspecific phylogenies and potential wild origins of domestication.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1255}, pmid = {39725934}, issn = {1471-2229}, abstract = {BACKGROUND: Dioscorea polystachya and its closely related species are original plants of the tuber crop "yam", which had been intensively use for medicinal and food purposes and widely cultivated in northern China and its surrounding areas with a long history. Many cultivars of these species are often confused with one another because of similar tuber morphology, however, conventional DNA barcoding faces practical limitations restricting the method to effectively identify closely related species. In addition, phylogenetic relationships among various cultivar groups of Chinese yam (D. polystachya) remains unclear. To solve these problems, genomic DNAs of 15 Dioscorea samples were sequenced to assemble and annotate chloroplast genomes, which were used for analyzing their structural characteristics and identifying phylogenetic relationships at the inter- and intraspecific levels.<br><br>RESULTS: The size of chloroplast genomes of the tested samples is about 153&#xa0;kb, and 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes are annotated. Phylogenetic analysis showed that D. polystachya were sister to Dioscorea japonica, and for Huaishan yams, Dioscorea persimilis did not cluster with Dioscorea alata and Dioscorea fordii. Four cultivar groups of Chinese yam were determined, namely Tiegun group, Anping group, Foshou group and Taihang complex group. Among these cultivar groups, Foshou and Taihang complex are clustered with different wild yams, respectively. Amino acid preferences are similar at the inter- and intraspecific levels, while synonymous codon usage reflects distinct patterns in the majority of cultivars of D. polystachya. There are distinct SSR variations among species, as well as four cultivar groups. Collinearity and SNP analyses show that nucleotide hypervariable regions among Dioscorea species are mainly concentrated in trnK-atpA, rps16-trnQ, atpA-atpH, rpoB-psbD, atpH-atpI, trnV-ndhC in the LSC region, and ccsA-ndhF in the SSC region, while intraspecific variation of Chinese yam is enriched in the intergenic spacers of rpoB-psbC, ndhD-ndhF, and trnQ-trnS, as well as the gene ycf1.<br><br>CONCLUSION: Phylogenetic analysis supports that Huaishan yams are not of monophyletic origin and the cultivated Chinese yam has at least two wild origins of domestication, which is consistent with the historical records of these wild yams from Mt. Dabie and Mt. Taihang. The identification efficiency of the newly developed barcodes for cultivar groups based on chloroplast genome SNP screening is significantly better than those of conventional barcodes. This approach to generate viable candidate markers based on the comparison from interspecific and intraspecific hypervariable regions of chloroplast genomes can be applied to conduct phylogenetic relationships of more important crop species and their close relatives, which are difficult to identify, as well as their wild origins of domestication.}, }
@article {pmid39719730, year = {2024}, author = {Bergin, R and Samperton, K and Bronikowski, M and Hoar, E and Rolison, J and Shollenberger, Q and Marks, N and Wellons, M and Scott, S}, title = {Synthesis and characterization of isotopically barcoded nickel, molybdenum, and tungsten taggants for intentional nuclear forensics.}, journal = {Talanta}, volume = {285}, number = {}, pages = {127425}, doi = {10.1016/j.talanta.2024.127425}, pmid = {39719730}, issn = {1873-3573}, abstract = {Intentional nuclear forensics is a concept wherein the deliberate addition of benign and persistent material signatures to nuclear material can be used to reduce the time between the discovery of material outside of regulatory control and determination of its original provenance. One concept within intentional nuclear forensics involves the use of perturbed stable isotopes to generate unique isotope ratio "barcodes" to encode information (e.g., production batch, location, etc.) and track material throughout the nuclear fuel cycle. Synthesis of taggant species of nickel (Ni), molybdenum (Mo), and tungsten (W) was undertaken via a double-spike mechanism, wherein two highly enriched isotopes of interest per elemental taggant were mixed to form an enriched "double-spike" which was subsequently isotopically diluted with bulk material having a natural isotopic composition. Two taggant species perturbing isotopic ratios, alpha (α) and beta (β), for each of Ni, Mo, and W were synthesized. Independent measurements of double spikes and alpha and beta taggant species agreed within uncertainty and are clearly resolvable from natural compositions. High-precision analyses were independently performed by MC-ICP-MS at two U.S. National Laboratories, with consensus values and uncertainties calculated for all samples. Observed isotopic perturbations in the final taggant species measured on the order of hundreds to thousands of permille (‰) with respect to natural for isotope ratios of interest (e.g., [60]Ni/[58]Ni, [100]Mo/[98]Mo, [186] W/[183]W). Discrepancies between modeled and measured isotopic compositions were observed and are largely attributed to imprecise vendor assay values for starting materials. Using measured starting material compositions as inputs for the mixing model improved the level of agreement between predicted and measured α and β taggant isotope ratios. Overall, characterization of all taggant species demonstrates that this "barcode" concept could have viability for use in nuclear forensics. It is expected that for any two-isotope mixing array dozens of isotopic barcodes could be encoded into a material system and subsequently resolved utilizing modern mass spectrometric methods.}, }
@article {pmid39719062, year = {2024}, author = {Long, Y and Mora, A and Li, FZ and Gürsoy, E and Johnston, KE and Arnold, FH}, title = {LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.4c00625}, pmid = {39719062}, issn = {2161-5063}, abstract = {Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq's ability to accurately detect variants under various experimental conditions. Finally, we show LevSeq's utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.}, }
@article {pmid39718626, year = {2024}, author = {Dhabal, S and Chakrabarty, AK and Banerjee, D and Katiyar, CK and Rai, RK and Dubey, SK}, title = {Internal transcribed spacer (ITS): The powerful DNA barcode and phylogenetic marker for successful authentication of Withania somnifera.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {77}, pmid = {39718626}, issn = {1573-4978}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Withania/genetics/classification ; Genetic Markers ; *DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Understanding the evolutionary history of plants and accurately identifying biologically important species and their families is crucial for the herbal and Ayurvedic industries. The genetic approach by DNA barcoding plays a pivotal role in accurate species identification, authentication and quality control. Due to various therapeutic properties, Withania somnifera has been used worldwide in traditional systems of medicine for centuries including Ayurveda and Unani. The increasing demand for W. somnifera products has led to concerns regarding the authenticity and quality of commercial herbal preparations. However, adulteration become major trouble for users and industry for safety reasons and authentication of the plant with proper DNA marker is a major concern.<br><br>METHODOLOGY: DNA barcoding techniques and Phylogenetic analysis were employed to authenticate W. somnifera plant species using universal genetic markers. The markers were PCR amplified, sequenced and analyzed using BLAST-based and phylogeny-based identification methods.<br><br>RESULTS: The BLAST result shows the percent identity (PI) of ITS1, ITS2, trnK, atpB, rbcL and matK was 100%, 100%, 100%, 97.59%, 100 and 99.20% respectively with the NCBI reference sequence. However, ITS1 and ITS2 show the maximum sequence similarity with W. somnifera of NCBI data. Phylogenetic analysis using NCBI data further supports the role of ITS in the discrimination of W. somnifera from closely related species.<br><br>CONCLUSION: Therefore, the ITS gene may be considered promising a candidate for DNA barcoding for discrimination of W. somnifera from other species, its authentication and quality control.}, }
@article {pmid39717638, year = {2024}, author = {Palandačić, A and Reier, S and Diripasko, OA and Jelić, D and Stroj, A and Wanka, A and Marić, D and Bogutskaya, NG}, title = {Substygophily in Dinaric Karst: A Model Case of Locally Endemic Minnows Phoxinellus (Leuciscinae).}, journal = {Ecology and evolution}, volume = {14}, number = {12}, pages = {e70648}, pmid = {39717638}, issn = {2045-7758}, abstract = {The Dinaric Karst extends along the Adriatic coast of the Western Balkan Peninsula and is home to a group of "karst minnows" of the genera Delminichthys, Phoxinellus, and Telestes, which have adapted to the highly variable water conditions in the karst by spending up to several months underground, but require surface habitats for spawning, defining them as substygophiles. The three species of the genus Phoxinellus, P. alepidotus, P. pseudalepidotus, and P. dalmaticus, are defined by restricted ranges, making them vulnerable to pollution and extended draughts caused by the climate change. In this study, the phylogeny of Leusciscinae was reconstructed using 15 Phoxinellus and one Delminichthys adspersus, one Pelasgus epiroticus, and one Telestes polylepis complete mitochondrial genomes and the position of the genus Phoxinellus within the subfamily as sister species to the Chondrostoma clade was confirmed. The inter- and intrapopulation structure of the genus Phoxinellus was inferred using molecular (nuclear and mitochondrial data) and morphological analyses. For the molecular analysis, more than 150 historical specimens were analyzed for a short fragment of the cytochrome oxidase I (COI) barcoding region and 15 Phoxinellus specimens were subjected to single nucleotide polymorphism analysis. For morphological analysis, 121 Phoxinellus specimens were analyzed for 51 measurements and 8 counts. All analyses confirmed the clear delimitation of the three Phoxinellus species, but were insufficient to fully resolve the intrapopulation structure within the species. This study also included data from field surveys of Phoxinellus collected over the past 20 years, which showed that abundance is declining and ranges are shrinking. Phoxinellus are also threatened by invasive/introduced species. Based on cave observations/occurrence and morphological analysis, P. dalmaticus was classified as an advanced substygophile and P. alepidotus and P. pseudalepidotus were classified as basic stygophiles.}, }
@article {pmid39716438, year = {2024}, author = {Liu, X and Yang, X and Xiang, S and Lv, Y and Zhang, Z}, title = {Coordination-Defect-Driven Construction of Responsive Pure-MOF Microspheres for Switchable Mode-Dependent Anticounterfeiting Labels.}, journal = {ACS applied materials &amp; interfaces}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsami.4c19719}, pmid = {39716438}, issn = {1944-8252}, abstract = {Luminescent metal-organic frameworks (MOFs) with exceptional dynamics and diverse active sites possess tremendous potential in information security and anticounterfeiting applications. However, traditional MOF systems are based on broadband spectral signals with spectrum overlap, which easily leads to low-resolution signal identification, compromising the overall security level. Here, we report the coordination-defect-induced amorphous pure-MOF microsphere with switchable whispering-gallery-mode (WGM) signals as a mode-dependent security platform. Amorphous MOF microspheres are prepared by a chlorine coordination-defect-driven growth strategy based on the aperiodic arrangement in coordinate networks. The as-prepared amorphous MOF microspheres with well-defined circular morphology display the typical WGM resonance with dimension-dependent character, permitting the creation of photonic barcodes with substantial encoding capacity. Furthermore, the amorphous MOF microspheres exhibit optical mode switching behavior due to reversible framework shrinkage, which enables the design of covert photonic barcodes as anticounterfeiting labels, finally demonstrating responsive coding property and enhanced information security. The results provide a novel strategy for exploring an MOF-based security platform for information encryption and optical anticounterfeiting.}, }
@article {pmid39714325, year = {2024}, author = {Vaidya, K and Regan, M and Lin, J and Houle, J and Gupta, A and Stopka, S and Agar, N and Hammond, P and Boehnke, N}, title = {Pooled nanoparticle screening using a chemical barcoding approach.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202420052}, doi = {10.1002/anie.202420052}, pmid = {39714325}, issn = {1521-3773}, abstract = {We report the development of a small molecule-based barcoding platform for pooled screening of nanoparticle delivery. Using aryl halide-based tags (halocodes), we achieve high-sensitivity detection via gas chromatography coupled with mass spectrometry or electron capture. This enables barcoding and tracking of nanoparticles with minimal halocode concentrations and without altering their physicochemical properties. To demonstrate the utility of our platform for pooled screening, we synthesized a halocoded library of polylactide-co-glycolide (PLGA) nanoparticles and quantified uptake in ovarian cancer cells in a pooled manner. Our findings correlate with conventional fluorescence-based assays. Additionally, we demonstrate the potential of halocodes for spatial mapping of nanoparticles using mass spectrometry imaging (MSI). Halocoding presents an accessible and modular nanoparticle screening platform capable of quantifying delivery of pooled nanocarrier libraries in a range of biological settings.}, }
@article {pmid39714184, year = {2024}, author = {Leitner, DR and Zingl, FG and Morano, AA and Zhang, H and Waldor, MK}, title = {The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase.}, journal = {mBio}, volume = {}, number = {}, pages = {e0343324}, doi = {10.1128/mbio.03433-24}, pmid = {39714184}, issn = {2150-7511}, abstract = {UNLABELLED: Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote pathogen fitness in stationary phase. We discovered that the maintenance of lipid asymmetry (Mla) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type (WT) and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48 h stationary phase cultures. The mutant defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48 h. However, by 96 h the culturability of the WT and mutant strains were equivalent. By monitoring the abundances of genomically barcoded libraries of WT and ∆mlaE strains, we observed that a few barcodes dominated the mutant culture at 96 h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the defect of ∆mlaE. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for maintaining the culturability of V. cholerae because it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.<br><br>IMPORTANCE: Bacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction is limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promoting Vibrio cholerae re-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high-energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis that emerge in the absence of the Mla pathway underlie its importance in maintaining V. cholerae culturability.}, }
@article {pmid39713585, year = {2024}, author = {Wang, H and Wei, Z and Ren, G}, title = {A new species of Laena Dejean (Coleoptera, Tenebrionidae) from Sichuan Province, China, with an updated key.}, journal = {ZooKeys}, volume = {1221}, number = {}, pages = {165-173}, pmid = {39713585}, issn = {1313-2989}, abstract = {In this study, we describe and illustrate a new species of the genus Laena Dejean, 1821, Laenacostata sp. nov., which was collected in Micangshan Nature Reserve of Sichuan Province, China. Additionally, the COI mitochondrial gene was sequenced to provide additional evidence for this new species' validity. The results of phylogenetic analyses suggest that this new species is sister to L.maowenica Schawaller, 2008. Furthermore, an updated key to Laena species from Sichuan Province is provided.}, }
@article {pmid39713068, year = {2024}, author = {Douglas, HB and Hammond, G and Smith, TW and Mutz, J and Konstantinov, AS}, title = {Palaearctic flea beetle Phyllotretaochripes (Curtis) (Coleoptera, Chrysomelidae, Galerucinae), herbivore of Alliariapetiolata (garlic mustard), new to North America.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e135576}, pmid = {39713068}, issn = {1314-2828}, abstract = {BACKGROUND: The univoltine leaf beetle Phyllotretaochripes (Curtis, 1837b) is native to the Palaearctic Region from Japan to western Europe.This species was previously evaluated as a potential biological control agent against invasive populations of the woodland weed Alliariapetiolata (Bieb.) Cavara &amp; Grande (Brassicaceae) in North America, but rejected because it could harm native and at-risk populations of Brassicaceae.<br><br>NEW INFORMATION: First North American records are presented for Phyllotretaochripes (Curtis, 1837). Specimens were examined from the USA: Illinois, Maryland, Michigan, Ohio and Pennsylvania. Internet photographs of apparent additional individuals from USA: Indiana, Michigan, Minnesota, Ohio, Pennsylvania, Tennessee, Wisconsin and Canada: Ontario were also examined. DNA barcoding analysis showed high genetic variability and possible cryptic species within European populations of P.ochripes. Diagnostic information is presented to distinguish P.ochripes. from other North American Chrysomelidae and a species distribution model to assess its potential spread in North America is presented.Phyllotretaochripes breeds on invasive garlic mustard, Alliariapetiolata (Bieb.) Cavara &amp; Grande (Brassicaceae) and also non-native Rorippaamphibia (L.) Besser and other species of Brassicaceae.A species distribution model and the range of its host plant A.petiolata, indicates the most suitable conditions for this species are in humid areas of eastern North America. However, most of the known records of this species were discovered in areas projected to have low suitability. This is likely a consequence of sampling bias towards western Europe and away from the eastern Asian portion of its native range. The United States of America and Canada are now known to be home to 72 or more species of adventive Chrysomelidae.}, }
@article {pmid39711595, year = {2024}, author = {Harun, A and Song, S and You, X and Liu, H and Wen, X and Fang, Z and Cheng, Z and Chen, C}, title = {Comprehensive mapping of molecular cytogenetic markers in pitaya (Hylocereus undatus) and related species.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1493776}, pmid = {39711595}, issn = {1664-462X}, abstract = {Pitaya (Hylocereus undatus; 2n=22) is an important fruit crop from the Cactaceae family, originally domesticated in Mexico and the USA, and is now widely cultivated for its nutritional benefits. It is characterized by its distinctive triangular-shaped stems and large, showy flowers, thriving in arid and semi-arid environments, particularly in hot, dry climates. However, systematic chromosomal studies, including chromosomal mapping of cytogenetic markers in pitaya, are limited, presenting challenges for its cytogenetic improvement. To address this issue, we designed oligo-barcodes specific to thirty-three chromosome regions based on the pitaya reference genome and applied them to both pitaya and cactus (Selenicerus grandifloras; 2n=22) for oligo-barcodes mapping, karyotyping, and chromosome identification. We utilized FISH technology, employing oligo, rDNA, and tandem repeat probes for chromosomal mapping, identification, and karyotyping of pitaya and related species. We successfully localized oligo-barcodes on eleven pairs of chromosomes in both pitaya and cactus, demonstrating the effectiveness of the synthesized oligo-barcodes. We used two ribosomal DNA (rDNA) probes (45S and 5S) and two tandem repeat probes (GTR11 and STR3) in pitaya (both diploid and tetraploid) and two other Cactaceae species (S. grandifloras and Opuntia humifusa; 2n=40) for chromosomal mapping. The analysis of rDNA distribution and CMA (Chromomycin A3) banding across different chromosomes in pitaya and cacti highlights the concept of conserved rDNA. This study provides fundamental insights into cytogenetic markers and their localization across different chromosomes in pitaya and other Cactaceae species.}, }
@article {pmid39711562, year = {2024}, author = {Fan, R and Enninful, A and Zhang, Z and Klymyshyn, D and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Yang, M and Lu, Y and Zhang, N and Braubach, O and Xu, M and Ma, Z}, title = {Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-5398491/v1}, pmid = {39711562}, issn = {2693-5015}, abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.}, }
@article {pmid39711846, year = {2023}, author = {Adams, SJ and Walker, AK}, title = {Diversity of fungi from marine inundated wood from the Bay of Fundy, Nova Scotia, Canada.}, journal = {Botanica marina}, volume = {66}, number = {4}, pages = {319-329}, pmid = {39711846}, issn = {0006-8055}, abstract = {Marine fungi play an integral role in the decomposition of intertidal organic substrata but remain understudied in cold-water habitats including Atlantic Canada. Marine inundated wood from the intertidal zone was sampled from 30 sites along the Bay of Fundy coastline in Nova Scotia, Canada. Wood types studied included attached and loose intertidal wood, and driftwood. Emergent fungi were cultured and identified using ITS (internal transcribed spacers) rDNA barcoding. Two hundred and twenty cultures representing 86 fungi are reported. Sixty-one fungi were new records for the Bay of Fundy, 41 are first records from the marine environment, and 19 fungi are potentially new to science. Fungi identified included eight obligate marine fungi, with the remaining fungi being facultatively marine. Eight ascomycetes were soft rot fungi; this ecological strategy for decaying woody material in cold-water marine environments is discussed. Historical records and roles of wood type and site on fungal colonization are discussed.}, }
@article {pmid39704725, year = {2024}, author = {Wang, R and Hastings, WJ and Saliba, JG and Bao, D and Huang, Y and Maity, S and Kamal Ahmad, OM and Hu, L and Wang, S and Fan, J and Ning, B}, title = {Applications of Nanotechnology for Spatial Omics: Biological Structures and Functions at Nanoscale Resolution.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.4c11505}, pmid = {39704725}, issn = {1936-086X}, abstract = {Spatial omics methods are extensions of traditional histological methods that can illuminate important biomedical mechanisms of physiology and disease by examining the distribution of biomolecules, including nucleic acids, proteins, lipids, and metabolites, at microscale resolution within tissues or individual cells. Since, for some applications, the desired resolution for spatial omics approaches the nanometer scale, classical tools have inherent limitations when applied to spatial omics analyses, and they can measure only a limited number of targets. Nanotechnology applications have been instrumental in overcoming these bottlenecks. When nanometer-level resolution is needed for spatial omics, super resolution microscopy or detection imaging techniques, such as mass spectrometer imaging, are required to generate precise spatial images of target expression. DNA nanostructures are widely used in spatial omics for purposes such as nucleic acid detection, signal amplification, and DNA barcoding for target molecule labeling, underscoring advances in spatial omics. Other properties of nanotechnologies include advanced spatial omics methods, such as microfluidic chips and DNA barcodes. In this review, we describe how nanotechnologies have been applied to the development of spatial transcriptomics, proteomics, metabolomics, epigenomics, and multiomics approaches. We focus on how nanotechnology supports improved resolution and throughput of spatial omics, surpassing traditional techniques. We also summarize future challenges and opportunities for the application of nanotechnology to spatial omics methods.}, }
@article {pmid39704499, year = {2024}, author = {Wäneskog, M and Hoch-Schneider, EE and Garg, S and Kronborg Cantalapiedra, C and Schäfer, E and Krogh Jensen, M and Damgaard Jensen, E}, title = {Accurate phenotype-to-genotype mapping of high-diversity yeast libraries by heat-shock-electroporation (HEEL).}, journal = {mBio}, volume = {}, number = {}, pages = {e0319724}, doi = {10.1128/mbio.03197-24}, pmid = {39704499}, issn = {2150-7511}, abstract = {High-throughput DNA transformation techniques are invaluable when generating high-diversity mutant libraries, a cornerstone of successful protein engineering. However, transformation efficiencies have a direct correlation with the probability of introducing multiple DNA molecules into each cell, although reliable library screenings require cells that contain a single unique genotype. Thus, transformation methods that yield a high multiplicity of transformations are unsuitable for high-diversity library screenings. Here, we describe an innovative yeast library transformation method that is both simple and highly efficient. Our dual heat-shock and electroporation approach (HEEL) creates high-quality DNA libraries by increasing the fraction of mono-transformed yeast cells from 20% to over 70% of all transformed cells, thus allowing for near-perfect phenotype-to-genotype associations. HEEL also allows more than 10[7] yeast cells per reaction to be transformed with a circular plasmid molecule, which corresponds to an almost 100-fold improvement compared with current yeast transformation methods. To further refine our library screening approach, we integrated an automated yeast genotyping workflow with a dual-barcode design that employs both a single nucleotide polymorphism and a high-diversity region. This design allows for robust identification and quantification of unique genotypes within a heterogeneous population using standard Sanger sequencing. Our findings demonstrate that the longstanding trade-off between the size and quality of transformed yeast libraries can be overcome. By employing the HEEL method, large DNA libraries can be transformed into yeast with high-efficiency, while maintaining high library quality, essential for successful mutant screenings. This advancement holds significant promise for the fields of molecular biology and protein engineering.IMPORTANCEWith the recent expansion of artificial intelligence in the field of synthetic biology, there has never been a greater need for high-quality data and reliable measurements of phenotype-to-genotype relationships. However, one major obstacle to creating accurate computer-based models is the current abundance of low-quality phenotypic measurements originating from numerous high-throughput but low-resolution assays. Rather than increasing the quantity of measurements, new studies should aim to generate as accurate measurements as possible. The HEEL methodology presented here aims to address this issue by minimizing the problem of multi-plasmid uptake during high-throughput yeast DNA transformations, which leads to the creation of heterogeneous cellular genotypes. HEEL should enable highly accurate phenotype-to-genotype measurements going forward, which could be used to construct better computer-based models.}, }
@article {pmid39703419, year = {2024}, author = {Chamberlin, JT and Gillen, AE and Quinlan, AR}, title = {Improved characterization of 3' single-cell RNA-seq libraries with paired-end avidity sequencing.}, journal = {NAR genomics and bioinformatics}, volume = {6}, number = {4}, pages = {lqae175}, pmid = {39703419}, issn = {2631-9268}, abstract = {Prevailing poly(dT)-primed 3' single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site or in principle the polyadenylation site. Direct sequencing across this site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the 'barcode' end. Here, we evaluate the capability of 'avidity base chemistry' DNA sequencing from Element Biosciences to sequence through the primer and enable accurate paired-end read alignment and precise quantification of polyadenylation sites. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy. The additional sequence enables direct and independent assignment of reads to polyadenylation sites, which bypasses the complexities and limitations of conventional approaches but does not consistently improve read mapping rates compared to single-end alignment. We also characterize low-level artifacts and demonstrate necessary adjustments to adapter trimming and sequence alignment regardless of platform, particularly in the context of extended read lengths. Our analyses confirm that Element avidity sequencing is an effective alternative to Illumina sequencing for standard single-cell RNA-seq, particularly for polyadenylation site measurement but do not rule out the potential for similar performance from other emerging platforms.}, }
@article {pmid39702735, year = {2024}, author = {Fandrey, CI and Jentzsch, M and Konopka, P and Hoch, A and Blumenstock, K and Zackria, A and Maasewerd, S and Lovotti, M and Lapp, DJ and Gohr, FN and Suwara, P and Świeżewski, J and Rossnagel, L and Gobs, F and Cristodaro, M and Muhandes, L and Behrendt, R and Lam, MC and Walgenbach, KJ and Bald, T and Schmidt, FI and Latz, E and Schmid-Burgk, JL}, title = {NIS-Seq enables cell-type-agnostic optical perturbation screening.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39702735}, issn = {1546-1696}, abstract = {Optical pooled screening offers a broader-scale alternative to enrichment-based perturbation screening, using fluorescence microscopy to correlate phenotypes and perturbations across single cells. Previous methods work well in large, transcriptionally active cell lines, because they rely on cytosolic detection of endogenously expressed barcoded transcripts; however, they are limited by reliable cell segmentation, cytosol size, transcriptional activity and cell density. Nuclear In-Situ Sequencing (NIS-Seq) expands this technology by creating bright sequencing signals directly from nuclear genomic DNA to screen nucleated cells at high density and high library complexity. By inserting an inverted phage promoter downstream of the single guide RNA (sgRNA), many RNA copies of the sgRNA can be generated and sequenced independently of cellular transcription. In this study, we benchmarked NIS-Seq across eight cell types from two species and performed four genome-scale optical perturbation screens, identifying key players of inflammation-related cellular pathways. Finally, we performed a small-scale pooled optical screen in primary human macrophages from blood of healthy donors and demonstrated barcode identification in lentivirally transduced human skin tissue.}, }
@article {pmid39701988, year = {2024}, author = {Zhang, J and Ning, Y and Li, J and Deng, Y and Wang, L and Mao, S and Zhao, B}, title = {Comparative chloroplast genome analysis of Ardisia (Myrsinoideae, Primulaceae) in China and implications for phylogenetic relationships and adaptive evolution.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1198}, pmid = {39701988}, issn = {1471-2229}, support = {[2022]-KJ019 and [2021]-KJ014//Science and technology plan project of Guangzhou Construction Group/ ; 32060090//National Natural Science Foundation of China/ ; 2021JJA130119//Natural Science Foundation of Guangxi Province/ ; }, mesh = {*Genome, Chloroplast ; *Phylogeny ; China ; *Ardisia/genetics ; Evolution, Molecular ; Microsatellite Repeats/genetics ; }, abstract = {BACKGROUND: Numerous species of Ardisia are widely used for their medicinal and ornamental values in China. However, accurately identifying Ardisia species at the molecular level remains a challenge due to the morphological similarities among different species, the complexity of interspecific variation, and the limited availability of genetic markers. In this study, we reported 20 chloroplast genomes of Ardisia species from China and combined them with 8 previously published chloroplast genomes to conduct a comprehensive analysis for phylogenetic relationships and adaptive evolution.<br><br>RESULTS: For the 28 Ardisia species analyzed in this study, the size of the chloroplast genomes ranged from 155,088&#xa0;bp to 156,999&#xa0;bp, and all exhibited a typical tetrad structure with conserved gene content and number. Each genome contained 85-88 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. Comparative analysis showed that the genomic structures and gene order were relatively conserved with slight variations in the inverted repeat regions (IRs). Simple sequence repeats (SSRs) were predominantly single nucleotide repeats, while repeat sequences were mainly composed of palindromic and forward repeats. Twelve highly variable regions were identified as potential DNA barcodes for species identification and phylogenetic analysis of Ardisia. The phylogenetic tree supported the division of the subgenus Bladhia s.l. into two subgenera: Bladhia s.str. and Odontophylla (Yang) Huang. Further investigation revealed that two protein-coding genes (rbcL and rpoC2) were under positive selection and might be associated with the adaptation of Ardisia species to shaded environments.<br><br>CONCLUSION: Our study analyzed the chloroplast genomes of 20 Ardisia species from China to explore their phylogenetic relationships and adaptive evolution. By combining these results with data from eight previously published chloroplast genomes, the essential characteristics of Ardisia chloroplast genomes were clarified. The research establishes a theoretical basis for the classification, identification, and comprehension of the adaptive evolution of Ardisia species.}, }
@article {pmid39700063, year = {2024}, author = {Munusamy, S and Zheng, H and Jahani, R and Zhou, S and Chen, J and Kong, J and Guan, X}, title = {DNA-Assisted CRISPR-Cas12a Enhanced Fluorescent Assay for Protein Detection in Complicated Matrices.}, journal = {ACS applied bio materials}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsabm.4c01600}, pmid = {39700063}, issn = {2576-6422}, abstract = {Proteins are important biological macromolecules that perform a wide variety of functions in the cell and human body, and can serve as important biomarkers for early diagnosis and prognosis of human diseases as well as monitoring the effectiveness of disease treatment. Hence, sensitive and accurate detection of proteins in human biospecimens is imperative. However, at present, there is no ideal method available for the detection of proteins in clinical samples, many of which are present at ultralow (less than 1 pM) concentrations and in complicated matrices. Herein, we report an ultrasensitive and selective DNA-assisted CRISPR-Cas12a enhanced fluorescent assay (DACEA) for protein detection with detection limits reaching as low as attomolar concentrations. The high assay sensitivity was accomplished through the combined DNA barcode amplification (by using dual-functionalized AuNPs) and CRISPR analysis, while the high selectivity and high resistance to the matrix effects of our method were accomplished via the formation of protein-antibody sandwich structure and the specific recognition of Cas12a (under the guidance of crRNA) toward the designed target ssDNA. Given its ability to accurately and sensitively detect trace amounts of proteins in complicated matrices, the DACEA protein assay platform pioneered in this work has a potential application in routine protein biomarker testing.}, }
@article {pmid39698230, year = {2024}, author = {Huang, WC and Hibino, Y and Balisco, RA and Liao, TY}, title = {Description of a new uniformly brown estuarine moray eel (Anguilliformes, Muraenidae) from the Central Indo-Pacific Ocean.}, journal = {ZooKeys}, volume = {1220}, number = {}, pages = {15-34}, pmid = {39698230}, issn = {1313-2989}, abstract = {A new estuarine moray eel, Uropterygiushades sp. nov., is described based on 14 specimens from Japan, Taiwan, the Philippines, southern Indonesia, and Fiji. It is a small-bodied, slender, uniformly dark-brown moray separated from congeners within the U.concolor species complex. The new species can be distinguished from congeners by the anteriorly positioned small eyes (5.0-7.2% of head length), absence of branchial pores, and extended inner rows of teeth which reach the posterior end of the jaws. Uropterygiushades sp. nov. represents a rare species of moray eel that inhabits turbid estuarine environments, preferring soft, muddy substrates, and burrowing and hiding among rocks or in fallen mangrove leaves. Additionally, Uropterygiusmactanensis Huang, Balisco, Evacitas &amp; Liao, another species recently separated from the U.concolor species complex, is reported for the first time from Iriomote Island in the Ryukyu Archipelago based on two specimens; this new record expands the geographic range of U.mactanensis from the central Philippines to southern Japan.}, }
@article {pmid39696450, year = {2024}, author = {Wang, YW and Tan, PC and Li, QF and Xu, XW and Zhou, SB}, title = {Adipose tissue protects against skin photodamage through CD151- and AdipoQ- EVs.}, journal = {Cell communication and signaling : CCS}, volume = {22}, number = {1}, pages = {594}, pmid = {39696450}, issn = {1478-811X}, mesh = {Animals ; *Adiponectin/metabolism ; *Skin/metabolism ; *Fibroblasts/metabolism ; Mice ; *Adipose Tissue/metabolism/cytology ; *Extracellular Vesicles/metabolism ; Humans ; Mice, Nude ; Cell Proliferation ; }, abstract = {To clarify the protective effects of subcutaneous adipose tissue (SAT) against photodamage, we utilized nude mouse skin with or without SAT. Skin and fibroblasts were treated with adipose tissue-derived extracellular vesicles (AT-EVs) or extracellular vesicles derived from adipose-derived stem cells (ADSC-EVs) to demonstrate that SAT protects the overlying skin from photodamage primarily through AT-EVs. Surprisingly, AT-EVs stimulated fibroblast proliferation more rapidly than ADSC-EVs did. The yield of AT-EVs from the same volume of AT was 200 times greater than that of ADSC-EVs. To compare the differences between AT-EVs and ADSC-EVs, we used a proximity barcoding assay (PBA) to analyze the surface proteins on individual particles of these two types of EVs. PBA analysis revealed that AT-EVs contain diverse subpopulations, with 83.42% expressing CD151, compared to only 1.98% of ADSC-EVs. Furthermore, AT-EVs are internalized more rapidly by cells than ADSC-EVs, as our study demonstrated that CD151-positive AT-EVs were endocytosed more quickly than their CD151-negative counterparts. Additionally, adiponectin in AT-EVs activated the AMPK pathway and inhibited the NF-κB pathway, enhancing fibroblast protection against photodamage. The significantly higher yield and faster acquisition of AT-EVs compared to ADSC-EVs underscore their potential for broader applications.}, }
@article {pmid39695811, year = {2024}, author = {Jeon, J and Kim, HC and Donnelly, MJ and Choi, KS}, title = {Genetic diversity and Wolbachia infection in the Japanese encephalitis virus vector Culex tritaeniorhynchus in the Republic of Korea.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {518}, pmid = {39695811}, issn = {1756-3305}, mesh = {Animals ; *Culex/virology/microbiology ; *Wolbachia/genetics/isolation &amp; purification/classification ; *Genetic Variation ; *Mosquito Vectors/microbiology/virology ; Republic of Korea/epidemiology ; *Encephalitis Virus, Japanese/genetics/classification/isolation &amp; purification ; Phylogeny ; Encephalitis, Japanese/epidemiology/transmission/virology ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; }, abstract = {BACKGROUND: Culex tritaeniorhynchus, a major vector of Japanese encephalitis virus (JEV), is found across a broad geographical range, including Africa, Asia, Australia and Europe. Understanding the population structure and genetic diversity of pathogen vectors is increasingly seen as important for effective disease control. In China and Japan, two countries in close proximity to the Republic of Korea (ROK), Cx. tritaeniorhynchus has been categorized into two clades based on the DNA barcoding region of mitochondrial cytochrome c oxidase subunit I (COI), suggesting the presence of cryptic species. No comprehensive analysis of the genetic diversity in Cx. tritaeniorhynchus has been conducted in the ROK. To address this gap, we investigated the population structure of Cx. tritaeniorhynchus in the ROK.<br><br>METHODS: In Daegu, mosquito collections were conducted over a 2-year period from 2022 to 2023. For all other regions, Cx. tritaeniorhynchus specimens collected in 2023 were used. The COI barcoding region was analyzed to determine the genetic structure of the populations, supplemented with data from the 28S ribosomal DNA region. Each population was also examined for the eventual presence of Wolbachia infection. Finally, a back trajectory analysis was conducted to assess the possibility of international introduction of Cx. tritaeniorhynchus into the ROK.<br><br>RESULTS: The analysis of the COI region revealed the presence of two distinct clades within Cx. tritaeniorhynchus; these clades were the same as Cx. tritaeniorhynchus continental type (Ct-C) and C. tritaeniorhynchus Japanese type (Ct-J) previously reported. In contrast, the nuclear 28S region showed no significant genetic differentiation between these clades. Wolbachia infection was confirmed in some populations, but there was no evidence of an association with Wolbachia in Ct-C and Ct-J. It was also confirmed that the ROK is currently dominated by the Ct-J clade, with a possible introduction of Ct-C via air currents.<br><br>CONCLUSIONS: Determining the presence of cryptic species is important for preventing vector-borne diseases. The results of this study confirm the existence of two clades of Cx. tritaeniorhynchus in the ROK, with Ct-J being the dominant clade. Our findings enhance current understanding of the genetic diversity within Cx. tritaeniorhynchus and provide valuable insights for the prevention of JEV outbreaks and the effective management of Cx. tritaeniorhynchus populations in East Asia.}, }
@article {pmid39695748, year = {2024}, author = {Aupalee, K and Srisuka, W and Limsopatham, K and Sanit, S and Takaoka, H and Saeung, A}, title = {Reliability of wing morphometrics for species identification of human-biting black flies (Diptera: Simuliidae) in Thailand.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {508}, pmid = {39695748}, issn = {1756-3305}, support = {106-2565//Faculty of Medicine, Chiang Mai University/ ; }, mesh = {Animals ; Thailand ; *Wings, Animal/anatomy &amp; histology ; *Phylogeny ; *Simuliidae/anatomy &amp; histology/classification/genetics ; Female ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; Humans ; Reproducibility of Results ; }, abstract = {BACKGROUND: Fast and reliable species identification of black flies is essential for research proposes and effective vector control. Besides traditional identification based on morphology, which is usually supplemented with molecular methods, geometric morphometrics (GM) has emerged as a promising tool for identification. Despite its potential, no specific GM techniques have been established for the identification of black fly species.<br><br>METHODS: Adult female black flies collected using human bait, as well as those reared from pupae, were used in this study. Here, landmark-based GM analysis of wings was assessed for the first time to identify human-biting black fly species in Thailand, comparing this approach with the standard morphological identification method and DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene. To explore genetic relationships between species, maximum likelihood (ML) and neighbor-joining (NJ) phylogenetic trees were built. Additionally, three different methods of species delimitation, i.e., assemble species by automatic partitioning (ASAP), generalized mixed yule coalescent (GMYC), and single Poisson tree processes (PTP), were utilized to identify the morphologically defined species. The effectiveness of a COI barcode in identifying black fly species was further examined through the best match (BM) and best close match (BCM) methods.<br><br>RESULTS: Seven black fly species, namely Simulium tenebrosum Takaoka, Srisuka &amp; Saeung, 2018 (complex), S. doipuiense Takaoka &amp; Choochote, 2005 (complex), S. nigrogilvum Summers, 1911, S. nodosum Puri, 1933, S. asakoae Takaoka &amp; Davies, 1995, S. chamlongi Takaoka &amp; Suzuki, 1984, and S. umphangense Takaoka, Srisuka &amp; Saeung, 2017 were morphologically identified. Compared with the standard method, the GM analysis based on wing shape showed high success in separating species, achieving an overall accuracy rate of 88.54%. On the other hand, DNA barcoding surpassed wing GM for species identification with a correct identification rate of 98.57%. Species delimitation analyses confirmed the validity of most nominal species, with an exception for S. tenebrosum complex and S. doipuiense complex, being delimited as a single species. Moreover, the analyses unveiled hidden diversity within S. asakoae, indicating the possible existence of up to four putative species.<br><br>CONCLUSIONS: This study highlights the potential of wing GM as a promising and reliable complementary tool for species identification of human-biting black flies in Thailand.}, }
@article {pmid39695327, year = {2024}, author = {Schröder, LC and Hüttermann, L and Kliesow Remes, A and Voran, JC and Hille, S and Sommer, W and Lutter, G and Warnecke, G and Frank, D and Schade, D and Müller, OJ}, title = {AAV library screening identifies novel vector for efficient transduction of human aorta.}, journal = {Gene therapy}, volume = {}, number = {}, pages = {}, pmid = {39695327}, issn = {1476-5462}, abstract = {Targeted gene delivery to vascular smooth muscle cells (VSMCs) could prevent or improve a variety of diseases affecting the vasculature and particularly the aorta. Thus, we aimed to develop a delivery vector that efficiently targets VSMCs. We selected engineered adeno-associated virus (AAV) capsids from a random AAV capsid library and tested the top enriched motifs in parallel screening through individual barcoding. This approach allowed us to distinguish capsids that only transduce cells based on genomic DNA (gDNA) from those also mediating transgene expression based on transcribed cDNA reads. After three rounds of selection on primary murine VSMCs (mVSMCs), we identified a novel targeting motif (RFTEKPA) that significantly improved transduction and gene expression efficiency over AAV9-wild type (WT) and increased expression in mVSMCs by 70% compared to the previously identified SLRSPPS peptide. Further analysis showed that the novel motif also improved expression in human aortic smooth muscle cells (HAoSMCs) and human aortic tissue ex vivo up to threefold compared to SLRSPPS and approximately 70-fold to AAV9-WT. This high cross-species transduction efficiency makes the novel capsid motif a potential candidate for future clinical application in vascular diseases.}, }
@article {pmid39693934, year = {2024}, author = {Heo, EH and Abrol, R}, title = {Thermodynamic role of receptor phosphorylation barcode in cannabinoid receptor desensitization.}, journal = {Biochemical and biophysical research communications}, volume = {743}, number = {}, pages = {151100}, doi = {10.1016/j.bbrc.2024.151100}, pmid = {39693934}, issn = {1090-2104}, abstract = {The endocannabinoid signaling system is comprised of CB1 and CB2 G protein-coupled receptors (GPCRs). CB2 receptor subtype is predominantly expressed in the immune cells and signals through its transducer proteins (Gi protein and β-arrestin-2). Arrestins are signaling proteins that bind to many GPCRs after receptor phosphorylation to terminate G protein signaling (desensitization) and to initiate specific G protein-independent arrestin-mediated signaling pathways via a "phosphorylation barcode", that captures sequence patterns of phosphorylated Ser/Thr residues in the receptor's intracellular domains and can lead to different signaling effects. The structural basis for how arrestins and G proteins compete with the receptor for biased signaling and how different barcodes lead to different signaling profiles is not well understood as there is a lack of phosphorylated receptor structures in complex with arrestins. In this work, structural models of β-arrestin-2 were built in complex with the phosphorylated and unphosphorylated forms of the CB2 receptor. The complex structures were relaxed in the lipid bilayer environment with molecular dynamics (MD) simulations and analyzed structurally and thermodynamically. The β-arrestin-2 complex with the phosphorylated receptor was more stable than the non-phosphorylated one, highlighting the thermodynamic role of the receptor phosphorylation. It was also more stable than any of the G protein complexes with CB2 suggesting that phosphorylation signals receptor desensitization (end of G protein signaling) and arrest of the receptor by arrestins. These models are beginning to provide the thermodynamic landscape of CB2 signaling, which can help bias signaling towards therapeutically beneficial pathways in drug discovery applications.}, }
@article {pmid39695366, year = {2024}, author = {Pere, K and Mburu, K and Muge, EK and Wagacha, JM and Nyaboga, EN}, title = {Molecular identification, genetic diversity, and secondary structure predictions of Physalis species using ITS2 DNA barcoding.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1178}, pmid = {39695366}, issn = {1471-2229}, abstract = {BACKGROUND: The genus Physalis belongs to the Solanaceae family and has different species with important nutritional and medicinal values. Species within this genus have limited morphological differences, a characteristic that hinders accurate identification, safe utilization and genetic conservation of promising genotypes. In addition, to prevent the perceived loss of Physalis diversity due to habitat destruction, species delimitation needs attention. In this study, we used the sequence and structural information of the internal transcribed spacer 2 (ITS2) barcode to efficiently identify and discriminate Physalis species from a collection of 34 Physalis accessions.<br><br>METHODOLOGY: Physalis plant samples were collected from eight Counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. A total of 34 Physalis accessions were identified and accessed for diversity based on the ITS2 barcode region. The sequence similarity of the ITS2 genes was analyzed through the Basic Local Alignment Search Tool (BLAST), the nearest Kimura-2-parameter (K2P) genetic distances were calculated and a phylogenetic tree was constructed using the Bayesian inference (BI) method in MrBayes 3.2.7a software. The differences in the ITS2 secondary structure between the species were analyzed.<br><br>RESULTS: The success rate of PCR amplification and sequencing was 75% and 67%, respectively. The analyzed ITS2 sequences displayed significant inter-specific divergences, clear DNA barcoding gaps and high species identification efficiency. Based on the constructed phylogenetic tree, three Physalis species (Physalis peruviana, Physalis purpurea and Physalis cordata) were identified and were clustered in a homogenized distribution. High genetic diversity (0.36923) and genetic distance (0.703) were observed between Physalis peruviana and Physalis cordata. The highest genetic nucleotide diversity (0.26324) and distance (0.46) within species was obtained for Physalis peruviana. The differences in the secondary structures generated from this study discriminated between the Physalis species.<br><br>CONCLUSIONS: Our study demonstrated that ITS2 is a potential DNA barcode for effective identification and discrimination of Physalis species. The results of this study provide insights into the scientific basis of species identification, safe utilization, genetic conservation and future breeding strategies for this important nutritional and medicinal plant species.}, }
@article {pmid39695009, year = {2024}, author = {Herath, DR and Perera, HACC and Ranasinghe, VK and Amarakoon, AADG and Hettiarachchi, GHCM}, title = {Stomach content analysis of Euthynnus affinis, Auxis thazard and Auxis rochei of the coastal waters of Sri Lanka by DNA barcoding.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {63}, pmid = {39695009}, issn = {1573-4978}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Sri Lanka ; *Gastrointestinal Contents ; *Tuna/genetics ; Feeding Behavior/physiology ; Predatory Behavior ; Fishes/genetics/classification ; }, abstract = {BACKGROUND: Analysis of the content of the gut of fish helps in the understanding of their inter- and intra-specific interactions, fish behaviour, condition and energy intake. The stomach contents of the commercially important neritic tuna species of Sri Lanka, kawakawa (Euthynnus affinis), frigate tuna (Auxis thazard) and bullet tuna (Auxis rochei) were analysed to determine their feeding habits and to identify prey species.<br><br>METHODS AND RESULTS: The weighed stomachs of fish were dissected to reveal the types of prey found within. The prey was categorised into prey categories and each prey species was identified morphologically. Prey items which were partially digested were identified using DNA barcoding. The main prey category was small fish, followed by crustaceans and cephalopods. While the highest occurring prey category for E. affinis and A. rochei was fish, crustaceans dominated the A. thazard diet. DNA barcoding identified 11 prey items that were partially digested, which could not be identified to species-level morphologically. Of the prey items identified by DNA barcoding, four species of fish, three species of cephalopod and four species of crustaceans were identified. These prey item identifications confirmed that E. affinis, A. thazard and A. rochei are all nonspecific feeders.<br><br>CONCLUSIONS: This exhibits the value of molecular tools in the identification of species which have lost their distinguishable features due to digestion. Further, it illustrates the predator-prey relationships between these species, aiding in the management of prey and predator populations, ensuring that both populations remain stable, helping in the maintenance of the balance of the ecosystem.}, }
@article {pmid39693656, year = {2024}, author = {Eriksen, TE and Brittain, JE and Sandin, L and Friberg, N}, title = {Unveiling cryptic macroinvertebrate sentinels to enhance biomonitoring in tropical rivers: Bridging traditional approaches with DNA barcoding in the Indo-Burma biodiversity hotspot.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178064}, doi = {10.1016/j.scitotenv.2024.178064}, pmid = {39693656}, issn = {1879-1026}, abstract = {Human activities present significant threats to tropical freshwater ecosystems, notably in many global biodiversity hotspots, threats that are further increased by inadequate taxonomic knowledge and the lack of appropriate biomonitoring tools. This study integrates globally validated biomonitoring approaches with DNA-based identification methods to create a macroinvertebrate-based tool for diagnosing ecosystem health and assessing the biodiversity of tropical river ecosystems in Myanmar (Indo-Burma bioregion). To evaluate river site degradation, comprehensive data on water and habitat quality, as well as land use information, were collected. Riverine macroinvertebrates were sampled by kick sampling, and subsequent DNA barcoding analysis was used to establish molecular taxonomic units (MTUs) for key bioindicator groups, including Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, and Odonata (EPTCO) as species-level identification nomenclature was lacking. Tolerance scores for the local fauna were derived along an environmental degradation gradient to enable comparisons with widely adopted global assessment tools relying on macroinvertebrate metrics. In both study areas, the upper parts of the river networks were generally undisturbed by human activities while stressors associated with urban and agricultural land use were evident in the lower parts of the catchments. The highest precision for assessment of river health was found when establishing tolerance scores adjusted to local species composition in each study area separately. Although a family-level-based multimetric approach was significantly related to the main environmental degradation gradient, assessments utilizing cryptic species-level data (MTUs) emerged as the being most precise indicator in both areas. Our study highlights the synergistic benefits of merging traditional biomonitoring with DNA-based methods for species identification for biomonitoring in tropical river ecosystems. To halt biodiversity decline and curb the extent of the escalating nature crisis, such integrated approaches will be highly valuable in understudied and biodiversity-rich aquatic ecosystems.}, }
@article {pmid39688736, year = {2024}, author = {Singha, D and Patidar, A and Pal, S and Tyagi, K and Kumar, V}, title = {Mitochondrial genetic diversity of pest and vector species, Frankliniella schultzei (Thripidae: Thripinae).}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {55}, pmid = {39688736}, issn = {1573-4978}, support = {CRG/2023/000498//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Phylogeny ; *Genetic Variation/genetics ; *Haplotypes/genetics ; India ; *Thysanoptera/genetics/classification ; DNA Barcoding, Taxonomic/methods ; Australia ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Insect Vectors/genetics/classification ; Bayes Theorem ; Gene Flow ; }, abstract = {BACKGROUND: Frankliniella schultzei (Trybom) is a serious pest and a carrier of tospoviruses in major agricultural crops. This species is a historical and unresolved species complex that contains genetically different cryptic species across the globe.<br><br>METHODS AND RESULTS: DNA barcodes were generated from freshly collected specimens of F. schultzei from India and Australia using the sanger sequencing. Seventy-five COI sequences were generated from India and Australia. Moreover, 318 sequences were downloaded (India, Australia, Pakistan, and Africa) from the NCBI GenBank to explore the genetic diversity and phylogeny. The minimum and maximum mean interspecific distance between 393 sequences was found to be 7.97% and 21.50%, respectively. Bayesian and Neighbour joining clustering indicated the presence of five putative species within F. schultzei that had sympatry and allopatry. Moreover, 20 haplotypes and 140 polymorphic sites were identified. The African clade is unique; it does not share haplotypes with any other countries, suggesting it may represent the true F. schultzei. Haplotype network analysis showed shallow gene flow and deep genetic variation between the populations. Signatures of recent population history events were measured using Fu's Fs test and Tajima's D test. Morphometric analysis based on seven characters is also carried out.<br><br>CONCLUSION: Phylogeny and genetic distance revealed the presence of five putative species within F. schultzei. On the contrary, morphology does not unequivocally corroborate the phylogenetic results, as morphometric analysis showed overlap among these clades. To resolve F. schultzei species complex, whole genome-based sequencing data are very much necessitated.}, }
@article {pmid39687742, year = {2024}, author = {Haile, S and Corbett, RD and O'Neill, K and Xu, J and Smailus, DE and Pandoh, PK and Bayega, A and Bala, M and Chuah, E and Coope, RJN and Moore, RA and Mungall, KL and Zhao, Y and Ma, Y and Marra, MA and Jones, SJM and Mungall, AJ}, title = {Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1466338}, doi = {10.3389/fgene.2024.1466338}, pmid = {39687742}, issn = {1664-8021}, abstract = {The advent of long-read (LR) sequencing technologies has provided a direct opportunity to determine the structure of transcripts with potential for end-to-end sequencing of full-length RNAs. LR methods that have been described to date include commercial offerings from Oxford Nanopore Technologies (ONT) and Pacific Biosciences. These kits are based on selection of polyadenylated (polyA+) RNAs and/or oligo-dT priming of reverse transcription. Thus, these approaches do not allow comprehensive interrogation of the transcriptome due to their exclusion of non-polyadenylated (polyA-) RNAs. In addition, polyA + specificity also results in 3'-biased measurements of PolyA+ RNAs especially when the RNA input is partially degraded. To address these limitations of current LR protocols, we modified rRNA depletion protocols that have been used in short-read sequencing: one approach representing a ligation-based method and the other a template-switch cDNA synthesis-based method to append ONT-specific adaptor sequences and by removing any deliberate fragmentation/shearing of RNA/cDNA. Here, we present comparisons with poly+ RNA-specific versions of the two approaches including the ONT PCR-cDNA Barcoding kit. The rRNA depletion protocols displayed higher proportions (30%-50%) of intronic content compared to that of the polyA-specific protocols (5%-8%). In addition, the rRNA depletion protocols enabled ∼20-50% higher detection of expressed genes. Other metrics that were favourable to the rRNA depletion protocols include better coverage of long transcripts, and higher accuracy and reproducibility of expression measurements. Overall, these results indicate that the rRNA depletion-based protocols described here allow the comprehensive characterization of polyadenylated and non-polyadenylated RNAs. While the resulting reads are long enough to help decipher transcript structures, future endeavors are warranted to improve the proportion of individual reads representing end-to-end spanning of transcripts.}, }
@article {pmid39684314, year = {2024}, author = {Domingo-Bretón, R and Moroni, F and Toxqui-Rodríguez, S and Belenguer, &#xc1; and Piazzon, MC and Pérez-Sánchez, J and Naya-Català, F}, title = {Moving Beyond Oxford Nanopore Standard Procedures: New Insights from Water and Multiple Fish Microbiomes.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, doi = {10.3390/ijms252312603}, pmid = {39684314}, issn = {1422-0067}, support = {871108//Horizon H2020/ ; PRTR-C17.I1//Ministerio de Ciencia e Innovaci&#xf3;n/ ; THINKINAZUL/2021/024//Generalitat Valenciana/ ; }, mesh = {Animals ; *Microbiota/genetics ; *Fishes/microbiology ; Nanopores ; Feces/microbiology ; Water Microbiology ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Oxford Nanopore Technology (ONT) allows for the rapid profiling of aquaculture microbiomes. However, not all the experimental and downstream methodological possibilities have been benchmarked. Here, we aimed to offer novel insights into the use of different library preparation methods (standard-RAP and native barcoding-LIG), primers (V3-V4, V1-V3, and V1-V9), and basecalling models (fast-FAST, high-HAC, and super-accuracy-SUP) implemented in ONT to elucidate the microbiota associated with the aquatic environment and farmed fish, including faeces, skin, and intestinal mucus. Microbial DNA from water and faeces samples could be amplified regardless of the library-primer strategy, but only with LIG and V1-V3/V1-V9 primers in the case of skin and intestine mucus. Low taxonomic assignment levels were favoured by the use of full-length V1-V9 primers, though in silico hybridisation revealed a lower number of potential matching sequences in the SILVA database, especially evident with the increase in Actinobacteriota in real datasets. SUP execution allowed for a higher median Phred quality (24) than FAST (11) and HAC (17), but its execution time (6-8 h) was higher in comparison to the other models (0.6-7 h). Altogether, we optimised the use of ONT for water- and fish-related microbial analyses, validating, for the first time, the use of the LIG strategy. We consider that LIG-V1-V9-HAC is the optimal time/cost-effective option to amplify the microbial DNA from environmental samples. However, the use of V1-V3 could help to maximise the dataset microbiome diversity, representing an alternative when long amplicon sequences become compromised by microbial DNA quality and/or high host DNA loads interfere with the PCR amplification/sequencing procedures, especially in the case of gut mucus.}, }
@article {pmid39682398, year = {2024}, author = {Zhou, J and Zhang, X and Wang, Y and Liang, H and Yang, Y and Huang, X and Deng, J}, title = {Contamination Survey of Insect Genomic and Transcriptomic Data.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {23}, pages = {}, doi = {10.3390/ani14233432}, pmid = {39682398}, issn = {2076-2615}, support = {2022FY100500, KFB23016//the Special Investigation Program for National Science and Technology Basic Resources, the Special Fund for Science and Technology Innovation of Fujian Agriculture and Forestry University/ ; }, abstract = {The rapid advancement of high-throughput sequencing has led to a great increase in sequencing data, resulting in a significant accumulation of contamination, for example, sequences from non-target species may be present in the target species' sequencing data. Insecta, the most diverse group within Arthropoda, still lacks a comprehensive evaluation of contamination prevalence in public databases and an analysis of potential contamination causes. In this study, COI barcodes were used to investigate contamination from insects and mammals in GenBank's genomic and transcriptomic data across four insect orders. Among the 2796 WGS and 1382 TSA assemblies analyzed, contamination was detected in 32 (1.14%) WGS and 152 (11.0%) TSA assemblies. Key findings from this study include the following: (1) TSA data exhibited more severe contamination than WGS data; (2) contamination levels varied significantly among the four orders, with Hemiptera showing 9.22%, Coleoptera 3.48%, Hymenoptera 7.66%, and Diptera 1.89% contamination rates; (3) possible causes of contamination, such as food, parasitism, sample collection, and cross-contamination, were analyzed. Overall, this study proposes a workflow for checking the existence of contamination in WGS and TSA data and some suggestions to mitigate it.}, }
@article {pmid39678441, year = {2024}, author = {Hamdi, I and Benmansour, B and Ahmed, M and Gulsher, M and Bouguerche, C}, title = {A new genus and a new species of microcotylids (Polyopisthocotyla, Platyhelminthes), gill parasite of the pink dentex Dentex gibbosus (Teleostei, Sparidae) off Tunisia and notes on Polyopisthocotyla and Monopisthocotyla from Dentex spp.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {25}, number = {}, pages = {101016}, pmid = {39678441}, issn = {2213-2244}, abstract = {The study of the polyopisthocotylan parasites of marine fishes in the western Mediterranean is carried on using an integrative approach combining morphology and DNA barcodes. Ktarius patrickbrueli n. gen. n. sp (Polyopisthocotyla, Microcotylidae), from the gills of the pink dentex Dentex gibbosus (Teleostei, Sparidae) from the western Mediterranean Sea off Tunisia, is described. Anatomical and morphological features of the new genus are described, and the molecular barcodes for nuclear and mitochondrial markers (28S rRNA and cox1) are generated. The new genus is closely related to Microcotyle by sharing a symmetrical haptor, inverted question mark-shaped ovary and unarmed vagina. However, Ktarius n. gen. can be distinguished from Microcotyle and other Microcotylinae taxa by an unarmed male copulatory organ, formed by a long muscular cirrus, a basal layer of concentric muscles, and an elongated thick-walled ejaculatory bulb. A partial 28S rDNA sequence of K. patrickbrueli n. gen. n. sp. was obtained and found to be distinct from all known microcotylid sequences, with a p-distance of 5-13%. A phylogenetic tree constructed from available microcotylid sequences revealed that K. patrickbrueli n. gen. n. sp. clustered in a strongly supported clade of Microcotylinae, containing species of Omanicotyle, Bivagina, and Microcotyle confirming its belonging to the Microcotylinae subfamily. The cox1 sequences of K. patrickbrueli n. gen. n. sp. were highly divergent from the closely related genus Pauciconfibula and confirmed its distinction. This new genus is the third polyopisthocotylan genus to be described from sparids of Dentex.}, }
@article {pmid39677764, year = {2024}, author = {Cho, S and Moon, W and Martino, N and Yun, SH}, title = {Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.29.626128}, pmid = {39677764}, issn = {2692-8205}, abstract = {Laser particles (LPs) emitting narrowband spectra across wide spectral ranges are highly promising for high-multiplex optical barcoding. Here, we present LPs based on indium phosphide (InP) nanodisks, operating in the near-infrared wavelength range of 740-970 nm. Utilizing low-order whispering gallery resonance modes in size-tuned nanodisks, we achieved an ultrawide color palette with 27% bandwidth utilization and nanometer-scale linewidth. The minimum laser size was 430 nm in air and 560 nm within the cytoplasm, operating at mode order 4 or 5. We further demonstrated spectral detection of laser peaks with high signal-to-background ratios in highly-scattering media, including 1-cm-thick chicken breast tissue and blood vessels in live mice.}, }
@article {pmid39677603, year = {2024}, author = {Twa, GM and Phillips, RA and Robinson, NJ and Day, JJ}, title = {Accurate sample deconvolution of pooled snRNA-seq using sex-dependent gene expression patterns.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39677603}, issn = {2692-8205}, abstract = {Single nucleus RNA sequencing (snRNA-seq) technology offers unprecedented resolution for studying cell type-specific gene expression patterns. However, snRNA-seq poses high costs and technical limitations, often requiring the pooling of independent biological samples and loss of individual sample-level data. Deconvolution of sample identity using inherent features would enable the incorporation of pooled barcoding and sequencing protocols, thereby increasing data throughput and analytical sample size without requiring increases in experimental sample size and sequencing costs. In this study, we demonstrate a proof of concept that sex-dependent gene expression patterns can be leveraged for the deconvolution of pooled snRNA-seq data. Using previously published snRNA-seq data from the rat ventral tegmental area, we trained a range of machine learning models to classify cell sex using genes differentially expressed in cells from male and female rats. Models that used sex-dependent gene expression predicted cell sex with high accuracy (90-92%) and outperformed simple classification models using only sex chromosome gene expression (69-89%). The generalizability of these models to other brain regions was assessed using an additional published data set from the rat nucleus accumbens. Within this data set, model performance remained highly accurate in cell sex classification (89-90% accuracy) with no additional re-training. This work provides a model for future snRNA-seq studies to perform sample deconvolution using a two-sex pooled sample sequencing design and benchmarks the performance of various machine learning approaches to deconvolve sample identification from inherent sample features.}, }
@article {pmid39675106, year = {2024}, author = {Mutum, RS and Das, A and Ghosh, SK and Wangkheimayum, VD}, title = {The origins of "Kaunayen" game fowls of Manipur, India: Insights from mitochondrial D-loop sequence analysis.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104667}, doi = {10.1016/j.psj.2024.104667}, pmid = {39675106}, issn = {1525-3171}, abstract = {Notably, poultry animals-particularly chickens-are recognized globally for their valuable contributions to the food, ornamental, and game economies. Further, more robust local and regional breeds can be parental donors for these area-specific consumable breeds' resilient traits. Game birds that are locally significant economically or on a much smaller scale are frequently excluded from the procedure. One such breed is the fighting chicken of Manipur, India, known locally as the Kaunayen breed and listed as the 17th breed at the ICAR, the National Bureau of Animal Genetic Resources, India. When Kaunayen fowl from throughout Manipur are considered, they have anatomical characteristics and common behavioural traits despite the breed's extreme genetic heterogeneity. With this gap in mind, we attempted to use mitochondrial D-loop sequences to characterize Manipur's Kaunayen fowls concerning the global breeds of nearly similar molecular characteristics. We found that Kaunayen fowls share evolutionary traits such as a similar transition/transversion ratio with some Southeast Asian breeds, including a few red jungle fowls. Overall Kaunayen are also more closely related to Southeast Asian birds phylogenetically, after which with a few breeds from East Asian, Bangladesh, North-East India, and the Indian island of Nicobar. The global database including our query has 19 haplotypes, and majority of the Kaunayen fowls share haplotypes with North East Indian fowls; the remaining haplotypes are primarily associated with South East Asia and East Asia. The findings additionally indicated that Kaunayen's and the global breed's D-loop region tended to fixed neutral substitution, contributing to the distinct varieties. Further, migration research demonstrated that Kaunayen fowls originated from a substantial maternal genome influx from Southeast Asia, which may have later made a substantial contribution to East Asian and South Asian breeds. We also display a portion of the D-loop that demonstrates the majority of the substitution diversity across all breeds, and we suggest using sequence stretch to create miniature breed-specific identifying barcodes.}, }
@article {pmid39673434, year = {2024}, author = {Krasilnikova, LA and Tomkins-Tinch, C and Gayton, A and Schaffner, SF and Dobbins, ST and Gladden-Young, A and Siddle, KJ and Park, DJ and Sabeti, PC}, title = {Polyphonia: detecting inter-sample contamination in viral genomic sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae698}, pmid = {39673434}, issn = {1367-4811}, abstract = {SUMMARY: In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, and detection of superinfections and recombination events. While sample barcoding methods exist to track inter-sample contamination, they are not always used and can only detect contamination in the experimental pipeline from the point they are added. The underlying genomic information in a sample, however, carries information about inter-sample contamination occurring at any stage. Here, we present Polyphonia, a tool for detecting inter-sample contamination directly from deep sequencing data without the need for additional controls, using intrahost variant frequencies. We apply Polyphonia to 1 102 SARS-CoV-2 samples sequenced at the Broad Institute and already tracked using molecular barcoding for comparison.<br><br>Polyphonia is available as a standalone Docker image and is also included as part of viral-ngs, available in Dockstore. Full documentation, source code, and instructions for use are available at https://github.com/broadinstitute/polyphonia.<br><br>SUPPLEMENTARY INFORMATION: Data for reproducing results are available at Bioinformatics online.}, }
@article {pmid39672980, year = {2024}, author = {Garcia-Gonzalez, I and Gambera, S and Rocha, SF and Regano, A and Garcia-Ortega, L and Lytvyn, M and Diago-Domingo, L and Sanchez-Muñoz, MS and Garcia-Cabero, A and Zagorac, I and Luo, W and De Andrés-Laguillo, M and Fernández-Chacón, M and Casquero-Garcia, V and Lunella, FF and Torroja, C and Sánchez-Cabo, F and Benedito, R}, title = {iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {39672980}, issn = {1548-7105}, support = {101001814//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 638028//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; HR22-00316//"la Caixa" Foundation (Caixa Foundation)/ ; HR19-00120//"la Caixa" Foundation (Caixa Foundation)/ ; CX-SO-16-1//"la Caixa" Foundation (Caixa Foundation)/ ; CX_E-2015-01//"la Caixa" Foundation (Caixa Foundation)/ ; PRE2018-085283//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a (Ministerio de Econom&#xed;a, Industria y Competitividad)/ ; }, abstract = {To understand gene function, it is necessary to compare cells carrying the mutated target gene with normal cells. In most biomedical studies, the cells being compared are in different mutant and control animals and, therefore, do not experience the same epigenetic changes and tissue microenvironment. The experimental induction of genetic mosaics is essential to determine a gene cell-autonomous function and to model the etiology of diseases caused by somatic mutations. Current technologies used to induce genetic mosaics in mice lack either accuracy, throughput or barcoding diversity. Here we present the iFlpMosaics toolkit comprising a large set of new genetic tools and mouse lines that enable recombinase-dependent ratiometric induction and single-cell clonal tracking of multiple fluorescently labeled wild-type and Cre-mutant cells within the same time window and tissue microenvironment. The labeled cells can be profiled by multispectral imaging or by fluorescence-activated flow cytometry and single-cell RNA sequencing. iFlpMosaics facilitate the induction and analysis of genetic mosaics in any quiescent or progenitor cell, and for any given single or combination of floxed genes, thus enabling a more accurate understanding of how induced genetic mutations affect the biology of single cells during tissue development, homeostasis and disease.}, }
@article {pmid39672483, year = {2024}, author = {Houpt, TA and Houpt, CE and Cassell-Erquiaga, CB}, title = {BarTender: A system for recording intakes and body weights in ingestive behavior experiments.}, journal = {Physiology &amp; behavior}, volume = {}, number = {}, pages = {114783}, doi = {10.1016/j.physbeh.2024.114783}, pmid = {39672483}, issn = {1873-507X}, abstract = {A system is described for the semi-automated collection of fluid bottle, food jar, and rodent body weights. Items are labeled with barcodes, which are scanned by a Macintosh application connected via USB to a scale. Body weights are collected in the animal room by an iPad application connected to a Bluetooth scale. Simple summary statistics are automatically calculated, and data are stored with experiment metadata in a cloud database. Up-to-date graphs of the data are rendered by a web application from any browser, from which data can be downloaded for further analysis. Such a system makes ingestive behavior experiments more accurate, rapid, and higher throughput.}, }
@article {pmid39670108, year = {2024}, author = {Díaz, JA and Ordines, F and Massutí, E and Cárdenas, P}, title = {From caves to seamounts: the hidden diversity of tetractinellid sponges from the Balearic Islands, with the description of eight new species.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16584}, pmid = {39670108}, issn = {2167-8359}, mesh = {Animals ; *Porifera/classification/anatomy &amp; histology ; Spain ; Caves ; Phylogeny ; Biodiversity ; Ecosystem ; DNA Barcoding, Taxonomic ; }, abstract = {The sponge fauna of the Western Mediterranean stands as one of the most studied in the world. Yet sampling new habitats and a poorly studied region like the Balearic Islands highlights once again our limited knowledge of this group of animals. This work focused on demosponges of the order Tetractinellida collected in several research surveys (2016-2021) on a variety of ecosystems of the Balearic Islands, including shallow caves, seamounts and trawl fishing grounds, in a broad depth range (0-725 m). Tetractinellid material from the North Atlantic and more than twenty type specimens were also examined and, for some, re-described in this work. All species were barcoded with the traditional molecular markers COI (Folmer fragment) and 28S (C1-C2 or C1-D2 fragment). A total of 36 species were identified, mostly belonging to the family Geodiidae (15 species), thereby bringing the number of tetractinellids recorded in the Balearic Islands from 15 to 39. Eight species from this study are new: Stelletta mortarium sp. nov., Penares cavernensis sp. nov., Penares isabellae sp. nov., Geodia bibilonae sp. nov., Geodia microsphaera sp. nov. and Geodia matrix sp. nov. from the Balearic Islands; Geodia phlegraeioides sp. nov. and Caminus xavierae sp. nov. from the North East Atlantic. Stelletta dichoclada and Erylus corsicus are reported for the first time since their description in Corsica in 1983. Pachastrella ovisternata is documented for the first time in the Mediterranean Sea. Finally, after comparisons of type material, we propose new synonymies: Geodia anceps as a junior synonym of Geodia geodina, Erylus cantabricus as a junior synonym of Erylus discophorus and Spongosorites maximus as a junior synonym of Characella pachastrelloides.}, }
@article {pmid39664260, year = {2024}, author = {Albaina, A and Garić, R and Yebra, L}, title = {Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa.}, journal = {Journal of plankton research}, volume = {46}, number = {6}, pages = {581-595}, pmid = {39664260}, issn = {0142-7873}, abstract = {Eleven years after the publication of the first work applying deoxyribonucleic acid (DNA) metabarcoding to zooplankton communities, the commonly known "miniCOI" barcode is widely used, becoming the marker of choice. However, several primer combinations co-exist for this barcode and a critical evaluation of their performance is needed. This article reviews the misperformance of miniCOI metabarcoding with marine zooplankton communities, comparing them to microscopy and/or other universal markers. In total, misperformances were reported for 26 zooplankton taxa, including 18 copepods and five tunicates. We report a detection failure with Class Appendicularia and contrasting performances for Oithona similis (from good correspondence to detection failure), two worldwide abundant taxa with a crucial role in the marine pelagic realm. A combination of forward primer mismatches, the presence of long poly-T inserts and a low number of reference sequences would explain the failure to detect appendicularians. However, the contrasting performance with O. similis would correspond to distinct numbers of mismatches in the forward primer in different lineages within this cryptic taxon. This is reinforced by the report of similar patterns with other locally abundant zooplankton taxa. Therefore, we strongly call for the use of miniCOI in combination with alternative methods capable of addressing these limitations.}, }
@article {pmid39663496, year = {2024}, author = {Hu, M and Yang, L and Twarog, N and Ochoada, J and Li, Y and Vrettos, EI and Torres-Hernandez, AX and Martinez, JB and Bhatia, J and Young, BM and Price, J and McGowan, K and Nguyen, TH and Shi, Z and Anyanwu, M and Rimmer, MA and Mercer, S and Rankovic, Z and Shelat, AA and Blair, DJ}, title = {Continuous collective analysis of chemical reactions.}, journal = {Nature}, volume = {636}, number = {8042}, pages = {374-379}, pmid = {39663496}, issn = {1476-4687}, mesh = {*Mass Spectrometry ; High-Throughput Screening Assays/methods ; Chemistry Techniques, Synthetic/methods ; }, abstract = {The automated synthesis of small organic molecules from modular building blocks has the potential to transform our capacity to create medicines and materials[1-3]. Disruptive acceleration of this molecule-building strategy broadly unlocks its functional potential and requires the integration of many new assembly chemistries. Although recent advances in high-throughput chemistry[4-6] can speed up the development of appropriate synthetic methods, for example, in selecting appropriate chemical reaction conditions from the vast range of potential options, equivalent high-throughput analytical methods are needed. Here we report a streamlined approach for the rapid, quantitative analysis of chemical reactions by mass spectrometry. The intrinsic fragmentation features of chemical building blocks generalize the analyses of chemical reactions, allowing sub-second readouts of reaction outcomes. Central to this advance was identifying that starting material fragmentation patterns function as universal barcodes for downstream product analysis by mass spectrometry. Combining these features with acoustic droplet ejection mass spectrometry[7,8] we could eliminate slow chromatographic steps and continuously evaluate chemical reactions in multiplexed formats. This enabled the assignment of reaction conditions to molecules derived from ultrahigh-throughput chemical synthesis experiments. More generally, these results indicate that fragmentation features inherent to chemical synthesis can empower rapid data-rich experimentation.}, }
@article {pmid39660837, year = {2024}, author = {Lewin, GR}, title = {mSphere of Influence: How the single cell contributes to the collective.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0043124}, doi = {10.1128/msphere.00431-24}, pmid = {39660837}, issn = {2379-5042}, abstract = {Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq-"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing" by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192-1201, 2020, https://doi.org/10.1038/s41564-020-0729-6) and "Microbial single-cell RNA sequencing by split-pool barcoding" by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021, https://doi.org/10.1126/science.aba5257)-impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.}, }
@article {pmid39660352, year = {2024}, author = {Yu, T and Ren, Z and Gao, X and Li, G and Han, R}, title = {Generating barcodes for nanopore sequencing data with PRO.}, journal = {Fundamental research}, volume = {4}, number = {4}, pages = {785-794}, pmid = {39660352}, issn = {2667-3258}, abstract = {DNA barcodes, short and unique DNA sequences, play a crucial role in sample identification when processing many samples simultaneously, which helps reduce experimental costs. Nevertheless, the low quality of long-read sequencing makes it difficult to identify barcodes accurately, which poses significant challenges for the design of barcodes for large numbers of samples in a single sequencing run. Here, we present a comprehensive study of the generation of barcodes and develop a tool, PRO, that can be used for selecting optimal barcode sets and demultiplexing. We formulate the barcode design problem as a combinatorial problem and prove that finding the optimal largest barcode set in a given DNA sequence space in which all sequences have the same length is theoretically NP-complete. For practical applications, we developed the novel method PRO by introducing the probability divergence between two DNA sequences to expand the capacity of barcode kits while ensuring demultiplexing accuracy. Specifically, the maximum size of the barcode kits designed by PRO is 2,292, which keeps the length of barcodes the same as that of the official ones used by Oxford Nanopore Technologies (ONT). We validated the performance of PRO on a simulated nanopore dataset with high error rates. The demultiplexing accuracy of PRO reached 98.29% for a barcode kit of size 2,922, 4.31% higher than that of Guppy, the official demultiplexing tool. When the size of the barcode kit generated by PRO is the same as the official size provided by ONT, both tools show superior and comparable demultiplexing accuracy.}, }
@article {pmid39659773, year = {2024}, author = {Xue, XL and Lu, XQ and Du, XC}, title = {The new genus Purpurata (Lepidoptera, Crambidae, Spilomelinae), with descriptions of two new species from China.}, journal = {ZooKeys}, volume = {1219}, number = {}, pages = {175-194}, pmid = {39659773}, issn = {1313-2989}, abstract = {The male genitalia characters of four species, Botysiopasalis Walker, 1859, Pleuroptyaobfuscalis Yamanaka, 1998, Botysplagiatalis Walker, 1859 and Pataniashompen Singh et Ahmad, 2022, placed in the genus Patania Moore, 1888 before the present study, do not conform to the diagnosis of Patania. A new genus, Purpurata gen. nov., is established for these four species, and two new species, Purpuratadirecta sp. nov. and Purpuratalurida sp. nov. are described based on their external morphology and genitalia characters. Purpuratadirecta sp. nov. is designated as the type species of the new genus. Five species of the new genus were clearly separated from Patania species in the Maximum likelihood phylogenetic tree constructed based on COI sequence data. Compared to Patania, the new genus Purpurata exhibits distinctive characters in male genitalia: the uncus is short, broad, and arc-shaped posteriorly; the gnathos is present and setose, or reduced; and the fibula is very small and setose. In addition, Pataniaclava (Xu &amp; Du), syn. nov. is synonymized with Purpurataiopasalis comb. nov. An identification key to species of the new genus is presented based on morphological characters of habitus and genitalia. Images of the habitus and genitalia are provided.}, }
@article {pmid39659496, year = {2024}, author = {Shih, HT and Cai, Y and Niwa, N and Yoshigou, H and Nakahara, Y}, title = {Integrative Taxonomy Reveals Freshwater Shrimp Diversity (Decapoda: Atyidae: Neocaridina) from Kyushu and Southern Honshu of Japan, with a Discussion on Introduced Species.}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e18}, pmid = {39659496}, issn = {1810-522X}, abstract = {Correct identification of species is crucial for invasion ecology and management, particularly in aquatic systems. In this study, specimens of the freshwater shrimp genus Neocaridina from Kyushu and southern Honshuof Japan were identified by using an integrative approach that combined DNA barcoding of mitochondrial cytochrome oxidase subunit I (COI) and morphological examination. Among the eight species detected, two are native, viz. N. denticulata and N. ikiensis. Four are regarded as non-indigenous, viz. N. davidi, N. koreana, N. palmata, N. aff. palmata, which are believed to have been introduced from other East Asian countries either by the aquarium trade or as live fish bait. The remaining two species are likely cryptic native species, which have either been mistaken for known species, e.g., N. aff. denticulata, or species that have not been discovered before, e.g., N. aff. fukiensis. While the four alien species have spread widely in central Honshu, northern Kyushu and Tsushima Island, their impacts on the native species and the overall ecology remain mostly unexplored. Problems associated with using DNA barcoding for species identification are highlighted for further research.}, }
@article {pmid39657551, year = {2024}, author = {Zhang, D and Zhang, N and Zhao, J and Li, X and Bian, F and Zhang, Y and Ge, Y and Li, Z}, title = {Label-free multiplexed detection based on core-shell photonic barcodes integrated RCA.}, journal = {Biosensors &amp; bioelectronics}, volume = {271}, number = {}, pages = {117037}, doi = {10.1016/j.bios.2024.117037}, pmid = {39657551}, issn = {1873-4235}, abstract = {Multiplexed, rapid, and accurate virus quantification is of great value in biomedical detection. Herein, we proposed a label-free multiplexed virus screening quantitative biosensor based on color core-shell hydrogel photonic crystal (PhC) barcode integrated rolling circle amplification (RCA). The composite hydrogel shell was formed by acrylic acid and polyethylene glycol diacrylate, and the core silica photonic crystal was used as a detector. In addition, by adjusting the internal periodic structure, the PhC microcarrier was able to perform various color barcodes for the detection of different targets. Based on these excellent properties of the nanocomposite barcode, the biosensor not only demonstrated the ability to rapidly and accurately detect SARS-COV-2-N, SARS-COV-2-S, and H1N1 simultaneously in one tube, but also converting the signal of target protein to nucleic acid signal based on DNA decorated antibody complex combine with the blocked primer and RCA strategy. As a result, the platform achieved highly sensitive multiplexed quantitative detection with a detection limit in the range of 0.30 pg/mL. In addition, the platform we developed was validated by clinical sample analysis with acceptable accuracy and high specificity, demonstrating the good potential applicability of the proposed detection method in clinical screening and diagnosis.}, }
@article {pmid39654309, year = {2024}, author = {Frankenburg, R and Oreg, A}, title = {"As long as they remember me, I am alive": Commemoration and memory through stickers.}, journal = {Death studies}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/07481187.2024.2435929}, pmid = {39654309}, issn = {1091-7683}, abstract = {This study explores the phenomenon of memorial stickers commemorating victims of the October 7, 2023, massacre and subsequent Israel-Hamas war. Analyzing 600 stickers collected across Israel, we examine how these artifacts shape personal and collective memory of these tragic events. Using content analysis, visual data analysis, and ethnography of texts, we investigate the stickers' distribution, textual content, and visual elements. Three key findings emerged: (1) The widespread distribution of stickers expands commemoration beyond cemeteries, creating a larger community of remembrance; (2) Diverse textual content, from personal traits to universal messages, aims to keep the deceased's values alive in social awareness; (3) Visual elements balance public recognition with private mourning through strategic use of photographs, colors, and barcodes. Drawing on theories of collective memory and continuing bonds, we argue that these stickers symbolically bring the deceased into daily life and public spaces, contributing to the processing of personal and national trauma.}, }
@article {pmid39653555, year = {2024}, author = {Fuchs, KJ and Göransson, M and Kester, MGD and Ettienne, NW and van de Meent, M and de Jong, RCM and Koster, EAS and Halkes, CJM and Scheeren, F and Heemskerk, MHM and van Balen, P and Falkenburg, JHF and Hadrup, SR and Griffioen, M}, title = {DNA barcoded peptide-MHC multimers to measure and monitor minor histocompatibility antigen-specific T cells after allogeneic stem cell transplantation.}, journal = {Journal for immunotherapy of cancer}, volume = {12}, number = {12}, pages = {}, doi = {10.1136/jitc-2024-009564}, pmid = {39653555}, issn = {2051-1426}, mesh = {Humans ; *Minor Histocompatibility Antigens/immunology/metabolism ; *Transplantation, Homologous ; *Graft vs Host Disease/immunology ; Middle Aged ; Hematopoietic Stem Cell Transplantation/methods ; Male ; Female ; Adult ; Peptides/immunology ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Stem Cell Transplantation/adverse effects ; Aged ; Graft vs Leukemia Effect/immunology ; }, abstract = {Allogeneic stem cell transplantation (alloSCT) provides a curative treatment option for hematological malignancies. After HLA-matched alloSCT, donor-derived T cells recognize minor histocompatibility antigens (MiHAs), which are polymorphic peptides presented by HLA on patient cells. MiHAs are absent on donor cells due to genetic differences between patient and donor. T cells targeting broadly expressed MiHAs induce graft-versus-leukemia (GvL) reactivity as well as graft-versus-host disease (GvHD), while T cells for MiHAs with restricted or preferential expression on hematopoietic or non-hematopoietic cells may skew responses toward GvL or GvHD, respectively. Besides tissue expression, overall strength of GvL and GvHD is also determined by T-cell frequencies against MiHAs.Here, we explored the use of DNA barcode-labeled peptide-MHC multimers to detect and monitor antigen-specific T cells for the recently expanded repertoire of HLA-I-restricted MiHAs. In 16 patients who experienced an immune response after donor lymphocyte infusion, variable T-cell frequencies up to 30.5% of CD8[+] T cells were measured for 49 MiHAs. High T-cell frequencies above 1% were measured in 12 patients for 19 MiHAs, with the majority directed against mismatched MiHAs, typically 6-8 weeks after donor lymphocyte infusion and at the onset of GvHD. The 12 patients included 9 of 10 patients with severe GvHD, 2 of 3 patients with limited GvHD and 1 of 3 patients without GvHD.In conclusion, we demonstrated that barcoded peptide-MHC multimers reliably detect and allow monitoring for MiHA-specific T cells during treatment to investigate the kinetics of immune responses and their impact on development of GvL and GvHD after HLA-matched alloSCT.}, }
@article {pmid39652422, year = {2025}, author = {Ashkin, EL and Tang, YJ and Xu, H and Hung, KL and Belk, JA and Cai, H and Lopez, SS and Dolcen, DN and Hebert, JD and Li, R and Ruiz, PA and Keal, T and Andrejka, L and Chang, HY and Petrov, DA and Dixon, JR and Xu, Z and Winslow, MM}, title = {A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.}, journal = {The Journal of experimental medicine}, volume = {222}, number = {1}, pages = {}, doi = {10.1084/jem.20240765}, pmid = {39652422}, issn = {1540-9538}, support = {GT14928/HHMI/Howard Hughes Medical Institute/United States ; F99CA284289/CA/NCI NIH HHS/United States ; MFE-176568//Canadian Institute of Health Research/ ; 28FT-0019//Tobacco-Related Disease Research Program/ ; PF-21-112-01-MM//American Cancer Society/ ; DGE-2146755//National Science Foundation Graduate Research Fellowship Program/ ; R01-CA231253/NH/NIH HHS/United States ; //Stanford University/ ; }, mesh = {*Lung Neoplasms/pathology/metabolism/genetics ; Humans ; Animals ; *Cell Cycle Proteins/metabolism/genetics ; Cell Line, Tumor ; Mice ; *Carcinogenesis/genetics/metabolism ; Gene Expression Regulation, Neoplastic ; CRISPR-Cas Systems ; Antigens, Nuclear/metabolism/genetics ; Tumor Suppressor Proteins/metabolism/genetics ; Cohesins ; }, abstract = {The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and showed that STAG2 is uniquely tumor-suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. STAG2 inactivation elicits changes in gene expression, chromatin accessibility, and 3D genome conformation that impact the cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relate STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin-mediated mechanisms of lung tumor suppression.}, }
@article {pmid39649949, year = {2024}, author = {Rocha, LA and Pinheiro, HT and Najeeb, A and Rocha, CR and Shepherd, B}, title = {Chromisabadhah (Teleostei, Pomacentridae), a new species of damselfish from mesophotic coral ecosystems of the Maldives.}, journal = {ZooKeys}, volume = {1219}, number = {}, pages = {165-174}, doi = {10.3897/zookeys.1219.126777}, pmid = {39649949}, issn = {1313-2989}, abstract = {A new species of Chromis (Teleostei, Pomacentridae) is described from four specimens collected between 95 and 110 m depth in mesophotic coral ecosystems in the Maldives, Indian Ocean. Chromisabadhah sp. nov. can be distinguished from all of its congeners by the following combination of characters: dorsal-fin rays XIII, 12-13; anal-fin rays II,11-12; pectoral-fin rays 17-18; tubed lateral-line scales 17; gill rakers 7+17-18 = 24-25; pearly white body with a large black marking covering the anterior two-thirds of the anal fin. The closest DNA barcode sequence (5.1% average uncorrected genetic distance on the mitochondrial COI gene), among those available, is Chromiswoodsi, a similar mesophotic species known from the coastal western Indian Ocean (Somalia to South Africa). The new species is easily distinguished from C.woodsi by having 13 dorsal spines (versus 14 in C.woodsi), the absence of a black band on the base of the tail (present in C.woodsi), and by the genetic difference.}, }
@article {pmid39649948, year = {2024}, author = {Lehr, E and Moravec, J and Wang, Y and Uvizl, M}, title = {A new species of Pristimantis (Amphibia, Anura, Strabomantidae) from a montane forest of the Pui Pui Protected Forest in central Peru.}, journal = {ZooKeys}, volume = {1219}, number = {}, pages = {143-163}, doi = {10.3897/zookeys.1219.129773}, pmid = {39649948}, issn = {1313-2989}, abstract = {Herpetological inventories conducted in the Pui Pui Protected Forest in the central Peruvian Andes between 2012 and 2014 revealed unusually high local anuran richness and endemism. Herein, we describe a new species of Pristimantis discovered in the buffer zone of the protected area between 1550 and 1730 m a.s.l. The description is based on one subadult male (snout-vent length 14.4 mm), one adult female (snout-vent length 26.4 mm), and six juvenile specimens collected in the montane forest between 1550 and 1730 m a.s.l. DNA barcoding placed P.vrazi sp. nov. as the sister taxon to P.rhabdocnemus and in the clade also containing P.lindae, P.sinschi, P.quaquaversus, and one still unnamed Pristimantis species. Pristimantisvrazi sp. nov. differs from all these closely related species by the combination of the following characters: tuberculate dorsum, presence of the tympanum, presence of dentigerous processes on the vomer, absence of vocal slits, a red median horizontal streak across the iris, a narrow black median vertical streak on the lower half of the eye, cream to dark brown dorsal ground coloration, and cream to gray ventral ground coloration.}, }
@article {pmid39649432, year = {2024}, author = {Ollivier, M and Rivers-Moore, J and Pichon, M and Andrieu, E and Carrié, R and Rudelle, R and Sarthou, JP and Ouin, A}, title = {Wild bees (Apoidea, Anthophila) of south-west France: more than 10 years of inventories in mosaic landscapes of "Vallées et Coteaux de Gascogne" (ZA-PYGAR).}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e135157}, pmid = {39649432}, issn = {1314-2828}, abstract = {BACKGROUND: The reported massive decline of arthropods and particularly of pollinators such as wild bees, in terms of abundance and richness, is a threat for crop production and wild plant biodiversity conservation. This decline is mainly explained by a combination of drivers at local- and landscape-scale related to intensive farming practices. Assessing the evolution of wild bee communities in agricultural ecosystems and their response to such practices is needed to address conservation purposes.<br><br>NEW INFORMATION: We provide here data for the 24,329 wild bee specimens held in the collection of DYNAFOR Lab (UMR 1201 INRAE, INP-ENSAT, EI PURPAN), located at INP-ENSAT (Toulouse, France). All bee specimens were collected from the long term socio-ecological research site, ZA-PYGAR, located in south-west France, for more than 10 years (2010 to 2022) within the framework of different research programmes conducted by the DYNAFOR Lab. At least 270 species, representative of the six wild bee families, were identified from this area. The identified specimens are considered reliable as identifications were performed or have been verified by community-recognised experts. In addition, ongoing DNA barcoding performed on certain specimens helped clarify questionable morphological characters and provided cross-validation of species identification.}, }
@article {pmid39648853, year = {2024}, author = {Shi, R and Chen, H and Zhang, W and Leak, RK and Lou, D and Chen, K and Chen, J}, title = {Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges, and future perspectives on transcriptomic profiling.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {}, number = {}, pages = {271678X241305914}, doi = {10.1177/0271678X241305914}, pmid = {39648853}, issn = {1559-7016}, abstract = {Single-cell RNA sequencing (scRNA-seq) is a high-throughput transcriptomic approach with the power to identify rare cells, discover new cellular subclusters, and describe novel genes. scRNA-seq can simultaneously reveal dynamic shifts in cellular phenotypes and heterogeneities in cellular subtypes. Since the publication of the first protocol on scRNA-seq in 2009, this evolving technology has continued to improve, through the use of cell-specific barcodes, adoption of droplet-based systems, and development of advanced computational methods. Despite induction of the cellular stress response during the tissue dissociation process, scRNA-seq remains a popular technology, and commercially available scRNA-seq methods have been applied to the brain. Recent advances in spatial transcriptomics now allow the researcher to capture the positional context of transcriptional activity, strengthening our knowledge of cellular organization and cell-cell interactions in spatially intact tissues. A combination of spatial transcriptomic data with proteomic, metabolomic, or chromatin accessibility data is a promising direction for future research. Herein, we provide an overview of the workflow, data analyses methods, and pros and cons of scRNA-seq technology. We also summarize the latest achievements of scRNA-seq in stroke and acute traumatic brain injury, and describe future applications of scRNA-seq and spatial transcriptomics.}, }
@article {pmid39647154, year = {2024}, author = {Liu, YX and Xue, HJ and Liu, GQ}, title = {Two new species of the brachypterous Scirtetellus (Hemiptera: Heteroptera: Miridae) from China.}, journal = {Zootaxa}, volume = {5497}, number = {2}, pages = {244-254}, doi = {10.11646/zootaxa.5497.2.4}, pmid = {39647154}, issn = {1175-5334}, mesh = {Animals ; Male ; China ; *Heteroptera/anatomy &amp; histology/classification ; Female ; *Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; DNA Barcoding, Taxonomic ; Phylogeny ; }, abstract = {Two new species of the genus Scirtetellus Reuter, 1890 (Heteroptera: Miridae: Orthotylinae: Halticini) are described as new to science from China: Scirtetellus qinghaiensis sp. nov. and Scirtetellus shanxiensis sp. nov. Detailed morphological description, photographs of the dorsal habitus and male parameres, key to species of Scirtetellus from China and species list of Scirtetellus of the world are provided. The 658 bp long fragments of the mitochondrial gene COI (DNA barcode) are provided as a part of the diagnosis of the new species. The type specimens and the DNA sample were deposited in the Institute of Entomology, Nankai University, Tianjin, China.}, }
@article {pmid39647119, year = {2024}, author = {Prieto, C and Pinilla, C and Lorenc-Brudecka, J and Balke, M}, title = {Integrative description of Thaeides ramoni sp. nov. (Lepidoptera: Lycaenidae), a sympatric sibling species of Thaeides theia (Hewitson, 1870) found in the Sierra Nevada de Santa Marta, Colombia.}, journal = {Zootaxa}, volume = {5501}, number = {1}, pages = {181-190}, doi = {10.11646/zootaxa.5501.1.9}, pmid = {39647119}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Colombia ; *Animal Distribution ; *Butterflies/anatomy &amp; histology/classification ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Sympatry ; Phylogeny ; Ecosystem ; }, abstract = {We present evidence from DNA barcodes, wing pattern and distribution to support the hypothesis that an entity flying in sympatry with Thaeides theia in the Sierra Nevada de Santa Marta, is an undescribed biological species named herein as Thaides ramoni Prieto, sp. nov. Adult specimens and genital structures are illustrated for both species along with molecular and morphological diagnostic characters. In addition, we present some considerations about the taxonomy of the species in the Thaeides muela group.}, }
@article {pmid39647095, year = {2024}, author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM and Lisanovskaya, EA}, title = {Morphological description and DNA barcoding of Thalassomya paraskevae sp. nov. (Diptera: Chironomidae: Telmatogetoninae) from coast of the Black Sea.}, journal = {Zootaxa}, volume = {5501}, number = {4}, pages = {524-530}, doi = {10.11646/zootaxa.5501.4.2}, pmid = {39647095}, issn = {1175-5334}, mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; *Chironomidae/anatomy &amp; histology/classification/genetics ; Black Sea ; Female ; *Animal Distribution ; Organ Size ; Body Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Illustrated description of adult male, as well as DNA barcoding, of Thalassomya paraskevae sp. nov. in comparison with close related species T. frauenfeldi Schiner from coast of the Black Sea are provided. Interspecific p-distances using gene COI 5P between T. paraskevae sp. nov. and T. frauenfeldi from Madeira (Portugal) were 8.94%. Divergence between described species and T. frauenfeldi collected near the type locality (Friuli Venezia-Giulia, Italy) using COI 3P were 7.72%. Obtained values corresponds to species level.}, }
@article {pmid39647062, year = {2024}, author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Helmick, EE and Bahder, BW}, title = {A new species of planthopper in the genus Platocerella (Hemiptera: Auchenorrhyncha: Derbidae) from palms in Costa Rica, a key to the genus and an updated molecular phylogeny of available New World Otiocerinae.}, journal = {Zootaxa}, volume = {5512}, number = {2}, pages = {222-232}, doi = {10.11646/zootaxa.5512.2.6}, pmid = {39647062}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera/classification/anatomy &amp; histology/genetics ; Costa Rica ; *Phylogeny ; Male ; Female ; Animal Distribution ; Arecaceae/parasitology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Electron Transport Complex IV/genetics ; }, abstract = {The genus Platocerella is a monotypic otiocerine genus (Derbidae: Otiocerinae: Otiocerini) reported from Guyana. A new species of Platocerella associated with palms is herein described from Costa Rica. Molecular data for the barcoding region cytochrome c oxidase subunit I (COI), 18S rRNA gene, and D9-D10 expansion region of the 28S rRNA gene is provided to produce a preliminary phylogenetic tree including the new species and related taxa to place the new species relative to other otiocerine planthoppers.}, }
@article {pmid39647046, year = {2024}, author = {Mukherjee, B and Ray, N and Mukherjee, A and Naskar, A and Banerjee, D}, title = {First report of acifer group of the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from India, with a new species and updated world checklist.}, journal = {Zootaxa}, volume = {5512}, number = {4}, pages = {531-552}, doi = {10.11646/zootaxa.5512.4.4}, pmid = {39647046}, issn = {1175-5334}, mesh = {Animals ; Male ; India ; *Chironomidae/classification/anatomy &amp; histology/growth &amp; development ; *Animal Distribution ; *Checklist ; Phylogeny ; Female ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {A new species of the acifer group of the subgenus Tripodura and genus Polypedilum Kieffer is described on the basis of adult male. The acifer species group is recorded firstly from India. The molecular barcoding of the new species is provided. Moreover, molecular phylogeny of all available species of the subgenus Tripodura, along with an Indian key based on adult males of this subgenus have been designed here. Additionally, a world checklist of the subgenus Tripodura has also been furnished in this study.}, }
@article {pmid39647038, year = {2024}, author = {Godfray, HCJ and Achterberg, CV}, title = {Annotated Checklist of the European Dacnusini and the Dapsilarthra genus group of the Alysiini (Hymenoptera: Braconidae, Alysiinae).}, journal = {Zootaxa}, volume = {5513}, number = {1}, pages = {1-73}, doi = {10.11646/zootaxa.5513.1.1}, pmid = {39647038}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; *Wasps/classification/anatomy &amp; histology ; *Checklist ; *Animal Distribution ; Europe ; Hymenoptera/classification/anatomy &amp; histology ; Body Size ; DNA Barcoding, Taxonomic ; }, abstract = {An annotated checklist of the European Dacnusini (426 species) and the Dapsilarthra genus group of the Alysiini (16 species) (Hymenoptera: Braconidae, Alysiinae) is provided. In addition to a species list with synonymy, further details are given of: (i) intrageneric groupings; (ii) a reference to each species' treatment in the unindexed and multipart major revisions of Nixon &amp; Griffith as well as the long keys of Tobias; (iii) a hypothesis about host range for the 60% of species which have been reared, and the evidence upon which it is based; (iv) whether a DNA barcode sequence is available (30% of species); (v) for species published after Griffiths' revision a reference to similar species; (vi) any further relevant notes. One new synonym is established: Chorebus luzulae Griffiths syn. nov. is synonymised with Chorebus aphantus Marshall. Mesocrina Förster is excluded from the Dapsilartha genus group and whether Grandia Goidanich and Lodbrokia Hedqvist are in the Dacnusini is considered uncertain.}, }
@article {pmid39647031, year = {2024}, author = {Nazarov, RA and Nabizadeh, H and Rajabizadeh, M and Melnikov, DA and Volkova, VR and Poyarkov, NA and Rastegar-Pouyani, E}, title = {Taxonomy of Iranian Asaccus (Squamata: Phyllodactylidae) with description of a new species from southern Iran.}, journal = {Zootaxa}, volume = {5514}, number = {2}, pages = {101-128}, doi = {10.11646/zootaxa.5514.2.1}, pmid = {39647031}, issn = {1175-5334}, mesh = {Animals ; Iran ; *Lizards/anatomy &amp; histology/classification/genetics ; *Phylogeny ; Female ; Male ; *Animal Distribution ; *Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {We provide the first diversity assessment of Iranian species of the genus Asaccus based on COI DNA-barcoding. We analyzed 53 samples of Iranian Asaccus representing nine OTU corresponding to 10 currently recognzied nominal species, and evaluated both morphological and genetic data to support the recognition of a new species from Bandar-e Jask, Hormozgan Province, southern Iran-Asaccus authenticus sp. nov. The new species is characterized by medium body size (SVL max 55.5 mm), elongated limbs, and relatively small dorsal tubercles arranged in 12-14 regular rows. Morphologically Asaccus authenticus sp. nov. resembles both Arabian and Iranian representatives of the genus; phylogenetically it forms a highly divergent lineage with sister relationships to all other Iranian congeners. We applied the geometric morphometrics method to compare the position and shape of postmental plates for almost all members of Asaccus and evaluated the importance of this character in species diagnostics in this group. We also critically evaluate the recent phylogenetic data on Asaccus and discuss the most problematic questions on taxonomy of this genus. We also revalidate Asaccus ingae (Eiselt, 1973) as a full species; overall our work raises the total number of species of the genus Asaccus to 20.}, }
@article {pmid39647018, year = {2024}, author = {Bahder, BW and Randretsiferana, SA and Randretsiferana, A and Stroiński, A and Łukasik, P and Bartlett, CR and Pilet, F and Hasinjaka, RH}, title = {A new species of planthopper in the genus Eumyndus (Hemiptera: Cixiidae) from palms in eastern Madagascar and molecular evidence for the synonymy of Eumyndus kraussi and Eumyndus metcalfi.}, journal = {Zootaxa}, volume = {5514}, number = {4}, pages = {338-352}, doi = {10.11646/zootaxa.5514.4.3}, pmid = {39647018}, issn = {1175-5334}, mesh = {Animals ; Madagascar ; *Hemiptera/anatomy &amp; histology/classification/genetics ; Male ; Female ; *Animal Distribution ; Phylogeny ; Organ Size ; Electron Transport Complex IV/genetics ; Arecaceae/parasitology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; RNA, Ribosomal, 18S/genetics ; }, abstract = {A new species of Eumyndus Synave, 1956, a genus endemic to Madagascar, is here described as Eumyndus jeanjacquei sp. nov. The new species was collected from the palm Vonitra fibrosa (C.H.Wright) Becc., 1911. Molecular data are provided for the new species from the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene and support placement of the new species in Eumyndus. A new synonymy is proposed based on examination of type material: E. metcalfi Synave, 1956 equals E. kraussi Synave, 1956, new synonym.}, }
@article {pmid39646982, year = {2024}, author = {Pyrcz, TW and Boyer, P and Petit, JC and Garlacz, R and Garlacz, KSZ and Espeland, M and Willmott, KR}, title = {Bedazzled: a new, striking species of Corades from the outskirts of Quito questions our knowledge of Andean cloud forest butterflies (Lepidoptera, Nymphalidae, Satyrinae).}, journal = {Zootaxa}, volume = {5453}, number = {2}, pages = {255-262}, doi = {10.11646/zootaxa.5453.2.6}, pmid = {39646982}, issn = {1175-5334}, mesh = {Animals ; *Butterflies/anatomy &amp; histology/classification ; Male ; Ecuador ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Forests ; Phylogeny ; }, abstract = {A new butterfly species in the genus Corades, C. yanacocha Pyrcz, Boyer &amp; Petit sp. n., belonging to the diverse, predominantly Andean subtribe Pronophilina (Nymphalidae, Satyrinae), is described from the Yanacocha Reserve situated only a couple of kilometres west of Quito, Ecuador. This is an extremely surprising discovery in a region whose butterfly fauna was considered to be fairly well known, underlying the need to protect remnants of high elevation forests in such overpopulated regions of the Andes. Morphological characters, in particular male genitalia, indicate an affinity of C. yanacocha sp. n. with C. trimaculata from northern Peru. A preliminary molecular study using COI barcodes indicates, however, the widely distributed north Andean C. dymantis as the closest relative.}, }
@article {pmid39646949, year = {2024}, author = {Riccardi, PR and Ang, Y}, title = {New species and new records of Chloropinae from Singapore (Diptera: Chloropidae).}, journal = {Zootaxa}, volume = {5458}, number = {1}, pages = {83-92}, doi = {10.11646/zootaxa.5458.1.4}, pmid = {39646949}, issn = {1175-5334}, mesh = {Animals ; Singapore ; Male ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; Organ Size ; Phylogeny ; Biodiversity ; }, abstract = {Chloropidae biodiversity in the Oriental region is remarkably diverse and yet poorly understood. In this study, we used integrative taxonomy to tackle the species diversity of the subfamily Chloropinae from Singapore. We describe the first Oriental species of Cryptonevra Lioy, C. argenteum Riccardi, sp. nov., a new species of Chloropsina Becker, C. flavipes Riccardi, sp. nov., provide the first record of Eutropha noctilux (Walker) from Singapore and DNA barcodes of Chloropsina minima (Becker), Ensiferella kanmiyai Nartshuk. In addition, we increased the number of Chloropinae records from Singapore from two (Anthracophagella Anderson and Chlorops Meigen) to nine (addition of Cerais van der Wulp, Chloropsina, Cryptonevra, Elliponeura Loew, Ensiferella Andersson, Eutropha Loew, and Thressa Walker) genera and from two to seven described species plus four morphospecies. The species were discovered using NGS barcodes and are part of an ongoing campaign to document the biodiversity of Singapore.}, }
@article {pmid39646947, year = {2024}, author = {Béarez, P and Zavalaga, F and Miranda, J and Mennesson, MI and Campos-León, S and Jiménez-Prado, P}, title = {Aulopus chirichignoae, a new flagfin from the eastern Pacific Ocean (Teleostei, Aulopiformes, Aulopidae).}, journal = {Zootaxa}, volume = {5458}, number = {1}, pages = {108-118}, doi = {10.11646/zootaxa.5458.1.6}, pmid = {39646947}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Pacific Ocean ; Ecuador ; *Animal Distribution ; *Body Size ; Peru ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; }, abstract = {A new species of the Aulopidae is described from the waters of southern Ecuador and northern Peru. Aulopus chirichignoae sp. nov. was previously confused with Aulopus bajacali Parin &amp; Kotlyar, 1984, but it differs from this species by a significantly marked elongation of the dorsal fin rays in males (absent in females), a smaller head, modal differences in dorsal and anal ray counts (15 vs 14 and 11 vs 12, respectively), a higher number of vertebrae (50-51 vs 47-49), and color differences, especially on the dorsal fin. DNA barcoding analysis supported the status of new species, evidencing a 4.2% and 2.8% divergence with Aulopus filamentosus (Bloch, 1792) and A. bajacali, respectively. A sequence of an Aulopus sp., collected in the Tropical Eastern Pacific, matches the new species with only a 0.4% divergence, indicating that Aulopus chirichignoae sp. nov. is distributed at least as far north as the Paramount Seamount at 3°20.35'N, ca. 400 km north of the Galápagos Islands.}, }
@article {pmid39646945, year = {2024}, author = {Fitrian, T and Rahayu, DL and Ismet, MS}, title = {A new species of hermit crab genus Diogenes Dana, 1851 from Papua, Indonesia (Crustacea, Decapoda, Anomura, Diogenidae).}, journal = {Zootaxa}, volume = {5458}, number = {1}, pages = {130-140}, doi = {10.11646/zootaxa.5458.1.8}, pmid = {39646945}, issn = {1175-5334}, mesh = {Animals ; Indonesia ; *Anomura/anatomy &amp; histology/classification/genetics ; Male ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {A new species of hermit crab from the genus Diogenes Dana, 1851 is described on the basis of a specimen from Papua, Indonesia. Diogenes hawisi n. sp. is distinguished from the closest allied species, D. edwardsii (De Haan, 1849) and D. laevicarpus Rahayu, 1996, by the shape and armature of the left cheliped. Morphological differences of these three species are also supported by genetic analysis, through DNA barcoding using the CO1 gene marker.}, }
@article {pmid39646930, year = {2024}, author = {Kaila, L}, title = {A review of Coelopoetinae (Lepidoptera, Gelechioidea, Pterolonchidae), a moth subfamily confined to western North America, with descriptions of seven new species.}, journal = {Zootaxa}, volume = {5458}, number = {3}, pages = {361-384}, doi = {10.11646/zootaxa.5458.3.3}, pmid = {39646930}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Moths/anatomy &amp; histology/classification ; *Animal Distribution ; North America ; Phylogeny ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Systematics and taxonomy of the gelechioid subfamily Coelopoetinae are reviewed. Following the current classification, this group is considered to form its own monotypic subfamily in Pterolonchidae with one recognized genus, Coelopoeta, after a convoluted and, in part, arguably conjectural, historical systematic treatment. On morphological basis (appearance, male genitalia) and with support from DNA barcodes, the genus is divided into two discrete units probably meriting recognition as separate genera. The species groups are informally treated as the nominate C. glutinosi species group, and the C. fissurina species group. In the absence of knowledge of females or the biologies of any of the species of the C. fissurina group, species of both groups are here provisionally included in Coelopoeta. In total, 10 species are recognized, seven of which are here described as new: C. glutinosi species group: C. alboflava Kaila, sp. nov., C. aprica Kaila, sp. nov., C. aurora Kaila, sp. nov., C. fulminea Kaila, sp. nov. and C. sariae Kaila, sp. nov.; C. fissurina species group: C. fissurina Kaila, sp. nov. and C. valalbui Kaila, sp. nov. The three previously known species, C. glutinosi Walsingham, 1907, C. maiadella Kaila, 1995 and C. phaceliae Kaila, 1995 are redescribed. All three of these species belong to the glutinosi species group. A lectotype is designated for C. glutinosi Walsingham, 1907. Some southwestern Coelopoeta species are potentially under threat of decline or even extinction due to the apparently increasingly intense and frequent forest fires. This threat is significant as the species with known life histories spend their entire life cycles above ground in low vegetation.}, }
@article {pmid39646926, year = {2024}, author = {Kim, J and Lee, T}, title = {A new species of Janiralata Menzies, 1951 (Isopoda: Asellota, Janiridae) from Korea.}, journal = {Zootaxa}, volume = {5458}, number = {3}, pages = {427-441}, doi = {10.11646/zootaxa.5458.3.7}, pmid = {39646926}, issn = {1175-5334}, mesh = {*Isopoda/classification/anatomy &amp; histology ; Animals ; Male ; Republic of Korea ; *Animal Distribution ; Female ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Phylogeny ; Electron Transport Complex IV/genetics ; }, abstract = {A new isopod species, Janiralata kwangsooi sp. nov., from Dokdo Island located in the East Sea off the Korean Peninsula is described here. This species is distinguished from its congeners by the number of antennular articles, setation of mouthparts and pereopods, length and width ratio of appendages, and shape of male pleopods I and II. To aid species identification, a taxonomic key to species of Janiralata Menzies, 1951 in the Japanese and Korean waters is provided. A partial sequence of mitochondrial cytochrome-c-oxidase (COI) of this new species is also provided for DNA barcoding and compared with those of congeners publicly available in GenBank.}, }
@article {pmid39646853, year = {2024}, author = {Triberti, P and Staude, H and Sharp, I and Lopez-Vaamonde, C}, title = {Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species.}, journal = {Zootaxa}, volume = {5529}, number = {1}, pages = {1-51}, doi = {10.11646/zootaxa.5529.1.1}, pmid = {39646853}, issn = {1175-5334}, mesh = {Animals ; South Africa ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Plants ; Biodiversity ; }, abstract = {Despite relatively extensive historical exploration being carried out on Lepidopteran fauna of South Africa, leaf-mining micromoths of the family Gracillariidae remain a source of discovery, with many new species awaiting description. In the present work, 32 gracillariid species from South Africa are treated. For each species, hostplant and distribution information is provided, supplemented by taxonomic and molecular analysis where necessary. Nine species are described here as new to science: Ectropina spirostachydis sp. nov., Leucocercops curatellifoliae sp. nov., Phodoryctis tephrosiella sp. nov., Telamoptilia cordati sp. nov., Phyllonorycter pseudogrewiella sp. nov., Cameraria melhaniella sp. nov., Phyllocnistis magalismontani sp. nov., P. allisonae sp. nov. and P. faureae sp. nov. Sixteen host plant species are reported for the first time for the family Gracillariidae: Searsia pyroides (Anacardiaceae), Parinari curatellifolia (Chrysobalanaceae), Combretum zeyheri, Terminalia sericea (Combretaceae), Euclea divinorum (Ebenaceae), Spirostachys africana (Euphorbiaceae), Peltophorum africanum, Tephrosia rhodesica, Schotia brachypetala (Fabaceae), Cryptocarya transvaalensis (Lauraceae), Melhania acuminata (Malvaceae), Syzygium guineense (Myrtaceae), Ochna pretoriensis (Ochnaceae), Protea rubropilosa, Faurea saligna (Proteaceae), Englerophytum magalismontanum (Sapotaceae). Caloptilia mwamba De Prins, 2015 is recorded for the first time in South Africa.}, }
@article {pmid39646830, year = {2024}, author = {Orr, AGW and Dow, RA and Steinhoff, POM}, title = {Descriptions of larvae of four mainly DNA barcode-matched species of chlorocyphids from south-east Asia (Odonata: Chlorocyphidae) with notes on the generic and species level larval identification of Oriental region members of the family.}, journal = {Zootaxa}, volume = {5486}, number = {3}, pages = {301-337}, doi = {10.11646/zootaxa.5486.3.1}, pmid = {39646830}, issn = {1175-5334}, mesh = {Animals ; *Larva/anatomy &amp; histology/classification/growth &amp; development/genetics ; Female ; Male ; *DNA Barcoding, Taxonomic ; *Animal Distribution ; Asia, Southeastern ; *Odonata/anatomy &amp; histology/classification/genetics/growth &amp; development ; Phylogeny ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; }, abstract = {The final stadium larvae of the following four species of south-east Asian Chlorocyphidae are described and compared: Aristocypha fenestrella (Rambur), Heliocypha biseriata (Selys), Libellago hyalina (Selys) and Sundacypha petiolata (Selys), including both sexes for the latter two species. Excepting one L. hyalina specimen from Brunei, identified by supposition based on habitat, all specimens were identified by comparing and matching the mitochondrial marker COI with that of known adult specimens from Sarawak, Brunei and several localities throughout tropical Asia. The specimens presented close matches with all adults in this gene. An assessment of the efficacy of this method of identification is provided, noting that in some cases close species cannot be separated by bar-code matching and ultimate determination is partially based on known distributions of adults. Some aspects of the relationships among genera revealed by the genetic analyses are also discussed. In addition, an exuvia of Libellago lineata (Burmeister) from northern Thailand, identified by supposition, is partially described for the purpose of comparison with L. hyalina. For the morphological analysis the unique features of chlorocyphid anatomy are discussed, and some new terminology is introduced. Overall, the morphological analysis revealed numerous clear differences between the four species studied, and comparisons with available literature suggest that some of these may be characteristic of their genera. It is also evident that in some cases clear interspecific differences occur within genera. It is however concluded that a generic level larval key for the Oriental region Chlorocyphidae based on morphology may never be attainable, although local generic or even species level keys addressing the fauna of limited geographic areas may be possible in many places, especially as the larvae of more species come to be known and described in detail.}, }
@article {pmid39646800, year = {2024}, author = {Ahrens, D and Zhao, MZ and Pham, PV and Liu, WG}, title = {Taxonomic updates on Pachyserica Brenske, 1898 and Serica MacLeay, 1819 reveal 38 new species and new challenges of Sericini systematics regarding DNA barcodes and genus-level diagnostic key characters (Coleoptera: Scarabaeidae: Sericinae).}, journal = {Zootaxa}, volume = {5491}, number = {1}, pages = {1-89}, doi = {10.11646/zootaxa.5491.1.1}, pmid = {39646800}, issn = {1175-5334}, mesh = {Animals ; *Coleoptera/classification/anatomy &amp; histology/genetics ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Animal Distribution ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; }, abstract = {Here we present updates on the taxonomy and distribution of the genera Pachyserica Brenske, 1898 and Serica MacLeay, 1819 from East Asia. Thirty eight new species are desribed from China, Myanmar, South Korea, and Vietnam: Pachyserica chenchangchini Ahrens, Zhao, Pham &amp; Liu, new species, P. dieuthuyae Ahrens, Zhao, Pham &amp; Liu, new species, P. hoabinhensis Ahrens, Zhao, Pham &amp; Liu, new species, P. motuo Ahrens, Zhao, Pham &amp; Liu, new species, P. natmatoung Ahrens, Zhao, Pham &amp; Liu, new species, P. sanqingshanensis Ahrens, Zhao, Pham &amp; Liu, new species, P. sunfengyii Ahrens, Zhao, Pham &amp; Liu, new species, P. tayyentu Ahrens, Zhao, Pham &amp; Liu, new species, P. tianxuani Ahrens, Zhao, Pham &amp; Liu, new species, P. wangzizhaoi Ahrens, Zhao, Pham &amp; Liu, new species, P. yaonani Ahrens, Zhao, Pham &amp; Liu, new species, P. yinhengi Ahrens, Zhao, Pham &amp; Liu, new species, P. zhanbaoxiangi Ahrens, Zhao, Pham &amp; Liu, new species, Serica (s. l.) anhua Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) camura Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) fengxue Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) nhiae Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) paracallosericoides Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) taythien Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) wuyishan Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) yuechengling Ahrens, Zhao, Pham &amp; Liu, new species, S. (Serica) assingi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) bomi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) christophreuteri Ahrens, Zhao, Pham &amp; Liu, Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) cuona Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) fansipan Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) gongtonggouensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) guangxiensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) gwangjuensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) hongyii Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) jiangda Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) jiulaoci Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) lushui Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) liyitengi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) qizhihaoi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) xizang Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) zhamu Ahrens, Zhao, Pham &amp; Liu, new species, and S. (Taiwanoserica) yexiaohani Ahrens, Zhao, Pham &amp; Liu, new species. The lectotype of Pachyserica scalaris Arrow, 1946 is designated and its male genitalia is illustrated. Additional records of 66 other species are provided.}, }
@article {pmid39646795, year = {2024}, author = {Zhang, JY and Sun, XL and Wang, N and Hao, LI and Ma, CX and Zhao, NA and Li, HP and Zhao, M and Yang, ST}, title = {Tardigrades in the alpine region of Northeast China with an integrative description of Crenubiotus liangshuiensis sp. nov.}, journal = {Zootaxa}, volume = {5492}, number = {1}, pages = {96-108}, doi = {10.11646/zootaxa.5492.1.5}, pmid = {39646795}, issn = {1175-5334}, mesh = {Animals ; *Tardigrada/classification/anatomy &amp; histology ; China ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; DNA Barcoding, Taxonomic ; Ecosystem ; RNA, Ribosomal, 18S/genetics ; Female ; Male ; }, abstract = {A new species of tardigrade, Crenubiotus liangshuiensis sp. nov. (Eutardigrada: Parachela: Macrobiotoidea: Adorybiotidae), was identified by combining DNA barcoding and classical morphological analyses (including both light contrast microscopy and scanning electron microscopy) of animals and an egg found in moss Collected in Yichun Liangshui National Nature Reserve. Moreover, nucleotide sequences of the 18S rRNA and COI markers from used to analyse the diversity of the local tardigrade fauna indicated the presence of at least 16 species representing 11 genera.}, }
@article {pmid39646779, year = {2024}, author = {Liang, QR and Shi, L}, title = {Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences.}, journal = {Zootaxa}, volume = {5492}, number = {3}, pages = {325-342}, doi = {10.11646/zootaxa.5492.3.2}, pmid = {39646779}, issn = {1175-5334}, mesh = {Animals ; *Lizards/classification/genetics/anatomy &amp; histology ; *Phylogeny ; *DNA, Mitochondrial/genetics ; *Animal Distribution ; Male ; Female ; China ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; DNA Barcoding, Taxonomic ; }, abstract = {The rock lizard genus Laudakia is representative agamid species from the arid zone, and its genus division has not been resolved yet. Laudakia stoliczkana, which occurs in both Xinjiang, China, and the Gobi Altai, Mongolia, is divided into two subspecies, Laudakia stoliczkana stoliczkana and Laudakia stoliczkana altaica, based on morphological differences, but little is known about the molecular genetic differences between the two subspecies. This study reconstructs the phylogenetic tree of Laudakia and analyses molecular differences between two subspecies of L. stoliczkana by DNA barcoding (COI and 16S). Our results show that: (1) Laudakia is monophyletic and the phylogenetic tree is broadly divided into three main branches, namely branch A (L. caucasia and L. stoliczkana), which occurs mainly in Central Asia and the Gobi Altai region to the north, branch B (L. stellio), which occurs in the Middle East, and branch C (L. tuberculata, L. papenfussi, L. himalayana, L. wui, L. stellio), which occurs mainly near the Himalayas; (2) The biogeographic analysis of Laudakia suggests that the genus probably originated at 43.72 Ma (95% confidence interval HPD: 23.53-66.12Ma) and is associated with the uplift of the Tibetan Plateau and the aridification of Central Asias subsequently; (3) Molecular genetic distances and morphological differences support the delimitation of the two subspecies of L. stoliczkana, with divergence between the two subspecies estimated to have occurred at 3.27 Ma (95% confidence interval HPD: 1.58-5.87Ma), in associated with the recent uplift of the Tian Shan Mountains. The results highlight the importance of the uplift of the Central Asian mountains and the Tibetan Plateau for the divergence of Laudakia.}, }
@article {pmid39646691, year = {2024}, author = {Yu, T and Kallies, A and Arita, Y and He, J and Li, H and Yata, N and Li, X}, title = {Two new species of the genus Taikona Arita &amp; Gorbunov, 2001 (Lepidoptera, Sesiidae) from Yunnan, China.}, journal = {Zootaxa}, volume = {5443}, number = {1}, pages = {135-140}, doi = {10.11646/zootaxa.5443.1.8}, pmid = {39646691}, issn = {1175-5334}, mesh = {Animals ; Male ; China ; *Animal Distribution ; *Moths/anatomy &amp; histology/classification ; Female ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Two new species, Taikona gaoligongshana Yu, Arita &amp; Kallies, sp. nov. and Taikona extraordinaria Yu, Kallies &amp; Arita sp. nov. are described from Yunnan Province, China. Illustrations of the holotypes and the male genitalia are provided, along with a key to all currently known species of the genus. DNA barcoding sequences are also provided.}, }
@article {pmid39646654, year = {2024}, author = {David, KJ and Hancock, DL and Salini, S and Ningthoujam, K and Khemrajji, HN and Abhishek, V and Gracy, RG and Sushil, SN}, title = {New species and new records of fruit flies of tribe Acanthonevrini (Diptera: Tephritidae: Phytalmiinae) from India.}, journal = {Zootaxa}, volume = {5506}, number = {3}, pages = {301-321}, doi = {10.11646/zootaxa.5506.3.1}, pmid = {39646654}, issn = {1175-5334}, mesh = {Animals ; India ; Female ; Male ; *Animal Distribution ; *Tephritidae/classification/anatomy &amp; histology ; *Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Phylogeny ; }, abstract = {Two new species of Phytalmiinae belonging to the tribe Acanthonevrini are described from India, namely Ptilona confracta David &amp; Hancock, sp. nov. from Arunachal Pradesh and Tritaeniopteron obscurum David, Salini &amp; Nikhil, sp. nov. from Karnataka. Tritaeniopteron de Meijere is recorded for the first time from India based on the new species T. obscurum; male and female syntypes of T. punctatipleurum (Senior-White) are dissected and illustrated. A female of Erectovena desperata (Hering), both sexes of Felderimyia gombakensis Hancock &amp; Drew and Phorelliosoma hilaratum Hering, recorded for the first time from India are dissected and illustrated. An illustrated key to 23 species of Acanthonevrini belonging to 12 genera from India is included. DNA barcode sequences of Felderimyia fuscipennis Hendel, Ptilona confracta, P. confinis (Walker), Rioxoptilona dunlopi (van der Wulp) and Themara yunnana Zia were obtained and reported.}, }
@article {pmid39646638, year = {2024}, author = {Teslenko, VA and Palatov, DM and Semenchenko, AA}, title = {Overview of the Caucasian Perla Geoffroy, 1762 (Plecoptera: Perlidae) based on morphological and molecular data with description of two new species.}, journal = {Zootaxa}, volume = {5507}, number = {1}, pages = {1-56}, doi = {10.11646/zootaxa.5507.1.1}, pmid = {39646638}, issn = {1175-5334}, mesh = {Male ; Female ; Animals ; *Insecta/anatomy &amp; histology/classification/growth &amp; development/genetics ; Russia ; *Animal Distribution ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; }, abstract = {Six species of Caucasian Perla are reviewed, and diagnostic morphological characteristics of all stages of development (where possible) are described, supplemented, and illustrated in detail with comparative light microscope and scanning electron microscopy images. The DNA barcoding of five species is presented. Two new morphologically and genetically distinct species, Perla schapsugica sp. nov. and Perla palatovi sp. nov., are described for both sexes and all life stages in the North Caucasus, Russia, Krasnodar Kray. Reinstatement of Perla persica Zwick, 1975, as a valid species distinct from P. caucasica Guérin-Méneville, 1843, is proposed. A new record of P. persica is reported for the Greater Caucasus, Russia, North-Ossetia-Alania for the first time. Morphologically, these two latter species can be separated in male adults by the shape of the hemitergal hook on terga X, an additional ventral brush on the penis of P. caucasica, wing length, and color.}, }
@article {pmid39646583, year = {2024}, author = {DU, H and Liu, J and Heller, K and Shah, B and Wang, Q and Huang, J}, title = {Morphology and DNA barcodes of four species of Bradysia hilaris group from China (Diptera, Sciaridae).}, journal = {Zootaxa}, volume = {5493}, number = {2}, pages = {129-140}, doi = {10.11646/zootaxa.5493.2.2}, pmid = {39646583}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; China ; *Diptera/anatomy &amp; histology/classification/genetics ; *Phylogeny ; Male ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {Four morphologically allied species of the Bradysia hilaris group were studied from China. In a DNA metabarcoding based dipteran diversity study in Zhejiang, eastern China, a hyper-abundant sciarid species was discovered. It was further recognized in this study to be new to science, Bradysia tianmuensis Du &amp; Huang sp. nov., as well as a morphologically similar species, Bradysia curvula Du &amp; Huang sp. nov. Both new species were found to be fairly similar morphologically to the holotype of Bradysia noduspina Yang, Zhang &amp; Yang, 1993 from Guizhou in western China. However, the paratype of B. noduspina appeared to be different from the holotype and determined to be new to science, Bradysia chikunae Du &amp; Huang sp. nov. A phylogenetic tree of all the available 31 COI sequences of the Bradysia hilaris group was provided. Molecular work conducted in the current study also supports Bradysia tianmuensis Du &amp; Huang sp. nov. and Bradysia curvula Du &amp; Huang sp. nov. as new to science thus the four species were described or redescribed accompanied by detailed imagery of habitus and other characters useful for determination.}, }
@article {pmid39646580, year = {2024}, author = {Liu, WB and Wang, CY and Tang, YN and Pei, WX and Yan, CC}, title = {DNA barcodes and morphology reveal new species within the Cryptochironomus Kieffer from Oriental China (Diptera: Chironomidae).}, journal = {Zootaxa}, volume = {5493}, number = {2}, pages = {165-174}, doi = {10.11646/zootaxa.5493.2.5}, pmid = {39646580}, issn = {1175-5334}, mesh = {Animals ; *Chironomidae/classification/anatomy &amp; histology/genetics/growth &amp; development ; Male ; China ; *DNA Barcoding, Taxonomic ; Female ; Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {The genus Cryptochironomus has a cosmopolitan distribution including over 140 valid described species worldwide. The morphological characteristics and DNA barcode data of Cryptochironomus inflatus Liu, sp. nov. based on specimens collected from Oriental China. DNA barcode analysis including the partial COI sequences of species of genus Cryptochironomus is conducted. An updated key to adult males of the genus is provided.}, }
@article {pmid39646562, year = {2024}, author = {Makarchenko, EA}, title = {Pseudokiefferiella ferringtoni sp. nov. (Diptera: Chironomidae: Diamesinae) from North America.}, journal = {Zootaxa}, volume = {5493}, number = {4}, pages = {446-450}, doi = {10.11646/zootaxa.5493.4.10}, pmid = {39646562}, issn = {1175-5334}, mesh = {Animals ; Male ; *Chironomidae/classification/anatomy &amp; histology/growth &amp; development/genetics ; North America ; Female ; *Animal Distribution ; *Body Size ; Organ Size ; Pupa/anatomy &amp; histology/classification/growth &amp; development ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {In this article I continue to publish the data obtained as a result of the revision of the subfamily Diamesinae, namely of the genus Pseudokiefferiella Zavřel, 1941. As we noted earlier (Makarchenko &amp; Semenchenko 2023), before the start of molecular genetic study this genus was considered as monotypic, that is, with one species of Ps. parva (Edwards) in Holarctic region (Ashe &amp; O'Connor 2009). According to work of Stur and Ekrem (2020), as well as the results of our research and data of GenBank, there are at least 6 species in the genus Pseudokiefferiella that are well separated by DNA barcoding, while adult males poorly differ morphologically. However, species of this genus can be successfully identified by the morphological structures of the pupa, if it is associated with a male imago. As confirmation of this, below is provided a description of Pseudokiefferiella ferringtoni sp. nov. from North America based on the adult male and pupa, in which the originality of a new species is corroborated by the morphological structures of the pupa.}, }
@article {pmid39646561, year = {2024}, author = {Saha, S and Bogorodsky, SV and Baki, MA and Gao, T and McKay, RJ and Alpermann, TJ and Song, NA}, title = {Assessment of the diversity of the family Sillaginidae in the Indian Ocean with emphasis on the taxonomic identity of Sillago sihama.}, journal = {Zootaxa}, volume = {5493}, number = {5}, pages = {451-485}, doi = {10.11646/zootaxa.5493.5.1}, pmid = {39646561}, issn = {1175-5334}, mesh = {Animals ; Indian Ocean ; *Phylogeny ; *Animal Distribution ; Male ; Female ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Biodiversity ; Ecosystem ; }, abstract = {The present study contributes to the taxonomy of the family Sillaginidae, with comments on the distribution of its species in the Indian Ocean and an emphasis on the taxonomy and distribution of Sillago sihama. Thirty described and putative species with Indian Ocean distribution are listed, and a distribution range for each species is provided based on published data and results from the present study. A comprehensive phylogenetic analysis of the barcoding portion of the mitochondrial COI gene is provided together with three approaches for molecular species delimitation, which includes 44 to 47 genetic lineages (depending on the species delimitation approach used) in the family Sillaginidae, 33 of them applying to described species and also 8 putative species, formerly misidentified as S. sihama. Inclusion of specimens from South Africa, Iran, Pakistan, India, Bangladesh and the southern Red Sea (type locality) reveals one genetic lineage representing the true Sillago sihama. Distribution of the species is confined to the Red Sea and the Indian Ocean, and other records under the name S. sihama are based on misidentifications. Several undescribed species identified as S. sihama are distributed in the Indo-West Pacific region and closely resemble S. sihama, but are not identical with this species and can be identified as members of different evolutionary lineages. Two species, S. sihama and S. soringa, reported from Bangladesh, represent the easternmost record of both species. These two species are described in detail, including swimbladder morphology. The study also shows that specimens from India identified as Sillago ingenuua McKay, 1985 are nested within a lineage previously referred to as S. ingenuua A, but are different from the lineage S. ingenuua B, representing a confirmed record of the clade S. ingenuua in the northern Indian Ocean. Comments on misidentifications of S. sihama from the Indian Ocean and western Pacific are provided. Furthermore, we propose that Sillago erythraea should be resurrected from its synonymy with S. sihama. As Sillago suezensis is identical with the former species, it becomes a junior synonym of S. erythraea.}, }
@article {pmid39646546, year = {2024}, author = {Li, D and Xia, L and Wang, H}, title = {DNA barcodes and morphological evidence reveal a new genus of Nygmiini (Lepidoptera: Erebidae: Lymantriinae) from China.}, journal = {Zootaxa}, volume = {5496}, number = {1}, pages = {101-110}, doi = {10.11646/zootaxa.5496.1.5}, pmid = {39646546}, issn = {1175-5334}, mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics/growth &amp; development ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; }, abstract = {A new genus Aurivalva Li &amp; Wang gen. nov. is proposed for Nygmiini to accommodate three species previously placed in Euproctis Hübner: A. yunnanpina (Chao, 1984) comb. nov., A. telephanes (Collenette, 1939) comb. nov. and A. conistica (Collenette, 1936) comb. nov.. The new genus is supported by DNA barcodes and morphological evidence. A key to all currently recognized Aurivalva species in China is provided, with illustrations of the adults, wing venations and genitalia, together with a barcode-based tree.}, }
@article {pmid39646525, year = {2024}, author = {Shah, B and Shao, Y and DU, H and Wang, Y and Huang, J}, title = {Taxonomy and DNA barcoding of the dark-winged fungus gnat genus Zygoneura Meigen (Diptera: Sciaridae) from China, with revision of the type materials.}, journal = {Zootaxa}, volume = {5496}, number = {3}, pages = {377-400}, doi = {10.11646/zootaxa.5496.3.5}, pmid = {39646525}, issn = {1175-5334}, mesh = {Animals ; China ; Male ; *DNA Barcoding, Taxonomic ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Phylogeny ; Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {The genus Zygoneura Meigen is revised thoroughly from China, and 14 species are recognized and illustrated, including four new species: Zygoneura (Allozygoneura) xizangensis Shah &amp; Huang sp. nov., Zygoneura (Pharetratula) minuscula sp. nov., Zygoneura (Pharetratula) motuoensis sp. nov. and Zygoneura (Pharetratula) yangi sp. nov. In addition, Zygoneura (Pharetratula) divergens (Mamaev), Zygoneura (Pharetratula) flavicornis (Mamaev), and Zygoneura (Pharetratula) subdivergens (Mohrig &amp; Mamaev) are reported for the first time from China. The identification of these species is supported by both morphological characteristics and sequence data obtained from cytochrome oxidase subunit one (COI) in the DNA barcode analysis. Furthermore, a checklist of the known Zygoneura species in China is also provided, along with an identification key for males.}, }
@article {pmid39646519, year = {2024}, author = {Almeida, LH and Duarte, T and Bispo, PDC}, title = {Complementary studies of the Perlidae (Insecta: Plecoptera) fauna from the Paranapiacaba Mountains using DNA barcode data.}, journal = {Zootaxa}, volume = {5496}, number = {4}, pages = {500-508}, doi = {10.11646/zootaxa.5496.4.2}, pmid = {39646519}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Brazil ; Female ; Male ; *Animal Distribution ; Phylogeny ; Insecta/classification/anatomy &amp; histology/genetics ; Nymph/anatomy &amp; histology/classification/growth &amp; development/genetics ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {The Paranapiacaba Mountains are a region of Brazil where the stonefly fauna is relatively well known. Despite this, there are still gaps in knowledge that need to be filled. In this study, through field sampling and molecular analyses, we have updated the taxonomic knowledge of Perlidae species in this region. Our study employed DNA barcoding methods to complement traditional morphological approaches, facilitating the association and description of the nymphs of Anacroneuria itajaimirim Bispo &amp; Froehlich 2004. Additionally, we generated DNA barcode sequences for Anacroneuria iporanga Bispo &amp; Froehlich 2004. Our results contributed to knowledge about Perlidae from the Paranapiacaba Mountains, highlighting the importance of DNA barcode data in the association of immature stages and species delimitations. Although the stoneflies of Paranapiacaba Mountains have been relatively well-studied, our results reveal that we still have deficits in knowledge of the fauna of this region.}, }
@article {pmid39646485, year = {2024}, author = {Gordon, ML and Colville, JF and Engelbrecht, A and Couldridge, VCK}, title = {Ancient Grasshoppers: A revision of the genus Bullacris (Orthoptera: Pneumoridae).}, journal = {Zootaxa}, volume = {5474}, number = {4}, pages = {301-354}, doi = {10.11646/zootaxa.5474.4.1}, pmid = {39646485}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Grasshoppers/anatomy &amp; histology/classification/genetics ; *Phylogeny ; *Animal Distribution ; Body Size ; Organ Size ; South Africa ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The genus Bullacris in the family Pneumoridae was most recently revised by Dirsh in 1965 based on morphological comparisons between species. However, since that time, new information about the genus and the family has come to light, necessitating a revision of the genus. In addition, the species B. boschimana was originally described based on a single female specimen. Here we present and describe the male of the species for the first time. The aim of this study was to update the current species descriptions by including additional specimens and incorporating additional methods for a more comprehensive comparison. Analyses consisted of morphometric measurements from high-quality images of type specimens, existing South African museum specimens, as well as personally collected specimens. Acoustic signals are also presented and compared between species. In addition, phylogenetic analyses were conducted on the barcoding mitochondrial gene COI and two nuclear genes, namely ITS and 18S. Results show that according to morphological, acoustic and genetic data, B. discolor and B. serrata as well as B. intermedia and B. membracioides share notable similarities. Bullacris discolor and B. serrata share similar phenotypic traits, in which B. discolor can either appear uniform in colour or have a speckled variation that is very similar in appearance to B. serrata. Bullacris intermedia and B. membracioides have a 5% mitochondrial DNA pairwise distance, suggesting that they may have not be fully diverged; however, morphological analysis shows that these species are morphologically distinguishable. It is suggested that these species may have undergone spatial separation at one point; however, further investigation is required. Additional sampling across a wider geographic range is essential to clarify the relationships between B. discolor and B. serrata, as well as between B. intermedia and B. membracioides.}, }
@article {pmid39646451, year = {2024}, author = {Jimenez, PJ and Chang, K and Shih, HT and Yasuhara, M}, title = {Confirming the occurrence of two fiddler crabs, Tubuca dussumieri (H. Milne Edwards, 1852) and T. coarctata (H. Milne Edwards, 1852) (Crustacea: Decapoda: Ocypodidae), in Hong Kong by DNA barcoding and morphology.}, journal = {Zootaxa}, volume = {5476}, number = {1}, pages = {177-191}, doi = {10.11646/zootaxa.5476.1.17}, pmid = {39646451}, issn = {1175-5334}, mesh = {Animals ; *Brachyura/classification/anatomy &amp; histology/genetics ; Male ; Female ; Hong Kong ; *DNA Barcoding, Taxonomic ; *Animal Distribution ; Body Size ; Ecosystem ; Organ Size ; Phylogeny ; Electron Transport Complex IV/genetics ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The Indo-West Pacific region has a rich fiddler crab fauna. In East Asia, some species of fiddler crabs, such as Tubuca coarctata (H. Milne Edwards, 1852) and T. dussumieri (H. Milne Edwards, 1852), are considered insular, being present in the Philippines, Taiwan, and Ryukyus, but with no consistent record on continental China. Although T. dussumieri has been previously recorded in continental China, these records were considered dubious or misidentified. The nature of the Kuroshio Current and the colder waters of the China Coastal Current, compared to the currents along the eastern coasts of the Philippines and Taiwan, are considered barriers to the entrance of larvae of these species into the region. Nonetheless, using the cytochrome oxidase subunit I (COI) gene and morphological evidence, we present the first record of T. coarctata and show the presence of a T. dussumieri population in Hong Kong SAR, China. We hypothesize that the newly found T. coarctata in Hong Kong may be related to water temperature increases due to anthropogenic climate change, which allows its larvae to survive in this region and develop into adult crabs. Furthermore, our findings corroborate previous records of T. dussumieri in continental China. The restricted distribution of T. dussumieri in China and the smaller size of individuals, however, may indicate suboptimal habitats for arriving larvae. The limited presence of the two crabs on Chinese shores indicates that the intense coastal development in the country, such as in Hong Kong, may destroy suitable habitats and render these species susceptible to local extinction.}, }
@article {pmid39646447, year = {2024}, author = {Ma, L and Wu, Y and Li, XZ}, title = {A new species of the genus Porirualia Huys &amp; Mu, 2021 (Copepoda, Harpacticoida, Parastenheliidae) from the intertidal zone of Qingdao, China, with a key to species of the genus.}, journal = {Zootaxa}, volume = {5476}, number = {1}, pages = {241-252}, doi = {10.11646/zootaxa.5476.1.21}, pmid = {39646447}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; China ; *Animal Distribution ; *Copepoda/classification/anatomy &amp; histology/genetics ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Ecosystem ; Phylogeny ; }, abstract = {A new species belonging to the genus Porirualia Huys &amp; Mu, 2021 was identified and described here based on samples collected from No. 1 Bathing Beach, Qingdao, China. The new species differs from Porirualia pyriformis mainly in the following characteristics: P3 and P4 exp-3 with three inner setae (two inner setae in P. pyriformis), ratio of length to maximum width of female P5 3.83 (3.25 in P. pyriformis). The new species differs from Porirualia megarostrum by the characters including rostrum reaching to distal margin of third segment of antennule (reaching to distal margin of fifth segment of antennule in P. megarostrum), ratio of length to maximum width of female P5 3.83 (2.2 in P. megarostrum); male P2 and P3 two-segmented (three-segmented in P. megarostrum); male P5 bearing five elements (six in P. megarostrum). This is the first report of the genus Porirualia from the China Seas. The DNA barcode (COI) sequence of the new species was obtained and submitted to GenBank (PP761118), which is the first submission of COI sequence of the family Parastenheliidae to GenBank.}, }
@article {pmid39646433, year = {2024}, author = {Wong, KJH and Meij, SETV and Chan, BKK}, title = {A new species of coral-dwelling crab (Decapoda: Brachyura: Cryptochiridae: Opecarcinus) from the West Pacific.}, journal = {Zootaxa}, volume = {5476}, number = {1}, pages = {474-504}, doi = {10.11646/zootaxa.5476.1.35}, pmid = {39646433}, issn = {1175-5334}, mesh = {Animals ; *Brachyura/classification/anatomy &amp; histology/genetics ; Female ; Male ; *Animal Distribution ; *Body Size ; *Anthozoa/classification/anatomy &amp; histology ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Taiwan ; Pacific Ocean ; Phylogeny ; }, abstract = {Based on material acquired from Green Island, Taiwan, using a combined approach of traditional morphology-based taxonomy and molecular barcoding, we describe a new species of coral-dwelling crab, Opecarcinus ngankeeae sp. nov., from the scleractinian hosts Pavona decussata and P. varians (family Agariciidae). The DNA sequences of the present species matched with O. sp. SET6, associated with plate-forming Leptoseris and Pavona corals, available on Genbank, provided by Xu et al. (2022). The geographical distribution of O. ngankeeae sp. nov. spans from the Coral Triangle and Taiwan to Japan in West Pacific.}, }
@article {pmid39646432, year = {2024}, author = {Yang, CH and Kumar, AB and Chan, TY}, title = {On the differences between the two widely distributed and closely related rock shrimps Sicyonia japonica Balss, 1914 and S. parajaponica Crosnier, 2003 (Dendrobranchiata, Penaeoidea, Sicyoniidae), with a new record of S. japonica from Taiwan.}, journal = {Zootaxa}, volume = {5476}, number = {1}, pages = {505-513}, doi = {10.11646/zootaxa.5476.1.36}, pmid = {39646432}, issn = {1175-5334}, mesh = {Animals ; Taiwan ; Male ; Female ; *Animal Distribution ; Penaeidae/classification/anatomy &amp; histology ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {The rock shrimp Sicyonia japonica Balss, 1914 is recorded from Taiwan for the first time. The availability of many fresh specimens of S. japonica and S. parajaponica Crosnier, 2003 from various localities in the Indo-West Pacific allowed a detailed comparison of the morphology, fresh coloration and genetics between these two closely related species. Their major differences are illustrated by line drawings, micro-computed tomography (micro-CT) images and color photographs. DNA barcoding comparison supports the specific status of these two species and reveals that the western Indian Ocean material of S. japonica may represent another cryptic taxon.}, }
@article {pmid39646412, year = {2024}, author = {Radashevsky, VI and Al-Kandari, M and Malyar, VV and Pankova, VV}, title = {A twin of Polydora hoplura (Annelida: Spionidae) from the Arabian (Persian) Gulf, with review of primers used for barcoding of Spionidae.}, journal = {Zootaxa}, volume = {5529}, number = {2}, pages = {245-268}, doi = {10.11646/zootaxa.5529.2.2}, pmid = {39646412}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Polychaeta/classification/genetics/anatomy &amp; histology ; *Phylogeny ; Male ; Indian Ocean ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; }, abstract = {The spionid polychaete Polydora hoplura Claparède, 1868 has been widely recorded boring in shells of abalone, oysters, clams, barnacle tests and sponges in temperate and subtropical waters. Molecular studies have suggested conspecificity of individuals collected worldwide but showed high genetic variability of the species with the highest diversity of haplotypes in the South African population. We have compared the morphology and genetic data of shell-boring worms from Kuwait, which were previously assigned to P. hoplura, with American, Asian and European individuals, including those from the type locality in Italy. The Kuwaiti individuals share key diagnostic morphological characters with P. hoplura but differ in ochre pigment on the anterior chaetigers in life, pattern of pigmentation after fixation in formalin, and pattern of methyl green staining of fixed specimens. They also differ in the dimensions of mature spermatozoa. The analysis of sequence data of five gene fragments (total 3483 bp) showed that the intraspecific diversity of P. hoplura and the variability of Polydora individuals from Kuwait are less than the divergences in all studied genes, except for 28S rDNA, between these two groups. These data, as well as the absence of common cytochrome c oxidase subunit I (COI) and 16S haplotypes, and morphological differences between individuals from Kuwait and P. hoplura, allowed us to conclude that the Kuwaiti population is not conspecific with P. hoplura. This conclusion was confirmed by the results of the species delimitation analysis. In the Bayesian inference analysis of the sequence data individuals from Kuwait formed a well-supported clade sister to P. hoplura. These individuals are described and illustrated here as a new species, Polydora mohammadi sp. nov. Primers used for successful amplification of the mitochondrial COI gene in various species of Spionidae are reviewed and we suggest future studies on Polydora use a combination of two primer pairs (2F-spionid-LCO/1R-spionid-HCO and Dorid_COI.3F/Dorid_COI.1R) to target sequences that include the barcode fragments covered with "Folmer" and "Dorid" primers.}, }
@article {pmid39646401, year = {2024}, author = {Wesener, T}, title = {Five new species and numerous locality records of Spirobolida millipedes from Madagascar (Diplopoda, Spirobolida, Pachybolidae).}, journal = {Zootaxa}, volume = {5529}, number = {3}, pages = {461-486}, doi = {10.11646/zootaxa.5529.3.3}, pmid = {39646401}, issn = {1175-5334}, mesh = {Madagascar ; Animals ; Male ; *Animal Distribution ; Female ; *Arthropods/classification/anatomy &amp; histology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Ecosystem ; }, abstract = {Based mainly on the results of generalized American biodiversity inventory programmes, several samples of Malagasy Spirobolida millipedes became available to study. Based on this material, five new species of Spirobolida are described from Madagascar: four potential microendemic species, Aphistogoniulus amberivery sp. nov. from the Amberivery forest, A. manombo sp. nov., from the lowland rainforest of Manombo, Spiromimus endemicus sp. nov. from the Montagne des Français, and a species from the littoral forest of Tampolo, tentatively placed in the genus Eucarlia Brölemann, 1913, E. tampolo sp. nov.. A fifth species appears to be more widespread and is a morphologically unusual species of the genus Alluviobolus Wesener, 2009, A. omega sp. nov.. Aphistogoniulus manombo sp. nov. was previously described as a population of A. jeekeli Decker &amp; Wesener, 2011. One of the most enigmatic Malagasy millipede species, Spirobolus olympiacus Karsch, 1881, is redescribed based on topotypic material as Colossobolus olympiacus (Karsch, 1881) new combination. Additional locality data is provided for 14 other Spirobolida species, of which 11 are listed on the IUCN Red List: Aphistogoniulus aridus Wesener, 2009, A. diabolicus Wesener, 2009, A. erythrocephalus (Pocock, 1893), A. hova (de Saussure &amp; Zehntner, 1897), Colossobolus semicyclus Wesener, 2009, Spiromimus albipes Wesener &amp; Enghoff, 2009, S. litoralis Wesener &amp; Enghoff, 2009, S. simplex Wesener &amp; Enghoff, 2009, S. triaureus Wesener &amp; Enghoff, 2009, S. univirgatus deSaussure &amp; Zehntner, 1901, Flagellobolus pauliani Wesener, 2009, Dactylobolus bivirgatus (Karsch, 1881), Madabolus maximus Wesener &amp; Enghoff, 2008 and Hylekobolus rufus Wesener, 2009. Fourteen new genetic barcoding COI sequences are provided for nine species: Hylekobolus rufus, Colossobolus semicyclus, Aphistogoniulus amberivery sp. nov., A. aridus, A. diabolicus, A. erythrocephalus, A. hova, Spiromimus univirgatus and S. scapularis Wesener &amp; Enghoff, 2009.}, }
@article {pmid39646399, year = {2024}, author = {Zuñiga, R and Valerio, AA and Hanson, P and Smith, MA and Hallwachs, W and Janzen, DH}, title = {Cryptic diversity of Leurus wasps (Hymenoptera: Ichneumonidae: Metopiinae), parasitoids of caterpillars in Area de Conservación Guanacaste, Costa Rica.}, journal = {Zootaxa}, volume = {5529}, number = {3}, pages = {511-531}, doi = {10.11646/zootaxa.5529.3.5}, pmid = {39646399}, issn = {1175-5334}, mesh = {Animals ; Costa Rica ; *Wasps/anatomy &amp; histology/classification ; Male ; Female ; *Larva/anatomy &amp; histology/growth &amp; development ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Moths/anatomy &amp; histology/parasitology ; Ecosystem ; }, abstract = {As a consequence of COI barcoding hundreds of reared specimens of what appeared to be Leurus caeruliventris, a parasitoid of leaf-rolling Crambidae (Lepidoptera) from the Area de Conservación Guanacaste, northwestern Costa Rica, and matching them with their host caterpillars and morphological traits, we describe ten new sympatric species and redescribe L. caeruliventris. The new species, authored by Zuñiga &amp; Valerio, are: Leurus billeberhardi, L. henrytownesi, L. hugokonsi, L. iangauldi, L. jesusugaldei, L. marjorietownesae, L. maryjanewestae, L. pammitchellae, L. sondrawardae, and L. wahli. We also provide an illustrated key to the eleven species and an ecological glimpse into the lives of these very similar wasp species.}, }
@article {pmid39646383, year = {2024}, author = {Haÿ, V and Mennesson, MI and Dahruddin, H and Sauri, S and Limmon, G and Wowor, D and Hubert, N and Keith, P and Lord, C}, title = {A new freshwater pipefish species (Syngnathidae: Microphis) from the Sunda shelf islands, Indonesia.}, journal = {Zootaxa}, volume = {5536}, number = {1}, pages = {139-152}, doi = {10.11646/zootaxa.5536.1.5}, pmid = {39646383}, issn = {1175-5334}, mesh = {Animals ; Indonesia ; Male ; Female ; *Animal Distribution ; *Smegmamorpha/genetics/classification/anatomy &amp; histology ; Islands ; Phylogeny ; Organ Size ; Fresh Water ; Body Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {A new species of freshwater pipefish, Microphis arrakisae sp. nov., is described from the West Indonesian Islands (Java, Bali and Lombok). This species is morphologically very close to Microphis retzii (Bleeker, 1856), which is found in the eastern Indonesian Islands (Sulawesi, Ceram, Ambon and Papua). However, it can be distinguished by its in vivo coloration. Furthermore, genetic analysis of the partial COI gene (barcoding) indicates that it represents a distinct genetic lineage in the Indonesian region.}, }
@article {pmid39646344, year = {2024}, author = {Selis, M and Fateryga, AV and Cilia, G}, title = {The genus Euodynerus Dalla Torre in Europe and the Maghreb (Hymenoptera: Vespidae: Eumeninae).}, journal = {Zootaxa}, volume = {5537}, number = {2}, pages = {151-194}, doi = {10.11646/zootaxa.5537.2.1}, pmid = {39646344}, issn = {1175-5334}, mesh = {Animals ; Europe ; *Wasps/anatomy &amp; histology/classification ; Male ; Female ; *Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {The genus Euodynerus Dalla Torre, 1904 (= Extraepipona Gusenleitner, 2014, syn. nov.; Euodynerus occultus (Gusenleitner, 2014), comb. nov.) is revised in Europe and the Maghreb, combining morphological data and DNA barcoding. New synonymies are proposed for E. (Pareuodynerus) Blüthgen, 1938 (= E. (Incolepipona) Giordani Soika, 1994, syn. nov.), E. annae (Kostylev, 1937) (= Euodynerus shirazensis Giordani Soika, 1970, syn. nov.), E. caspicus (Morawitz, 1873) (= Euodynerus caspicus armeniacus Gusenleitner, 2016, syn. nov.), E. curictensis Blüthgen, 1940 (= Euodynerus curictensis sardous Borsato, 2006, syn. nov.), E. dantici (Rossi, 1790) (= Euodynerus dantici poggii Giordani Soika, 1986, syn. nov.; = Euodynerus minoricensis Sanza, 2003, syn. nov.), E. quadrifasciatus (Fabricius, 1793) (= Euodynerus quadrifasciatus atripes Giordani Soika, 1976, syn. nov.; = Euodynerus quadrifasciatus rufipes Gusenleitner, 1984, syn. nov.; = Euodynerus quadrifasciatus eburnus Yamane, 1987, syn. nov.), E. rubrosignatus Gusenleitner, 1984, stat. nov. (= Euodynerus notatus cyrenaicus Giordani Soika, 1986, syn. nov.) and E. variegatus (Fabricius, 1793) (= Odynerus crenatus kruegeri von Schulthess, 1928, syn. nov.). Euodynerus quadrifasciatus rubrosignatus Gusenleitner, 1984 is raised to species-level (E. rubrosignatus, stat. nov.), and E. bidentoides (Giordani Soika, 1953), sp. resurr. is removed from synonymy with E. bidentiformis (Giordani Soika, 1942). Euodynerus bidentatus (Lepeletier, 1841) is transferred from the subgenus Pareuodynerus to Euodynerus s. str. A key for the identification of the Euro-Maghrebi species of Euodynerus and reference photos for each species are provided.}, }
@article {pmid39646260, year = {2024}, author = {Makarchenko, EA and Semenchenko, AA and Krasheninnikov, AB and Yanygina, LV and Yavorskaya, NM}, title = {Review of archaic nymphomyiids (Diptera, Nymphomyiidae) of the Russian Far East and bordering territories, with describing of new taxa and DNA barcoding of known species.}, journal = {Zootaxa}, volume = {5448}, number = {2}, pages = {183-211}, doi = {10.11646/zootaxa.5448.2.2}, pmid = {39646260}, issn = {1175-5334}, mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Animal Distribution ; Russia ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; Ecosystem ; }, abstract = {Nymphomyiidae from the Russian Far East and bordering territories are revised, including data on taxonomy, redescriptions, and results of DNA barcoding. Nymphomyia orientalis sp. nov. with two subspecies N orientalis orientalis subsp. nov. and N. orientalis makcha subsp. nov. are described and information on biology, ecology and distribution are presented. Key of Nymphomyia species for adult males and females of the world is provided. Three species delimitation approaches (ASAP, mPTP, GMYC) using the mitochondrial gene cytochrome c oxidase I (COI) confirm validity of described taxa as well as available nymphomyiids in GenBank. Morphologically indistinguishable specimens of N. orientalis sp. nov. from Makcha and Polovinka rivers belongs to separate mOTUs with the lowest distances in the genus 1.99% that is the lower interspecific threshold.}, }
@article {pmid39646227, year = {2024}, author = {Sanz-Veiga, PA and Leivas, FWT and Díaz-Grisales, V and Anzaldo, S and Rosado-Neto, GH and Lampert, S and Maggio, DH and Corrêa, AS and Savaris, M}, title = {Sympatric species of Heilipus Germar (Coleoptera: Curculionidae: Hylobiini) on fruits of Lauraceae: a new species from Brazil and redescription of Heilipus draco (Fabricius, 1801).}, journal = {Zootaxa}, volume = {5463}, number = {1}, pages = {63-83}, doi = {10.11646/zootaxa.5463.1.4}, pmid = {39646227}, issn = {1175-5334}, mesh = {Animals ; Brazil ; *Weevils/anatomy &amp; histology/classification ; Male ; Female ; *Animal Distribution ; *Fruit ; Lauraceae/classification ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; Sympatry ; }, abstract = {The genus Heilipus Germar (Curculionidae: Hylobiini) is an American weevil group with 89 described species, of which 28 species are known from Brazil. Here, we describe a new species of Heilipus from Brazil and redescribe H. draco (Fabricius, 1801). Heilipus vividaensis Sanz-Veiga, Savaris &amp; Leivas, sp. nov. and H. draco are similar sympatric species, reared from fruits of Ocotea puberula (Rich.) Nees and Nectandra angustifolia (Schrad.) Nees &amp; Mart. (Lauraceae) in south and southeast Brazil. External morphological and genitalia descriptions, illustrations, distribution records, notes on the host plant, and a barcode DNA sequence are provided for both species.}, }
@article {pmid39646215, year = {2024}, author = {Lee, I and Park, KH}, title = {A new species of Homidia (Collembola: Entomobridae) from Korea, with notes on its DNA data.}, journal = {Zootaxa}, volume = {5463}, number = {2}, pages = {262-272}, doi = {10.11646/zootaxa.5463.2.6}, pmid = {39646215}, issn = {1175-5334}, mesh = {Animals ; Republic of Korea ; *Arthropods/classification/anatomy &amp; histology/genetics ; Male ; Female ; *DNA Barcoding, Taxonomic ; Animal Distribution ; Phylogeny ; Organ Size ; Electron Transport Complex IV/genetics ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {A new species, Homidia pseudokoreana sp. nov., from South Korea described based on morphological data and DNA barcodes. This species is morphologically characterized by the body color pattern with a longitudinal dark stripe on medial area of Th. II to Th. III, coxal macrochaetal formula as 3/4+1,3/4+2, and unguis III with three inner teeth. In this study, DNA sequences of mitochondrial cytochrome c oxidase subunit I (COI) gene were used as DNA barcode to distinguish species. It showed distinct differences in genetic distances between Homidia species. DNA barcoding was a useful tool when identifying morphologically closely related species in Homidia.}, }
@article {pmid39646203, year = {2024}, author = {Bahder, BW and Myrie, W and Helmick, EE and Bartlett, CR}, title = {A new species of planthopper in the genus Patara (Hemiptera: Auchenorrhyncha: Fulgoroidea: Derbidae) from central Jamaica.}, journal = {Zootaxa}, volume = {5463}, number = {3}, pages = {429-440}, doi = {10.11646/zootaxa.5463.3.8}, pmid = {39646203}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera/classification/anatomy &amp; histology/genetics ; Male ; Female ; Jamaica ; *Animal Distribution ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {During survey work for planthoppers associated with palms in Jamaica, one new species of Patara was collected at the Castleton Botanic Garden and is here described as Patara euryfrons sp. n. The species is unusual in having a much broader head than is normally found in members of the genus. Supplementary molecular data for the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI), 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene is provided to support the placement of the novel taxon in Patara.}, }
@article {pmid39646164, year = {2024}, author = {Lukhtanov, VA and Botman, RV and Gagarina, AV}, title = {DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe.}, journal = {Zootaxa}, volume = {5468}, number = {3}, pages = {505-522}, doi = {10.11646/zootaxa.5468.3.5}, pmid = {39646164}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Phylogeography ; Male ; *Animal Distribution ; Female ; Europe ; Butterflies/classification/genetics/anatomy &amp; histology ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {The complex of taxa closely related to Aricia anteros includes the species A. anteros sensu stricto, A. crassipuncta, A. bassoni, and A. vandarbani. All of them are sometimes considered as subspecies of a single polytypic species. Representatives of this complex are found in the Balkan Peninsula, Asia Minor, the Levant, the Caucasus, Transcaucasia, and Northern and Western Iran. In addition, an isolated population of A. anteros occurs in the Northern Black Sea region. In this work, based on DNA barcodes of all species and main populations of the complex, we show the existence of seven differentiated mitochondrial lineages: anteros (predominant in the Balkans), crassipuncta (predominant in Asia Minor), bassoni (the Levant), vandarbani (Talysh Mts), varicolor (Zagros Mts), dombaiensis (the Caucasus) and kalmius (Kalmius River basin in the Northern Black Sea region). The taxa of the A. anteros species complex are allopatric, except for A. anteros s.s. and A. crassipuncta, which have a mosaic distribution in eastern Anatolia and Transcaucasia. On the Balkan Peninsula, within the species A. anteros s.s, both the anteros and the crassipuncta mitochondrial haplogroups are found. This pattern is likely a consequence of interspecific hybridization and mitochondrial introgression. Based on mitochondrial DNA, the taxon A. crassipuncta mehmetcik from SE Anatolia is indistinguishable from A. crassipuncta crassipuncta, and the taxon varicolor from Central Iran is closer to the geographically distant European A. anteros than to the Anatolian A. crassipuncta. The geographically isolated and genetically differentiated population from the Kalmius River basin in the Northern Black Sea region is described here as a new subspecies.}, }
@article {pmid39646142, year = {2024}, author = {Wesener, T}, title = {Integrative redescription of Glomeris cingulata C. L. Koch, 1847, an almost forgotten microendemic pill millipede (Diplopoda, Glomerida, Glomeridae).}, journal = {Zootaxa}, volume = {5541}, number = {3}, pages = {326-338}, doi = {10.11646/zootaxa.5541.3.4}, pmid = {39646142}, issn = {1175-5334}, mesh = {Animals ; *Arthropods/classification/anatomy &amp; histology ; Male ; Female ; *Animal Distribution ; *Phylogeny ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Slovenia ; Ecosystem ; }, abstract = {Among the more than 80 species of the common pill millipede genus Glomeris Latreille, 1803, there are several microendemic species that have not been recorded for the last 80-120 years. To discover whether these species are colour morphs of widespread species or true local endemics is important from a conservation point of view as well as for understanding the biogeography and evolution of the group. The author received three specimens that were morphologically identical to C. L. Koch's 175-year-old first description of Glomeris cingulata Koch, 1847 from the Triglav Mountain in Slovenia, close to the border with Italy. No clear specimen-based records are available for G. cingulata and the type specimen is apparently lost. In order to clarify the taxonomy of this microendemic species, an integrative redescription was conducted, including scanning electron microscopy and DNA barcoding. Glomeris cingulata is a distinct species, with genetic distances of 12.6-15.5% compared to the seven syntopic and numerous other widespread Glomeris species. Based on characters of the first description and following other authors, the synonymy of Glomeris cingulata intercedens Latzel, 1884 under Glomeris transalpina Koch, 1836 is confirmed. The dark colour with posterior red bands closely resembles that of some other high-altitude Glomeris species like G. transalpina Koch, 1836, Glomeris aurita Koch, 1847 and Glomeris oropensis Verhoeff, 1936. Glomeris cingulata is genetically close to, but distant enough from the small-bodied and widespread taxa like Glomeris pustulata Latreille, 1804 and Glomeris tetrasticha Brandt, 1833.}, }
@article {pmid39646033, year = {2024}, author = {Krupitsky, AV and Naderi, A and Hagen, WT and Lukhtanov, VA and Nazari, V}, title = {New data on distribution of Phoenicurusia transcaucasicus (Miller, 1923) (Lepidoptera, Lycaenidae) with description of a new subspecies from Iran.}, journal = {Zootaxa}, volume = {5481}, number = {3}, pages = {373-383}, doi = {10.11646/zootaxa.5481.3.6}, pmid = {39646033}, issn = {1175-5334}, mesh = {Animals ; Iran ; Male ; Female ; *Animal Distribution ; *Phylogeny ; Butterflies/anatomy &amp; histology/classification/genetics/growth &amp; development ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Distribution of Phoenicurusia transcaucasicus (Miller, 1923) in Iran and neighbouring territories is clarified based on analysis of DNA barcodes, the male genitalia and wing pattern of adults. Our study revealed the widespread distribution of Ph. transcaucasicus throughout northern, northeastern and central Iran. Based on integrative analysis, a new subspecies, Ph. transcaucasicus flamma ssp. n., is described from the Zagros Mountains, the Central Iranian Range and the Alborz Mountains. Compared to the nominotypical subspecies, the new subspecies differs in well-developed orange pattern both of dorsal and ventral sides of the wings, shape of the valva in the male genitalia and distinct COI haplotypes. Additionally, distinct phylogenetic lineage of Ph. transcaucasicus is reported from Kerman Province. Diagnostic characters of the species of Ph. phoenicurus (Lederer, 1870) group of Iran are illustrated.}, }
@article {pmid39646026, year = {2024}, author = {Baldizzone, G and Huemer, P}, title = {Coleophora elea Baldizzone &amp; Huemer, new species of the Coleophora oriolella Zeller, 1849 species-group (Lepidoptera, Coleophoridae).}, journal = {Zootaxa}, volume = {5481}, number = {4}, pages = {463-470}, doi = {10.11646/zootaxa.5481.4.4}, pmid = {39646026}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics ; *Animal Distribution ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; }, abstract = {Coleophora elea Baldizzone &amp; Huemer, sp. nov., is described based on specimens collected from the Peloponnese peninsula (Greece). This species is closely related to C. oriolella Zeller, 1849, but it differs in external appearance and in characters of the male and female genitalia. Additionally, the two species are genetically distinct as evidenced by a p-distance of approximately 4% between their DNA barcodes (cytochrome c-oxidase subunit 1). Adult specimens and the genitalia of both species are illustrated for comparative purposes.}, }
@article {pmid39646024, year = {2024}, author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM}, title = {Morphological description and DNA barcoding of Diamesa achipseensis sp. nov. (Diptera: Chironomidae: Diamesinae) from Southwestern Caucasus.}, journal = {Zootaxa}, volume = {5481}, number = {4}, pages = {477-482}, doi = {10.11646/zootaxa.5481.4.6}, pmid = {39646024}, issn = {1175-5334}, mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; *Chironomidae/anatomy &amp; histology/classification/genetics/growth &amp; development ; Female ; Body Size ; Animal Distribution ; Phylogeny ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Illustrated description of adult male, as well as DNA barcoding, of Diamesa achipseensis sp. nov. in comparison with close related species D. caucasica Kownacki et Kownacka from Southwestern Caucasus are provided. Interspecific distances between D. achipseensis sp. nov. and D. caucasica are extremely low (0.64% in average) despite the identified morphological differences. High similarity of these species is new example of genetically indistinguishable of some species of the genus Diamesa Meigen.}, }
@article {pmid39645963, year = {2024}, author = {Gebremeskel, A and Salnitska, M and Solodovnikov, A}, title = {DNA barcode polymorphism within a common widespread rove beetle Quedius molochinus (Coleoptera: Staphylinidae).}, journal = {Zootaxa}, volume = {5519}, number = {4}, pages = {538-548}, doi = {10.11646/zootaxa.5519.4.3}, pmid = {39645963}, issn = {1175-5334}, mesh = {Animals ; *Coleoptera/genetics/classification/anatomy &amp; histology ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Phylogeny ; *Animal Distribution ; Body Size ; Polymorphism, Genetic ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Phylogenetic assessment of COI barcodes from 22 specimens identified as Q. molochinus based on external morphology and shape of the aedeagus revealed three non-sister clades within this recently revised species, with large molecular distance (6.3-7.8%) among them, suggesting their species status. On the contrary, preliminary study of the aedeagal internal sac (endophallus) of the available males from these clades and from the more numerous additional non-sequenced materials of Q. molochinus did not reveal notable variants. We report this case here because firstly, this goes against some cases observed in other beetles where endophallic characters may be the only morphological traits supporting molecular-based cryptic species, and secondly, these molecular clades are unexpected within a species we thought to be well-known. DNA barcoding, exploration of nuclear DNA markers and an in-depth examination of the fully everted endophallus for a wider sample of freshly collected specimens are required for further study and explanation of the detected molecular polymorphism of Q. molochinus. An illustration of the everted internal sac as a reference and new distributional data for this species are provided.}, }
@article {pmid39645938, year = {2024}, author = {Ballon-Estacio, R and Alvarado, M}, title = {Three new species of parasitoid wasps of the genus Mnioes Townes, 1946 (Ichneumonidae: Banchinae) in a humid forest in Peru.}, journal = {Zootaxa}, volume = {5523}, number = {2}, pages = {269-283}, doi = {10.11646/zootaxa.5523.2.8}, pmid = {39645938}, issn = {1175-5334}, mesh = {Animals ; Peru ; Female ; Male ; *Forests ; *Animal Distribution ; *Wasps/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; }, abstract = {Mnioes is a predominantly Neotropical genus of Banchinae (Ichneumonidae), currently including 26 species. Three new species of Mnioes are described, found in a humid montane forest in southern Peru, M. chunka sp. nov, M. chusaq sp. nov. and M. isqun sp. nov, and the male of M. huk Alvarado 2020 is also described. DNA barcoding for all the species treated here is included and provides information to match females with males, especially for M. chunka sp. nov., M. chusaq sp. nov., and M. soqta Alvarado 2020 where females are similar to each other and occur in sympatry. Additionally, an updated key to the Peruvian species is provided.}, }
@article {pmid39645925, year = {2024}, author = {Jiang, ZH and Yan, M and Wang, JX and Hu, SJ}, title = {Review of the genus Pseudodolbina Rothschild, 1894, with the description of a new species from Yunnan, China (Lepidoptera: Sphingidae).}, journal = {Zootaxa}, volume = {5523}, number = {4}, pages = {423-436}, doi = {10.11646/zootaxa.5523.4.2}, pmid = {39645925}, issn = {1175-5334}, mesh = {Animals ; China ; Male ; Female ; *Animal Distribution ; *Phylogeny ; *Moths/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The two species currently included in the genus Pseudodolbina Rothschild, 1894, Pseudodolbina fo (Walker, 1856) and Pseudodolbina aequalis Rothschild &amp; Jordan, 1903, were studied and a new species, Pseudodolbina yunnana sp. nov., was described from Yunnan, China. The diagnostic features and a distribution map of three species are provided, with a phylogenetic analysis based on DNA barcodes.}, }
@article {pmid39645924, year = {2024}, author = {Huemer, P and Özden, &#xd6;}, title = {Scrobipalpa chardonnayi Huemer and Özden, sp. nov.: a new presumably endemic species from Cyprus (Lepidoptera, Gelechiidae).}, journal = {Zootaxa}, volume = {5523}, number = {4}, pages = {437-447}, doi = {10.11646/zootaxa.5523.4.3}, pmid = {39645924}, issn = {1175-5334}, mesh = {Animals ; Cyprus ; Female ; Male ; *Animal Distribution ; *Moths/anatomy &amp; histology/classification ; *Phylogeny ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; }, abstract = {Scrobipalpa chardonnayi Huemer &amp; Özden, sp. nov. is described from the limestone mountains of northern Cyprus and considered as a possible island endemism. The new species shows closer phylogenetic relationships to S. vasconiella (Rössler, 1877) and some related species, but differs phenotypically and in male and female genitalia, as well as through significant divergences in DNA barcode. Morphologically relevant diagnostic characters are compared and figured. Finally, S. vasconiella is reported from Kyrgyzstan for the first time.}, }
@article {pmid39645904, year = {2024}, author = {Komai, T and Hanai, M}, title = {A new shallow water species of the palaemonid shrimp genus Palaemon Weber, 1795 (Decapoda: Caridea) from Japan.}, journal = {Zootaxa}, volume = {5443}, number = {3}, pages = {417-430}, doi = {10.11646/zootaxa.5443.3.6}, pmid = {39645904}, issn = {1175-5334}, mesh = {Animals ; *Palaemonidae/classification/anatomy &amp; histology/genetics ; Japan ; Male ; Female ; *Animal Distribution ; *Body Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; }, abstract = {During a survey of the shallow water decapod fauna in the Miura Peninsula, Kanagawa Prefecture, central Japan, four specimens of a new palaemonid shrimp, Palaemon parvibrachium n. sp., were collected from sea grass beds of Nanozostera japonica (Ascherson &amp; Graebner) Tomlinson &amp; Posluszny, 2001. The new species appears morphologically similar to P. serrifer (Stimpson, 1860), one of the most common representatives of Palaemon Weber, 1795 in Japanese waters, but the short carpus of the second pereopod and the different live colouration readily differentiate the new species from the latter. A DNA barcode (a partial fragment of the mitochondrial CO1 gene), as well as a partial fragment of the mitochondrial 16S rRNA gene, are provided to genetically characterize the new species.}, }
@article {pmid39645896, year = {2024}, author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Helmick, EE and Bahder, BW}, title = {A new species of planthopper in the genus Myconus (Hemiptera: Auchenorrhyncha: Fulgoroidea: Achilidae) from the Osa Peninsula in Costa Rica.}, journal = {Zootaxa}, volume = {5443}, number = {4}, pages = {580-590}, doi = {10.11646/zootaxa.5443.4.6}, pmid = {39645896}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera/anatomy &amp; histology/classification ; Costa Rica ; Male ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; }, abstract = {Recent surveys of palm-associated planthoppers in Costa Rica have revealed many new species, primarily in the families Derbidae and Cixiidae, but also Myconus jacquelinae Bahder &amp; Bartlett, in the Achilidae. Here a new species of Myconus from the the Osa peninsula is described as Myconus florae sp. n. with supplemental molecular data for the barcoding region (5'-half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and histone 3 (H3) gene. A key to all species of Myconus is provided.}, }
@article {pmid39645882, year = {2024}, author = {Samoh, A and Grootaert, P}, title = {New species and records of the genus Hercostomus Loew (Diptera: Dolichopodidae) from Thailand mangroves, with notes on the Hercostomus fauna of Singapore mangroves.}, journal = {Zootaxa}, volume = {5446}, number = {2}, pages = {179-204}, doi = {10.11646/zootaxa.5446.2.2}, pmid = {39645882}, issn = {1175-5334}, mesh = {Animals ; Thailand ; Female ; *Animal Distribution ; *Diptera/classification/anatomy &amp; histology/genetics ; Singapore ; Male ; *Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Wetlands ; }, abstract = {The long-legged fly genus Hercostomus Loew, 1857 is reported for the first time from mangrove habitats in Thailand. Two new species, H. obtusus sp. nov. and H. squamatus sp. nov. are described based on external morphology and supported by NGS barcoding. Four described species, namely, H. brevicornis Zhang, Yang &amp; Grootaert, 2008, H. brevidigitalis Zhang, Yang &amp; Grootaert, 2008, H. lanceolatus Zhang, Yang &amp; Grootaert, 2008, and H. plumatus Zhang, Yang &amp; Grootaert, 2008, previously known only from Singapore mangroves, are recorded for the first time from Thailand mangroves. In addition, species distributions are mapped and taxonomic notes are provided.}, }
@article {pmid39645866, year = {2024}, author = {Yagi, S and Goto, K and Sohn, JC}, title = {A new species of Caloptilia (Lepidoptera: Gracillariidae) from Japan and Korea.}, journal = {Zootaxa}, volume = {5446}, number = {3}, pages = {420-432}, doi = {10.11646/zootaxa.5446.3.6}, pmid = {39645866}, issn = {1175-5334}, mesh = {Animals ; Male ; Republic of Korea ; Japan ; *Moths/classification/anatomy &amp; histology/genetics/growth &amp; development ; Female ; *Animal Distribution ; Larva/growth &amp; development/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; }, abstract = {A new species of Caloptilia, C. rhynchosiae n. sp. is described, based on 16 specimens from Japan and Korea. The species is characterized by the presence of the saccular process in the male genitalia. A fabaceous vine, Rhynchosia tomentosa (L.) Hook. &amp; Arn. is reported as the larval host of C. rhynchosiae n. sp. Larval feeding preference, biology and pupation process are described for the species. The species turned out to be host-specific. Two sets of COI barcodes were generated for C. rhynchosiae n. sp. The genetic distances of COI barcodes between the new species and other congeners in the public databases are compared. The conclusion was made that C. rhynchosiae n. sp. was misidentified as C. soyella in the BOLD and GenBank DNA barcode depositories.}, }
@article {pmid39645854, year = {2024}, author = {Xue, G and Xie, Y and Shen, G and Li, X and Li, M and Guo, Y}, title = {Study on the intraspecific variation of Capila lineata lineata Chou &amp; Gu, 1994, with some taxonomic notes on the related taxa (Hesperiidae, Pyrginae).}, journal = {Zootaxa}, volume = {5446}, number = {4}, pages = {573-580}, doi = {10.11646/zootaxa.5446.4.9}, pmid = {39645854}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Animal Distribution ; Organ Size ; Phylogeny ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; }, abstract = {The history with regard to questions on Capila lineata lineata Chou &amp; Gu, 1994, C. lineata magna Devyatkin &amp; Monastyrskii, 1999, C. lineata irregularis Devyatkin &amp; Monastyrskii, 2002 and C. neolineata Fan, Wang &amp; Huang, 2003 was reviewed. The intraspecific variation of C. lineata lineata was explored by DNA barcoding and morphological comparison. The results revealed a remarkable variability in wing patterns and a slight variability in female genitalia, whereas characters of the male genitalia were uniform. C. lineata irregularis syn. n. and C. neolineata syn. n. are treated as junior subjective synonyms of C. lineata lineata because morphological characters of the two taxa fall into the range of individual variation of the latter.}, }
@article {pmid39645812, year = {2024}, author = {Navarro-Rodríguez, CI and Valdez-Mondragón, A}, title = {Violins we see, species we don't… Species delimitation of the spider genus Loxosceles Heineken &amp; Lowe (Araneae: Sicariidae) from North America using morphological and molecular evidence.}, journal = {Zootaxa}, volume = {5428}, number = {4}, pages = {527-548}, doi = {10.11646/zootaxa.5428.4.4}, pmid = {39645812}, issn = {1175-5334}, mesh = {Animals ; *Spiders/anatomy &amp; histology/classification/genetics ; Male ; Female ; North America ; *Phylogeny ; DNA Barcoding, Taxonomic ; Animal Distribution ; Electron Transport Complex IV/genetics ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {In modern systematics, different sources of evidence are commonly used for the discovery, identification, and delimitation of species, especially when morphology fails to delineate between species or in underestimated species complexes or cryptic species. In this study, morphological data and two DNA barcoding markers-cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2)-were used to delimit species in the spider genus Loxosceles from North America. The molecular species delimitation analyses were carried out using three different methods under the corrected p-distance Neighbor-Joining (NJ) criteria: 1) Assemble Species by Automatic Partitioning (ASAP), 2) General Mixed Yule Coalescent model (GMYC), and 3) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 192 terminals corresponding to 43 putative species of Loxosceles, of which 15 are newly recognized herein, as putative new species, based on morphology and congruence between molecular methods with COI. The average intraspecific genetic distance (p-distance) was <2%, whereas the average interspecific genetic distance was 15.6%. The GMYC and bPTP molecular methods recovered 65-79 and 69 species respectively, overestimating the diversity in comparison with morphology, whereas the ASAP method delimited 60 species. The morphology of primary sexual structures (males palps and female seminal receptacles) was congruent with most of the molecular methods mainly with COI, showing that they are robust characters for identification at the species level. For species delimitation COI was more informative than ITS2. The diversity of Loxosceles species is still underestimated for North America, particularly in Mexico which holds the highest diversity of this genus worldwide.}, }
@article {pmid39645769, year = {2024}, author = {Jia, J and Zhao, X and Skarżyński, D and Wu, R and Cheng, L and An, J}, title = {Morphological description and DNA barcoding of Ceratophysella gracilimucronata sp. nov. (Collembola: Hypogastruridae) from China, with a key to species of the C. armata group of the Sino-Japanese Region.}, journal = {Zootaxa}, volume = {5432}, number = {4}, pages = {555-566}, doi = {10.11646/zootaxa.5432.4.5}, pmid = {39645769}, issn = {1175-5334}, mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; *Arthropods/anatomy &amp; histology/classification/genetics ; Female ; Male ; Phylogeny ; Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; }, abstract = {A new species, Ceratophysella gracilimucronata sp. nov. from Nan Ling Mountains (Guangdong Province, China), is described. It resembles C. ainu (Yosii, 1972), C. glancei Hammer, 1953 and C. falcifer Cassagnau, 1959 due to the B type chaeotataxy and short and slender mucro. Mitochondrial COI gene sequence of C. gracilimucronata sp. nov. is provided. A key to species of the C. armata group of the Sino-Japanese Region is given.}, }
@article {pmid39645686, year = {2024}, author = {Oh, JI and Lee, JY and Kim, SY and Jeong, JH and Song, YG and Byun, BK}, title = {Discovery of Bucculatrix koreana sp. nov. and newly recorded Bucculatrix duanwuia (Lepidoptera: Bucculatricidae) in Korea.}, journal = {Zootaxa}, volume = {5538}, number = {5}, pages = {485-491}, doi = {10.11646/zootaxa.5538.5.9}, pmid = {39645686}, issn = {1175-5334}, mesh = {Animals ; Republic of Korea ; Male ; Female ; *Moths/anatomy &amp; histology/classification ; *Animal Distribution ; *Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; }, abstract = {In this study, we describe a new species, Bucculatrix koreana sp. nov., and report B. duanwuia Liu, 2020, for the first time in Korea. Adults and genitalia of both species are illustrated. Additionally, we provide and discuss DNA barcode sequences for Bucculatrix species known from Korea.}, }
@article {pmid39645681, year = {2024}, author = {Röll, B and Pinto, PV and Lobón-Rovira, J}, title = {A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest.}, journal = {Zootaxa}, volume = {5538}, number = {6}, pages = {561-574}, doi = {10.11646/zootaxa.5538.6.3}, pmid = {39645681}, issn = {1175-5334}, mesh = {Animals ; *Lizards/classification/anatomy &amp; histology/genetics ; Female ; Male ; *Animal Distribution ; *Phylogeny ; Rainforest ; Body Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Guinea ; }, abstract = {The genus Lygodactylus Gray is a species-rich group of small, diurnal geckos distributed in Africa, Madagascar, and South America. The genus is divided into several species groups based on morphological characters, biogeographical affinities and/or phylogenetic investigations. To date, some of these groups still contain candidate species. One of these candidate species, provisionally designed as L. sp. B (a single female from Cameroon), had been placed phylogenetically within the East African Lygodactylus scheffleri-group. Furthermore, it shares typical scale characters with all members of this group. However, L. fischeri Boulenger, eponym and member of the West/Central African L. fischeri-group, also shares these scale characters with the L. scheffleri-group and with L. sp. B. While it could be ruled out that L. sp. B was conspecific with any member of the L. scheffleri-group, it could not be ruled out that L. sp. B represents a female of L. fischeri, as there is no female type material nor a clear description of a female of L. fischeri. Only when a male of this taxon was discovered in Cabinda (Angola) in a case of barcoding, the problem could be solved. We here describe the female L. sp. B from Cameroon and the male from Cabinda as new species Lygodactylus lobeke sp. nov. It is a small nondescript species without any bold color markings, such as dark blotches above the shoulder and on the flanks, which mark the male L. fischeri. The male and the female do not differ in coloration. In captivity, the female showed distinct 'mood dependent' colorations, including a 'pyjamas' coloration. For phylogenetic analysis, only sequences of L. laterimaculatus Pasteur, L. gravis Pasteur and L. lobeke sp. nov. were available. Lygodactylus lobeke sp. nov. was recovered as an independent clade which differs greatly in 16S uncorrected pairwise distance (>10%) from these two congeners. The new species is known from two localities in the Lower Guinea rainforests, with a linear distance of about 850 km. Despite this great distance, both specimens of L. lobeke sp. nov. are genetically surprisingly similar (3.5%). Presumably, the species has a wide distribution within the Lower Guinea region and a continuous gene flow within the population.}, }
@article {pmid39645676, year = {2024}, author = {Wu, J and Liu, X}, title = {Systematics of the green lacewing tribe Ankylopterygini Navás, 1910 (Neuroptera: Chrysopidae: Chrysopinae) from China.}, journal = {Zootaxa}, volume = {5540}, number = {1}, pages = {1-169}, doi = {10.11646/zootaxa.5540.1.1}, pmid = {39645676}, issn = {1175-5334}, mesh = {China ; Animals ; Male ; Female ; *Animal Distribution ; Insecta/anatomy &amp; histology/classification ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {A systematic revision of the taxonomy of the green lacewing tribe Ankylopterygini (Neuroptera: Chrysopidae: Chrysopinae) from China is present. Sixty-six species belonging to six genera are recorded and described. Keys to genera, subgenera and species are provided. A total of 201 COI barcodes (partial sequence of cytochrome c oxidase subunit I (COI)) from 49 species of the tribe are provided and used for molecular species delimitation. Nineta Navás, 1912 is treated as a subgenus of Tumeochrysa Needham, 1909. Two new generic synonyms are proposed: Tibetochrysa Yang, 1988, junior synonym of Retipenna Brooks, 1986; Sencera Navás, 1925, junior synonym of Ankylopteryx Brauer, 1864. Sixteen new species are described: Ankylopteryx hainanensis sp. nov., A. montipunctata sp. nov., A. stena sp. nov., Chrysopidia arcta sp. nov., C. macrosterna sp. nov., C. abdominata sp. nov., Tumeochrysa acuta sp. nov., T. breva sp. nov., T. biloba sp. nov., T. minina sp. nov., T. yangi sp. nov., Retipenna interrupta sp. nov., R. triphlebia sp. nov., Semachrysa pura sp. nov., Se. triloba sp. nov. and Signochrysa jianfenglingensis sp. nov. Twelve specific synonyms are proposed: Ankylopteryx yangi Ma, Yang &amp; Liu, 2020, junior synonym of Ankylopteryx octopunctata candida (Fabricius, 1798), Chrysopidia yangi Yang &amp; Lin, 1977, junior synonym of Chrysopidia junbesiana Hölzel, 1973; Chrysopidia fuscata Navás, 1914 and Chrysopidia tjederi Ma, 2022, junior synonyms of Chrysopidia regulata Navás, 1914; Tumeochrysa hui Yang, 1987, junior synonym of Tumeochrysa praeclara Hölzel, 1973; Tumeochrysa nyingchiana Yang, 1987, junior synonym of Tumeochrysa yunica Yang, 1986; Retipenna inordinata, Yang, 1997, junior synonym of Retipenna dasyphlebia (McLachlan, 1894); Retipenna chione (Banks, 1942 [1940]), junior synonym of Retipenna grahami (Banks, 1942 [1940]); Retipenna chaoi Yang &amp; Yang, 1987, Retipenna guangdongana Yang &amp; Yang, 1987 and Retipenna huai Yang &amp; Yang, 1987, junior synonyms of Retipenna burmana Brooks, 1986; and Signochrysa hainanus (Yang &amp; Yang, 1991), junior synonym of Signochrysa ornatissima (Nakahara, 1955). Eight new combinations are proposed: Retipenna phanera (Yang, 1987) comb. nov., R. sinica (Yang, 1988) comb. nov., Tumeochrysa abunda (Yang &amp; Yang, 1989) comb. nov., T. dolichoptera (Navás, 1910) comb. nov., T. grandis (Navás, 1915) comb. nov., T. inpunctata (Reuter, 1894) comb. nov., T. shaanxiensis (Yang &amp; Yang, 1989) comb. nov. and T. vittata (Wesmael, 1841) comb. nov. Ten species are newly recorded from China: Chrysopidia junbesiana Hölzel, 1973, C. nigrata Navás, 1910, C. ciliata (Wesmael, 1841), C. orientalis (Hölzel, 1973), Tumeochrysa inpunctata (Reuter, 1894), T. praeclara Hölzel, 1973, T. magnifica Hölzel, 1973, Retipenna burmana Brooks, 1986, R. variegata Brooks, 1986, and Semachrysa contorta Brooks, 1983. One species is transferred from Ankylopterygini to Chrysopini: Chrysopa yananica (Yang &amp; Yang, 1989) comb. nov.}, }
@article {pmid39645675, year = {2024}, author = {Kasparek, M}, title = {New species, new synonyms, and resurrected taxa: A review of West and Central Palaearctic members of the genus Pseudoanthidium (Apoidea: Megachilidae).}, journal = {Zootaxa}, volume = {5541}, number = {1}, pages = {1-50}, doi = {10.11646/zootaxa.5541.1.1}, pmid = {39645675}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Animal Distribution ; Bees/anatomy &amp; histology/classification ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; Organ Size ; Ecosystem ; Morocco ; }, abstract = {Wool carder bees of the genus Pseudoanthidium comprise approximately 60-65 species, which are found in the Palaearctic, Indo-Malayan and Afrotropical realms. Their taxonomic relationships are little understood. Herein, I revised West and Central Palaearctic members of the genus. Four species are described as new, namely P. farsiense sp. nov. from Iran, P. microrubrum sp. nov. from Morocco, P. syriacum sp. nov. from Syria, and P. tajikistanicum sp. nov. from Tajikistan. The largely overlooked species Anthidium fulviventre Friese, 1917, described from Russia, and Anthidium ivanovi Mavromoustakis, 1954, described from Tajikistan, are recognized as members of the Pseudoanthidium genus, as P. fulviventre (Friese, 1917) comb. nov. and P. ivanovi (Mavromoustakis, 1954) stat. resurrect. &amp; comb. nov. Anthidium moricei Friese, 1911, from Jordan, and A. royoi Dusmet, 1915, from Morocco, are resurrected from synonymy with P. melanurum and suggested to be treated as P. moricei (Friese, 1911) stat. resurrect. and P. royoi (Dusmet, 1915) stat. resurrect. &amp; comb. nov. The hitherto unknown males of P. moricei (Friese, 1911) and P. rubellulum Pasteels, 1969 are described based on material from Jordan and Israel, respectively. Royanthidium bicoloripenne Pasteels, 1981 (syn. nov.) from Morocco, is revealed to be a junior synonym of P. octodentatum (Pérez, 1895). Morphological traits, along with DNA sequences of the mitochondrial COI gene ("barcoding gene"), allowed clustering the species in five polytypic and five monotypic species groups. As key character traits of the type species of nominate Pseudoanthidium largely fit the subgeneric characters of the subgenus Royanthidium Pasteels, 1969, Royanthidium is regarded as a junior synonym (syn. nov.) of nominate Pseudoanthidium. The species of the subgenus Exanthidium Pasteels, 1969 form a uniform clade both in terms of morphology and DNA marker. An examination of the non-Palaearctic Pseudoanthidium species is suggested to determine whether Exanthidium deserves subgenus status.}, }
@article {pmid39645672, year = {2024}, author = {Wang, S and Jiang, J and Wei, C}, title = {A review of the cicada genus Mata Distant, 1906 (Hemiptera: Cicadidae) with description of one new species from China.}, journal = {Zootaxa}, volume = {5541}, number = {1}, pages = {73-83}, doi = {10.11646/zootaxa.5541.1.4}, pmid = {39645672}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera/anatomy &amp; histology/classification/genetics ; China ; Male ; Female ; *Phylogeny ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The cicada genus Mata Distant, 1906 was reviewed based on the description of one new species, Mata uncinulata sp. nov., from China. Mata kama (Distant, 1881) and Mata meghalayana Sarkar, Mahapatra, Mohapatra, Nair &amp; Kunte, 2021 are reported for the first time in China. Morphological phylogenetic analysis reveals the relationships among related species of Mata. Partial mitochondrial COI gene (DNA barcoding) of M. uncinulata sp. nov. and M. kama rec. nov. are sequenced and uploaded to GenBank. A key to species of Mata is provided.}, }
@article {pmid39644641, year = {2024}, author = {Leidenberger, S and Wiese, V and Schaumann, F and Pleiss, F and Langen, K and Bourlat, SJ}, title = {Freshwater mollusc community screening - Classical and eDNA monitoring methods to detect rare, indicator and invasive species.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177763}, doi = {10.1016/j.scitotenv.2024.177763}, pmid = {39644641}, issn = {1879-1026}, abstract = {Freshwater habitats and their quality have always been of utmost importance for human subsistence. Water quality assessment is an important tool, covering biological, chemical and hydromorphological aspects. Bioindicators such as the bivalves can be used as evidence for good water quality, but widespread groups such as species of the family Sphaeriidae Deshayes,1855 (1822) and genus Pisidium/Euglesa/Odhneripidisium also known as 'pea clams' are poorly known and lack taxonomic expertise. The situation is similar for many other benthic macroinvertebrate species used in biomonitoring. In this study, we tested if pea clams can be detected using eDNA metabarcoding methods applied to sediment and plankton samples from 15 lakes and rivers in Sweden. Additionally, we detected benthic macroinvertebrates, so-called indicator species used in freshwater monitoring, as well as rare or red-listed and invasive species. We created a COI reference barcode library of 22 species of Swedish freshwater molluscs, of which one species is new, and five species have less than five records on NCBI and BOLD. From 272 sediment and plankton samples, we detected 497 benthic macroinvertebrate indicator species, 20 mollusc species and 3 invasive species in 15 freshwater environments in Sweden using eDNA metabarcoding. We show that one of the sediment sampling methods (M42) can detect slightly more species in autumn compared to the plankton or sediment kick-net methods, or to collecting samples in spring. A clear advantage is that biological water quality indices formerly calculated using taxa identified to the family level can now be calculated using the species level, giving higher precision. We suggest that future freshwater monitoring efforts can be greatly improved and sped up through large-scale and strategic habitat screening using barcoding and metabarcoding methods to support decision-making and help fulfill the goals of the UN 2030 Agenda.}, }
@article {pmid39642167, year = {2024}, author = {Buri, MC and Shoeb, MR and Bykov, A and Repiscak, P and Baik, H and Dupanovic, A and David, FO and Kovacic, B and Hall-Glenn, F and Dopa, S and Urbanus, J and Sippl, L and Stofner, S and Emminger, D and Cosgrove, J and Schinnerl, D and Poetsch, AR and Lehner, M and Koenig, X and Perie, L and Schumacher, TN and Gotthardt, D and Halbritter, F and Putz, EM}, title = {Natural killer cell-mediated cytotoxicity shapes the clonal evolution of B cell leukaemia.}, journal = {Cancer immunology research}, volume = {}, number = {}, pages = {}, doi = {10.1158/2326-6066.CIR-24-0189}, pmid = {39642167}, issn = {2326-6074}, abstract = {The term cancer immunoediting describes the dual role by which the immune system can suppress and promote tumour growth and is divided into three phases: elimination, equilibrium and escape. The role of NK cells has mainly been attributed to the elimination phase. Here we show that NK cells play a role in all three phases of cancer immunoediting. Extended co-culturing of DNA barcoded mouse BCR/ABLp185+ B-cell acute lymphoblastic leukaemia (B-ALL) cells with NK cells allowed for a quantitative measure of NK cell-mediated immunoediting. Although most tumour cell clones were efficiently eliminated by NK cells, a certain fraction of tumour cells harboured an intrinsic primary resistance. Furthermore, DNA barcoding revealed tumour cell clones with secondary resistance, which stochastically acquired resistance to NK cells. NK cell-mediated cytotoxicity put a selective pressure on B-ALL cells, which led to an outgrowth of primary and secondary resistant tumour cell clones, which were characterised by an IFN-γ signature. Besides well-known regulators of immune evasion, our analysis of NK cell-resistant tumour cells revealed the upregulation of genes, including Ly6a, which we found to promote leukaemic-cell resistance to NK cells. Translation of our findings to the human system showed that high expression of LY6E on tumour cells impaired their physical interaction with NK cells and led to worse prognosis in leukaemia patients. Our results demonstrate that tumour cells are actively edited by NK cells during the equilibrium phase and use different avenues to escape NK cell-mediated eradication.}, }
@article {pmid39641628, year = {2024}, author = {Hossain, A and Cetnar, DP and LaFleur, TL and McLellan, JR and Salis, HM}, title = {Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.4c00661}, pmid = {39641628}, issn = {2161-5063}, abstract = {Oligopool synthesis and next-generation sequencing enable the construction and characterization of large libraries of designed genetic parts and systems. As library sizes grow, it becomes computationally challenging to optimally design large numbers of primer binding sites, barcode sequences, and overlap regions to obtain efficient assemblies and precise measurements. We present the Oligopool Calculator, an end-to-end suite of algorithms and data structures that rapidly designs many thousands of oligonucleotides within an oligopool and rapidly analyzes many billions of barcoded sequencing reads. We introduce several novel concepts that greatly increase the design and analysis throughput, including orthogonally symmetric barcode design, adaptive decision trees for primer design, a Scry barcode classifier, and efficient read packing. We demonstrate the Oligopool Calculator's capabilities across computational benchmarks and real-data projects, including the design of over four million highly unique and compact barcodes in 1.2 h, the design of universal primer binding sites for one million 200-mer oligos in 15 min, and the analysis of about 500 million deep sequencing reads per hour, all on an 8-core desktop computer. Overall, the Oligopool Calculator accelerates the creative use of massively parallel experiments by eliminating the computational complexity of their design and analysis.}, }
@article {pmid39641617, year = {2024}, author = {Jiang, H and Qian, C and Deng, Y and Lv, X and Liu, Y and Li, A and Li, X}, title = {Novel Multimode Assay Based on Asymmetrically Competitive CRISPR and Raman Barcode Spectra for Multiple Hepatocellular Carcinoma Biomarkers Detection.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.4c04593}, pmid = {39641617}, issn = {1520-6882}, abstract = {Commercial pregnancy test strips (PTS) possess the advantages of lower price, higher stability, and better repeatability and have been popularized to integrate with novel sensing strategies to detect other disease biomarkers, which accelerates the commercialization process of those novel sensing strategies. However, the current integration of novel sensing strategies into commercial PTS still faced the problems of insufficient quantification, low sensitivity, and lack of multiple detection capabilities. Hence, we proposed the concept of "visual classification recognition, spectral signal subdivision" for multiple hepatocellular carcinoma biomarkers (miRNA122 and miRNA233) detection with dual signals based on asymmetric competitive CRISPR (acCRISPR) and surface-enhanced Raman spectroscopy coupling with PTS, named the acCRISPR-PTS-SERS assay. In this assay, acCRISPR was used as a nonamplified cascaded signal amplification method to improve the sensitivity of detection. Two AuNPs-based core-shell Raman tags, each corresponding to different miRNA biomarkers, were used to achieve both visual recognition and spectral segmentation to enhance the quantification of PTS detection and the capability for multiple detection. Under the optimal conditions, the LOD for miRNA122 and miRNA223 were 10.36 and 4.65 fM, respectively. The sensitivity was enhanced by nearly 2 orders of magnitude. In the future, simultaneous hand-held detection for fingerprint barcodes of different cancers can be achieved with the assistance of a microfluidic chip and smartphone.}, }
@article {pmid39640376, year = {2024}, author = {Tabares-Medina, J and García-Blandón, K and García-Montoya, GM and Soto-Calderón, ID}, title = {Redefining infections with trypanosomatids in Neotropical primates: Case study of the white-footed tamarin (Oedipomidas leucopus).}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {25}, number = {}, pages = {101021}, pmid = {39640376}, issn = {2213-2244}, abstract = {Trypanosomes are blood parasites capable of infecting nearly any vertebrate. Many Neotropical primates frequently host trypanosomes and are considered potential reservoirs for Trypanosoma cruzi and other human-pathogenic trypanosomatids. However, diagnostic methods originally developed for detecting these trypanosomatids in humans and domestic species must be validated to reliably diagnose infections in non-human primates. Without such validation, taxonomic biases and incorrect assignments of wildlife reservoirs can occur. The white-footed tamarin (Oedipomidas leucopus), a primate endemic to northwestern Colombia, is classified by the World Health Organization as a reservoir of T. cruzi. However, this classification is based on studies with small sample sizes, ambiguous diagnostic methods, and questionable geographic records. In this study, the 18S ribosomal RNA gene was amplified via PCR and sequenced to estimate trypanosome infection rates and identify species in natural populations of O. leucopus across a wide geographic range, as well as in (ex situ) specimens. This molecular approach was also compared with traditional microscopy diagnosis using blood smears. The molecular diagnosis revealed that over 60% of the tested specimens were infected, whereas traditional microscopy resulted in 58% false negatives compared to the molecular method. A Bayesian phylogeny of the 18S gene identified T. minasense as the sole trypanosomatid species present in O. leucopus, with no detections of T. cruzi or other trypanosomatids of concern to human or domestic animal health. This study highlights the risk of overestimating the presence of human-infecting trypanosomes, such as T. cruzi, in tamarins and other vertebrates, and underscores the importance of validating diagnostic methods to accurately assess the zoonotic potential of wild species. Accurate identification of wildlife reservoirs is essential for understanding parasite life cycles and implementing effective management and conservation strategies for primates and other potential reservoirs.}, }
@article {pmid39638898, year = {2024}, author = {Aggarwal, SD and Lokken-Toyli, KL and Weiser, JN}, title = {Pneumococcal pneumonia is driven by increased bacterial turnover due to bacteriocin-mediated intra-strain competition.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1628}, pmid = {39638898}, issn = {2399-3642}, support = {R01 AI50893//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI038446/AI/NIAID NIH HHS/United States ; }, mesh = {*Bacteriocins/metabolism/genetics ; *Streptococcus pneumoniae/genetics/metabolism ; Animals ; Mice ; *Pneumonia, Pneumococcal/microbiology/metabolism ; *Streptolysins/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Lung/microbiology/metabolism/pathology ; Mice, Inbred C57BL ; Female ; Disease Models, Animal ; Quorum Sensing ; }, abstract = {Using chromosomal barcoding, we observed that >97% of the Streptococcus pneumoniae (Spn) population turns over in the lung within 2 days post-inoculation in a murine model. This marked collapse of diversity and bacterial turnover was associated with acute inflammation (severe pneumococcal pneumonia), high bacterial numbers in the lungs, bacteremia, and mortality. Intra-strain competition mediated by the blp locus, which expresses bacteriocins in a quorum-sensing-dependent manner, was required for each of these effects. Bacterial turnover from the activity of Blp-bacteriocins increased the release of the pneumococcal toxin, pneumolysin (Ply), which was sufficient to account for the lung pathology. The ability of Ply to evade complement, rather than its pore-forming activity, prevented opsonophagocytic clearance of Spn enabling its multiplication in the lung, facilitating the inflammatory response and subsequent invasion into the bloodstream. Thus, our study demonstrates how an appreciation for bacterial population dynamics during infection provides new insight into pathogenesis.}, }
@article {pmid39636545, year = {2024}, author = {Dlauchy, D and Kachalkin, A and Glushakova, A and Buda, K and Fehér, C and Péter, G}, title = {Description of Wickerhamia europaea sp. nov. and revisitation of the ascospore number of W. fluorescens.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39636545}, issn = {1618-1905}, support = {075-15-2021-1396//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1396//Ministry of Science and Higher Education of the Russian Federation/ ; TKP2021-EGA//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; TKP2021-EGA//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; }, abstract = {During the course of two independent studies, six conspecific yeast strains were recovered from flowers, soil, bird faeces and wood of different geographical origins. The six strains share identical DNA sequences in two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2). According to sequence comparisons and phylogenetic analysis, they represent an undescribed Wickerhamia species. The novel species is not only genetically distinct from W. fluorescens, the single species of the genus but can also be distinguished from it by some phenotypic characters. We propose Wickerhamia europaea sp. nov. (holotype: NCAIM Y.01938; isotype: CBS 18675; MycoBank no.: 856571) to accommodate the above noted strains. Under certain fermentation conditions, we detected the production of phenyllactic acid, a potential broad-spectrum antimicrobial compound against food-borne pathogens, by the type strain of the novel species, although in smaller concentrations than in the case of W. fluorescens. Comparing our observations on the formation and properties of the ascospores of Wickerhamia europaea sp. nov. and the ambiguous data on the number of ascospores per ascus of W. fluorescens, we suggest a possible explanation to reconcile the different data regarding the number of ascospores per ascus formed by W. fluorescens.}, }
@article {pmid39636286, year = {2024}, author = {Ayika, MG and Bansal, K and Chakrabarti, S and Gazis, R and Dhillon, B}, title = {Lasiodiplodia theobromae causes rachis blight on coconut palms (Cocos nucifera L.) in Florida.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-09-24-1925-PDN}, pmid = {39636286}, issn = {0191-2917}, abstract = {Lasiodiplodia, a genus in the family Botryosphaeriaceae, has a broad host range and causes dieback, root rot, fruit rot, leaf rot, and blights in many plant species across sub-tropical and tropical geographical areas (Alves et al., 2008). In palms, this fungal pathogen is known to cause fruit and heart rot, wood decay and leaf blight around the globe (Atallah et al., 2024; Santos et al., 2020). In field-grown coconut palms symptoms usually start on older fronds progressing to younger fronds. Symptoms including discoloration of internal tissue, profuse pathogen sporulation, fruiting body formation, and death of entire fronds, universally characterize rachis blight caused by Lasiodiplodia. In summer 2023, a disease incidence of 30% and severity ranging from 20% to 100% of the canopy was observed in Florida. Three diseased coconut palms were sampled from a five-acre plot and the symptomatic tissue (internal rachis discoloration) was excised at the margin of the advancing lesion, and surface sterilized (30s 75% EtOH, 1 min 3% sodium hypochlorite, 1 min rinse in sterile water). Six pieces were plated on one Potato Dextrose Agar (PDA, Difco) plate supplemented with three antibiotics, penicillin, streptomycin, and neomycin, each at 5mg/L (Gibco PSN), and a total of three PDA plates per sample were processed. Plates were incubated at 25°C under darkness and Lasiodiplodia-like colonies were consistently recovered from all 54 rachis pieces. Initially white in color, the fungal colony grew radially, turned gray, and eventually took on a darker shade, with an abundance of aerial mycelium and rare occurrence of conidiomata and conidia in older plates. Two morphologically similar isolates Las1A and Las1B were obtained from single spores and grown at 28°C in the dark for 7 days. DNA was extracted using the quick DNA extraction protocol (Liu et al., 2000) and regions from two fungal barcoding genes, nuclear ribosomal internal transcribed spacer (nrITS) and translation elongation factor 1-α (TEF1-α) were amplified using primers ITS1/ITS4 (White et al., 1990) and EF1-728F/EF1-986R (Carbone &amp; Kohn, 1999), respectively, and sequenced. The ITS (PQ282128 and PQ282129) and TEF1-α sequences from both isolates (PQ278132 and PQ278133) were 100% identical to Lasiodiplodia theobromae isolate G112-8 (OR453211 and OR482955, respectively). One-year-old seedlings of coconut palm (Cocos nucifera L.) were used for pathogenicity tests. Agar plugs from margins of actively growing cultures of Las1A and Las1B were placed on cut end of petioles from fronds close to the spear leaf and covered with parafilm. The control palms were treated with distilled water. The onset of disease symptoms was observed about 14 days post inoculation. The inoculated petioles were soft, listless, lost turgidity, and could be easily bent without snapping about 1 month following inoculation. In contrast, the palm control seedlings that were inoculated with water remained turgid, healthy and alive. Fruiting body development was observed on inoculated petioles, the pathogen was reisolated, and examination of its colony and spore morphology as well as presence of paraphyses was used to verify its identity. This is the first report of Lasiodiplodia theobromae causing disease on Cocos nucifera in Florida. This pathogen is a potential threat to coconut palm production in Florida and further research on pathogen diversity, pathogenicity, and distribution is needed to develop options for disease management.}, }
@article {pmid39633475, year = {2024}, author = {Evasco, KL and Brockway, C and Falkingham, T and Hall, M and Wilson, NG and Potter, A}, title = {First detection of Culex tritaeniorhynchus in Western Australia using molecular diagnostics and morphological identification.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {500}, pmid = {39633475}, issn = {1756-3305}, mesh = {*Culex/virology/classification/genetics ; Animals ; Western Australia ; *Phylogeny ; *Mosquito Vectors/virology/classification/genetics ; Electron Transport Complex IV/genetics ; Female ; Encephalitis Virus, Japanese/genetics/isolation &amp; purification/classification ; Encephalitis, Japanese/virology/transmission/epidemiology ; }, abstract = {BACKGROUND: Culex tritaeniorhynchus has long been considered the primary vector of Japanese encephalitis virus (JEV), but until recently, it was considered exotic to Australia. When the species was detected in the country's Northern Territory (NT) for the first time, the Western Australia (WA) Department of Health was cognisant of the risk it posed to the State because of the shared border and continuous mosquito habitat adjoining the two jurisdictions. The aim of this study was to undertake intensive mosquito surveillance in the Kimberley region to ascertain whether Cx. tritaeniorhynchus was present in WA, define the extent of its distribution and undertake phylogenetic analysis of select specimens to support hypothesized routes of entry into the state.<br><br>METHODS: Carbon dioxide (CO2)-baited encephalitis virus surveillance (EVS) mosquito traps were deployed at various sites throughout the Kimberley region by surveillance officers within the Medical Entomology unit of the Western Australia (WA) Department of Health. Mosquitoes were then morphologically identified, and a subset of four specimens were confirmed as Cx. tritaeniorhynchus by molecular identification using Cytochrome Oxidase I (COI) DNA data and phylogenetic analysis.<br><br>RESULTS: From 31 March 2021 to 30 May 2024, a total of 211 female Cx. tritaeniorhynchus specimens were collected from 21 unique trap sites in the Kimberley's Shire of Wyndham-East Kimberley (SWEK). Four COI DNA barcode regions were amplified and successfully sequenced for analysis. These sequences fell within a clade recognised as Cx. tritaeniorhynchus and specifically all sequences were in a clade with other specimens from the NT and Timor-Leste.<br><br>CONCLUSIONS: This study represents the first detection of Cx. tritaeniorhynchus in WA. Given the widespread nature of trap sites that yielded the species and consecutive seasons over which it was observed, the authors surmise that Cx. tritaeniorhynchus is now established within the northeast Kimberley region. The findings are significant given the detection of the species coincides with the first significant outbreak of JEV activity on mainland Australia involving an estimated 45 human cases of Japanese encephalitis, 80 impacted commercial piggeries and widespread feral pig activity. Although the role that Cx. tritaeniorhynchus&#xa0;may play in JEV transmission into the future is not yet understood, it presents a potential risk to public health in the region.}, }
@article {pmid39632768, year = {2024}, author = {Martínez-Sánchez, A and Szpila, K and Villet, MH and Ståhls, G and Thomas-Cabianca, A and Velásquez, Y and Parrott, JJ and Rojo, S}, title = {Morphology, biology and molecular characterisation of the endemic Canary Islands blowfly Calliphora splendens Macquart, 1838 (Diptera: Calliphoridae).}, journal = {Medical and veterinary entomology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mve.12777}, pmid = {39632768}, issn = {1365-2915}, support = {//Universidad de Alicante/ ; //Horizon 2020/ ; //Rhodes University/ ; }, abstract = {The Canary Islands are an excellent natural laboratory for understanding ecological and evolutionary processes such as biogeographical colonisation. The morphology of the larva, puparium and adult of the endemic Canarian copper fly, Calliphora splendens, is described, illustrated and contrasted with those of the other species of Calliphora that occur in Africa, the Iberian Peninsula and Macaronesia. Partial cytochrome oxidase I sequences show a connection between C. splendens, Calliphora vicina, Calliphora loewi and Calliphora croceipalpis, but more distant relationship with Calliphora vomitoria. Calliphora splendens produced unisexual offspring in captivity. This work confirms the relict character of the Canarian copper fly associated with the endemic laurel forest habitat.}, }
@article {pmid39635013, year = {2022}, author = {Liu, Y and Li, X and Chen, Y and Geng, G and Li, J and Wang, Y and Huang, L}, title = {Imaging-based optical barcoding for relative humidity sensing based on meta-tip.}, journal = {Nanophotonics (Berlin, Germany)}, volume = {11}, number = {1}, pages = {111-118}, pmid = {39635013}, issn = {2192-8614}, abstract = {In a wide range of applications such as healthcare treatment, environmental monitoring, food processing and storage, and semiconductor chip manufacturing, relative humidity (RH) sensing is required. However, traditional fiber-optic humidity sensors face the challenges of miniaturization and indirectly obtaining humidity values. Here, we propose and demonstrate an optical barcode technique by cooperating with RH meta-tip, which can predict the humidity values directly. Such RH meta-tip is composed of fiber-optic sensor based on surface plasmon resonance (SPR) effect and graphene oxide film as humidity sensitizer. While SPR sensor is composed of multimode fiber (MMF) integrated with metallic metasurface. Dynamic time warping (DTW) algorithm is used to obtain the warp path distance (WPD) sequence between the measured reflection spectrum and the spectra of the precalibrated database. The distance sequence is transformed into a pseudo-color barcode, and the humidity value is corresponded to the lowest distance, which can be read by human eyes. The RH measurement depends on the collective changes of the reflection spectrum rather than tracking a single specific resonance peak/dip. This work can open up new doors to the development of a humidity sensor with direct RH recognition by human eyes.}, }
@article {pmid39629927, year = {2024}, author = {Ma, W and Li, J and Qu, X and Sun, S and Zhou, Y and Liu, Y and Wang, P and Sha, Z}, title = {Liquid-Solid Triboelectric Nanogenerator-Based DNA Barcode Detection Biosensor for Species Identification.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2408718}, doi = {10.1002/advs.202408718}, pmid = {39629927}, issn = {2198-3844}, support = {2022LSL050102//Laoshan Laboratory/ ; No. 42276216//National Natural Science Foundation of China/ ; No. GuiKeAD24010036//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; SDCX-ZG-202400209//Shandong Postdoctoral Science Foundation/ ; }, abstract = {DNA barcode detection method is widely applied for species identification, which is imperative to evaluate the effect of human economic activities on the biodiversity of ecosystem. However, the wide utilization of existing detection biosensors is limited by bulky and expensive instruments, such as Raman spectroscopy and electrochemical station. Herein, a liquid-solid triboelectric nanogenerator (TENG)-based DNA barcode detection biosensor is proposed, which consists of water flow, fluid channel, and PDMS film attached by specifically designed capture probe. Through sequentially combining capture probe, targeted DNA barcode, and signal probe with Au nanoparticles (NPs), the surface charge density of friction layer of TENG decreases under the effect of AuNPs, verified by the density functional theory (DFT) method. Consequently, the peak value of output current spike signal for targeted DNA is smaller than that for other DNA, which is the working mechanism of the present TENG-based biosensor. Such biosensor successfully recognizes Alvinocaris muricola among different types of Alvinocarididae shrimps, and its low limit detection can reach 1×10[-12] m. The present work provides a paradigm-shift way to develop an inexpensive and accurate technique to detect DNA barcode for species identification, and paves a novel way for the application of liquid-solid TENG.}, }
@article {pmid39628840, year = {2024}, author = {Mukalel, AJ and Hamilton, AG and Billingsley, MM and Li, J and Thatte, AS and Han, X and Safford, HC and Padilla, MS and Papp, T and Parhiz, H and Weissman, D and Mitchell, MJ}, title = {Oxidized mRNA Lipid Nanoparticles for In Situ Chimeric Antigen Receptor Monocyte Engineering.}, journal = {Advanced functional materials}, volume = {34}, number = {27}, pages = {}, pmid = {39628840}, issn = {1616-301X}, abstract = {Chimeric antigen receptor (CAR) monocyte and macrophage therapies are promising solid tumor immunotherapies that can overcome the challenges facing conventional CAR T cell therapy. mRNA lipid nanoparticles (mRNA-LNPs) offer a viable platform for in situ engineering of CAR monocytes with transient and tunable CAR expression to reduce off-tumor toxicity and streamline cell manufacturing. However, identifying LNPs with monocyte tropism and intracellular delivery potency is difficult using traditional screening techniques. Here, ionizable lipid design and high-throughput in vivo screening are utilized to identify a new class of oxidized LNPs with innate tropism and mRNA delivery to monocytes. A library of oxidized (oLNPs) and unoxidized LNPs (uLNPs) is synthesized to evaluate mRNA delivery to immune cells. oLNPs demonstrate notable differences in morphology, ionization energy, and pKa, therefore enhancing delivery to human macrophages, but not T cells. Subsequently, in vivo library screening with DNA barcodes identifies an oLNP formulation, C14-O2, with innate tropism to monocytes. In a proof-of-concept study, the C14-O2 LNP is used to engineer functional CD19-CAR monocytes in situ for robust B cell aplasia (45%) in healthy mice. This work highlights the utility of oxidized LNPs as a promising platform for engineering CAR macrophages/monocytes for solid tumor CAR monocyte therapy.}, }
@article {pmid39626340, year = {2024}, author = {Huang, Z and Wu, K and Ju, F and He, R and Tang, Y and Chen, Y and He, X and Zhang, J and Nie, L}, title = {Copper nanocluster based cascade amplified DNA electrochemical detection combining with bio-barcode assay and surface-initiated enzyme polymerization.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {163}, number = {}, pages = {108857}, doi = {10.1016/j.bioelechem.2024.108857}, pmid = {39626340}, issn = {1878-562X}, abstract = {Early cancer diagnosis is paramount for enhancing treatment efficacy, extending patient survival, and improving the quality of life. We developed a highly sensitive electrochemical biosensor for the detection of target DNA (tDNA) associated with gastric cancer. This advancement integrates dual signal amplification strategies: bio-barcode amplification (BCA) and surface-initiated enzyme polymerization (SIEP), with copper nanoclusters (CuNCs) serving as signal labels. Silica nanoparticles (SiO2) were covalently linked with polythymine (poly T) and complementary DNA to create bio-barcode probes. These probes, through hybridization, were immobilized on the reduced graphene oxide and Au nanoparticle (rGO-AuNPs) modified interface and marking the first amplification of the electrical signal. Subsequently, the extended poly T prompted by SIEP bound additional CuNCs through the combination of T-Cu[2+], leading to a second round of signal amplification. The biosensor demonstrated a minimum detection limit of 0.13 fmol/L over a linear response range from 1 fmol/L to 1 nmol/L. It also showcased excellent specificity, repeatability, and stability, making it a promising tool for the sensitive detection of gastric cancer biomarkers.}, }
@article {pmid39623507, year = {2024}, author = {Chen, Y and Shentu, J and Lou, H and Xia, Y and Jiang, Y and Duan, S}, title = {Hematopoietic stem cell heterogeneity and age-related platelet bias: implications for bone marrow transplantation and blood disorders.}, journal = {Stem cell research &amp; therapy}, volume = {15}, number = {1}, pages = {459}, pmid = {39623507}, issn = {1757-6512}, support = {210000-581835//the Qiantang Scholars Fund in Hangzhou City University/ ; 20221JCGY010610//the Natural Science Foundation of Ningbo Municipality, Zhejiang Province/ ; }, abstract = {Hematopoietic stem cells (HSCs) are critical for maintaining lifelong blood production and immune function, especially in the context of bone marrow transplantation, where their ability to reconstruct multiple blood lineages is essential. However, recent studies have revealed that certain HSCs exhibit a bias toward platelet differentiation, termed platelet-biased HSCs (P-HSCs). This lineage bias, particularly pronounced with aging, can lead to imbalances in post-transplant blood recovery, negatively affecting patient outcomes. Research by Claus Nerlov's team has provided key insights into the heterogeneity of HSCs, focusing on the age-related expansion of P-HSCs. Using advanced techniques such as single-cell RNA sequencing and molecular barcoding, their work highlights the evolutionary conservation of platelet bias in HSCs across species. This work delves into these findings, discussing their clinical implications for bone marrow transplantation, aging-related blood disorders, and potential therapeutic strategies. Moreover, we address limitations in current methodologies and propose future directions for research to optimize HSC-based therapies and improve clinical outcomes in hematological diseases.}, }
@article {pmid39622837, year = {2024}, author = {Kuo, LY and Tang, SK and Huang, YH and Xie, PJ and Chen, CW and Chang, ZX and Hsu, TC and Chang, YH and Chao, YS and Chen, CW and Fawcett, S and Nitta, JH and Sundue, M and Kao, TT and Luu, HT and Mustapeng, AMA and Coritico, FP and Amoroso, VB and Thai, YK}, title = {A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1314}, pmid = {39622837}, issn = {2052-4463}, mesh = {*DNA Barcoding, Taxonomic ; *Ferns/genetics/classification ; *Biodiversity ; *Phylogeny ; DNA, Plant/genetics ; }, abstract = {Ferns belong to species-rich group of land plants, encompassing more than 11,000 extant species, and are crucial for reflecting terrestrial ecosystem changes. However, our understanding of their biodiversity hotspots, particularly in Southeast Asia, remains limited due to scarce genetic data. Despite harboring around one-third of the world's fern species, less than 6% of Southeast Asian ferns have been DNA-sequenced. In this study, we addressed this gap by sequencing 1,496 voucher-referenced and expert-identified fern samples from (sub)tropical Asia, spanning Malaysia, the Philippines, Taiwan, and Vietnam, to retrieve their rbcL and trnL-F sequences. This DNA barcode collection of Asian ferns encompasses 956 species across 152 genera and 34 families, filling major gaps in fern biodiversity understanding and advancing research in systematics, phylogenetics, ecology and conservation. This dataset significantly expands the Fern Tree of Life to over 6,000 species, serving as a pivotal and global reference for worldwide barcoding identification of ferns.}, }
@article {pmid39621694, year = {2024}, author = {Mata-Somarribas, C and Cardoso das Graças, G and de Oliveira R Pereira, L and Côrtes Boité, M and Motta Cantanhêde, L and Braga Filgueira, CP and Fallas, A and Quirós-Rojas, L and Morelli, KA and Ferreira, GEM and Cupolillo, E}, title = {Applying a cytochrome c oxidase I barcode for Leishmania species typing.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0309277}, doi = {10.1371/journal.pone.0309277}, pmid = {39621694}, issn = {1932-6203}, mesh = {*Electron Transport Complex IV/genetics ; *Leishmania/genetics/enzymology/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Species Specificity ; }, abstract = {Species delimitation has always been a challenge for taxonomists and for Leishmania studies there is no exception. Herein we attempt to display the usefulness of the mitochondrial gene Cytochrome Oxidase I-coI in classical and barcode-based approaches for Leishmania characterization. A total of 228 samples were analyzed, comprising 28 Leishmania related taxa, mainly from cultures of the Oswaldo Cruz Foundation`s Leishmania Collection. Primers were designed for amplification of coI; sequences were analyzed by distance-based indicators and both the Neighbor Joining and NeighborNet as species grouping techniques. Automatic Barcode Gap Discovery was applied to define species delimitation while for the character-based analysis a software for Barcoding with Logic formulas was employed. Final sequences of 486 bp with 238 parsimonious sites were aligned and edited. Robust groups were formed for most of the genus species, distinctive nucleotide positions in the barcode sequence were observed for 11 of them. A good agreement between the techniques applied and the original characterization was observed. Few species were not distinguished by coI: (i) L. (V.) peruviana, L. (V.) lindenbergi, and L. (V.) utingensis; (ii) L. (L.) venezuelensis and (iii) L. colombiensis and L. equatorensis with identical sequences. Some of these taxa have been, at one time or another, classified as controversial and, for most of them, a higher number of isolates should be studied to properly infer their taxonomic status. CoI represents a mitochondrial target that stands out as a taxonomically important asset with multiple advantages over other genes. This paper corresponds to the first report of coI analysis in Leishmania, a potentially advantageous target for the characterization of this parasite.}, }
@article {pmid39619925, year = {2024}, author = {Santanumurti, MB and Nugraha, MAR and Dewi, NR and Awaluddin, M and Tang, PW and Pardede, HI and Solami, LA and Sulmartiwi, L and El-Regal, MAA}, title = {Fish diversity assessment through conventional morphological identification and recent advances in Saudi Arabia: A review.}, journal = {Veterinary world}, volume = {17}, number = {10}, pages = {2267-2285}, pmid = {39619925}, issn = {0972-8988}, abstract = {Fish identification in the Red Sea, particularly in Saudi Arabia, has a long history. Because of the vast fish diversity in Saudi Arabia, proper species identification is required. Indeed, identifying fish species is critical for biodiversity conservation, food and drug safety, and sustainable fishery management. Numerous approaches have been used to identify fish species, including conventional morphological identification, next-generation sequencing (NGS), nanopore sequencing, DNA barcoding, and environmental DNA analysis. In this review, we collected as much scientific information as possible on species identification in Saudi Arabia. Our findings suggest that the identification process has advanced and spread rapidly and broadly, as evidenced by the discovery of new fish species in Saudi Arabia. The advantages and disadvantages of each method were discussed as part of a comprehensive comparison. This study aimed to provide further scientific knowledge to promote the growth of fish diversity worldwide.}, }
@article {pmid39619666, year = {2024}, author = {Réblová, M and Nekvindová, J and Kolařík, M and Jurjević, &#x17d; and Kolář, M and Hubka, V}, title = {Re-evaluation of Ceratostomella and Xylomelasma with introduction of two new species (Sordariomycetes).}, journal = {MycoKeys}, volume = {110}, number = {}, pages = {319-360}, pmid = {39619666}, issn = {1314-4049}, abstract = {In this study, we assessed the phylogenetic relationships among members of Ceratostomella and the morphologically similar genus Xylomelasma, currently classified within the Sordariomycetes. Our phylogenetic analyses, utilising three and five gene markers, revealed that species from these two genera are congeneric, supporting the transfer of Xylomelasma to Ceratostomella. Consequently, we propose two new combinations: C.sordida comb. nov. and C.novae-zelandiae comb. nov. In addition, we identified two cryptic species within the C.sordida species complex, which are described as C.crypta sp. nov. and C.melanospora sp. nov. Traditional micromorphological characters have proven insufficient for differentiating these new species; however, they are clearly distinguishable by molecular data, particularly using the internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) of the nuclear rRNA cistron, and genes encoding the second largest subunit of RNA polymerase II (rpb2), and translation elongation factor 1-α (tef1-α) as primary and secondary barcodes. This study provides new insights into the morphological characteristics of Ceratostomella, identifying the ascogenous system as an important diagnostic trait at the generic level, which distinguishes Ceratostomella from morphologically similar fungi. Ceratostomella is currently recognised with eight species. We also investigated the relationship between Ceratostomella and the closely related Barbatosphaeria. The lack of statistical support in the Maximum likelihood analysis is discussed and the inclusion of Ceratostomella in Barbatosphaeriaceae is not supported. Ceratostomella is accepted as a genus incertae sedis, while Barbatosphaeriaceae remains a monotypic family. The global diversity of Ceratostomella is inferred from metabarcoding data and published field observations. Biogeographic analysis indicates that members of Ceratostomella are widespread, found in soil and decaying wood, as well as in air, dust, roots, shoots, and water across temperate, subtropical and tropical regions in both the Northern and Southern Hemispheres. We are concurrently publishing whole-genome analyses of three ex-type strains of Ceratostomella, i.e. C.crypta, C.melanospora and C.sordida. This effort aims to establish a new standard for high-quality taxonomic studies, which, in accordance with current trends, should incorporate whole-genome sequencing data for future research and application. Our findings underscore the importance of integrating morphological, biogeographic and molecular data for accurate species delineation and highlight the complexity within the genus Ceratostomella.}, }
@article {pmid39619289, year = {2024}, author = {Iqbal, Z and Azad, R and Jin, X and Hassan, MA and Abbas, M and Nasir, MF and Bodlah, I and Ali, M and Szawaryn, K and Nie, RE}, title = {The review of the genus Coccinella (Coleoptera, Coccinellidae) from Pakistan.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e137417}, pmid = {39619289}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Coccinella is reviewed with seven species found in Pakistan: C.luteopicta (Mulsant, 1866), C.marussii Kapur, 1973, C.iranica Dobzhansky, 1926, C.transversalis Fabricius, 1781, C.septempunctata Linnaeus, 1758, C.transversoguttatatransversoguttata Faldermann, 1835 and C.undecimpunctata Linnaeus, 1758. Information on prey, host plants, distribution and an identification key for Coccinella species in Pakistan is provided. Additionally, newly-sequenced partial COI (cytochrome-c-oxidase subunit I) for C.luteopicta and C.marussii were used to determine their phylogenetic positions within the genus Coccinella.<br><br>NEW INFORMATION: This study comprehensively reviews the genus Coccinella in Pakistan and highlights Coccinellaluteopicta as a new country record. Morphological features of adults, including male genital characters and an identification key to known species in Pakistan are presented. Records of prey, host plants and distributions for all identified species are included. The new data (COI-barcode) shows that C.luteopicta (Mulsant, 1866) was recorded first in Pakistan.}, }
@article {pmid39619181, year = {2024}, author = {McCartin, L and Saso, E and Vohsen, SA and Pittoors, N and Demetriades, P and McFadden, CS and Quattrini, AM and Herrera, S}, title = {Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18607}, pmid = {39619181}, issn = {2167-8359}, mesh = {*Anthozoa/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; DNA Primers/genetics ; Gulf of Mexico ; RNA, Ribosomal, 28S/genetics ; Polymerase Chain Reaction/methods ; Coral Reefs ; }, abstract = {The distributions of anthozoan corals are undercharacterized due to their wide bathymetric ranges, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a noninvasive strategy to complement conventional approaches for mapping and monitoring the distribution and biodiversity of coral communities. Primers for eDNA metabarcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA metabarcoding of all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the 28S rRNA gene (28S rDNA). We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in eDNA from octocorals, black corals and scleractinians, with up to 99.9% of the reads originating from these corals. Further, the 28S barcode amplified using the primers distinguished coral genera and species in many cases, like previously developed methods that target eDNA in only octocorals or scleractinians. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA metabarcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.}, }
@article {pmid39616387, year = {2024}, author = {Huang, G and Peng, X}, title = {Genus Bithynia: morphological classification to molecular identification.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {496}, pmid = {39616387}, issn = {1756-3305}, support = {82060376//National Natural Science Foundation of China/ ; No.2024GXNSFAA010039//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, mesh = {Animals ; *Snails/parasitology ; Trematode Infections/parasitology/veterinary ; Phylogeny ; Humans ; }, abstract = {Snails of the genus Bithynia, whose primary habitat is slow-flowing ponds and ditches, serve as the first intermediate hosts of liver fluke. Currently, approximately 200 million individuals worldwide are at risk of liver fluke infection, yet questions still persist regarding the taxonomic identification of Bithynia genus, a crucial player in the transmission of this disease. Accurate taxonomic classification of the Bithynia genus could significantly enhance current understanding of the disease's transmission mechanisms. In this article we comprehensively review the extensive research conducted on Bithynia genus, spanning past inquiries up to the latest findings. The primary emphasis is placed on exploring the taxonomic identification of this genus within various technological settings. We then present a consolidated analysis of the morphological taxonomic identification methods, highlighting their strengths and limitations. We also introduce a novel perspective on the future direction of identification and classification efforts for the members of this genus, emphasizing the crucial role Bithynia plays in the epidemiological cycle of liver fluke transmission. We conclude by urging researchers to prioritize the significance of the members of this genus in the epidemiological cycle of liver fluke transmission and in control measures for disease dissemination, within the context of the vector organisms.}, }
@article {pmid39615483, year = {2024}, author = {Michaels, YS and Major, MC and Bonham-Carter, B and Zhang, J and Heydari, T and Edgar, JM and Siu, MM and Greenstreet, L and Vilarrasa-Blasi, R and Kim, S and Castle, EL and Forrow, A and Ibanez-Rios, MI and Zimmerman, C and Chung, Y and Stach, T and Werschler, N and Knapp, DJHF and Vento-Tormo, R and Schiebinger, G and Zandstra, PW}, title = {Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells.}, journal = {Cell systems}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cels.2024.11.001}, pmid = {39615483}, issn = {2405-4720}, abstract = {T cells develop from hematopoietic progenitors in the thymus and protect against pathogens and cancer. However, the emergence of human T cell-competent blood progenitors and their subsequent specification to the T lineage have been challenging to capture in real time. Here, we leveraged a pluripotent stem cell differentiation system to understand the transcriptional dynamics and cell fate restriction events that underlie this critical developmental process. Time-resolved single-cell RNA sequencing revealed that downregulation of the multipotent hematopoietic program, upregulation of >90 lineage-associated transcription factors, and cell-cycle exit all occur within a highly coordinated developmental window. Gene-regulatory network inference uncovered a role for YBX1 in T lineage specification. We mapped the differentiation cell fate hierarchy using transcribed lineage barcoding and discovered that mast and myeloid potential bifurcate from each other early in hematopoiesis, upstream of T lineage restriction. Our systems-level analyses provide a quantitative, time-resolved model of human T cell fate specification. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid39613881, year = {2024}, author = {Ghauri, MSZ and Soomro, S and Novianto, D and Arnuphapprasert, A and Kaewthamasorn, M}, title = {Molecular detection and genetic characterization of hemotropic mycoplasmas in goats and fleas from Thailand.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29702}, pmid = {39613881}, issn = {2045-2322}, mesh = {Animals ; *Goats/microbiology ; Thailand/epidemiology ; *Mycoplasma/genetics/isolation &amp; purification ; *Siphonaptera/microbiology ; Goat Diseases/microbiology/epidemiology ; Mycoplasma Infections/veterinary/epidemiology/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {Arthropod vectors play a crucial role in the transmission of hemotropic mycoplasmas, small bacteria that infect red blood cells in a wide range of animals and humans globally, leading to intravascular infections. Traditional Giemsa-stained thin blood smears, used for diagnosing hemotropic mycoplasmas through microscopic examination, have low sensitivity and are effective only when bacteremia levels are high. This study aimed to employ molecular methods to detect and genetically characterize hemotropic mycoplasmas in goats as well as investigate the potential role of fleas as vectors. Blood and flea samples were collected concurrently from goats on 16 farms across seven provinces in Thailand from January 2017 to October 2023. The 16 S rRNA, 23 S rRNA, and rnpB genes of hemoplasmas were amplified and sequenced. All fleas were identified morphologically and molecularly through DNA barcoding of the cytochrome oxidase I gene. A total of 78 out of 500 goats (15.6%), three pooled flea samples (3/6, 50%), and one individual flea (1/49, 2.04%) tested positive for hemoplasmas and all fleas were identified as Ctenocephalides orientis. BLASTN searches utilizing the three genetic markers revealed that the hemoplasmas detected in this study showed 97.81-100% similarity to Mycoplasma ovis and Candidatus Mycoplasma haemovis, which have been previously reported in sheep, goats, and humans, suggesting their zoonotic potential. The sequences were grouped into 28 unique nucleotide sequence types (ntSTs) based on minor variations in the 16 S rRNA gene. Hemotropic mycoplasma infection was significantly associated with farm locations and seasonality of sample collection (p < 0.0001), indicating that farm management practices or environmental conditions may play a critical role in the epidemiology of these infections. This study represents the first report of hemotropic mycoplasmas in goats in Thailand, confirms their presence in fleas, and provides valuable insights for farm management, such as guiding the rational use of insecticides and antibiotics.}, }
@article {pmid39610807, year = {2024}, author = {Wang, C and Gan, J and Mi, X}, title = {On two species of Phintella Strand, 1906 from Hainan, China (Araneae, Salticidae).}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e138400}, pmid = {39610807}, issn = {1314-2828}, abstract = {BACKGROUND: In our recent examination of the Phintella specimens collected from Hainan Tropical Rainforest National Park, a new species and the unknown female of P.liae Wang, Mi &amp; Peng, 2023 were recognised, based on the morphological characteristics and molecular evidence.<br><br>NEW INFORMATION: A new species of Phintella Strand, 1906 is described: P.hongkan sp. nov. (&#x2642;&#x2640;) from Hainan, China. The unknown female of P.liae Wang, Mi &amp; Peng, 2023 is also described for the first time. Diagnostic photos of both species are provided.}, }
@article {pmid39609739, year = {2024}, author = {Li, JW and Li, RY and Chen, YM and Wu, YH and Zou, LH and Tang, SL and Zhai, JW}, title = {Comprehensive characterization and phylogenetic analysis of the complete plastomes of two ant-orchids, Caularthron bicornutum and Myrmecophila thomsoniana.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1146}, pmid = {39609739}, issn = {1471-2229}, support = {2023YFD1600504//the National Key Research and Development Program of China/ ; KH230350A//the Construction and Management Program of the Research Center for the Protection and Utilization of Orchids in Motuo County, Xizang Autonomous Region, China/ ; }, mesh = {*Phylogeny ; Animals ; *Orchidaceae/genetics/classification ; Genome, Plastid ; Ants/genetics/classification ; Plastids/genetics ; Symbiosis ; Gryllidae ; }, abstract = {BACKGROUND: Myrmecophytes, characterized by specialized structures like hollow stems that facilitate mutualistic relationships with ants, serve as an important system for studying ant-plant interactions and the adaptation mechanisms. Caularthron and Myrmecophila are exemplary myrmecophytes within Orchidaceae. Previous studies suggested a genetic relationship between these two genera, placing them within Laeliinae (Epidendreae), yet the precise phylogenetic positioning remained uncertain. The absence of available plastome resources has hindered investigations into plastome evolution and phylogeny.<br><br>RESULTS: In this study, we sequenced and assembled the complete plastomes of Caularthron bicornutum and Myrmecophila thomsoniana to elucidate their plastome characteristics and phylogenetic relationships. The determined plastome sizes were 150,557&#xa0;bp for C. bicornutum and 156,905&#xa0;bp for M. thomsoniana, with GC contents of 37.3% and 37.1%, respectively. Notably, M. thomsoniana exhibited a distinctive IR expansion and SSC contraction, with the SSC region measuring only 4532&#xa0;bp and containing five genes (ccsA, ndhD, rpl32, psaC, and trnL-UAG), a unique feature observed for the first time in Epidendreae. Comparative analyses with species from the related genus Epidendrum revealed that C. bicornutum plastome exhibited conserved genome size, GC content, gene content, and gene order. A total of 32 and 33 long sequence repeats, 50 and 40 tandem repeats, and 99 and 109 SSRs were identified in the plastomes of C. bicornutum and M. thomsoniana, respectively. The RSCU analysis demonstrated a consistent pattern in both plastomes, with 29 out of 30 codons with RSCU values greater than 1 featuring A/U at the third codon position. Leucine was the most prevalent amino acid, while Cysteine was the least common. Four potential DNA barcoding regions with Pi values exceeding 0.07, namely ycf1, ccsA-psaC, petN-psbM, and accD-psaI, were identified for subsequent phylogenetic reconstructions within Laeliinae. Phylogenetic analysis underscored the close relationships among Caularthron, Epidendrum, and Myrmecophila.<br><br>CONCLUSIONS: This study represents the first comprehensive analysis of the plastome characteristics of Caularthron bicornutum and Myrmecophila thomsoniana. Through our characterization and phylogenetic analyses, we unveiled the unique IR expansion/SSC contraction and further elucidated their phylogenetic positions. Our research contributes significant data and insights into the dynamic evolution of ant-orchid plastomes and the phylogeny of the Laeliinae.}, }
@article {pmid39608688, year = {2024}, author = {Devan, J and Sandalova, M and Bitterli, P and Herger, N and Mengis, T and Brender, K and Heggli, I and Distler, O and Dudli, S}, title = {Massively parallel flow-cytometry-based screening of hematopoietic lineage cell populations from up to 25 donors simultaneously.}, journal = {Methods (San Diego, Calif.)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ymeth.2024.11.014}, pmid = {39608688}, issn = {1095-9130}, abstract = {This study aimed to develop a method allowing high-dimensional and technically uniform screening of surface markers on cells of hematopoietic origin. High-dimensional screening of cell phenotypes is primarily the domain of single-cell RNA sequencing (RNAseq), which allows simultaneous analysis of the expression of thousands of genes in several thousands of cells. However, rare cell populations can often substantially impact tissue homeostasis or disease pathogenesis, and dysregulation of rare populations can easily be missed when only a few thousand cells are analyzed. With the presented methodological approach it is possible to screen hundreds of markers on millions of cells in a technically uniform manner and thus identify and characterize changes in rare populations. We utilize the highly expressed markers CD45 on immune cells and CD71 on erythroid progenitors to create unique fluorescent barcodes on each of the 25 samples. Double-barcoded samples are co-stained with a broad immunophenotyping panel. The panel is designed in such a way that allows the addition of PE-labelled antibody, which was used for screening purposes. Multiplexed samples are divided into hundreds of aliquots and co-stained, each aliquot with a different PE-labelled antibody. Utilizing a broad immunophenotyping panel and machine-learning algorithms, we can predict the co-expression of hundreds of screened markers with a high degree of precision. This technique is suitable for screening immune cells in bone marrow from different locations, blood specimens, or any tissue with a substantial presence of immune cells, such as tumors or inflamed tissue areas in autoimmune conditions. It represents an approach that can significantly improve our ability to recognize dysregulated immune cell populations and, if needed, precisely target subsequent experiments covering lower cell counts such as RNAseq.}, }
@article {pmid39606648, year = {2024}, author = {Alvarez Rojas, CA and Bonacic, C and Salgado, R and Peters, L and Fredes, D and Rubio, AV and Muñoz-Leal, S and Oyarzún-Ruiz, P and Aguirre, AA}, title = {Genetic and biological insights into Hydatigera taeniaeformis in invasive black rats from southern Chile.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1466409}, pmid = {39606648}, issn = {2297-1769}, abstract = {INTRODUCTION: This study investigates the genetic variability of Hydatigera taeniaeformis in black rats (Rattus rattus), a common tapeworm that infects cats and rodents worldwide. Despite its widespread presence and zoonotic potential, little is known about the genetic diversity of this parasite in the Americas.<br><br>METHODS: We conducted DNA barcoding analysis using mitochondrial cox1 gene sequences using samples collected from 171 invasive wild black rats, captured in the temperate rainforest of Southern Chile. We also included two adult parasites isolated from road killed Kodkods (Leopardus guigna), a small felid species native to the Americas.<br><br>RESULTS: Our findings revealed only two haplotypes, suggesting low genetic variability in a parasite that arrived in the Americas with the Spanish colonization.<br><br>DISCUSSION: These haplotypes are more closely related to parasite populations from Peru, Africa, Australia, and Europe, suggesting an origin linked to the Spanish colonization, possibly from North Africa via the Canary Islands. The study also analyzed infection rates, parasite size, and their correlation with host body size, age, and weight, revealing significant patterns. These results provide new insights into the biogeography and genetic diversity of H. taeniaeformis in a new geographical area, enhancing our understanding of its evolutionary history.}, }
@article {pmid39606254, year = {2024}, author = {Ding, M and Cheng, H and Li, X and Li, X and Zhang, M and Cui, D and Yang, Y and Tian, X and Wang, H and Yang, W}, title = {Phytochemistry, quality control and biosynthesis in ginseng research from 2021 to 2023: A state-of-the-art review concerning advances and challenges.}, journal = {Chinese herbal medicines}, volume = {16}, number = {4}, pages = {505-520}, pmid = {39606254}, issn = {2589-3610}, abstract = {Panax L. (Araliaceae) has a long history of medicinal and edible use due to its significant tonifying effects, and ginseng research has been a hot topic in natural products research and food science. In continuation of our recent ginseng review, we highlighted the advances in ginseng research from 2021 to 2023 with 157 citations, which exhibited the increasingly systematic, collaborative, and intelligent characteristics. In this review, we firstly updated the progress in phytochemistry involving the ginsenosides and polysaccharides and summarized the researches on the active components. Then, some specific applications by feat of the multidimensional chromatography, mass spectrometry imaging, DNA barcoding, and metabolomics, were analyzed, which could provide rich information supporting the multi-component characterization, authentication, and quality control of ginseng and the versatile products. Finally, the recent biosynthesis studies concerning ginsenosides were retrospected. Additionally, the current challenges and future trends with respect to ginseng research were discussed.}, }
@article {pmid39605649, year = {2024}, author = {Diamond, B and Chahar, D and Jain, MD and Poos, AM and Durante, M and Ziccheddu, B and Kaddoura, M and Papadimitriou, M and Maclachlan, K and Jelinek, T and Davies, F and Figura, NB and Morgan, G and Mai, E and Weisel, KC and Fenk, R and Raab, MS and Usmani, S and Landgren, O and Locke, FL and Goldschmidt, H and Schatz, JH and Weinhold, N and Maura, F}, title = {Mutagenic impact and evolutionary influence of radiotherapy in hematologic malignancies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.15.623836}, pmid = {39605649}, issn = {2692-8205}, abstract = {Ionizing radiotherapy (RT) is a widely used palliative and curative treatment strategy for malignancies. In solid tumors, RT-induced double strand breaks lead to the accumulation of indels, and their repair by non-homologous end-joining has been linked to the ID8 mutational signature in resistant cells. However, the extent of RT-induced DNA damage in hematologic malignancies and its impact on their evolution and interplay with commonly used chemotherapies has not yet been explored. Here, we interrogated 580 whole genome sequencing (WGS) from patients with large B-cell lymphoma, multiple myeloma, and myeloid neoplasms and identified ID8 only in relapsed disease. Yet, it was detected after exposure to both RT and mutagenic chemotherapy (i.e., platinum). Using WGS of single-cell colonies derived from treated lymphoma cells, we revealed a dose-response relationship between RT and platinum and ID8. Finally, using ID8 as a genomic barcode we demonstrate that a single RT-resistant cell may seed systemic relapse.}, }
@article {pmid39605582, year = {2024}, author = {Meleshko, D and Yang, R and Maharajan, S and Danko, DC and Korobeynikov, A and Hajirasouliha, I}, title = {Blackbird: structural variant detection using synthetic and low-coverage long-reads.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.17.624011}, pmid = {39605582}, issn = {2692-8205}, abstract = {Recent benchmarks of structural variant (SV) detection tools revealed that the majority of human genome structural variations (SVs), especially the medium-range (50-10,000 bp) SVs cannot be resolved with short-read sequencing, but long-read SV callers achieve great results on the same datasets. While improvements have been made, high-coverage long-read sequencing is associated with higher costs and input DNA requirements. To decrease the cost one can lower the sequence coverage, but the current long-read SV callers perform poorly with coverage below 10X. Synthetic long-read (SLR) technologies hold great potential for structural variant (SV) detection, although utilizing their long-range information for events smaller than 50 kbp has been challenging. Results: In this work, we propose a hybrid novel integrated alignment- and local-assembly-based algorithm, Blackbird, that uses SLR together with low-coverage long reads to improve SV detection and assembly. Without the need for a computationally expensive whole genome assembly, Blackbird uses a sliding window approach and barcode information encoded in SLR to accurately assemble small segments and use long reads for an improved gap closing and contig assembly. We evaluated Blackbird on simulated and real human genome datasets. Using the HG002 GIAB benchmark set, we demonstrated that in hybrid mode, Blackbird demonstrated results comparable to state-of-the-art long-read tools, while using less long-read coverage. Blackbird requires only 5X coverage to achieve F1 scores (0.835 and 0.808 for deletions and insertions) similar to PBSV (0.856 and 0.812) and Sniffles2 (0.839 and 0.804) using 10X Pacbio Hi-Fi long-read coverage.}, }
@article {pmid39605581, year = {2024}, author = {Enninful, A and Zhang, Z and Klymyshyn, D and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Yang, M and Lu, Y and Zhang, N and Braubach, O and Xu, ML and Ma, Z and Fan, R}, title = {Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.07.622523}, pmid = {39605581}, issn = {2692-8205}, abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.}, }
@article {pmid39605504, year = {2024}, author = {Yan, Y and Cheung, E and Verzier, LH and Appetecchia, F and March, S and Craven, AR and Du, E and Probst, AS and Rinvee, TA and de Vries, LE and Kauffman, J and Bhatia, SN and Nelson, E and Singh, N and Peng, D and Shaw, WR and Catteruccia, F}, title = {Mapping Plasmodium transitions and interactions in the Anopheles female.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.12.623125}, pmid = {39605504}, issn = {2692-8205}, abstract = {The human malaria parasite, Plasmodium falciparum , relies on Anopheles mosquitoes for transmission. Once ingested during blood feeding, most parasites die in the mosquito midgut lumen or during epithelium traversal. How surviving ookinetes interact with midgut cells and form oocysts is unknown, yet these steps are essential to initiate a remarkable, similarly uncharacterized growth process culminating in the production of thousands of infectious sporozoites. Here, using single-cell RNA sequencing of both parasites and mosquito cells across four time points and two metabolic conditions, we unveil key processes shaping developmental transitions and mosquito-parasite interactions occurring in the midgut. In depth functional analyses reveal processes regulating oocyst growth and identify the transcription factor Pf SIP2 as essential for sporozoite infection of human hepatocytes. By combining the analysis of shared mosquito-parasite barcodes with confocal microscopy, we discover that parasites preferentially interact with midgut progenitor cells during epithelial crossing, potentially using their basal location as an exit landmark. Additionally, we unveil tight connections between extracellular late oocysts and surrounding muscle cells that may ensure parasites adhere to the midgut without damaging it. Ultimately, our study provides fundamental insight into the molecular events characterizing previously inaccessible biological transitions and mosquito-parasite interactions, and identifies candidates for transmission-blocking strategies.}, }
@article {pmid39605487, year = {2024}, author = {Delamarre, A and Bailey, B and Yavid, J and Koche, R and Mohibullah, N and Whitehouse, I}, title = {Chromatin architecture mapping by multiplex proximity tagging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.12.623258}, pmid = {39605487}, issn = {2692-8205}, abstract = {Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate in 3D space. Using this method - Proximity Copy Paste (PCP) - we mapped the connectivity of individual nucleosomes in Saccharomyces cerevisiae . We show that chromatin is predominantly organized into regularly spaced nucleosome arrays whose properties differ according to transcriptional activity. Additionally, by mapping long-range, multi-way interactions we provide evidence that metaphase chromosomes are compacted by arrayed cohesin hubs. Using single-molecule nuclease footprinting data we define distinct chromatin states within a mixed population to show that noncanonical nucleosomes are a stable feature of chromatin. PCP is a versatile method allowing the connectivity of individual molecules to be mapped at high-resolution.}, }
@article {pmid39604449, year = {2024}, author = {Holzmann, M and Nguyen, NL and Angeles, IB and Pawlowski, J}, title = {BFR2: a curated ribosomal reference dataset for benthic foraminifera.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1292}, pmid = {39604449}, issn = {2052-4463}, support = {Exploring abyssal and hadal biodiversity of foraminifera in the North Pacific//Fondation Ernst et Lucie Schmidheiny (Ernst and Lucie Schmidheiny Foundation)/ ; 221959//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_179125//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_159709//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 316030_150817//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Foraminifera/genetics/classification ; *DNA Barcoding, Taxonomic ; RNA, Ribosomal, 18S/genetics ; DNA, Ribosomal/genetics ; }, abstract = {Benthic foraminifera are one of the major groups of marine protists that also occur in freshwater and terrestrial habitats. They are widely used to monitor current and past environmental conditions. Over the last three decades, thousands of DNA sequences have been obtained from benthic foraminiferal isolates. The results of this long-term effort are compiled here in the form of the first curated benthic foraminiferal ribosomal reference dataset (BFR2). The present dataset contains over 5000 sequences of a fragment of the 18S rDNA gene, which is recognized as the DNA barcode of foraminifera. The sequences represent 279 species and 204 genera belonging to 91 families. Thirteen percent of these sequences have not been assigned to any morphologically described group and may represent species new to science. Furthermore, forty-five percent of the sequences have not been previously published. The BFR[2] dataset aims to collect all DNA barcodes of benthic foraminifera and to provide a much-needed reference dataset for the rapidly developing field of molecular foraminiferal studies.}, }
@article {pmid39604411, year = {2024}, author = {Purushothaman, S and Meola, M and Roloff, T and Rooney, AM and Egli, A}, title = {Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29531}, pmid = {39604411}, issn = {2045-2322}, support = {310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Humans ; Bacteria/genetics/isolation &amp; purification/classification ; }, abstract = {During a bacterial infection or colonization, the detection of antimicrobial resistance (AMR) is critical, but slow due to culture-based approaches for clinical and screening samples. Culture-based phenotypic AMR detection and confirmation require up to 72 hours (h) or even weeks for slow-growing bacteria. Direct shotgun metagenomics by long-read sequencing using Oxford Nanopore Technologies (ONT) may reduce the time for bacterial species and AMR gene identification. However, screening swabs for metagenomics is complex due to the range of Gram-negative and -positive bacteria, diverse AMR genes, and host DNA present in the samples. Therefore, DNA extraction is a critical initial step. We aimed to compare the performance of different DNA extraction protocols for ONT applications to reliably identify species and AMR genes using a shotgun long-read metagenomic approach. We included three different sample types: ZymoBIOMICS Microbial Community Standard, an in-house mock community of ESKAPE pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE Mock), and anonymized clinical swab samples. We processed all sample types with four different DNA extraction kits utilizing different lysis (enzymatic vs. mechanical) and purification (spin-column vs. magnetic beads) methods. We used kits from Qiagen (QIAamp DNA Mini and QIAamp PowerFecal Pro DNA) and Promega (Maxwell RSC Cultured Cells and Maxwell RSC Buccal Swab DNA). After extraction, samples were subject to the Rapid Barcoding Kit (RBK004) for library preparation followed by sequencing on the GridION with R9.4.1 flow cells. The fast5 files were base called to fastq files using Guppy in High Accuracy (HAC) mode with the inbuilt MinKNOW software. Raw read quality was assessed using NanoPlot and human reads were removed using Minimap2 alignment against the Hg38 genome. Taxonomy identification was performed on the raw reads using Kraken2 and on assembled contigs using Minimap2. The AMR genes were identified using Minimap2 with alignment against the CARD database on both the raw reads and assembled contigs. We identified all bacterial species present in the Zymo Mock Community (8/8) and ESKAPE Mock (6/6) with Qiagen PowerFecal Pro DNA kit (chemical and mechanical lysis) at read and assembly levels. Enzymatic lysis retrieved fewer aligned bases for the Gram-positive species (Staphylococcus aureus and Enterococcus faecium) from the ESKAPE Mock on the assembly level compared to the mechanical lysis. We detected the AMR genes from Gram-negative and -positive species in the ESKAPE Mock with the QIAamp PowerFecal Pro DNA kit on reads level with a maximum median time of 1.9 h of sequencing. Long-read metagenomics with ONT may reduce the turnaround time in screening for AMR genes. Currently, the QIAamp PowerFecal Pro DNA kit (chemical and mechanical lysis) for DNA extraction along with the Rapid Barcoding Kit for the ONT sequencing captured the best taxonomy and AMR identification for our specific use case.}, }
@article {pmid39603810, year = {2024}, author = {Gong, X and Zhang, H and Guo, Y and Yu, S and Tang, M}, title = {Chromosome-level genome assembly of Iodes seguinii and its metabonomic implications for rheumatoid arthritis treatment.}, journal = {The plant genome}, volume = {}, number = {}, pages = {e20534}, doi = {10.1002/tpg2.20534}, pmid = {39603810}, issn = {1940-3372}, support = {SH2023078//Science and Technology Plan Projects of Zhenjiang/ ; JDYY2023009//Medical Education Collaborative Innovation Fund of Jiangsu University/ ; 32002235//National Natural Science Foundation of China/ ; }, abstract = {Iodes seguinii is a woody vine known for its potential therapeutic applications in treating rheumatoid arthritis (RA) due to its rich bioactive components. Here, we achieved the first chromosome-level assembly of the nuclear genome of I. seguinii using PacBio HiFi and chromatin conformation capture (Hi-C) sequencing data. The initial assembly with PacBio data produced contigs with an N50 length of 9.71 Mb, and Hi-C data anchored these contigs into 13 chromosomes, achieving a total length of 273.58 Mb, closely matching the estimated genome size. Quality assessments, including BUSCO, long terminal repeat assembly index, transcriptome mapping rates, and sequencing coverage, confirmed the high quality, completeness, and continuity of the assembly, identifying 115.28 Mb of repetitive sequences, 1062 RNA genes, and 25,270 protein-coding genes. Additionally, we assembled and annotated the 150,599 bp chloroplast genome using Illumina sequencing data, containing 121 genes including key DNA barcodes, with maturase K (matK) proving effective for species identification. Phylogenetic analysis positioned I. seguinii at the base of the Lamiales clade, identifying significant gene family expansions and contractions, particularly related to secondary metabolite synthesis and DNA damage repair. Metabolite analysis identified 84 active components in I. seguinii, including the discovery of luteolin, with 119 targets predicted for RA treatment, including core targets like AKT1, toll-like receptor 4 (TLR4), epidermal growth factor receptor (EGFR), tumor necrosis factor (TNF), TP53, NFKB1, janus kinase 2 (JAK2), BCL2, mitogen-activated protein kinase 1 (MAPK1), and spleen-associated tyrosine kinase (SYK). Key active components such as flavonoids and polyphenols with anti-inflammatory activities were highlighted. The discovery of luteolin, in particular, underscores its potential therapeutic role. These findings provide a valuable genomic resource and a scientific basis for the development and application of I. seguinii, addressing the genomic gap in the genus Iodes and the order Icacinales and underscoring the need for further research in genomics, transcriptomics, and metabolomics to fully explore its potential.}, }
@article {pmid39603754, year = {2024}, author = {Maladan, Y and Retnaningrum, E and Daryono, BS and Sarassari, R and Sari, RF and Balqis, SA and Wahid, GA and Safari, D}, title = {A New Serotyping Method of Streptococcus pneumoniae Based on CRISPR/Cas9-Targeted Sequencing.}, journal = {The Journal of molecular diagnostics : JMD}, volume = {26}, number = {12}, pages = {1045-1054}, doi = {10.1016/j.jmoldx.2024.08.009}, pmid = {39603754}, issn = {1943-7811}, mesh = {*Streptococcus pneumoniae/genetics/classification ; *CRISPR-Cas Systems/genetics ; *Serotyping/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Pneumococcal Infections/microbiology/genetics ; Genome, Bacterial ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) application for targeted sequencing has made a breakthrough in the genomic research era. High diversity in the capsular polysaccharide (cps) locus of Streptococcus pneumoniae has hampered identification of the serotype. This study developed a new serotyping method for S. pneumoniae using CRISPR/Cas9-targeted sequencing with the Oxford Nanopore Technologies platform. A probe was designed at the position of the cps locus using an excision approach on two sides flanking genes between the dexB and aliA genes with approximately 20 kb. A native barcoding method was used for multiplexing. The probe will attach to a specific side followed by attachment of CRISPR/Cas9 to cut the recognition area. The study used de novo assembly to reconstruct sequence reads, which were analyzed using PneumoCRISPR, a new serotyping pipeline for Oxford Nanopore Technologies sequencing data output. Four CRISPR/Cas9 probes have been designed and recognize the cps locus of S. pneumoniae. Serotyping results align precisely with serotyping data from whole-genome sequencing. This serotyping method also allows researchers to use multiple samples in a single run. The new serotyping method based on CRISPR/Cas9-targeted sequencing holds immense promise for serotype identification of S. pneumoniae.}, }
@article {pmid39603242, year = {2024}, author = {Pahl, V and Lubrano, P and Troßmann, F and Petras, D and Link, H}, title = {Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {100908}, doi = {10.1016/j.crmeth.2024.100908}, pmid = {39603242}, issn = {2667-2375}, abstract = {Detecting strain-specific barcodes with mass spectrometry can facilitate the screening of genetically engineered bacterial libraries. Here, we introduce intact protein barcoding, a method to measure protein-based library barcodes and metabolites using flow injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin with N-terminal tags of six amino acids. We demonstrate that FI-MS detects intact ubiquitin proteins and identifies the mass of N-terminal barcodes. In the same analysis, we measured relative concentrations of primary metabolites. We constructed six ubiquitin-barcoded CRISPR interference (CRISPRi) strains targeting metabolic enzymes and analyzed their metabolic profiles and ubiquitin barcodes. FI-MS detected barcodes and distinct metabolome changes in CRISPRi-targeted pathways. We demonstrate the scalability of intact protein barcoding by measuring 132 ubiquitin barcodes in microtiter plates. These results show that intact protein barcoding enables fast and simultaneous detection of library barcodes and intracellular metabolites, opening up new possibilities for mass spectrometry-based barcoding.}, }
@article {pmid39602973, year = {2024}, author = {Um, DH and Knowles, DA and Kaiser, GE}, title = {Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries.}, journal = {Computational biology and chemistry}, volume = {114}, number = {}, pages = {108251}, doi = {10.1016/j.compbiolchem.2024.108251}, pmid = {39602973}, issn = {1476-928X}, abstract = {This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ[5]). By assigning a unique vector embedding to each short sequence, it is possible to more efficiently cluster and improve upon compression performance for the string representations of cDNA libraries. Furthermore, by studying alternative coordinate vector embeddings trained on the context of codon triplets, we can demonstrate clustering based on amino acid properties. Employing this sequence embedding method to encode barcodes and cDNA sequences, we can improve the time complexity of similarity searches. By pairing vector embeddings with an algorithm that determines the vector proximity in Euclidean space, this approach enables quicker and more flexible sequence searches.}, }
@article {pmid39602792, year = {2024}, author = {Lancioni, GE and Alberti, G and Filippini, C and Singh, NN and O'Reilly, MF and Sigafoos, J and Orlando, I and Desideri, L}, title = {A Technology System to Help People With Intellectual Disability and Blindness Find Room Destinations During Indoor Traveling: Case Series Study.}, journal = {JMIR rehabilitation and assistive technologies}, volume = {11}, number = {}, pages = {e65680}, doi = {10.2196/65680}, pmid = {39602792}, issn = {2369-2529}, abstract = {BACKGROUND: People with severe or profound intellectual disability and visual impairment tend to have serious problems in orientation and mobility and need assistance for their indoor traveling. The use of technology solutions may be critically important to help them curb those problems and achieve a level of independence.<br><br>OBJECTIVE: This study aimed to assess a new technology system to help people with severe to profound intellectual disability and blindness find room destinations during indoor traveling.<br><br>METHODS: A total of 7 adults were included in the study. The technology system entailed a barcode reader, a series of barcodes marking the room entrances, a smartphone, and a special app that controlled the presentation of different messages (instructions) for the participants. The messages varied depending on whether the participants were (1) in an area between room entrances, (2) in correspondence with a room entrance to bypass, or (3) in correspondence with a room entrance representing the destination to enter. The intervention with the technology system was implemented according to a nonconcurrent multiple baseline design across participants. Sessions included 7 traveling trials, in each of which the participants were to reach and enter a specific room (1 of the 7 or 9 available) to deliver an object they had carried (transported) during their traveling.<br><br>RESULTS: The participants' mean frequency of traveling trials completed correctly was between zero and 2 per session during the baseline (without the system). Their mean frequency increased to between about 6 and nearly 7 per session during the intervention (with the system).<br><br>CONCLUSIONS: The findings suggest that the new technology system might be a useful support tool for people with severe to profound intellectual disability and blindness.}, }
@article {pmid39599554, year = {2024}, author = {Morelli, M and D'Attoma, G and Saldarelli, P and Minafra, A}, title = {The Evolution of Wisteria Vein Mosaic Virus: A Case Study Approach to Track the Emergence of New Potyvirus Threats.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/pathogens13111001}, pmid = {39599554}, issn = {2076-0817}, abstract = {Wisteria vein mosaic virus (WVMV, Potyvirus wisteriae), a virus belonging to the genus Potyvirus, is responsible for Wisteria vein mosaic disease (WMD), a severe disease that affects Wisteria, a genus of garden plants acclaimed worldwide. Although probably originating in the Far East, WVMV infection was first reported in the US, and subsequently in numerous countries. Following the first molecular detection of an Italian isolate, WVMV Bari, its full-length genome was achieved using NGS barcoding technology. A PhyML phylogenetic analysis, supported by clustering algorithm validation, identified a clear separation between two phylogroups. One major clade comprised WVMV strains isolated from Wisteria spp. A second clade grouped three highly divergent strains, at the borderline species threshold, all found in non-wisteria hosts. Relying on a Relative Time Dated Tips (RTDT) molecular clock, the first emergence of WVMV clades has been traced back to around the 17th century. A network inference analysis confirmed the sharp separation between the two host-related phylogroups, also highlighting the presence of potential intermediate variants. Inter-population genetic parameters revealed a very high genetic differentiation in both populations, which was made reliable by statistically significant permutation tests. The migrant number (Nm) and fixation index (FST) evidenced a restricted gene flow and strong population structures. According to the dN/dS ratio and negative neutrality tests, it was derived that purifying selection at the expense of non-silent variants is underway within WVMV populations. Targeting WVMV evolutionary traits, the present effort raised interesting questions about the underestimated potential of this culpably neglected species to spread in economically relevant crops. The main intention of our study is, therefore, to propose an evolution-based analysis approach that serves as a case study to investigate how other potyviruses or newly emerging viruses may spread.}, }
@article {pmid39599494, year = {2024}, author = {Alkathiri, B and Lee, S and Ahn, K and Youn, SY and Yoo, MS and Lee, HS and Cho, YS and Jung, J and Seo, K and Kim, S and Umemiya-Shirafuji, R and Xuan, X and Kwak, D and Shin, S and Lee, SH}, title = {DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/pathogens13110941}, pmid = {39599494}, issn = {2076-0817}, support = {//Animal and Plant Quarantine Agency/ ; 2024//Chungbuk National University BK21 program/ ; }, abstract = {The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely Hepatozoon canis, Theileria luwenshuni, and Gregarine sp. However, the number and abundance of protists detected were different depending on the primer sets, and T. gondii was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of H. canis, Toxoplasma gondii, T. luwenshuni, and Theileria sp. in the collected ticks. This study identified H. canis and T. gondii in Ixodes nipponensis for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.}, }
@article {pmid39599378, year = {2024}, author = {De Luca, D and Del Guacchio, E and Cennamo, P and Minutillo, F and Bernardo, L and Caputo, P}, title = {Genetics and Distribution of the Italian Endemic Campanula fragilis Cirillo (Campanulaceae).}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {22}, pages = {}, doi = {10.3390/plants13223169}, pmid = {39599378}, issn = {2223-7747}, abstract = {Campanula fragilis Cirillo is a species distributed in central and southern Italy and includes two subspecies with uncertain taxonomic position and distribution. By means of nuclear and chloroplast markers, we attempted at testing the genetic distinctness of the two subspecies, as well as their possible correspondence with geographical or ecological patterns. After a revision of geographic occurrences based on herbarium data, we carried out species distribution modeling to assess the present and future distribution of this species under different ecological variables, also for conservation purposes. Our findings support the recognition of two weakly differentiated taxa, here accepted at subspecific rank, in agreement with the current taxonomic treatment. We found that C. fragilis subsp. cavolinii is monophyletic and limited to mountains and hills of central Italy. On the contrary, C. fragilis subsp. fragilis shows a higher genetic variability and a broader distribution in central and southern Italy, with a wider altitudinal range from coasts to mountain cliffs. We confirmed that both subspecies are narrowly calcicolous and have similar ecological requirements, but C. fragilis subsp. cavolinii occurs in colder habitats. Our results forecast a significant distribution contraction in the long term.}, }
@article {pmid39597591, year = {2024}, author = {Chen, H and Yin, X and Chen, Y and Wang, Y and Li, Q and Ji, N and Zhou, L and Hu, G and Shen, X}, title = {Characterization of a Levanderina fissa Bloom in Aquaculture Ponds and Its Utilization of Dissolved Organic Phosphorus.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112202}, pmid = {39597591}, issn = {2076-2607}, support = {SF2303//Lianyungang Key Research and Development Program/ ; }, abstract = {Harmful algal blooms (HABs) pose significant threats to ecosystems and human health worldwide, with their frequency and intensity increasing substantially. The present study reports an algal bloom observed in an aquaculture pond near Haizhou Bay in July 2022. The causative species, identified through morphological observation and DNA barcoding analysis, was the dinoflagellate Levanderina fissa (Levander) Moestrup, Hakanen, Gert Hansen, Daugbjerg &amp; M. Ellegaard, 2014, known for causing extensive HAB events in the coastal waters of China. A sharp decline in phytoplankton species diversity was observed during the transition from the pre-bloom to the bloom phase. Furthermore, the uptake of four types of dissolved organic phosphorus (DOP), including glucose-6-phosphate (G6P), adenosine-5-triphosphate (ATP), sodium tripolyphosphate (TPP), and glyphosate, by isolated L. fissa was investigated in the laboratory. The results showed that G6P, ATP, and TPP supported L. fissa growth as effectively as orthophosphate. Additionally, the elevated concentrations of dissolved inorganic phosphorus in the media of the three treatments indicated the involvement of extracellular hydrolysis. However, alkaline phosphatase was not responsible for the hydrolysis of these three forms of DOP. This study demonstrates that the ability of L. fissa to utilize DOP may confer a competitive advantage within phytoplankton communities, potentially leading to algal blooms in aquaculture ponds.}, }
@article {pmid39596906, year = {2024}, author = {Ismailaj, M and Zangaro, F and Specchia, V and Sangiorgio, F and Marcucci, F and Kiçaj, H and Basset, A and Pinna, M}, title = {Biodiversity Patterns and DNA Barcode Gap Analysis of COI in Coastal Lagoons of Albania.}, journal = {Biology}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/biology13110951}, pmid = {39596906}, issn = {2079-7737}, support = {101082327//EU commission/ ; }, abstract = {Aquatic biodiversity includes a variety of unique species, their habitats, and their interactions with each other. Albania has a large hydrographic network including rivers, lakes, wetlands and coastal marine areas, contributing to a high level of aquatic biodiversity. Currently, evaluating aquatic biodiversity relies on morphological species identification methods, but DNA-based taxonomic identification could improve the monitoring and assessment of aquatic ecosystems. This study aims to evaluate the coverage of COI DNA barcodes in the reference libraries for the known aquatic animal species present in the coastal lagoons of Albania. In this study, the six most studied coastal lagoons of Albania were selected. Species data were gathered from the scientific literature and publicly available sites and studies. The collected species lists were taxonomically standardised using global public taxonomic databases like WORMS. The standardised lists were used to analyse the barcode gap of COI based on two public DNA barcode libraries: Barcode of Life Data Systems (BOLD) and NCBI GenBank. The results show that the COI DNA barcode gap in the coastal lagoons of Albania ranges from 7% (Lagoon of Patok) to 33% (Karavasta Lagoon). Fishes and Amphibia represent the groups with the lowest barcode gap (8% each), while Annelida shows the highest (47%). In conclusion, the COI gene marker for DNA-based biodiversity assessments is reliable for the coastal lagoons of Albania.}, }
@article {pmid39596647, year = {2024}, author = {Almerekova, S and Yermagambetova, M and Ivashchenko, A and Abugalieva, S and Turuspekov, Y}, title = {Assessment of Complete Plastid Genome Sequences of Tulipa alberti Regel and Tulipa greigii Regel Species from Kazakhstan.}, journal = {Genes}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/genes15111447}, pmid = {39596647}, issn = {2073-4425}, support = {AP14870612//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {*Phylogeny ; *Genome, Plastid ; Kazakhstan ; *Tulipa/genetics ; Microsatellite Repeats/genetics ; Plastids/genetics ; RNA, Transfer/genetics ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Tulipa species are economically, culturally, scientifically, and ecologically important. Tulips present taxonomic complexities that cannot be adequately resolved by examining their morphological characteristics alone or by relying on a limited selection of genetic markers.<br><br>METHODS: In the present study, we assessed the complete plastid sequences of Tulipa alberti Regel and Tulipa greigii Regel collected from Kazakhstan. Additionally, 14 previously published plastomes were obtained from GenBank for comparison and phylogenetic analysis.<br><br>RESULTS: The plastid genome sizes of T. alberti and T. greigii were 152,359 bp and 152,242 bp, respectively. In the plastid genomes of T. alberti and T. greigii, 136 genes were annotated, 114 of which were unique. These unique genes comprised eighty protein-coding, thirty transfer RNA, and four ribosomal RNA genes. Additionally, 415 simple sequence repeats were identified, comprising 107 tandem, 40 forward, 49 palindromic, 8 reverse, and 1 complementary repeat. Notably, the region containing ycf1 exhibited high variability and may serve as an informative DNA barcode for this genus.<br><br>CONCLUSION: Phylogenetic analysis showed strong support for the relationships among Tulipa species, indicating the utility of plastid genome data for further taxonomic studies within the genus.}, }
@article {pmid39596617, year = {2024}, author = {Sajjad, S and Islam, M and Muhammad, K and Ghafoor, SU and Ullah, I and Khan, A and Siraj, M and Alrefaei, AF and Shah, JA and Ali, S}, title = {Comprehensive Evaluation of Cryptic Juglans Genotypes: Insight from Molecular Markers and Phylogenetic Analysis.}, journal = {Genes}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/genes15111417}, pmid = {39596617}, issn = {2073-4425}, mesh = {*Juglans/genetics/classification ; *Phylogeny ; *Genotype ; Genetic Markers/genetics ; DNA Barcoding, Taxonomic/methods ; Pakistan ; }, abstract = {Background/Objectives: The current research work aimed to evaluate the cryptic walnut genotypes of the Hazara region in Pakistan by using DNA barcoding and phylogenetic analysis. Methods: Based on morphological traits such as nut size, nut shape, and the number of leaflets, five genotypes were chosen and samples were collected for the current study. For molecular analysis, gDNA was isolated from the fresh leaves, and the five most effective angiosperm-specific markers, ITS2, rbcLa, rbcLc, rpoC1, and UBE3, were utilized. Based on amplification, sequencing, and identification success rates, ITS2 and UBE3 were recorded as the most efficient markers followed by rbcLa, rbcLc, and rpoC1. Results: During phylogenetic analysis, the query genotype-1 based on ITS2 and genotype-2 based on UBE3 clustered with (KF454101.1-Juglans regia) and (KC870919.1-J. regia) with bootstraps of 56 and 100, respectively. Genotype-3 based on rbcla clustered in a major clade with J. regia L., cultivars (MN397935.1 J. regia 'Vina') and (MN397934.1-J. regia 'Serr'), (MN397933.1 J. regia 'Pedro'), (MN397932.1 J. regia 'Lara'), (MN397931.1 J. regia 'Howard'), and (MN397930.1 J. regia 'Hartley') with bootstrap of 100. Meanwhile, genotype-4 and genotype-5 based on rbclc and rpoC1 clustered with (MN397935.1 J. regia 'Vina') and (MN397934.1 J. regia 'Serr'), across the database sequences. To clarify the taxonomic status of cryptic walnut genotypes, it is necessary to combine diverse DNA barcodes. The results of ITS2 and UBE3, followed by rbcL barcoding markers, are promising taxonomic tools for cryptic walnut genotypes in Pakistan. Conclusions: It has been determined that the genotypes of walnuts in the study area are both J. regia L. and its cultivars and that the accuracy of discrimination regarding the genus Juglans L. is greater than 90%. The reported DNA barcodes are recommended for the correct identification and genetic evaluation of Juglans taxa and its population.}, }
@article {pmid39596209, year = {2024}, author = {Wang, X and Wang, Z and Yang, F and Lin, R and Liu, T}, title = {Assembly, Annotation, and Comparative Analysis of Mitochondrial Genomes in Trichoderma.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, doi = {10.3390/ijms252212140}, pmid = {39596209}, issn = {1422-0067}, support = {XTCX2022NYB12//Collaborative Innovation Center Project of Hainan University/ ; }, mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Trichoderma/genetics ; *Molecular Sequence Annotation ; RNA, Transfer/genetics ; Base Composition/genetics ; Evolution, Molecular ; Introns/genetics ; }, abstract = {Trichoderma is a widely studied ascomycete fungal genus, including more than 400 species. However, genetic information on Trichoderma is limited, with most species reporting only DNA barcodes. Mitochondria possess their own distinct DNA that plays a pivotal role in molecular function and evolution. Here, we report 42 novel mitochondrial genomes (mitogenomes) combined with 18 published mitogenomes of Trichoderma. These circular mitogenomes exhibit sizes of 26,276-94,608 bp, typically comprising 15 core protein-coding genes (PCGs), 2 rRNAs, and 16-30 tRNAs; however, the number of endonucleases and hypothetical proteins encoded in the introns of PCGs increases with genome size enlargement. According to the result of phylogenetic analysis of the whole mitogenome, these strains diverged into six distinct evolutionary branches, supported by the phylogeny based on 2830 single-copy nuclear genes. Comparative analysis revealed that dynamic Trichoderma mitogenomes exhibited variations in genome size, gene number, GC content, tRNA copy, and intron across different branches. We identified three mutation hotspots near the regions encoding nad3, cox2, and nad5 that caused major changes in the mitogenomes. Evolutionary analysis revealed that atp9, cob, nad4L, nad5, and rps3 have been influenced by positive selection during evolution. This study provides a valuable resource for exploring the important roles of the genetic and evolutionary dynamics of Trichoderma mitogenome in the adaptive evolution of biocontrol fungi.}, }
@article {pmid39595947, year = {2024}, author = {Hoffmann, M and Jang, JH and Tallent, SM and Gonzalez-Escalona, N}, title = {Single Laboratory Evaluation of the Q20+ Nanopore Sequencing Kit for Bacterial Outbreak Investigations.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, doi = {10.3390/ijms252211877}, pmid = {39595947}, issn = {1422-0067}, support = {FDA Foods Program Intramural Funds//United States Food and Drug Administration/ ; FDA Foods Program Intramural Funds//United States Food and Drug Administration/ ; }, mesh = {*Nanopore Sequencing/methods ; *Disease Outbreaks ; Humans ; Polymorphism, Single Nucleotide ; Genome, Bacterial ; Foodborne Diseases/microbiology ; Phylogeny ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/epidemiology/diagnosis ; Sequence Analysis, DNA/methods ; Pilot Projects ; }, abstract = {Leafy greens are a significant source of produce-related Shiga toxin-producing Escherichia coli (STEC) outbreaks in the United States, with agricultural water often implicated as a potential source. Current FDA outbreak detection protocols are time-consuming and rely on sequencing methods performed in costly equipment. This study evaluated the potential of Oxford Nanopore Technologies (ONT) with Q20+ chemistry as a cost-effective, rapid, and accurate method for identifying and clustering foodborne pathogens. The study focuses on assessing whether ONT Q20+ technology could facilitate near real-time pathogen identification, including SNP differences, serotypes, and antimicrobial resistance genes. This pilot study evaluated different combinations of two DNA extraction methods (Maxwell RSC Cultured Cell DNA kit and Monarch high molecular weight extraction kits) and two ONT library preparation protocols (ligation and the rapid barcoding sequencing kit) using five well-characterized strains representing diverse foodborne pathogens. High-quality, closed bacterial genomes were obtained from all combinations of extraction and sequencing kits. However, variations in assembly length and genome completeness were observed, indicating the need for further optimization. In silico analyses demonstrated that Q20+ nanopore sequencing chemistry accurately identified species, genotype, and virulence factors, with comparable results to Illumina sequencing. Phylogenomic clustering showed that ONT assemblies clustered with reference genomes, though some indels and SNP differences were observed, likely due to sequencing and analysis methodologies rather than inherent genetic variation. Additionally, the study evaluated the impact of a change in the sampling rates from 4 kHz (260 bases pair second) to 5 kHz (400 bases pair second), finding no significant difference in sequencing accuracy. This evaluation workflow offers a framework for evaluating novel technologies for use in surveillance and foodborne outbreak investigations. Overall, the evaluation demonstrated the potential of ONT Q20+ nanopore sequencing chemistry to assist in identifying the correct strain during outbreak investigations. However, further research, validation studies, and optimization efforts are needed to address the observed limitations and fully realize the technology's potential for improving public health outcomes and enabling more efficient responses to foodborne disease threats.}, }
@article {pmid39595309, year = {2024}, author = {Figura, A and Gryzinska, M and Jakubczak, A}, title = {Comparison of Universal mtDNA Primers in Species Identification of Animals in a Sample with Severely Degraded DNA.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {22}, pages = {}, doi = {10.3390/ani14223256}, pmid = {39595309}, issn = {2076-2615}, abstract = {Analysis of mitochondrial DNA, specifically the cytochrome b gene (cyt b), has become an essential tool for species identification. In the case of degraded samples, in which DNA is fractionated, universal primers, which are highly effective at amplifying the target region, are necessary. The material analysed in this study was a keychain made of bone, which was secured at a border crossing due to the suspicion that it was made of ivory. Due to processing of the bone and the likelihood of DNA degradation, five pairs of universal primers with different product lengths (from 148 to 990 base pairs) were used for species identification. Fragments of mtDNA from the cyt b and the 12S rRNA and 16S rRNA subunits were analysed. The analysis showed that only one pair of primers (L15601/H15748) enabled identification of the species, which is very common in samples with highly degraded DNA. The material was bone tissue belonging to the species Bos taurus (cattle). Species identification by molecular methods is extremely important in analysis of material when the species cannot be identified on the basis of morphological characteristics.}, }
@article {pmid39591964, year = {2024}, author = {Lu, X and Zhang, Q and Wang, Z and Cheng, X and Yan, H and Cai, S and Zhang, H and Liu, Q}, title = {Development of an inducible DNA barcoding system to understand lineage changes in Arabidopsis regeneration.}, journal = {Developmental cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.devcel.2024.10.023}, pmid = {39591964}, issn = {1878-1551}, abstract = {Plants demonstrate a high degree of developmental plasticity, capable of regenerating entire individuals from detached somatic tissues-a regenerative phenomenon rarely observed in metazoa. Consequently, elucidating the lineage relationship between somatic founder cells and descendant cells in regenerated plant organs has long been a pursuit. In this study, we developed and optimized both DNA barcode- and multi-fluorescence-based cell-lineage tracing toolsets, employing an inducible method to mark individual cells in Arabidopsis donor somatic tissues at the onset of regeneration. Utilizing these complementary methods, we scrutinized cell identities at the single-cell level and presented compelling evidence that all cells in the regenerated Arabidopsis plants, irrespective of their organ types, originated from a single progenitor cell in the donor somatic tissue. Our discovery suggests a single-cell passage directing the transition from multicellular donor tissue to regenerated plants, thereby creating opportunities for cell-cell competition during plant regeneration-a strategy for maximizing survival.}, }
@article {pmid39590688, year = {2024}, author = {Chen, TQ and Yang, C and Xu, XL and Yang, L and He, HQ and Weng, MT and Ying, ZH and Shi, XK and Ding, MG}, title = {Comparative Mitogenomics Provides Valuable Insights for the Phylogeny and New DNA Barcodes of Ganoderma.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, doi = {10.3390/jof10110769}, pmid = {39590688}, issn = {2309-608X}, support = {2023R1106//Science &amp; Technology Department of Fujian Province, the Public Welfare Competitive Research Project/ ; }, abstract = {Ganoderma is the most important genus in the family Ganodermataceae; many species have attracted much attention and widely cultivated because of their medicinal values, but so far, not a sequenced mitogenome derived from dikaryon strains has been explicitly recorded. Herein, four novel mitogenomes of commonly cultivated Ganoderma (G. leucocontextum H4, G. lucidum G6, G. sinense MZ96 and G. tsugae SS) were de novo assembled and given detail functional annotations. Collinearity analysis revealed that the four mitogenomes shared 82.93-92.02% similarity with their corresponding reference mitogenomes at the nucleotide level. A total of 15 core protein-coding genes (PCGs), along with rrnL and rrnS (mtLSU and mtSSU) were chosen as potential candidates for constructing their individual phylogenetic trees. These trees were compared with those derived from the concatenated sequences of 15 core PCGs. And finally, we found that the atp9 and nad4L were the most reliable markers for the phylogenetic analysis of Ganoderma and chosen as standard sequences to generate new DNA barcodes. This finding was further verified by comparing it against almost all available Ganoderma mitogenomes in the NCBI, with Trametes versicolor (Polyporaceae) and Rigidoporus microporus (Meripilaceae) as two outgroups. A total of 52 mitogenomes from three families were highly conserved, with identical gene lengths for atp9 (222 bp) and nad4L (267 bp). These genes were capable of distinguish distinctly different various species, which are grouped into separate clades within the phylogenetic trees. The closest related clades (I and II), including at least 30 samples of the three classical taxonomic species (G. lingzhi, G. sichuanense and G. lucidum), differed in only one SNP. The single base mutation rate increased with the evolutionary divergence of the phylogenetic clades, from two to three SNPs in earlier clades (e.g., clade IV containing G. leucocontextum) to five to six SNPs in later clades (e.g., clade X containing G. sinense). Despite these variations between species, the atp9 and nad4L genes of Ganoderma mitogenomes consistently encoded the same ATP synthase F0 subunit c (73 aa) and NADH dehydrogenase subunit 4L (88 aa). These two genes have been identified as reliable markers of new DNA barcodes, offering valuable insights and contributing significantly to understanding the evolutionary relationships and phylogeny of the Ganoderma genus and even the Ganodermataceae family.}, }
@article {pmid39590509, year = {2024}, author = {Xie, TT and Wang, MQ and Li, Y and Su, CY and Zhang, D and Zhou, QS and Niu, ZQ and Yuan, F and Liu, XW and Ma, KP and Zhu, CD and Hao, JS and Chesters, D}, title = {Blue Vane and Pan Traps Are More Effective for Profiling Multiple Facets of Bee Diversity in Subtropical Forests.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/insects15110909}, pmid = {39590509}, issn = {2075-4450}, abstract = {The choice of trap in entomological surveys affects the composition of captured insects, though previous comparative studies have been limited in the types of composition measured, and the effects of environmental context. We assessed the sampling bias of several traps commonly used in pollinator monitoring: blue, yellow, and white pan traps, and blue vane traps, towards different taxonomic and functional groups and their efficiency in measuring taxonomic, phylogenetic, and functional diversity. Analyses were performed in monoculture and mixed forests to understand the environmental context of trap efficiency. We found that blue pan traps generally outperformed other types in bee capture and exhibited a preference for Halictidae bees. Blue pan traps yielded the highest species richness and phylogenetic diversity, while blue vane traps captured the highest functional richness. Bias differences were frequently detected in mixed forests compared with monoculture forests. We also found the combination of blue vane and pan traps consistently correlated highest with a complete survey among two-method combinations. Based on our findings, we recommend a combination of blue vane and pan traps to obtain a more comprehensive bee collection in an efficient manner. Additionally, it is crucial to consider habitat type when designing bee trapping protocols to ensure an accurate representation of bee communities.}, }
@article {pmid39590449, year = {2024}, author = {Schmid-Egger, C and Schmidt, S and Rosa, P and Niehuis, O}, title = {DNA Barcoding of German Cuckoo Wasps (Hymenoptera: Chrysididae) Suggests Cryptic Species in Several Widely Distributed Species.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/insects15110850}, pmid = {39590449}, issn = {2075-4450}, support = {NI 1387/1-1, NI 1387/2-1, NI 1387/5-1, NI 1387/6-1/2//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Germany is home to a rich cuckoo wasp fauna (Hymenoptera: Chrysididae) with about 108 species. However, several nomenclatural changes, the lack of identification keys, and the discovery of cryptic species difficult to identify based on external morphology have made the identification of several species a challenge. COI barcoding has been instrumental in the identification of some cuckoo wasp species and could help alleviate some of the above problems, but a reliable large reference database containing the cuckoo wasp barcodes is lacking. We present the COI barcodes of more than 800 specimens of 101 cuckoo wasp species native to Germany to lay the foundation for the barcode-based identification of German species. An analysis of the COI barcode sequences suggested groups that are largely consistent with the current taxonomy of the group. We found a few cases of over- or undersplitting of taxa. In some common species, the high degree of barcode divergence suggests the presence of cryptic species that need to be further assessed by integrative approaches. Our library of cuckoo wasp reference barcodes will enhance researchers' ability to reliably identify species within this fascinating group of insects, in particular for identifying life stages that offer few or no morphological features for species-level identification.}, }
@article {pmid39590434, year = {2024}, author = {Zhu, J and van Achterberg, C and Chen, X and Tang, P}, title = {New Records and New Species of Dacnusini (Hymenoptera: Braconidae, Alysiinae) Based on Morphological and Molecular Evidence.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/insects15110835}, pmid = {39590434}, issn = {2075-4450}, support = {2023FY100200//Science &amp; Technology Fundamental Resources Investigation Program of China/ ; 31920103005//Key International Joint Research Program of National Natural Science Foundation of China/ ; 32070467//General Program of National Natural Science Foundation of China/ ; (32200355)//National Natural Science Foundation of China/ ; 226-2024-00095//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Dacnusini is a species-rich tribe in the subfamily Alysiinae, with most species exclusively serving as parasitoids of leaf-mining Diptera (Agromyzidae). The number of genera discovered in China remains limited, which is apparently insufficient considering the global diversity of species and genera within this tribe, particularly given the vast and ecologically diverse landscapes of China. In the present study, three new record genera, Victorovita Tobias, Coloneura Foerster, and Laotris Nixon, were documented for the first time in China. In addition, the species delimitation approach and haplotype network analyses based on the COI sequences, combined with morphological evidence, were employed to delimit species. The findings indicated three new species: Laotris glabella sp. nov., Laotris aethidentata sp. nov., and Victorovita aequalis sp. nov. Additionally, K2P divergences showed no overlap between intra- and interspecific genetic distances in the Laotris and Victorovita species. Detailed descriptions for new species and keys to the species of Laotris and Victorovita are provided in this paper, along with the documentation of two new species records for China: Victorovita caudata (Szépligeti, 1901) and Coloneura stylata Foerster, 1863.}, }
@article {pmid39590432, year = {2024}, author = {Ramos-Lagunes, VH and Laredo-Tiscareño, SV and González-Peña, R and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and de Jesús de Luna-Santillana, E and Hernández-Triana, LM and Velasco-Chino, LE and Laredo-Tiscareño, AG and Garza-Hernández, JA}, title = {Aedes (Georgecraigius) epactius from Zacatecas and Chihuahua Mexico: New Geographical Distribution and Altitude Records.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/insects15110833}, pmid = {39590432}, issn = {2075-4450}, support = {740742, 769056, and 842817//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; UACJ-PTC-399 and UACJ-PTC-267//Programa para el Desarrollo Profesional Docente, para el Tipo Superior/ ; No. 419-24-23//CONAHCYT CIENCIA DE FRONTERA 2023/ ; 397-24-01//Proyectos de Investigaci&#xf3;n con Impacto Social (PIISO) UACJ/ ; SV3045//Department for Environment Food and Rural Affairs (DEFRA), Scottish Government and Welsh Government/ ; }, abstract = {Adults and immatures of Aedes epactius were collected in July and December 2022 at sites of high elevation in the states of Chihuahua (2300 masl) and Zacatecas (2182 and 2595 masl), Mexico, respectively. Mosquitoes were identified morphologically and sequenced for a DNA barcode of the cytochrome c oxidase I (COX1). This is the first distributional record of Ae. epactius in Zacatecas and provides evidence of the highest altitude in the Americas, including Mexico. The geographical distribution of Ae. epactius in Mexico was reviewed, and the COX1 analysis, using phylogenetic Bayesian analysis to confirm species identification, was performed.}, }
@article {pmid39589980, year = {2024}, author = {Zhong, L and Chen, H and Cao, S and Hu, S}, title = {Single Nucleotide Recognition and Mutation Site Sequencing Based on a Barcode Assay and Rolling Circle Amplification.}, journal = {Biosensors}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/bios14110521}, pmid = {39589980}, issn = {2079-6374}, support = {2021Y9014//innovation of science and Technology, Fujian province/ ; XRCZX2019024//Fujian Medical University's Research Foundation for Talented Scholars/ ; }, mesh = {*Nucleic Acid Amplification Techniques ; *Polymorphism, Single Nucleotide ; *Helicobacter pylori/genetics ; Mutation ; DNA Barcoding, Taxonomic ; Quantum Dots ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Biosensing Techniques ; }, abstract = {Single nucleotide polymorphisms (SNPs) present significant challenges in microbial detection and treatment, further raising the demands on sequencing technologies. In response to these challenges, we have developed a novel barcode-based approach for highly sensitive single nucleotide recognition. This method leverages a dual-head folded complementary template probe in conjunction with DNA ligase to specifically identify the target base. Upon recognition, the system triggers rolling circle amplification (RCA) followed by the self-assembly of CdSe quantum dots onto polystyrene microspheres, enabling a single-particle fluorescence readout. This approach allows for precise base identification at individual loci, which are then analyzed using a bio-barcode array to screen for base changes across multiple sites. This method was applied to sequence a drug-resistant mutation site in Helicobacter pylori (H. pylori), demonstrating excellent accuracy and stability. Offering high precision, high sensitivity, and single nucleotide resolution, this approach shows great promise as a next-generation sequencing method.}, }
@article {pmid39589713, year = {2024}, author = {Guo, P and Deng, Y}, title = {Spatial Omics: Navigating Neuroscience Research into the New Era.}, journal = {Advances in neurobiology}, volume = {41}, number = {}, pages = {133-149}, pmid = {39589713}, issn = {2190-5215}, mesh = {Humans ; *Neurosciences ; *Brain/metabolism ; Proteomics ; Transcriptome ; High-Throughput Nucleotide Sequencing ; Animals ; Genomics ; In Situ Hybridization, Fluorescence ; Neurons/metabolism ; Epigenomics ; }, abstract = {The human brain's complexity is underpinned by billions of neurons and trillions of synapses, necessitating coordinated activities across diverse cell types. Conventional techniques like in situ hybridization and immunohistochemistry, while valuable, face limitations in resolution and comprehensiveness when analyzing neuron types. Advances in spatial omics technologies, especially those integrating transcriptomics and proteomics, have revolutionized our understanding of brain tissue organization. These technologies, such as FISH-based, in situ sequencing-based (ISS), and next-generation sequencing (NGS)-based methods, provide detailed spatial context, overcoming previous limitations. FISH techniques, including smFISH and its variants like seqFISH and MERFISH, offer high-resolution spatial gene expression data. ISS approaches leverage padlock probes and rolling circle amplification to yield spatial transcriptome information. NGS-based methods, such as spatial transcriptomics and spatial-epigenomics, integrate spatial barcodes with single-cell sequencing, enabling comprehensive profiling of gene expression and epigenetic states in tissues. These innovations have propelled insights into neural development and disease, identifying cellular heterogeneity and molecular alterations in conditions like Alzheimer's and major depression. Despite challenges in cost, speed, and data analysis, spatial omics technologies continue to evolve, promising deeper insights into the molecular mechanisms of the brain and neurodegenerative diseases.}, }
@article {pmid39589617, year = {2024}, author = {Argôlo, LA and Ramos, RTC and Bitencourt, JA and Galdino, JH and Sampaio, I and Affonso, PRAM}, title = {Hidden diversity revealed by DNA barcoding of paralichthyidae fish along the caribbean and brazilian coast.}, journal = {Genetica}, volume = {153}, number = {1}, pages = {4}, pmid = {39589617}, issn = {1573-6857}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; code 406489/2023-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Brazil ; *Electron Transport Complex IV/genetics ; *Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Caribbean Region ; Genetic Variation ; Fishes/genetics/classification ; }, abstract = {DNA barcoding based on COI sequences has been highly informative for the taxonomic assessment of many fish species due to its high rate of species identification. Accordingly, numerous studies have employed this method to encompass species checklists of different areas, assessment of cryptic diversity, biodiversity monitoring, and other applications. Furthermore, most of the success of COI DNA barcoding relies on a comprehensive database (BOLD Systems) that holds sequences and detailed records of millions of species and applies a system (BIN) that clusters short DNA barcodes to generate OTUs. Besides COI, the 16S rDNA has proven to be suitable for the molecular identification of several taxa, and the combination of both markers could be advantageous in investigating species composition in the Neotropics. The family Paralichthyidae comprises over 60 flatfish species. Most of them inhabit tropical areas and remain understudied. Here, we evaluated the diversity of Paralichthyidae species along the Brazilian coast through COI and 16S DNA barcodes. Combining our dataset with BOLD (COI) and GenBank (16S) public records, we conducted tree-based and genetic distance analyses along with BIN-based and species delimitation methods. Our results were consistent for both markers, and we identified eight species of paralichthyids among our samples with high confidence. Interestingly, our analyses indicate several cases where public records assigned to the same species might be sequences from multiple species. Therefore, we provide new records and occurrences and explore important issues regarding misidentification and putative cryptic diversity for several species.}, }
@article {pmid39588656, year = {2024}, author = {Jiang, Y and Wang, Y and Luo, W and Luan, X and Zhang, Z and Pan, Y and He, B and Gao, Y and Song, Y}, title = {Detecting telomerase activity at the single-cell level using a CRISPR-Cas12a-based chip.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4lc00619d}, pmid = {39588656}, issn = {1473-0189}, abstract = {The intimate association between telomerase activity and cancer has driven the exploration of diverse methodologies for its precise detection. However, detecting telomerase activity at the single-cell level remains a significant challenge. Herein, we present a MOF-DNA barcode-amplified CRISPR-Cas12a strategy integrated with a single-cell microfluidic chip for ultrasensitive detection of telomerase activity. DNA-functionalized UiO-66 nanoparticles act as signal transducers, effectively converting telomerase activity into DNA activation strands, which subsequently trigger the trans-cleavage activity of CRISPR-Cas12a. This amplification-based assay could be integrated with a microfluidic chip to enable highly sensitive detection of telomerase activity at the single-cell level, offering promising advancements in early cancer diagnosis.}, }
@article {pmid39587724, year = {2024}, author = {Tebaldi, ND and Mota, LCBM and Corrêa, JL and Santos, ACC and Santos, ARD and Ueira-Vieira, C}, title = {First report of Kosakonia cowanii causing bacterial blight on Coffea arabica.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-07-24-1572-PDN}, pmid = {39587724}, issn = {0191-2917}, abstract = {From 2012 to 2019, 6-month to 2-year-old coffee (Coffea arabica) plants showing leaf blight, stem blackening, brownish, necrotic, irregular leaf spots and shoot tip dieback (Figure 1A, B, C, and D) symptoms were observed at the municipalities of Araguari, Indianópolis, Monte Carmelo, Nova Ponte and Romaria, Minas Gerais State, Brazil. Bacterial exudates from infected tissues, mainly from the shoot tip, were observed under microscopy; no bacterial exudates were found in leaf tissues. Bacterial colonies were isolated from symptomatic disinfested tissues (leaves and shoot tip) using medium 523 (Figure 1E). The isolated bacteria were facultative anaerobe, Gram-negative, cream-colored on YDC medium, growth at 37 [o]C, arginine and oxidase negative, catalase and asparagine positive (Schaad et al. 2002), and positive hypersensitivity reaction in tobacco leaves. Pathogenicity was confirmed by spraying coffee plants (at the three-leaf stage) until runoff, with a 1 × 108 CFU/mL bacterial suspension inoculate. The plants were kept in the moist chamber for 24 hours, before and after inoculation under greenhouse conditions. No symptoms were observed under the mock-inoculated plants. Disease symptoms on inoculated plants were observed 13 days after inoculation. The bacteria were then reisolated to satisfy Koch's postulates, the colony phenotypes were identical to the original ones. Bacterial genomic DNA of four isolates (UFU D1, UFU G119, UFU H1, and UFU I87) was extracted, and the 16S rRNA gene region was amplified using the 8F and 1492R universal primers, and then compared with sequences deposited in the GenBank. The results aligned closely with those of Kosakonia cowanii (GenBank NR_025566.1), with 99.4% similarity and 96% query coverage for the sequence. In addition to sequencing the 16S rRNA gene, which is considered the barcode for bacteria, other single-copy genes are necessary for species confirmation. In this study, to confirm the species and generate more data on these new isolates, 150 bp paired-end libraries were constructed and sequenced using DNBSEQ. A minimum of 1 gigabase was obtained for each isolate, and the genomes were assembled using the SPAdes genome assembler v3.15.4. Subsequently, the in-house developed algorithm SpM (Species Matching) was used to identify the species. The phylogenetic tree for the 16S gene was constructed using the maximum likelihood algorithm available in PhyML (v3.1/3.0 aLRT). The Phylogeny.fr platform was used to perform the phylogenetic reconstruction. This analysis revealed that our K. cowanii isolates (H1, D1, G119, and I87) from the coffee tree clustered with other K. cowanii strains isolated from different locations (Figure 2A). The Average Nucleotide Identity (ANI) analysis was performed using the fastANI program on all complete genomes of the Kosakonia genus obtained from the NCBI database. The results indicated that our K. cowanii isolates from the coffee tree clustered closely with other strains of the K. cowanii species (Figure 2B). Genomic analyses confirmed that all isolates belong to the species K. cowanii, corroborating the 16S rRNA gene analyses. The genomes have been deposited in NCBI with the accession numbers CP160410 (K. cowanii strain UFU H1, size 4,749,805 bp and coverage 36.21x), CP160412 (strain UFU G119, size 4,509,735 bp and coverage 31.26x), CP162577 (strain UFU D1, size 4,867,107 bp and coverage 19.0x), and CP162576 (strain UFU I87, size 4,552,151 bp and coverage 18.23x). These results are of great importance for better understanding the role of K. cowanii as a disease-causing pathogen of coffee plants. K. cowanii has already been described infecting Eucalyptus with symptoms of bacterial blight in Uruguay (Brady et al. 2009), causing disease in soybeans (Krawczyk and Borodynko-Filas 2020), also associated as endophytic in plants (Thomas et al. 2007), and as human pathogens (Yang et al. 2018). Thus, to our knowledge, this is the first report of bacterial blight caused by K. cowanii on coffee plants. The isolates are deposited in the phytopathogenic bacteria collection at Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Brazil, under the codes UFU D1, UFU G119, UFU H1 and UFU I87.}, }
@article {pmid39587617, year = {2024}, author = {Landman, F and Jamin, C and de Haan, A and Witteveen, S and Bos, J and van der Heide, HGJ and Schouls, LM and Hendrickx, APA and , }, title = {Genomic surveillance of multidrug-resistant organisms based on long-read sequencing.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {137}, pmid = {39587617}, issn = {1756-994X}, mesh = {*Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Genome, Bacterial ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/drug effects/classification ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Multidrug-resistant organisms (MDRO) pose a significant threat to public health worldwide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for surveillance and infection prevention of MDRO. Molecular characterization based on long-read sequencing has emerged as a promising alternative to short-read sequencing. The aim of this study was to characterize MDRO for surveillance and transmission studies based on long-read sequencing only.<br><br>METHODS: Genomic DNA of 356 MDRO was automatically extracted using the Maxwell-RSC48. The MDRO included 106 Klebsiella pneumoniae isolates, 85 Escherichia coli, 15 Enterobacter cloacae complex, 10 Citrobacter freundii, 34 Pseudomonas aeruginosa, 16 Acinetobacter baumannii, and 69 methicillin-resistant Staphylococcus aureus (MRSA), of which 24 were from an outbreak. MDRO were sequenced using both short-read (Illumina NextSeq 550) and long-read (Nanopore Rapid Barcoding Kit-24-V14, R10.4.1) whole-genome sequencing (WGS). Basecalling was performed for two distinct models using Dorado-0.3.2 duplex mode. Long-read data was assembled using Flye, Canu, Miniasm, Unicycler, Necat, Raven, and Redbean assemblers. Long-read WGS data with&#x2009;>&#x2009;40&#x2009;&#xd7;&#x2009;coverage was used for multi-locus sequence typing (MLST), whole-genome MLST (wgMLST), whole-genome single-nucleotide polymorphisms (wgSNP), in silico multiple locus variable-number of tandem repeat analysis (iMLVA) for MRSA, and identification of resistance genes (ABRicate).<br><br>RESULTS: Comparison of wgMLST profiles based on long-read and short-read WGS data revealed&#x2009;>&#x2009;95% of wgMLST profiles within the species-specific cluster cut-off, except for P. aeruginosa. The wgMLST profiles obtained by long-read and short-read WGS differed only one to nine wgMLST alleles or SNPs for K. pneumoniae, E. coli, E. cloacae complex, C. freundii, A. baumannii complex, and MRSA. For P. aeruginosa, differences were up to 27 wgMLST alleles between long-read and short-read wgMLST and 0-10 SNPs. MLST sequence types and iMLVA types were concordant between long-read and short-read WGS data and conventional MLVA typing. Antimicrobial resistance genes were detected in long-read sequencing data with high sensitivity/specificity (92-100%/99-100%). Long-read sequencing enabled analysis of an MRSA outbreak.<br><br>CONCLUSIONS: We demonstrate that molecular characterization of automatically extracted DNA followed by long-read sequencing is as accurate compared to short-read sequencing and suitable for typing and outbreak analysis as part of genomic surveillance of MDRO. However, the analysis of P. aeruginosa requires further improvement which may be obtained by other basecalling algorithms. The low implementation costs and rapid library preparation for long-read sequencing of MDRO extends its applicability to resource-constrained settings and low-income countries worldwide.}, }
@article {pmid39587359, year = {2024}, author = {Ramani, V}, title = {Split-pool barcoding serves up an epigenomic smorgasbord.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {39587359}, issn = {1546-1718}, support = {DP2-HG012442//U.S. Department of Health &amp; Human Services | NIH | NIH Office of the Director (OD)/ ; }, }
@article {pmid39585955, year = {2024}, author = {Osborne, M and Chen, H and Kadhiresan, P and Mahbub, N and Malekjahani, A and Kozlowski, HN and Udugama, B and Nguyen, LNM and Perusini, S and Mubareka, S and Chan, WCW}, title = {QBox: An Automated Portable System for Multiplex Quantum Dot Barcode Diagnostics.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.4c12306}, pmid = {39585955}, issn = {1936-086X}, abstract = {The COVID-19 pandemic accelerated the development of automated systems for detecting molecular targets for the point-of-care. However, these systems have limited multiplexing capabilities because of the need to alter their hardware to accommodate additional targets and probes. Quantum dot barcodes address this multiplexing obstacle, but their assays have multiple steps that rely on extensive training and laboratory equipment. Here, we built a portable cartridge-and-instrument system that automates the extraction, reverse transcription, amplification, and detection steps of a quantum dot barcode assay. This entire workflow can be completed in 40 minutes. We clinically validated the system with SARS-CoV-2 patient samples (n = 50, 92% sensitivity, 100% specificity). We then demonstrated multiplexing with 4-barcode respiratory and 5-barcode bloodborne pathogen panels. Our portable system opens quantum dot barcodes for broad use in rapid multiplexed detection of infectious pathogens with the potential for detecting cancer and other genetic diseases.}, }
@article {pmid39585918, year = {2024}, author = {Ambu, J and Dufresnes, C}, title = {Genomic and bioacoustic variation in a midwife toad hybrid zone: A role for reinforcement?.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0314477}, doi = {10.1371/journal.pone.0314477}, pmid = {39585918}, issn = {1932-6203}, mesh = {Animals ; *Anura/genetics/physiology ; *Hybridization, Genetic ; Reproductive Isolation ; Vocalization, Animal/physiology ; Polymorphism, Single Nucleotide ; Genomics/methods ; Gene Flow ; France ; }, abstract = {Hybrid zones, i.e., geographic areas where diverging lineages meet, hybridize and eventually mix their genomes, offer opportunities to understand the mechanisms behind reproductive isolation and speciation. Hybrid zones are particularly well suited to study reinforcement, i.e., the process by which selection against hybridization increases reproductive barriers, which, in anuran amphibians, is typically expressed by increased divergence in advertisement calls-the main cue to assortative mating-in parapatric ranges. Using mitochondrial barcoding (16S sequences), population genomics (thousands of SNPs) and bioacoustic analyses (four call parameters), we examine the hybrid zone between two incipient species of midwife toads (Alytes obstetricans and A. almogavarii) in southern France, with the purposes of locating their transition, measuring genetic introgression, and documenting potential signatures of reinforcement. We map range boundaries in the Eastern Pyrenees and the southwestern foothills of the Massif Central, namely along the Ariège valley and the Montagne Noire area. Similarly to another transition between these species in Spain, we found the hybrid zone to be narrow, involving geographically restricted gene flow (~20 km wide allele frequency clines) and barrier loci (i.e., loci resisting introgression), both suggestive of partial post-zygotic isolation (hybrid incompatibilities). The calls of the species overlap less inside than outside the hybrid zone, due to a reduction of their standing variation rather than a shift towards distinctive variants. While neutral causes cannot be excluded, this pattern follows the general expectations of reinforcement, yet without reproductive character displacement. Our study highlights the potential of amphibian hybrid zones to assess the genetic and behavioral drivers of reproductive isolation in statu nascendi and under various evolutionary contexts.}, }
@article {pmid39582226, year = {2024}, author = {Wu, X and Zhao, Z and Yu, W and Liu, S and Zhou, M and Jiang, N and Du, X and Yang, X and Chen, J and Guo, H and Yang, R}, title = {Single-Cell Multiomics Identifies Glycan Epitope LacNAc as a Potential Cell-Surface Effector Marker of Peripheral T Cells in Bladder Cancer Patients.}, journal = {ACS chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acschembio.4c00635}, pmid = {39582226}, issn = {1554-8937}, abstract = {Cancer is a systemic disease continuously monitored and responded to by the human global immune system. Peripheral blood immune cells, integral to this surveillance, exhibit variable phenotypes during tumor progression. Glycosylation, as one of the most prevalent and significant post-translational modifications of proteins, plays a crucial role in immune system recognition and response. Glycan analysis has become a key method for biomarker discovery. LacNAc, a prominent glycosylation modification, regulates immune cell activity and function. Therefore, we applied our previously developed single-cell glycomic multiomics to analyze peripheral blood in cancer patients. This platform utilizes chemoenzymatic labeling with DNA barcodes for detecting and quantifying LacNAc levels at single-cell resolution without altering the transcriptional status of immune cells. For the first time, we systematically integrated single-cell transcriptome, T cell receptor (TCR) repertoire, and glycan epitope LacNAc analyses in tumor-patient-derived peripheral blood. Our integrated analysis reveals that lower-stage bladder cancer patients showed significantly higher levels of LacNAc in peripheral T cells, and peripheral T cells with high levels of cell-surface LacNAc exhibit higher cytotoxicity and TCR clonal expansion. In summary, we identified LacNAc as a potential cell-surface effector marker for peripheral T cells in bladder cancer patients, which enhances our understanding of peripheral immune cells and offers potential advancements in liquid biopsy.}, }
@article {pmid39582135, year = {2024}, author = {Seo, Y and Fowler, K and Flick, LM and Withers, TA and Savoldo, B and McKinnon, K and Iannone, MA}, title = {Barcoding of viable peripheral blood mononuclear cells with selenium and tellurium isotopes for mass cytometry experiments.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cyto.a.24907}, pmid = {39582135}, issn = {1552-4930}, support = {//University Cancer Research Fund (UCRF)/ ; //UNC Cancer Center Core Support Grant #P30CA016086/ ; }, abstract = {Barcoding viable cells combined with pooled sample staining is an effective technique that eliminates batch effects from serial cell staining and facilitates uninterrupted data acquisition. We describe three novel and isotopically pure selenium-containing compounds (SeMals) that are useful cellular labeling tools. The maleimide-functionalized selenophenes ([76]SeMal, [77]SeMal, and [78]SeMal) covalently react with cellular sulfhydryl groups and uniquely label cell samples. The SeMal reagents label viable and paraformaldehyde-fixed peripheral blood mononuclear cells (PBMC), are well resolved by the mass cytometer, and have little spill into adjacent channels. They appear non-toxic to viable cells at working concentrations. We used SeMal reagents in combination with four isotopically pure tellurium maleimide reagents ([124]TeMal, [126]TeMal, [128]TeMal, and [130]TeMal) to label 21 individual PBMC samples with unique combinations of selenium and tellurium isotopes (seven donors with three replicates using a 7 isotope pick 2 combinatorial schema). The individually barcoded samples were pooled, stained with an antibody cocktail as a pool, and acquired on the mass cytometer as a single suspension. The single-cell data were de-barcoded into separate sample-specific files after data acquisition, enabling an uninterrupted instrument run. Each donor sample retained its unique phenotypic profile with excellent replicate reproducibility. Unlike current live cell barcoding methods, this approach does not require antibodies to surface markers, allowing for the labeling of all cells regardless of surface antigen expression. Additionally, since selenium and tellurium isotopes are not currently utilized in CyTOF antibody panels, this method expands barcoding options and frees up commonly used isotopes for more detailed cell profiling.}, }
@article {pmid39581345, year = {2024}, author = {Parmar, DR and Johnston, NP and Wallman, JF and Szpila, K}, title = {Blowfly genomics: Current insights, knowledge gaps, and future perspectives.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {101305}, doi = {10.1016/j.cois.2024.101305}, pmid = {39581345}, issn = {2214-5753}, abstract = {Blowflies (Calliphoridae) form a diverse, species-rich group, yet publicly available genome assemblies are limited to only sixteen species despite recent genomic advances. This knowledge gap extends to mitogenomes and barcode databases, which mainly focus on medically and veterinary-important species. While blowfly phylogenetics has progressed, additional genome sequencing is crucial for various subfamilies given their diverse life histories. This review presents a quantitative overview of available genetic information for blowflies, highlighting substantial gaps in public databases. DNA barcodes, mitogenomes and genomes represent only 16.5% (342 species), ~3% (53 species) and <1% (16 species) of known family diversity, respectively. While 183 genomics-related calliphorid BioProjects are recorded by NCBI, many subfamilies and genera have limited or no genomic representation, impacting studies on identification, systematics, phylogenetics and evolution. We stress the urgent need for high-quality reference genomes and highlight target species representing all blowfly subfamilies to support new era of rapid, low-cost genomic research.}, }
@article {pmid39579652, year = {2024}, author = {Bates, SA and Budowle, B and Baker, L and Mittelman, K and Mittelman, D}, title = {A molecular framework for enhancing quality control and sample integrity in forensic genome sequencing.}, journal = {Forensic science international. Genetics}, volume = {75}, number = {}, pages = {103179}, doi = {10.1016/j.fsigen.2024.103179}, pmid = {39579652}, issn = {1878-0326}, abstract = {DNA typing is essential for identifying crime scene evidence and missing and unknown persons. Molecular tags historically have been incorporated into DNA typing reactions to improve result interpretation. Molecular tags like barcodes and unique identifiers are integral to MPS, aiding in sample tracking and error detection. However, these tags do not fully leverage sequence variation to enhance quality control. To address this need, molecular etches, which are synthetic oligonucleotides that serve as an internal molecular information management system, are introduced. Molecular etches encode detailed sample information improving sample workflow history, tracking, contamination detection, and authenticity verification. Validation studies demonstrate the robustness of molecular etches in genomic sequencing, making them a valuable quality tool for forensic DNA analysis.}, }
@article {pmid39578906, year = {2024}, author = {Schack, AK and Garrido-Navas, MC and Galevski, D and Madjarov, G and Krych, L}, title = {SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {131}, pmid = {39578906}, issn = {1479-7364}, mesh = {Humans ; *Aneuploidy ; Cost-Benefit Analysis ; Infant, Newborn ; Klinefelter Syndrome/genetics/diagnosis ; Genetic Testing/economics/methods ; Nanopore Sequencing/methods ; Neonatal Screening/economics/methods ; Nanopores ; Mass Screening/economics/methods ; Machine Learning ; }, abstract = {In developed countries, Newborn Screening (NBS) programs aim to detect treatable yet clinically silent disorders. The selection of disorders to be included in NBS considers severity, treatment availability, prevalence, and analysis cost. However, numerous genetic disorders remain excluded from routine testing due to high expenses and specialized equipment requirements. Here we present SCAN, a novel, non-invasive, and cost-effective decision-support tool utilizing nanopore sequencing for estimating proportions of chromosomes responsible for the most common aneuploidies. SCAN combines DNA enrichment (amplification), barcoding, nanopore sequencing, and machine learning predictive modeling. In a proof-of-concept study for Klinefelter Syndrome, SCAN achieved 100% sensitivity, specificity, and accuracy, becoming the world's first IVD-certified genetic test utilising nanopore sequencing. Further model training shows promise in expanding this assay to detect other chromosomal aneuploidies included in the protocol.}, }
@article {pmid39577343, year = {2024}, author = {Sanhueza, MI and Montes, CS and Sanhueza, I and Montoya-Gallardo, NI and Escalona, F and Luarte, D and Escribano, R and Torres, S and Godoy, SE and Amigo, JM and Castillo, RDP and Urbina, M}, title = {VIS-NIR hyperspectral imaging and multivariate analysis for direct characterization of pelagic fish species.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {328}, number = {}, pages = {125451}, doi = {10.1016/j.saa.2024.125451}, pmid = {39577343}, issn = {1873-3557}, abstract = {The identification of fish species and their physical and chemical characterization play a crucial role in the fishing industry, fish-food research and the management of marine resources. Traditional methods for species identification, such as expert observation, DNA barcoding and meta-barcoding, though effective, require labor-intensive laboratory work. Consequently, there is a pressing need for more objective and efficient methodologies for accurate fish species identification and characterization. This study proposes the use of multivariate analysis and visible-near infrared hyperspectral imaging (HSI) for a rapid characterization of fish, including the evaluation of specific morphological regions of interest (ROIs) in fish images or intrasample spectral variability, species differentiation, and freshness assessment. The study involves three pelagic species: sardine (Strangomera bentincki), silverside (Odontesthes regia) and anchovy (Engraulis ringens). Principal component analysis (PCA), support vector machine regression (SVM-R), partial least squares regression (PLS-R), and partial least squares discriminant analysis (PLS-DA) were applied as multivariate techniques for these purposes. Comparative studies of morphological ROIs revealed significant differences between the spectral characteristics of various fish zones. A decrease in reflectance intensity due to freshness loss was detected, and the prediction of this freshness, quantified as "time after capture," was achievable using SVM-R, with a 9% relative error of prediction. Overall, VIS-NIR HSI, supported by multivariate analysis, enables differentiation between the studied species, highlighting its potential as a robust fish species identification and characterization tool.}, }
@article {pmid39575683, year = {2024}, author = {Siniscalco, AM and Perera, RP and Greenslade, JE and Veeravenkatasubramanian, H and Masters, A and Doll, HM and Raj, B}, title = {Barcoding Notch signaling in the developing brain.}, journal = {Development (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1242/dev.203102}, pmid = {39575683}, issn = {1477-9129}, support = {R00HD098298/NH/NIH HHS/United States ; }, abstract = {Developmental signaling inputs are fundamental for shaping cell fates and behavior. However, traditional fluorescent-based signaling reporters have limitations in scalability and molecular resolution of cell types. We present SABER-seq, a CRISPR-Cas molecular recorder that stores transient developmental signaling cues as permanent mutations in cellular genomes for deconstruction at later stages via single-cell transcriptomics. We applied SABER-seq to record Notch signaling in developing zebrafish brains. SABER-seq has two components: a signaling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control while the recorder obtains mutations in ancestral cells where Notch is active. We combine SABER-seq with an expanded juvenile brain atlas to identify cell types derived from Notch-active founders. Our data reveals rare examples where differential Notch activities in ancestral progenitors are detected in terminally differentiated neuronal subtypes. SABER-seq is a novel platform for rapid, scalable and high-resolution mapping of signaling activity during development.}, }
@article {pmid39574722, year = {2024}, author = {Leitner, DR and Zingl, FG and Morano, AA and Zhang, H and Waldor, MK}, title = {The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.07.622497}, pmid = {39574722}, issn = {2692-8205}, abstract = {UNLABELLED: Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote the pathogen's fitness in stationary phase. We discovered that the Mla (m aintenance of lipid a symmetry) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48h stationary phase cultures. The mutant's defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48h. However, by 96h the culturability of the mutant and wild-type strains were equivalent. By monitoring the abundances of genomically barcoded libraries of wild-type and Δ mlaE strains, we observed that a few barcodes dominated the mutant culture at 96h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the mlaE mutant's defect. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for the maintenance of V. cholerae's culturability as it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.<br><br>IMPORTANCE: Bacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction are limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promoting Vibrio cholerae re-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis which emerge in the absence of the Mla pathway underlie its importance in maintaining V. cholerae culturability.}, }
@article {pmid39574588, year = {2024}, author = {Stevenson, ZC and Laufer, E and Estevez, AO and Robinson, K and Phillips, PC}, title = {Precise Lineage Tracking Using Molecular Barcodes Demonstrates Fitness Trade-offs for Ivermectin Resistance in Nematodes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.08.622685}, pmid = {39574588}, issn = {2692-8205}, abstract = {A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans (Stevenson et al., 2023) to implement the first randomly inserted genomic-barcode experimental evolution animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14 , avr-15 , and glc-1 , has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, yielding the largest animal experimental evolution study to date. The frequency of each barcode was determined at multiple time points via sequencing at deep coverage and then used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wildtype genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.}, }
@article {pmid39572229, year = {2024}, author = {Zhang, X and Huang, Y and Yang, Y and Wang, QE and Li, L}, title = {Advancements in prospective single-cell lineage barcoding and their applications in research.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.278944.124}, pmid = {39572229}, issn = {1549-5469}, abstract = {Single-cell lineage tracing (scLT) has emerged as a powerful tool, providing unparalleled resolution to investigate cellular dynamics, fate determination, and the underlying molecular mechanisms. This review thoroughly examines the latest prospective lineage DNA barcode tracing technologies. It further highlights pivotal studies that leverage single-cell lentiviral integration barcoding technology to unravel the dynamic nature of cell lineages in both developmental biology and cancer research. Additionally, the review navigates through critical considerations for successful experimental design in lineage tracing and addresses challenges inherent in this field, including technical limitations, complexities in data analysis, and the imperative for standardization. It also outlines current gaps in knowledge and suggests future research directions, contributing to the ongoing advancement of scLT studies.}, }
@article {pmid39570762, year = {2024}, author = {Wang, YC and Koster, J and Rooney-Latham, S and Blomquist, CL and Belisle, WH and Bourret, T}, title = {First report of Phytophthora taxon × salinaslettuce (Subclade 8b hybrid) causing stem and basal rot in lettuce in North America.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-10-24-2155-PDN}, pmid = {39570762}, issn = {0191-2917}, abstract = {More than 55% of U.S. lettuce (Lactuca sativa L.) production is in California, with Monterey Co. being the largest producer. Stunted mature romaine 'Valencia' and 'Stomper' and iceberg 'Frazier' lettuces with wilted outer leaves were collected from five commercial fields in Monterey Co. in spring 2023 and 2024. Brown internal stem and crown lesions progressed into sunken cavities and plant collapse. Incidence was approximately 5 to 75%. Margins of discolored stem and crown tissue were surface sterilized and plated on PARP-CMA (Jeffers and Martin 1986) and colonies resembling Phytophthora were recovered. Papillate sporangia ranged from 42 to 67.5 × 25 to 45 μm (avg. 56.1 × 37.0 μm, n = 30) and a length/breadth ratio of 1.4 to 1.7 (avg. 1.5). Globose, intercalary or terminal chlamydospores, 20 to 45 µm in diameter (avg. 32.6 µm, n = 30), and oospores, 17 to 29 μm in diameter (avg. 23.9 μm, n = 30) formed on 10 to 12-day-old cultures. Sequences from the two primary barcodes, ITS and COI (Robideau et al. 2011) were obtained from isolates collected from five different host cultivars and locations, finding identical multi-locus genotypes. ITS chromatograms contained six double-peaks, indicating interspecific hybridization. COI found the lettuce isolates forming a clade with the provisional P. taxon castitis, in Subclade 8b where hybrids are common (Bertier et al. 2013). If P. taxon castitis ITS is used as one parental ITS haplotype, the other haplotype is 1 bp different from P. lactucae and P. pseudolactucae ITS, suggesting one is the other parent of this hybrid taxon, provisionally introduced here as P. taxon ×salinaslettuce with accessions PQ427275-9 (ITS), and PQ424946-50 (COI). Pathogenicity assays were conducted on lettuce cultivars 'Bondi', 'El Guapo', and 'Valencia' (seven-week-old; 473-ml pots; 5 pots each for 'Bondi' and 'El Guapo', and 2 pots for 'Valencia'). Phytophthora inoculum of isolate 5411 was prepared as described in Hao et al. (2019) with oat seed replaced with long grain rice. Ten milliliter inoculum was added into two 6-cm-deep holes on opposite sides of the main stem. A non-colonized mixture was added to an equal number of control plants. All plants were maintained in a growth chamber with a 12-h photoperiod at 20°C/18°C. After one week, 'Bondi' and 'El Guapo' inoculated plants were stunted, and after two weeks, older leaves were chlorotic and wilted. After three weeks, 80% of the plants collapsed. Dark brown internal lesions were seen along the stem, crown, and tap roots of the collapsed plants after four weeks. 'Valencia' inoculated plants were stunted with no internal tissue discoloration observed over the same period. No symptoms were observed on any control plants; P. taxon ×salinaslettuce was reisolated and confirmed via ITS sequence from symptomatic stems, crowns, and tap roots of 'Bondi' and 'El Guapo', as well as non-symptomatic feeder roots of all three cultivars. No Phytophthora was recovered from the controls. This is the first report of P. taxon ×salinaslettuce detection on lettuce; P. taxon castitis has been isolated from strawberry and carrot in Sweden and Canada (Bertier et al. 2013), while P. lactucae and P. pseudolactucae have only been reported on lettuce in Greece and Japan (Elena et al. 2006; Rahman et al. 2015). Plans are underway to confirm the hybrid status and parentage of P. taxon ×salinaslettuce using genomics. This emerging pathogen may cause severe economic losses in CA lettuce production during the winter and spring growing seasons.}, }
@article {pmid39570496, year = {2024}, author = {Dilrukshi, HAC and Ruklani, NCS and Rubasinghe, SCK}, title = {Cryptogams as bio-indicators for ecosystem monitoring in Sri Lanka: a comprehensive review and recommendations.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1231}, pmid = {39570496}, issn = {1573-2959}, support = {22-101//National Research Council/ ; 22-101//National Research Council/ ; 22-101//National Research Council/ ; }, mesh = {Sri Lanka ; *Environmental Monitoring/methods ; *Ecosystem ; *Fungi ; *Biodiversity ; Lichens ; Climate Change ; Bryophyta ; }, abstract = {Cryptogams, encompassing algae, fungi, lichens, bryophytes, and pteridophytes play essential roles in soil formation, nutrient cycling, and ecological stability. Sri Lanka faces numerous environmental challenges, including habitat loss, climate change, and pollution and there is an urgent need for effective monitoring programs to assess and mitigate these changes. This comprehensive review compiles existing literature on the importance of cryptogams and their responses to various environmental stressors and highlights the specific characteristics that make cryptogams valuable bio-indicators, such as their sensitivity to pollution, climate change, and land-use changes in habitats such as forests, agricultural lands, and urban areas, as well as their ability to accumulate and retain pollutants over time. The diversity of cryptogams is integral to their effectiveness as bio-indicators, providing a comprehensive picture of ecosystem health. Furthermore, recommendations for the development of monitoring programs are provided for different areas in the country. These recommendations include establishing baseline data for cryptogam diversity and abundance and incorporating the integration of modern molecular techniques such as DNA barcoding which are widely used in biodiversity monitoring programs to track the responses of cryptogams to environmental changes. This review seeks to emphasize the importance of cryptogams in ecosystem health assessment raising awareness among policymakers, researchers, and conservationists in Sri Lanka. Through the implementation of effective monitoring programs, we can enhance our understanding of local ecosystem dynamics, improve conservation efforts, and contribute to the sustainable management of Sri Lanka's natural resources in the face of ongoing environmental changes.}, }
@article {pmid39570169, year = {2024}, author = {Oliveira, RCG and Silva, JLN and Silva, ACC and Sousa, PRS and Almeida, MS and Nascimento, MHS and Rodrigues-Filho, LFS and Barros, MC and Fraga, EC}, title = {DNA barcode reveals a new lineage of Astyanax bimaculatus (Linnaeus 1758) in the basins of the Western Northeast Atlantic Region, Brazil.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {96}, number = {4}, pages = {e20240161}, doi = {10.1590/0001-3765202420240161}, pmid = {39570169}, issn = {1678-2690}, mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; *Genetic Variation/genetics ; *Characidae/genetics/classification ; *Haplotypes/genetics ; Phylogeny ; Bayes Theorem ; DNA, Mitochondrial/genetics ; }, abstract = {Astyanax bimaculatus are small characids known as piabas or lambaris that form a complex encompassing 18 species, including cryptic species. The present study aimed to use DNA barcode to analyze populations of A. bimaculatus found in Maranhão hydrographic basins, comparing molecular diversity indices between populations from the other Brazilian basins. The results revealed the formation of 32 haplotypes (h = 0.9289; π = 0.0523). Seven haplogroups were formed with intrapopulation genetic distance ranging from 0 to 2%. The Maranhão populations of the Western Northeast Atlantic Region basins separated from the other analyzed basins, corroborating with the groups generated in BAPS and with the Bayesian Inference tree. The occurrence of exclusive OTUs for the Maranhão populations of the Western Northeast Atlantic Region was confirmed through delimitation models. Thus, the data from this study provide information on the genetic diversity of the A. bimaculatus complex with the detection of a different lineage for the State of Maranhão, contributing to the understanding of the group's systematics.}, }
@article {pmid39568955, year = {2024}, author = {Park, J and Yagi, S and Kobayashi, S and Hirowatari, T}, title = {A new species of the genus Dryadaula Meyrick (Lepidoptera, Dryadaulidae) from Japan, with a redescription of D.epischista (Meyrick, 1936).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {327-342}, pmid = {39568955}, issn = {1313-2989}, abstract = {Dryadaulaepischista (Meyrick, 1936), initially described from a single male specimen in Japan, is herein redescribed based on newly collected specimens from the type locality. Furthermore, we describe Dryadaulaorientalis Park &amp; Yagi, sp. nov., a new species from Japan that closely resembles D.epischista. The adults and genitalia of the two species are illustrated. The genitalia of D.epischista from a specimen collected at the type locality are shown for the first time. DNA barcodes of the two Dryadaula species and the genetic distances of barcode regions among them and other congeners are provided.}, }
@article {pmid39567484, year = {2024}, author = {Zhang, P and Tian, Z and Jin, K and Yang, K and Collyer, W and Rufo, J and Upreti, N and Dong, X and Lee, LP and Huang, TJ}, title = {Automating life science labs at the single-cell level through precise ultrasonic liquid sample ejection: PULSE.}, journal = {Microsystems &amp; nanoengineering}, volume = {10}, number = {1}, pages = {172}, pmid = {39567484}, issn = {2055-7434}, support = {UH3TR002978//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; UH3 TR002978/TR/NCATS NIH HHS/United States ; R01 GM141055/GM/NIGMS NIH HHS/United States ; R44 AG063643/AG/NIA NIH HHS/United States ; R01HD103727//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01GM141055//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R44 HL140800/HL/NHLBI NIH HHS/United States ; R44 OD024963/OD/NIH HHS/United States ; R01 HD103727/HD/NICHD NIH HHS/United States ; }, abstract = {Laboratory automation technologies have revolutionized biomedical research. However, the availability of automation solutions at the single-cell level remains scarce, primarily owing to the inherent challenges of handling cells with such small dimensions in a precise, biocompatible manner. Here, we present a single-cell-level laboratory automation solution that configures various experiments onto standardized, microscale test-tube matrices via our precise ultrasonic liquid sample ejection technology, known as PULSE. PULSE enables the transformation of titer plates into microdroplet arrays by printing nanodrops and single cells acoustically in a programmable, scalable, and biocompatible manner. Unlike pipetting robots, PULSE enables researchers to conduct biological experiments using single cells as anchoring points (e.g., 1 cell vs. 1000 cells per "tube"), achieving higher resolution and potentially more relevant data for modeling and downstream analyses. We demonstrate the ability of PULSE to perform biofabrication, precision gating, and deterministic array barcoding via preallocated droplet-addressable primers. Single cells can be gently printed at a speed range of 5-20 cell⋅s[-1] with an accuracy of 90.5-97.7%, which can then adhere to the substrate and grow for up to 72 h while preserving cell integrity. In the deterministic barcoding experiment, 95.6% barcoding accuracy and 2.7% barcode hopping were observed by comparing the phenotypic data with known genotypic data from two types of single cells. Our PULSE platform allows for precise and dynamic analyses by automating experiments at the single-cell level, offering researchers a powerful tool in biomedical research.}, }
@article {pmid39565827, year = {2024}, author = {Nazari, V and Yen, SH and Hsu, YF and Shapoval, G and Shapoval, N and Todisco, V}, title = {Wiped out by an earthquake? The 'extinct' Taiwanese swallowtail butterfly (Lepidoptera, Papilionidae) was morphologically and genetically distinct.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0310318}, pmid = {39565827}, issn = {1932-6203}, mesh = {Animals ; *Butterflies/genetics ; Taiwan ; *Earthquakes ; DNA Barcoding, Taxonomic ; Haplotypes ; Phylogeny ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Female ; Male ; }, abstract = {For the first time, we obtained for the first time a COI DNA barcode from museum specimens of the Old World swallowtail butterfly endemic to Taiwan, Papilio machaon ssp. sylvina, that has disappeared since the devastating Jiji earthquake in 1999 that shook Central Taiwan. We demonstrate that this population was not only phenotypically distinct, but also had a unique mitochondrial haplotype among all other Holarctic populations of P. machaon. The life history of P. m. sylvina from rearing experiments carried out in the 1990s is illustrated and discussed.}, }
@article {pmid39563389, year = {2024}, author = {Jumpato, W and Wannasingha, W and Jaroenchaiwattanachote, C and Mintara, R and Wongpakam, K and Adler, PH and Pramual, P}, title = {Diversity and prevalence of Leucocytozoon in black flies (Diptera: Simuliidae) of Thailand.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {475}, pmid = {39563389}, issn = {1756-3305}, support = {6720001/2567//Mahasarakham University/ ; }, mesh = {Animals ; Thailand/epidemiology ; *Simuliidae/parasitology/classification ; *Haemosporida/isolation &amp; purification/classification/genetics ; Prevalence ; Phylogeny ; Cytochromes b/genetics ; Insect Vectors/parasitology/classification ; Female ; Genetic Variation ; Birds/parasitology ; Bird Diseases/parasitology/epidemiology ; Protozoan Infections, Animal/epidemiology/parasitology ; DNA Barcoding, Taxonomic ; }, abstract = {BACKGROUND: Leucocytozoonosis, a parasitic disease of birds, is caused by haemosporidian protozoan parasites of the genus Leucocytozoon, which infect diverse avian species, including poultry. These parasites are transmitted by several black fly species, but knowledge of the factors determining the diversity and prevalence in these vectors, which is crucial for fully understanding disease epidemiology, is largely unexplored. In this study, we investigated factors associated with the prevalence and diversity of Leucocytozoon species in black flies from Thailand.<br><br>METHODS: Adults of two black fly taxa (Simulium asakoae Takaoka and Davies complex and S. khelangense Takaoka, Srisuka and Saeung) were collected using sweep nets at nine locations in northern and northeastern regions of Thailand. Specimens were identified morphologically and the results corroborated by DNA barcoding. Molecular methods using specific primers for amplification of the mitochondrial cytochrome b (cyt b) gene of Leucocytozoon were used to detect the parasite in black flies. Species and lineages of Leucocytozoon were determined using the MalAvi database of malaria parasites and related haemosporidians in avian hosts. Regression analysis was used to examine relationships between Leucocytozoon diversity and prevalence, black fly abundance and habitat characteristics.<br><br>RESULTS: A total of 11,718 adult black flies were collected, of which 4367 were members of the S. asakoae complex and 7351 were S. khelangense. For molecular detection of Leucocytozoon, we randomly selected 300 individual female black flies of the S. asakoae complex and 850 females of S. khelangense pooled into groups of five individuals (= 170 pools). A total of 34 of the 300 specimens of the S. asakoae complex and 118 of the 170 pools of S. khelangense were positive for Leucocytozoon. Fifty-four lineages (haplotypes) were identified, all of which belonged to those reported in domestic chickens, Gallus gallus, with one exception that was identified in S. khelangense and found to be closely related to the Leucocytozoon lineages reported in owls; this is the first record of the latter lineage in Asian black flies. Among these haplotypes, nine and 45 were exclusively found in the S. asakoae complex and S. khelangense, respectively. No lineage was shared between these black fly taxa. Analysis of similarity (ANOSIM) revealed significant Leucocytozoon lineage composition between the two black flies. Phylogenetic analysis found that Leucocytozoon lineages in the S. asakoae complex and S. khelangense are largely isolated, agreeing with the ANOSIM result. The overall prevalence of Leucocytozoon in the S. asakoae complex was 11.3% and ranged from 9% to 13% in each collection. Leucocytozoon prevalence in S. khelangense was 21%, varying from 13% to 37% in each collection. The Shannon H' index indicated greater Leucocytozoon diversity in S. khelangense (H'&#x2009;=&#x2009;3.044) than in the S. asakoae complex (H'&#x2009;=&#x2009;1.920). Regression analysis revealed that Leucocytozoon diversity was positively related to black fly abundance and negatively related to maximum air temperature.<br><br>CONCLUSIONS: The results of this study show that the prevalence and diversity of Leucocytozoon lineages in the S. asakoae complex and S. khelangense from Thailand were associated with the abundance of these black flies and with air temperature. The Leucocytozoon lineages identified also showed some degree of black fly taxon specificity, possibly related to different abundance peaks of these vectors. The environmental conditions that favor the development of black flies are possibly a driver of Leucocytozoon prevalence, diversity and vector-parasite co-evolution.}, }
@article {pmid39562752, year = {2024}, author = {Cipurko, D and Ueda, T and Mei, L and Chevrier, N}, title = {Repurposing large-format microarrays for scalable spatial transcriptomics.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {39562752}, issn = {1548-7105}, support = {DP2-AI145100//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U01-AI160418//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, abstract = {Spatiomolecular analyses are key to study tissue functions and malfunctions. However, we lack profiling tools for spatial transcriptomics that are easy to adopt, low cost and scalable in terms of sample size and number. Here, we describe a method, Array-seq, to repurpose classical oligonucleotide microarrays for spatial transcriptomics profiling. We generate Array-seq slides from microarrays carrying custom-design probes that contain common sequences flanking unique barcodes at known coordinates. Then we perform a simple, two-step reaction that produces mRNA capture probes across all spots on the microarray. We demonstrate that Array-seq yields spatial transcriptomes with high detection sensitivity and localization specificity using histological sections from mouse tissues as test systems. Moreover, we show that the large surface area of Array-seq slides yields spatial transcriptomes (i) at high throughput by profiling multi-organ sections, (ii) in three dimensions by processing serial sections from one sample, and (iii) across whole human organs. Thus, by combining classical DNA microarrays and next-generation sequencing, we have created a simple and flexible platform for spatiomolecular studies of small-to-large specimens at scale.}, }
@article {pmid39562573, year = {2024}, author = {Kunitake, K and Mizuno, T and Hattori, K and Oneyama, C and Kamiya, M and Ota, S and Urano, Y and Kojima, R}, title = {Barcoding of small extracellular vesicles with CRISPR-gRNA enables comprehensive, subpopulation-specific analysis of their biogenesis and release regulators.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9777}, pmid = {39562573}, issn = {2041-1723}, support = {24H00868//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJPR17H5//MEXT | JST | Precursory Research for Embryonic Science and Technology (PRESTO)/ ; CDA-00008/2019-C//Human Frontier Science Program (HFSP)/ ; K05 DA000008/DA/NIDA NIH HHS/United States ; JPMJCR19H1, JPMJCR23B7//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; }, mesh = {*Extracellular Vesicles/metabolism/genetics ; Humans ; *CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Tetraspanin 29/metabolism/genetics ; *Tetraspanin 30/metabolism/genetics ; HEK293 Cells ; Exosomes/metabolism/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; }, abstract = {Small extracellular vesicles (sEVs) are important intercellular information transmitters in various biological contexts, but their release processes remain poorly understood. Herein, we describe a high-throughput assay platform, CRISPR-assisted individually barcoded sEV-based release regulator (CIBER) screening, for identifying key players in sEV release. CIBER screening employs sEVs barcoded with CRISPR-gRNA through the interaction of gRNA and dead Cas9 fused with an sEV marker. Barcode quantification enables the estimation of the sEV amount released from each cell in a massively parallel manner. Barcoding sEVs with different sEV markers in a CRISPR pooled-screening format allows genome-wide exploration of sEV release regulators in a subpopulation-specific manner, successfully identifying previously unknown sEV release regulators and uncovering the exosomal/ectosomal nature of CD63[+]/CD9[+] sEVs, respectively, as well as the synchronization of CD9[+] sEV release with the cell cycle. CIBER should be a valuable tool for detailed studies on the biogenesis, release, and heterogeneity of sEVs.}, }
@article {pmid39559832, year = {2024}, author = {Grasshoff, M and Kalmer, M and Chatain, N and Kricheldorf, K and Maurer, A and Weiskirchen, R and Koschmieder, S and Costa, IG}, title = {SIngle cell level Genotyping Using scRna Data (SIGURD).}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39559832}, issn = {1477-4054}, support = {KO2155/7-1 and 7-2//German Research Foundation/ ; KO 2155/6-1//German Research Foundation/ ; //German Ministry of Education and Science/ ; }, mesh = {*Single-Cell Analysis/methods ; Humans ; Sequence Analysis, RNA/methods ; Genotype ; Genotyping Techniques/methods ; Computational Biology/methods ; Mitochondria/genetics/metabolism ; }, abstract = {MOTIVATION: By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3' ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones.<br><br>RESULTS: Here, we propose SIGURD (SIngle cell level Genotyping Using scRna Data) (SIGURD), which is an R-based pipeline for the clonal analysis of scRNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones, and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.}, }
@article {pmid39559559, year = {2024}, author = {Lu, SC and Lee, YY and Andres, FGM and Moyer, DA and Barry, MA}, title = {FastAd: A versatile toolkit for rapid generation of single adenoviruses or diverse adenoviral vector libraries.}, journal = {Molecular therapy. Methods &amp; clinical development}, volume = {32}, number = {4}, pages = {101356}, pmid = {39559559}, issn = {2329-0501}, abstract = {Adenoviruses (Ads) are potent gene delivery vectors for in vitro and in vivo applications. However, current methods for their construction are time-consuming and inefficient, limiting their rapid production and utility in generating complex genetic libraries. Here, we introduce FastAd, a rapid and easy-to-use technology for inserting recombinant "donor" DNA directly into infectious "receiver" Ads in mammalian cells by the concerted action of two efficient recombinases: Cre and Bxb1. Subsequently, the resulting mixed recombinant Ad population is subjected to negative selections by flippase recombinase to remove viruses that missed the initial recombination. With this approach, recombinant Ad production time is reduced from 2 months to 10 days or less. FastAd can be applied for inserting complex genetic DNA libraries into Ad genomes, as demonstrated by the generation of barcode libraries with over 3 million unique clones from a T25 flask-scale transfection of 3 million cells. Furthermore, we leveraged FastAd to construct an Ad library containing a comprehensive genome-wide CRISPR-Cas9 guide RNA library and demonstrated its effectiveness in uncovering novel virus-host interactions. In summary, FastAd enables the rapid generation of single Ad vectors or complex genetic libraries, facilitating not only novel applications of Ad vectors but also research in foundamental virology.}, }
@article {pmid39557939, year = {2024}, author = {Shah, HK and Fathima, PA and Ajithlal, PM and Kumar, A and Rawani, A and Thakur, MS and Mohanty, SS and Sarma, DK and Pandey, K and Kumar, A and Rahi, M and Saini, P}, title = {Nationwide cross-sectional surveillance of Leishmania donovani in phlebotomine sand flies and its impact on national kala-azar elimination in India.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28455}, pmid = {39557939}, issn = {2045-2322}, support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; }, mesh = {Animals ; *Leishmaniasis, Visceral/epidemiology/parasitology/prevention &amp; control/transmission ; *Leishmania donovani/genetics/isolation &amp; purification ; India/epidemiology ; Cross-Sectional Studies ; *Insect Vectors/parasitology ; Psychodidae/parasitology ; Phlebotomus/parasitology ; Humans ; Disease Eradication/methods ; }, abstract = {India is accelerating efforts to eliminate kala-azar by aligning its National Kala-Azar Elimination Program with the World Health Organization's (WHO) roadmap for Neglected Tropical Diseases (NTDs) 2021-2030. Elimination relies on comprehensive vector surveillance and integrated vector management. This study aimed to conduct nationwide entomological surveillance to detect Leishmania donovani in phlebotomine sand flies. A cross-sectional survey was conducted from January 2022 to December 2023 in five different biogeographical zones in India. Mechanical aspirator, light traps were used for sampling. The collected sand flies were identified to species level. Molecular xenomonitoring was conducted using kDNA qPCR, and parasite characterization targeting ITS1 gene sequencing and RFLP. Sand fly species was confirmed by DNA barcode. Molecular xenomonitoring revealed that Phlebotomus argentipes from Bihar, West Bengal, and Kerala exhibited high levels of L. donovani parasitic DNA. In Rajasthan, P. sergenti and P. papatasi and in Himachal Pradesh, P. longiductus, P. major, and P. bruneyi were positive. The high levels of L. donovani parasitic DNA detected in various Phlebotomus species, along with its presence in other sand fly species beyond the established vectors, underscore the urgent need for the National Kala-Azar Elimination Program to prioritize comprehensive and rigorous vector surveillance. Strengthening these efforts is crucial for achieving the program's goal of eliminating the disease.}, }
@article {pmid39555796, year = {2024}, author = {Yang, S and Chen, S and Mo, J and Liu, J and Pan, Q and Song, C}, title = {Application of DNA Barcoding to Identify Medicinal Plants.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {213}, pages = {}, doi = {10.3791/66925}, pmid = {39555796}, issn = {1940-087X}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants, Medicinal/genetics/classification ; *DNA, Plant/genetics ; }, abstract = {Medicinal plants are valuable resources globally and are used worldwide to maintain health and treat disease; however, the presence of adulteration obstructs their development. DNA barcoding, a technique for species identification by standard DNA regions, facilitates prompt and accurate identification of traditional medicinal plants. The process of DNA barcoding entails six basic steps: 1) processing the medicinal plants, 2) extracting high-quality total DNA from the medicinal plants using centrifugal column method, 3) amplifying target DNA region internal transcribed spacer 2 (ITS2) with universal primers of plants and performing Sanger sequencing, 4) splicing and aligning sequence to obtain the target sequence, 5) matching the barcode sequence against the barcode library for identification, 6) aligning sequence, comparing intraspecific and interspecific variation, constructing phylogenetic neighbor-joining tree. As shown in the results, the universal primer can amplify the target region. Basic Local Alignment Search Tool (BLAST) demonstrates the percentage identified was 100%, and the neighbor-joining tree demonstrates that the splicing sequences were clustered with the A. sinensis OR879715.1 clade, and the clade support value is 100. This protocol provides a reference for applying DNA barcoding technology as an effective method to identify medicinal plants and adulterants.}, }
@article {pmid39552916, year = {2024}, author = {Chen, HP and Chan, FT and Shiao, SF and Chiu, MC}, title = {New record of Carnidae (Diptera) from Taiwan and potential challenges in DNA barcode amplification due to pseudogene.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e137532}, pmid = {39552916}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Carnus Nitzsch, 1818 comprises small ectoparasites that feed on the blood of juvenile avians. They are characterised by dealated adults with setose abdominal intersegmental membranes. Carnusorientalis Maa, 1968 was previously recorded in Malaysia and the Ryukyu Islands of Japan, parasitising two owl species: Ketupaketupu (Horsfield, 1821) and Otuselegans (Cassin, 1852). This study confirms the occurrence of C.orientalis in Taiwan and presents a new host record, along with COI barcode sequences. Additionally, the study also elucidates the difficulties posed by blood meal contamination and pseudogene amplification as confounding factors intrinsic to the molecular taxonomic delineation of C.orientalis via universal DNA barcoding primers.<br><br>NEW INFORMATION: The following new information regarding C.orientalis is provided in this study: Carnusorientalis is first recorded in Taiwan, filling the gap in its East Asian distribution. This is also the first record of Carnidae from Taiwan.Otuslettia (Hodgson, 1836) (Aves, Strigidae) is reported as a new host for C.orientalis, identified on a fallen fledgling.Co-amplification of the host's COI is reported in this study using the universal PCR primer set LCO1490/HCO2198. Additionally, the amplification of a COI-like pseudogene using a newly-designed primer set is detected through abnormal translated amino acid sequences and the occurrence of a stop codon.New specific primers for the COI gene of Carnus were designed in this study. The new distribution and ecological data of C.orientalis enhance our understanding of this species. The provision of new COI primers is anticipated to contribute to future studies employing DNA barcoding in bird-parasitic flies.}, }
@article {pmid39552768, year = {2024}, author = {Jiang, YY and Zhao, H and Chen, Y}, title = {A new species of Proaphelinoides Girault (Hymenoptera, Aphelinidae) from China, with a phylogenetic analysis.}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {263-272}, pmid = {39552768}, issn = {1313-2989}, abstract = {A new species of Proaphelinoides Girault, Proaphelinoideshuangi Chen &amp; Jiang, sp. nov., is reported from China. A key to all species of the genus is provided. DNA standard barcode COI and partial nuclear ribosomal 28S-D2 from two individuals of Proaphelinoides were sequenced, and 28S-D2 rDNA was included in a phylogenetic analysis, confirming Proaphelinoides as the sister group to Aphytis.}, }
@article {pmid39552767, year = {2024}, author = {Kits, JH}, title = {Boreolimnus, a new leafhopper genus from northern North America, with a review of Cribrus Oman (Hemiptera, Cicadellidae, Deltocephalinae).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {273-290}, pmid = {39552767}, issn = {1313-2989}, abstract = {The poorly known leafhopper species described as Deltocephalus (Laevicephalus) concinnus var. incisurus DeLong, 1926 previously had no accepted generic placement. It is here redescribed and placed in Boreolimnus gen. nov. in the tribe Paralimnini, as Boreolimnusincisurus (DeLong) comb. nov. Cribrusmicmac Hamilton, 1987 is a junior syn. nov. of B.incisurus. Due to historic confusion, the species currently placed in Cribrus Oman, 1949 were also reviewed. Cribrusconcinnus (Sanders &amp; DeLong, 1917) is redescribed, and a lectotype is designated to clarify the application of the name. Deltocephalusplagus Ball &amp; DeLong, 1926 and Laevicephalusshingwauki Beamer &amp; Tuthill, 1934 are recognized as junior syn. nov. of C.concinnus, now the only recognized species in the genus.}, }
@article {pmid39549753, year = {2024}, author = {Pogner, CE and Antunes, C and Apangu, GP and Bruffaerts, N and Celenk, S and Cristofori, A and González Roldán, N and Grinn-Gofroń, A and Lara, B and Lika, M and Magyar, D and Martinez-Bracero, M and Muggia, L and Muyshondt, B and O'Connor, D and Pallavicini, A and Penha, MA and Pérez-Badia, R and Ribeiro, H and Rodrigues Costa, A and Tischner, Z and Xhetani, M and Ambelas Skjøth, C}, title = {Airborne DNA: State of the art - Established methods and missing pieces in the molecular genetic detection of airborne microorganisms, viruses and plant particles.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {177439}, doi = {10.1016/j.scitotenv.2024.177439}, pmid = {39549753}, issn = {1879-1026}, abstract = {Bioaerosol is composed of different particles, originating from organisms, or their fragments with different origin, shape, and size. Sampling, analysing, identification and describing this airborne diversity has been carried out for over 100 years, and more recently the use of molecular genetic tools has been implemented. However, up to now there are no established protocols or standards for detecting airborne diversity of bacteria, fungi, viruses, pollen, and plant particles. In this review we evaluated commonalities of methods used in molecular genetic based studies in the last 23 years, to give an overview of applicable methods as well as knowledge gaps in diversity assessment. Various sampling techniques show different levels of effectiveness in detecting airborne particles based on their DNA. The storage and processing of samples, as well as DNA processing, influences the outcome of sampling campaigns. Moreover, the decisions on barcode selection, method of analysis, reference database as well as negative and positive controls may severely impact the results obtained. To date, the chain of decisions, methodological biases and error propagation have hindered DNA based molecular sequencing from offering a holistic picture of the airborne biodiversity. Reviewing the available studies, revealed a great diversity in used methodology and many publications didn't state all used methods in detail, making comparisons with other studies difficult or impossible. To overcome these limitations and ensure genuine comparability across studies, it is crucial to standardize protocols. Publications need to include all necessary information to enable comparison among different studies and to evaluate how methodological choices can impacts the results. Besides standardization, implementing of automatic tools and combining of different analytical techniques, such as real-time evaluation combined with sampling and molecular genetic analysis, could assist in achieving the goal of accurately assessing the actual airborne biodiversity.}, }
@article {pmid39548171, year = {2024}, author = {Raupach, MJ and Charzinski, N and Villastrigo, A and Gossner, MM and Niedringhaus, R and Schäfer, P and Schmelzle, S and Strauß, G and Hendrich, L}, title = {The discovery of an overseen pygmy backswimmer in Europe (Heteroptera, Nepomorpha, Pleidae).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28139}, pmid = {39548171}, issn = {2045-2322}, mesh = {Animals ; *Heteroptera/genetics/classification/anatomy &amp; histology ; *Phylogeny ; Europe ; Male ; Genome, Mitochondrial ; DNA Barcoding, Taxonomic ; Female ; }, abstract = {The Pleidae, or pygmy backswimmers, is a family of aquatic bugs (Hemiptera, Heteroptera, Nepomorpha) containing four genera. Here, we describe Plea cryptica sp. nov. and redescribe its sister species, Plea minutissima Leach, 1817. Whereas the morphological distinction of these closely related species is only possible for males, molecular data clearly separate them. As part of our taxonomic study, we provide comprehensive molecular data including more than 200 DNA barcodes from all over Europe, complete nuclear ribosomal DNA, full mitochondrial genome data, and 3D scans for both species. Furthermore, the same molecular markers are also presented for Neoplea striola (Fieber, 1844). We used Maximum Likelihood (ML) analyses to reconstruct the phylogeny of the Pleidae and Notonectoidea based on available mitogenomic data. Our study represents a successful implementation of the proposed concept of taxonomics, using data from high-throughput sequencing technologies for integrative taxonomic studies, and allowing high confidence for both biodiversity and ecological research.}, }
@article {pmid39544525, year = {2024}, author = {López-Blanco, C and Tasevska, O and Kostoski, G and Vicente, E and Epp, LS and García-Alix, A}, title = {Ancient Endemic or Recent Invader? Phylogenetic Position and the Probable Origin of the Ccladoceran Diaphanosoma macedonicum (Diplostraca, Sididae) from the Ancient Lakes in the Balkans.}, journal = {Zoological studies}, volume = {62}, number = {}, pages = {e9}, pmid = {39544525}, issn = {1810-522X}, abstract = {Ancient lakes contain unique and very vulnerable fauna. Determining and understanding the origin of such biodiversity is a key factor in promoting conservation and management actions in some of the most singular ecosystems on the planet. Lake Ohrid in the Balkans is known as a natural laboratory for speciation, containing a high number of endemic species. However, the identity and origin of the planktonic cladoceran Diaphanosoma is uncertain. Representatives of the genus were long considered to have invaded the lake, but recent morphological studies have suggested that they belonged to the endemic taxon in the Balkans, D. macedonicum. Here, phylogenetic methods based on two mitochondrial gene fragments (COI and 16S) were used to identify Diaphanosoma specimens from the ancient Lake Ohrid and Lake Prespa in the Balkans and compare them with other species in Europe, including those living in nearby water bodies. Molecular evidence showed that D. macedonicum was constrained to the ancient lakes Ohrid, Prespa, and Mikri Prespa, which suggests reproductive isolation within the lakes. Phylogenetic analyses supported previous morphological assessments and situated D. macedonicum within the D. mongolianum species group, which contains three sibling species (D. mongolianum, D. lacustris, and D. macedonicum). Nuclear markers are needed to study intraspecific gene flow in these organisms and discard a potential formation of hybrids.}, }
@article {pmid39542856, year = {2024}, author = {Valkiūnas, G and Iezhova, TA and Duc, M and Dunn, JC and Bensch, S}, title = {A new blood parasite of the accentor birds: description, molecular characterization, phylogenetic relationships and distribution.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1017/S0031182024000878}, pmid = {39542856}, issn = {1469-8161}, support = {RG170086//Royal Society/ ; }, abstract = {Haemoproteus bobricklefsi sp. nov. (Haemosporida, Haemoproteidae) was found in the dunnock Prunella modularis and represents the first blood parasite described in accentor birds of the Prunellidae. The description is based on the morphology of blood stages and includes information about a barcoding segment of the mitochondrial cytochrome b gene (lineage hDUNNO01) and the full mitochondrial genome, which can be used for identification and diagnosis of this infection. The new parasite can be readily distinguished from described species of haemoproteids parasitizing passeriform birds due to markedly variable position of nuclei in advanced and fully grown macrogametocytes. Illustrations of blood stages of the new species are given, and phylogenetic analyses based on partial mitochondrial cytochrome b gene sequences and the full mitochondrial genome identified the closely related lineages. DNA haplotype networks showed that transmission occurs in Europe and North America. This parasite was found in the dunnock in Europe and several species of the Passerellidae in North America. It is probably of Holarctic distribution, with the highest reported prevalence in the UK. The parasite distribution seems to be geographically patchy, with preference for areas of relatively cool climates. Phylogenetic analysis suggests that H. bobricklefsi sp. nov. belongs to the Parahaemoproteus subgenus and is probably transmitted by biting midges belonging to Culicoides (Ceratopogonidae). The available data on molecular occurrence indicate that this pathogen is prone to abortive development, so worth attention in regard of consequences for bird health.}, }
@article {pmid39541669, year = {2024}, author = {Kusuda, K and Yamashita, K and Morishita, E and Ishibashi, N and Shiraishi, Y and Yamaguchi, H}, title = {Comparison of Reading Times of RFID-Tagged and Barcode-Engraved Surgical Instruments.}, journal = {The Journal of surgical research}, volume = {304}, number = {}, pages = {121-125}, doi = {10.1016/j.jss.2024.09.087}, pmid = {39541669}, issn = {1095-8673}, abstract = {INTRODUCTION: To improve patient safety and reduce burden on healthcare professionals and institutions, the individual management of surgical instruments is essential. There are two methods for individual item management: radio-frequency identification (RFID) and barcoding. However, there has been no examination of efficiency regarding reading times. Therefore, this study aimed to compare the reading times of RFID-tagged and barcode-engraved surgical instruments and evaluate the influence of operator proficiency.<br><br>METHODS: The participants included 8 individuals and 41 surgical instruments from a varicose vein set. RFID tags and barcodes were attached to the surgical instruments. Five trials were conducted for each, and the reading times were measured.<br><br>RESULTS: The reading times for RFID-tagged surgical instruments in the skilled and unskilled groups were 64.0&#xa0;&#xb1;&#xa0;9.0s and 79.4&#xa0;&#xb1;&#xa0;17.0&#xa0;s, respectively, whereas those for barcode-engraved surgical instruments were 190.4&#xa0;&#xb1;&#xa0;28.1&#xa0;s and 212.3&#xa0;&#xb1;&#xa0;40.3&#xa0;s, respectively. Barcodes took 3.0 and 2.7 times longer to read than RFID-tagged instruments for the skilled and unskilled groups, respectively. Additionally, skilled operators using barcodes required 2.4 times more time than unskilled operators using RFID. Even nonmedical individuals were able to achieve quick and accurate readings with RFID. The estimated labor hours per person were $24,146-$42,322 for RFID and $71,078-$110,898 for barcode scanning for a year (working 8&#xa0;h/d for 250&#xa0;d).<br><br>CONCLUSIONS: RFID-tagged surgical instruments impose a lighter workload and financial burden than barcode-engraved surgical instruments. RFID technology may also improve patient safety due to less dependency on operator proficiency.}, }
@article {pmid39538416, year = {2024}, author = {Hua, J and Wang, K and Chen, Y and Xu, X and Dong, G and Li, Y and Liu, R and Xiong, Y and Ding, J and Zhang, T and Zeng, X and Li, Y and Sun, H and Gu, Y and Liu, S and Ouyang, W and Liu, C}, title = {Molecular characterization of human HSPCs with different cell fates in vivo using single-cell transcriptome analysis and lentiviral barcoding technology.}, journal = {Clinical and translational medicine}, volume = {14}, number = {11}, pages = {e70085}, pmid = {39538416}, issn = {2001-1326}, support = {No.31970816//National Natural Science Foundation of China (NSFC)/ ; No.BGIRSZ20210006//Open fund project of Shenzhen BGI Institute of Life Science/ ; No. KJZD20230923114911023//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; No.SZSM202211033//Sanming Project of Medicine in Shenzen Municipality/ ; }, mesh = {Humans ; *Single-Cell Analysis/methods ; *Gene Expression Profiling/methods ; *Hematopoietic Stem Cells/metabolism/cytology ; Cell Differentiation/genetics ; Lentivirus/genetics ; Single-Cell Gene Expression Analysis ; }, abstract = {Hematopoietic stem and progenitor cells (HSPCs) possess the potential to produce all types of blood cells throughout their lives. It is well recognized that HSPCs are heterogeneous, which is of great significance for their clinical applications and the treatment of diseases associated with HSPCs. This study presents a novel technology called Single-Cell transcriptome Analysis and Lentiviral Barcoding (SCALeBa) to investigate the molecular mechanisms underlying the heterogeneity of human HSPCs in vivo. The SCALeBa incorporates a transcribed barcoding library and algorithm to analyze the individual cell fates and their gene expression profiles simultaneously. Our findings using SCALeBa reveal that HSPCs subset with stronger stemness highly expressed MYL6B, ATP2A2, MYO19, MDN1, ING3, and so on. The high expression of COA3, RIF1, RAB14, and GOLGA4 may contribute to the pluripotent-lineage differentiation of HSPCs. Moreover, the roles of the representative genes revealed in this study regarding the stemness of HPSCs were confirmed with biological experiments. HSPCs expressing MRPL23 and RBM4 genes may contribute to differentiation bias into myeloid and lymphoid lineage, respectively. In addition, transcription factor (TF) characteristics of lymphoid and myeloid differentiation bias HSPCs subsets were identified and linked to previously identified genes. Furthermore, the stemness, pluripotency, and differentiation-bias genes identified with SCALeBa were verified in another independent HSPCs dataset. Finally, this study proposes using the SCALeBa-generated tracking trajectory to improve the accuracy of pseudo-time analysis results. In summary, our study provides valuable insights for understanding the heterogeneity of human HSPCs in vivo and introduces a novel technology, SCALeBa, which holds promise for broader applications. KEY POINTS: SCALeBa and its algorithm are developed to study the molecular mechanism underlying human HSPCs identity and function. The human HSPCs expressing MYL6B, MYO19, ATP2A2, MDN1, ING3, and PHF20 may have the capability for high stemness. The human HSPCs expressing COA3, RIF1, RAB14, and GOLGA4 may have the capability for pluripotent-lineage differentiation. The human HSPCs expressing MRPL23 and RBM4 genes may have the capability to differentiate into myeloid and lymphoid lineage respectively in vivo. The legitimacy of the identified genes with SCALeBa was validated using biological experiments and a public human HSPCs dataset. SCALeBa improves the accuracy of differentiation trajectories in monocle2-based pseudo-time analysis.}, }
@article {pmid39538182, year = {2024}, author = {Anwar, A and Wahab, H and Wahab, A and Afshan, NUS and Moussa, IM and Elhindi, KM and Ahmed, M and Malik, A and Singh, MP and Gaidhane, S and Uddin, S}, title = {Molecular and morphoanatomical characterization of Urocystis heteropogonis sp. nov.: a novel smut fungus infecting Heteropogon contortus.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1070}, pmid = {39538182}, issn = {1471-2229}, mesh = {*Phylogeny ; DNA, Fungal/genetics ; Spores, Fungal/genetics ; Pakistan ; Animals ; }, abstract = {BACKGROUND: A new species of smut fungus, Urocystis heteropogonis, was discovered infecting Heteropogon contortus in Shawar Valley, Swat district, Khyber Pakhtunkhwa, Pakistan. The study aimed to characterize this fungus based on its morpho-anatomical and molecular features and clarify its phylogenetic position within the genus Urocystis.<br><br>RESULTS: Urocystis heteropogonis was identified as a novel species, distinct from other Urocystis species. Morphologically, it is characterized by larger spore balls (14-69&#x2009;&#xd7;&#x2009;11-45&#xa0;&#x3bc;m) and central spores that are 14-28&#x2009;&#xd7;&#x2009;11-20&#xa0;&#x3bc;m in size, with each spore containing1-8 central spores. The spore walls measure 0.9-2.5&#xa0;&#x3bc;m in thickness and the species differs in infection patterns compared to other Urocystis species. Phylogenetic analysis based on the ITS and LSU regions of nuclear ribosomal DNA (nrDNA) further confirmed the novelty of the species, placing it within a distinct clade alongside U. agropyri, U. occulta, U. piptatheri, and U. tritici.<br><br>CONCLUSIONS: The discovery of Urocystis heteropogonis adds to the diversity of smut fungi infecting grasses and highlights the need for further research into its ecological and agricultural implications. Future studies should focus on the disease's spread, management, and potential impact on host populations.}, }
@article {pmid39538137, year = {2024}, author = {El-Demerdash, MM and El-Sayed, ASA and Teleb, SS and Sadek, AM and Elsehely, HH}, title = {DNA barcoding, micromorphology and metabolic traits of selected Ficus L. (Moraceae) species from Egypt.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1067}, pmid = {39538137}, issn = {1471-2229}, mesh = {*DNA Barcoding, Taxonomic ; *Ficus/genetics/anatomy &amp; histology/classification ; Egypt ; Phylogeny ; DNA, Plant/genetics ; Plant Leaves/anatomy &amp; histology/genetics/metabolism ; Species Specificity ; }, abstract = {The genus Ficus of the family Moraceae, is one of the largest genera of angiosperms, with diverse pharmaceutical applications and biological activities. The traditional approaches based on the morphological traits have been frequently implemented for taxonomical identification of the different taxa of Ficus, however, encompassing these features are quite laborious, due to the dependence of these phenotypic traits on the environmental conditions. So, authenticating the taxonomical identity of the Ficus taxa with molecular barcoding and metabolic profiling, as relatively stable traits, could be a relevant approach for confirming the traditional phenotypic traits of this genus. Nine species of the genus Ficus namely F. amplissima Sm., F. benjamina L. F. binnendijkii, F. drupacea var. pubescens, F. elastica Roxb., F. microcarpa L., F. religiosa L., F. tinctoria subsp. gibbosa and F. virens var. sublancelata in Egypt, were selected for this study. From the anatomical features, three species of subsection Urostigma, F. religiosa, F. virens var. sublanceolata have cystoliths on the abaxial layer, whereas in F. amplissima it was on the adaxial layer. The UPGMA dendrogram of the studied Ficus taxa has been generated from the 21 anatomical characters, categorized the studied taxa into two clusters (I and II) of average distance ~ 3.5, each cluster has been further divided into subclusters I and II. The sub-cluster I includes F. religiosa, F. virens var. sublanceolata and F. tinctoria subsp. gibbosa were grouped together to subsection Urostigma, while the sub-cluster II of the cluster I includes F. benjamina and F. amplissima. From the DNA barcoding analysis, three clusters I, II and III were emerged, the cluster I includes F. benjamina, F. binnendjikee, and F. amplissima. The cluster II, F. virens var. sublanceolata and F. religiosa that belong to subsection Urostigma, while, the cluster III includes F. elastica and F. drupacea var. pubescens, F. microcarpa that belongs to subsection Conosycea. From the metabolic profiling of Ficus species, the major compounds; H-cycloprop-azulen-7-ol, 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, 2-(9-octadecenyloxy), pentadecanoic acid, phytol, sitosterol and 9,12-octadecadienoic acid were the common among the taxa, with an obvious fluctuation, that could be a chemotaxonomic markers for these species of Ficus. Based on the metabolic profiling, two distinct clusters I and II were evolved, the cluster I involve F. elastica, F. benjamina, F. drupacea var. pubescens, F. amplissima, while, the cluster II had F. tinctoria subsp. gibbosa and F. religiosa. The fluctuation on the metabolites of the tested Ficus species could be a metabolic fingerprint for each species. So, the delamination of the tested plants based on their anatomical traits was typically matched to the separation based on the ITS sequence analysis.}, }
@article {pmid39537812, year = {2024}, author = {Mingeot, D and Chavalle, S and Buhl, PN and Sonet, G and Dubois, B and Hautier, L}, title = {Molecular methods for the detection and identification of parasitoids within larval wheat midges.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27770}, pmid = {39537812}, issn = {2045-2322}, mesh = {Animals ; *Larva/parasitology ; *Triticum/parasitology ; *Diptera/parasitology ; *DNA Barcoding, Taxonomic/methods ; Hymenoptera/genetics ; }, abstract = {Three species of cecidomyiid midges (Diptera: Cecidomyiidae) cause significant yield losses on wheat in Europe: Sitodiplosis mosellana (Géhin), Contarinia tritici (Kirby) and Haplodiplosis marginata (von Roser). Eggs and young larvae may be parasitised by a complex of hymenopteran parasitoids belonging to the Pteromalidae and Platygastridae families which contributes to natural pest control. We have developed molecular tools for detecting and identifying seven parasitoid species previously encountered in Belgium inside individual wheat midge larvae. Barcode DNA sequences from COI, 18S and 28S genes were obtained from the midges and parasitoid species. Each of the three genes allowed all the species to be distinguished although 18S was the only one displaying a barcoding gap, both between parasitoids and midges, and at the species level. Based on the 18S gene, we developed a TaqMan assay to assess parasitism in midge larvae, regardless of the midge and parasitoid species. Next, two group-specific PCR primer pairs were generated, allowing the separate amplification of midge DNA or parasitoid DNA in parasitised individuals and subsequent identification by Sanger sequencing. Finally, species-specific primers were designed to identify six parasitoid species by simple PCR amplification. These tools were successfully applied to assess the parasitism rate of S. mosellana larvae in seven Belgian fields.}, }
@article {pmid39535995, year = {2024}, author = {Shah, SHA and Nisar, M and Ihsan, M and Zahoor, M and Ullah, R and Iqbal, Z and Shah, AB}, title = {Estimation of genetic polymorphism in quince (Cydonia oblonga Mill.) genotypes using morphological traits and molecular (DNA barcoding) characterizations.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0310048}, pmid = {39535995}, issn = {1932-6203}, mesh = {*Rosaceae/genetics ; *Genotype ; *Polymorphism, Genetic ; *DNA Barcoding, Taxonomic/methods ; Fruit/genetics/anatomy &amp; histology ; Pakistan ; Phylogeny ; DNA, Plant/genetics ; }, abstract = {Quince (Cydonia oblonga) is a medicinal plant and a member of family Rosaceae. It is native plant of Asia Minor and Europe. It is used in production of jam and jellies and also as a remedy of several ailments. The present study was conducted to evaluate the genetic polymorphism based on morphological and molecular traits. Different varieties of Quince were collected from different ecological zones of Khyber Pakhtunkhwa Pakistan and a total of 26 different morphological traits were recorded among studied genotypes. Based on qualitative morphological trait study, the variety collected from Tindodag was unique one with highest fruit weight (328.82 g). The lowest fruit weight (68.38 g) was recorded for Talash genotype. The Charbagh and Tindodag genotypes showed highest seed length (10.6 mm) while genotypes of Chitral was recorded as lowest (8.4 mm). Statistically, significant level of variation was noted with coefficient of variance ranged from 2.23% to 30.38%. Based on correlation analysis, fruit length had strongly correlation with fruit weight (r = 0.89**), Average Fruit width was found significant with fruit weight (r = 0.90**). Similarly, the Core Width was found strongly significant with Core Length (r = 0.95**). ANOVA analysis indicated 10 quantitative characters to be highly significant, 2 significant and 1 insignificant. Principal component analysis was also computed for the 13 quantitative traits with Eigen value of 0.48 and a total variance of 97.78%. The first principal component shows total variation of 52.52%. In PC2 the total variation was 80.15%, PC3 94.06% while in PC4 it was 97.78%. The NCBI BLAST results shows that all the genotypes have similar origin except Tindodag genotype, which shows differences in its origin. Accession number for all other genotypes is MN216014.1, while accession number of Tindodag genotype is KF861967.1. Based on this study, it can be concluded that Tindodag genotype is unique out of the studied localities. NCBI BLAST have provided further support for the drawn conclusion.}, }
@article {pmid39534104, year = {2024}, author = {Wang, L and Li, F and Zhao, K and Yang, J and Sun, H and Cui, X and Dong, W and Li, E and Wang, N}, title = {Comparative plastomes sheds light on phylogeny of Weigela.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1487725}, pmid = {39534104}, issn = {1664-462X}, abstract = {Weigela Thunb. is a genus in the family Caprifoliaceae. All species in this genus have high ornamental and medicinal value. However, the genetic divergence between species and the phylogeny within Weigela is still unclear. Therefore, we sequenced and analyzed four plastomes from four different Weigela species to reveal the genetic divergence among species of this genus, and the phylogeny within Weigela. The four plastomes from Weigela ranged from 156,909 bp to 157,739 bp in size, and presented a typical circular quadripartite structure. Each complete plastome contained a pair of inverted repeat regions (23,592~24,957 bp), a larger single-copy (LSC) region (89,922~90,229 bp), and a small single-copy (SSC) region (17,668~20,429 bp). We identified three types of repeats, corresponding to 268 forward repeats, 128 palindromic repeats, and 867 tandem repeats, for a total of 1,263 long repeats. A total of 352 SSRs were identified from the four plastomes, and most of them were concentrated in the LSC region and the noncoding regions. Mononucleotide repeat units were the most frequently detected types of repeats, of which A/T repeat units were the most abundant. Three mutational hotspots (trnH-psbA, trnR-ndhF, and trnN-ndhF) were identified as candidate barcodes for Weigela species. Weigela belongs to Diervilloideae located at an early diverging position in the Caprifoliaceae. Within Weigela, W. japonica and W. floribunda were sister with W. subsessilis and W. florida. This study revealed the plastome structure and variation of four well-known Weigela species, and found three candidate barcodes for further study of four well-known Weigela species. In addition, the phylogenetic location of Weigela within the Caprifoliaceae was identified.}, }
@article {pmid39528918, year = {2024}, author = {Filippov, I and Philip, CS and Schauser, L and Peterson, P}, title = {Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1069}, pmid = {39528918}, issn = {1471-2164}, support = {955321//Horizon 2020 Framework Programme/ ; 955321//Horizon 2020 Framework Programme/ ; PRG2011//Eesti Teadusagentuur/ ; }, mesh = {Animals ; *Thymocytes/metabolism/cytology ; *Single-Cell Analysis/methods ; Mice ; *Genomics/methods ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Transcriptome ; RNA-Seq/methods ; Single-Cell Gene Expression Analysis ; }, abstract = {BACKGROUND: Single-cell RNA sequencing experiments commonly use 10x Genomics (10x) kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences (Parse) introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. Parse enables the analysis of more cells from multiple samples in a single run without the need for additional reagents or specialized microfluidics equipment. To evaluate the performance of both platforms, we conducted a benchmark study using biological and technical replicates of mouse thymus as a complex immune tissue.<br><br>RESULTS: We found that Parse detected nearly twice the number of genes compared to 10x, with each platform detecting a distinct set of genes. The comparison of multiplexed samples generated from 10x&#xa0;and Parse techniques showed 10x&#xa0;data to have lower technical variability and more precise annotation of biological states in the thymus compared to Parse.<br><br>CONCLUSION: Our results provide a comprehensive comparison of the suitability of both single-cell platforms for immunological studies.}, }
@article {pmid39526042, year = {2024}, author = {Pešić, V and Zawal, A and Ferreira, S and Benitez-Bosco, L and Cruz-Oliveira, A and Girão, D and Padilha, A and Turaccio, P and Rossini, S and Ballini, L and Staffoni, G and Fratini, S and Ciofi, C and Iannucci, A and Ekrem, T and Stur, E}, title = {DNA barcode library of Portuguese water mites, with the descriptions of two new species (Acari, Hydrachnidia).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {119-171}, pmid = {39526042}, issn = {1313-2989}, abstract = {This study presents the first results from the analysis of water mites collected in Portugal as part of the Biodiversity Genomics Europe project. 307 COI DNA barcodes clustered into 75 BINs are provided, with 38 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). 65 species have been identified, of which 36 are new to the water mite fauna of Portugal. Two species, Torrenticolasoniae Pešić, sp. nov. and T.elisabethae Pešić, sp. nov. (Torrenticolidae), are described as new to science. 47% of the water mite species currently known from Portugal now have reference barcodes in BOLD. High intraspecific distances were recorded for some species, suggesting the presence of cryptic diversity and species complexes that needs further study. Our results improve the DNA barcode reference database for Portuguese water mites, enhancing species identification accuracy and stimulating future investigation.}, }
@article {pmid39524431, year = {2024}, author = {Kan, J and Nie, L and Mi, Z and Liu, X and Xu, D and Tembrock, LR and Wu, Z and Hong, Z}, title = {Insights into Aquilaria phylogenetics through comparative plastomic resources.}, journal = {Forestry research}, volume = {4}, number = {}, pages = {e030}, pmid = {39524431}, issn = {2767-3812}, abstract = {The plastid is an essential organelle for its role in photosynthesis and energy production and its genomic information is always employed as important evolutionary markers to explore the relationship among species. Agarwood (Aquilaria), prized for its aromatic blend, finds extensive use in various cultures as incense and perfume. Despite its high economic importance, the phylogenetic status among Aquilaria based on plastomes remains ambiguous due to the lack of available plastomic resources. To bridge this knowledge gap, 22 Aquilaria plastomes were newly sequenced, similar variation patterns in this genus were determined, including a shared 16 bp extension of the rps19 gene and seven highly variable regions. The analysis highlighted the highest prevalence of the A/T motif among simple sequence repeats in these plastomes. Further phylogenetic analysis revealed Aquilaria's phylogenetic implications with an expanded dataset. This comprehensive plastomic resource not only enhances our understanding of Aquilaria evolution but also presents potential molecular markers for DNA barcoding.}, }
@article {pmid39524315, year = {2024}, author = {Lamichhane, B and Brockway, C and Evasco, K and Nicholson, J and Neville, PJ and Mackenzie, JS and Smith, D and Imrie, A}, title = {DNA Barcoding for the Identification of Adult Mosquitoes (Diptera: Culicidae) in Western Australia.}, journal = {Ecology and evolution}, volume = {14}, number = {11}, pages = {e70493}, pmid = {39524315}, issn = {2045-7758}, abstract = {Precise mosquito identification is integral to effective arbovirus surveillance. Nonetheless, the conventional morphological approach to identifying mosquito species is laborious, demands expertise and presents challenges when specimens are damaged. DNA barcoding offers a promising alternative, surmounting challenges inherent in morphological identification. To integrate DNA barcoding into arbovirus surveillance effectively, a robust dataset of mosquito barcode sequences is required. This study established a comprehensive repository of Cytochrome Oxidase I (COI) barcodes, encompassing 177 samples representing 45 mosquito species from southern and northern Western Australia (WA), including 16 species which have not been previously barcoded. The average intraspecific and interspecific genetic distances were 1% and 6.8%, respectively. Anopheles annulipes sensu lato had the highest intraspecific distance at 9.1%, signifying a genetically diverse species. While validating the potential of COI barcodes to accurately differentiate mosquito species, we identified that some species pairs have low COI divergence. This includes Aedes clelandi and Ae. hesperonotius, Tripteroides atripes and Tp. punctolaeralis and Ae. turneri and Ae. stricklandi. In addition, we observed ambiguity in identification of the members of Culex sitiens subgroup (Cx. annulirostris, Cx. palpalis and Cx. sitiens) and three members of Cx. pipiens complex (Cx. australicus, Cx. globocoxitus, Cx. quinquefasciatus). In summary, despite presenting challenges in the identification of some mosquito species, the COI barcode accurately identified most of the species and generated a valuable resource that will support the WA arbovirus surveillance program and enhance public health intervention strategies for mosquito-borne disease control.}, }
@article {pmid39535538, year = {2024}, author = {Singh, Y and Farrelly, C and Hathaway, QA and Carlsson, G}, title = {Persistence barcodes: A novel approach to reducing bias in radiological analysis.}, journal = {Oncotarget}, volume = {15}, number = {}, pages = {784-786}, pmid = {39535538}, issn = {1949-2553}, mesh = {Humans ; *Bias ; Diagnostic Imaging/methods/standards ; Image Processing, Computer-Assisted/methods/standards ; Algorithms ; Neural Networks, Computer ; Radiology/methods/standards ; }, abstract = {Persistence barcodes emerge as a promising tool in radiological analysis, offering a novel approach to reduce bias and uncover hidden patterns in medical imaging. By leveraging topological data analysis, this technique provides a robust, multi-scale perspective on image features, potentially overcoming limitations in traditional methods and Graph Neural Networks. While challenges in interpretation and implementation remain, persistence barcodes show significant potential for improving diagnostic accuracy, standardization, and ultimately, patient outcomes in the evolving field of radiology.}, }
@article {pmid39534110, year = {2024}, author = {Oeum, K and Suong, M and Uon, K and Jobert, L and Bellafiore, S and Comte, A and Thomas, E and Kuok, F and Moulin, L}, title = {Comparison of plant microbiota in diseased and healthy rice reveals methylobacteria as health signatures with biocontrol capabilities.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1468192}, pmid = {39534110}, issn = {1664-462X}, abstract = {INTRODUCTION: Rice (Oryza sativa) is a staple food worldwide, but its production is under constant pressure from both abiotic and biotic stresses, resulting in high use of agrochemicals. The plant microbiome harbours microorganisms that can benefit plant health and provide alternatives to the use of agrochemicals. The composition of plant microbiomes depends on many factors (soil composition, age, and health) and is considered a primary driver of future plant health. To identify plant microbiomes that protect against disease, we hypothesised that asymptomatic rice plants in fields under high pathogen pressure (i.e., healthy islands of plants among predominantly diseased plants) might harbour a microbiota that protects them from disease.<br><br>MATERIAL AND METHODS: We sampled healthy and leaf-diseased plants in rice fields with high disease incidence in Cambodia and profiled their microbiota at leaf, root, and rhizosphere levels using 16S V3V4 and 18S V4 amplicon barcoding sequencing.<br><br>RESULTS: Comparison of amplicon sequence variants (ASV) of the microbiota of healthy and diseased samples revealed both disease and healthy signatures (significant enrichment or depletion at ASV/species/genus level) in both fields. The genera Methylobacterium and Methylorubrum were identified health taxa signatures with several species significantly enriched in healthy leaf samples (Methylobacterium indicum, Methylobacterium komagatae, Methylobacterium aerolatum, and Methylorubrum rhodinum). A cultivation approach on rice samples led to the isolation of bacterial strains of these two genera, which were further tested as bioinoculants on rice leaves under controlled conditions, showing for some of them a significant reduction (up to 77%) in symptoms induced by Xanthomonas oryzae pv. oryzae infection.<br><br>DISCUSSION: We validated the hypothesis that healthy plants in fields under high disease occurrence can host specific microbiota with biocontrol capacities. This strategy could help identify new microbes with biocontrol potential for sustainable rice production.}, }
@article {pmid39532481, year = {2024}, author = {Nazar, N and Saxena, A and Sebastian, A and Slater, A and Sundaresan, V and Sgamma, T}, title = {Integrating DNA Barcoding Within an Orthogonal Approach for Herbal Product Authentication: A Narrative Review.}, journal = {Phytochemical analysis : PCA}, volume = {}, number = {}, pages = {}, doi = {10.1002/pca.3466}, pmid = {39532481}, issn = {1099-1565}, support = {//Daphne Jackson Trust/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {INTRODUCTION: Existing methods for morphological, organoleptic, and chemical authentication may not adequately ensure the accurate identification of plant species or guarantee safety. Herbal raw material authentication remains a major challenge in herbal medicine. Over the past decade, DNA barcoding, combined with an orthogonal approach integrating various testing methods for quality assurance, has emerged as a new trend in plant authentication.<br><br>OBJECTIVE: The review evaluates DNA barcoding and common alternative testing in plant-related sectors to enhance quality assurance and accurate authentication.<br><br>METHOD: Studies were selected based on their relevance to the identification, quality assurance, and safety of herbal products. Inclusion criteria were peer-reviewed articles, systematic reviews, and relevant case studies from the last two decades focused on DNA barcoding, identification methods, and their applications. Exclusion criteria involved studies lacking empirical data, those not peer-reviewed, or those unrelated to the main focus. This ensured the inclusion of high-quality, pertinent sources while excluding less relevant studies.<br><br>RESULTS: An orthogonal approach refers to the use of multiple, independent methods that provide complementary information for more accurate plant identification and quality assurance. This reduces false positives or negatives by confirming results through different techniques, combining DNA barcoding with morphological analysis or chemical profiling. It enhances confidence in results, particularly in cases of potential adulteration or misidentification of plant materials.<br><br>CONCLUSION: This study highlights the persistent challenges in assuring the quality, purity, and safety of plant materials. Additionally, it stresses the importance of incorporating DNA-based authentication alongside traditional methods, to enhance plant material identification.}, }
@article {pmid39532139, year = {2024}, author = {Calderón-Gutiérrez, F and Labonté, JM and Gonzalez, BC and Iliffe, TM and Mejía-Ortíz, LM and Borda, E}, title = {Cryptic diversity patterns of subterranean estuaries.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2034}, pages = {20241483}, pmid = {39532139}, issn = {1471-2954}, support = {//T3: Texas A&amp;M Triads for transformation/ ; //Texas A&amp;M University Galveston/ ; //Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; //CONACYT- Texas A&amp;M University/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //National Science Foundation/ ; //Texas A&amp;M University San Antonio/ ; }, mesh = {*RNA, Ribosomal, 16S/analysis ; *Estuaries ; *Biodiversity ; Animals ; *Electron Transport Complex IV/genetics/analysis ; *DNA Barcoding, Taxonomic ; *Phylogeny ; Mexico ; Sequence Analysis, DNA ; Genetic Variation ; Invertebrates/genetics ; }, abstract = {Subterranean estuaries are coastal ecosystems characterized by vertically stratified groundwater. The biota within these ecosystems is relatively understudied due to the inherent difficulty of accessing such extreme environments. The fauna inhabiting these ecosystems is considered vulnerable to extinction, and the presence of cryptic species has major implications for research and conservation efforts. Most species lack molecular data; however, the evaluation of genetic data for some taxa has revealed that undocumented species are common. This study employs molecular species delimitation methods and DNA barcoding through the analysis of publicly and newly generated sequences, including individuals from type localities and non-crustacean phyla; the latter are typically overlooked in biodiversity assessments of subterranean estuaries. We analysed 376 cytochrome c oxidase subunit I (COI) gene sequences and 154 16S rRNA gene sequences. The COI sequences represented 32% of previously described species and 50% of stygobiont species from the Yucatan Peninsula and Cozumel Island, while sequences of the 16S rRNA represented 14% of described species and 22% of stygobionts. Our results revealed cryptic genetic lineages and taxonomic misidentification of species. As several species from these ecosystems are recognized as endangered, the use of molecular approaches will improve biodiversity estimates and highlight overlooked cryptic lineages in need of evaluation of conservation status.}, }
@article {pmid39529423, year = {2024}, author = {Bustamante, MI and Elfar, K and Carachure, C and Adaskaveg, A and Kabashima, JN and Shogren, C and Eskalen, A and Lynch, SC}, title = {Etiology of Pine Ghost Canker in Southern California Urban Forests.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-08-24-1718-SR}, pmid = {39529423}, issn = {0191-2917}, abstract = {Pine ghost canker is a recently described disease affecting multiple pine species in urban forests of Southern California. Symptoms include wedged cankers with irregular margins and cryptic discoloration on cross-sections of branches, which can lead to severe dieback and potentially tree death. In this study, we identified and characterized five Neofusicoccum species (N. luteum, N. mediterraneum, N. parvum, N. stellenboschianum, and N. vitifusiforme) as the primary etiological agents of pine ghost canker. These pathogens were consistently isolated from multiple symptomatic pine samples (n = 41) and identified by morphology and phylogenetic analyses using four DNA barcodes (rDNA ITS, tef1, tub2, and rpb2). Pathogenicity was confirmed on healthy branches of 15-year-old Monterey pines, where the five Neofusicoccum species, caused vascular lesions that were not significantly different in length. Secondary fungi (Diaporthe, Diplodia, Neopestalotiopsis, and Pestalotiopsis spp.) were also recovered from symptomatic tissues but did not cause vascular lesions in pathogenicity tests. The optimal temperature for mycelial growth of N. luteum and N. parvum was 30 °C, whereas for N. mediterraneum, N. stellenboschianum and N. vitifusiforme, it was 25 °C. All five species were able to resume growth at room temperature (20 °C) after showing no growth during a 7-day exposure to 5 °C and 40 °C. This study constitutes the first report of N. luteum, N. stellenboschianum, and N. vitifusiforme causing pine ghost canker in California. Environmental factors such as warmer temperatures, irrigation, and pest infestations are discussed as drivers of disease expression in pine trees. Management practices are also proposed.}, }
@article {pmid39526732, year = {2024}, author = {Soto-Serrano, A and Li, W and Panah, FM and Hui, Y and Atienza, P and Fomenkov, A and Roberts, RJ and Deptula, P and Krych, L}, title = {Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.}, journal = {Microbial genomics}, volume = {10}, number = {11}, pages = {}, doi = {10.1099/mgen.0.001316}, pmid = {39526732}, issn = {2057-5858}, mesh = {*Genome, Bacterial ; *Base Composition ; Nanopores ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Nanopore Sequencing/methods ; }, abstract = {The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at a lower cost, yet its error rate raises scepticism. Recent ONT advancements, such as new Flow cells (R10.4.1), chemistry (V14) and duplex mode, improve data quality. Our study compares ONT with PacBio and Illumina, including hybrid data. We used Propionibacterium freudenreichii, a bacterium with a genome known for being difficult to reconstruct. By combining data from ONT's Native Barcoding and a custom-developed BARSEQ method, we achieved high-quality, near-perfect genome assemblies. Our findings demonstrate, for the first time, that the combination of nanopore-only long-native with shorter PCR DNA reads (~3 kb) results in high-quality genome reconstruction, comparable to hybrid data assembly from two sequencing platforms. This endorses ONT as a cost-effective, stand-alone strategy for bacterial genome reconstruction. Additionally, we compared methylated motif detection between PacBio and ONT R10.4.1 data, showing that results comparable to PacBio are achievable using ONT, especially when utilizing the advanced Nanomotif tool.}, }
@article {pmid39523608, year = {2024}, author = {Hosuru, RV and Yang, J and Zhou, Y and Gin, A and Hayal, TB and Hong, SG and Dunbar, CE and Wu, C}, title = {Long-term tracking of haematopoietic clonal dynamics and mutations in non-human primate undergoing transplantation of lentivirally barcoded haematopoietic stem and progenitor cells.}, journal = {British journal of haematology}, volume = {}, number = {}, pages = {}, doi = {10.1111/bjh.19889}, pmid = {39523608}, issn = {1365-2141}, support = {/HI/NHLBI NIH HHS/United States ; }, abstract = {Haematopoietic stem and progenitor cell (HSPC) autologous gene therapies are promising treatment for a variety of blood disorders. Investigation of the long-term HSPC clonal dynamics and other measures of safety and durability following lentiviral-mediated gene therapies in predictive models are crucial for assessing risks and benefits in order to inform decisions regarding wider utilization. We established an autologous lentivirally barcoded HSPC transplantation model in rhesus macaque (RM), a model offering insights into haematopoiesis and gene therapies with direct relevance to human. Healthy young adult RMs underwent total body irradiation, followed by transplantation of autologous HSPCs transduced with a lentiviral vector containing a diverse genetic barcode library, uniquely labelling individual HSPCs and their progeny. With up to 131 months of follow-up, we now report quantitative clonal dynamics, characterizing the number, diversity, stability and lineage bias of hundreds of thousands of HSPC clones tracked in five RMs. We documented long-term stable and multi-lineage output from a highly polyclonal pool of HSPCs. Clonal succession after stable haematopoietic reconstitution was minimal. There was no evidence for accelerated acquisition of acquired somatic mutations following autologous lentivirally transduced HSPC transplantation. Our results provide relevant insights into long-term HSPC behaviours in vivo following transplantation and gene therapies.}, }
@article {pmid39521085, year = {2024}, author = {Bálint, M and Tumusiime, J and Nakintu, J and Baranski, D and Schardt, L and Romahn, J and Dusabe, MC and Tolo, CU and Kagoro, GR and Ssenkuba, F and Junginger, A and Albrecht, C}, title = {Environmental DNA barcoding reveals general biodiversity patterns in the large tropical rift Lake Albert.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177308}, doi = {10.1016/j.scitotenv.2024.177308}, pmid = {39521085}, issn = {1879-1026}, abstract = {Lake Albert, Africa's seventh-largest lake and a biodiversity hotspot, faces significant environmental challenges, including unregulated anthropogenic pressure and a lack of comprehensive biological studies. To address the scarcity of biodiversity data, we utilized environmental DNA (eDNA) metabarcoding to assess the lake's eukaryotic and metazoan communities. Surface water samples were collected at three distinct locations: close to the southern inflow of the Semliki River, the central part of the lake, and close to the northern inflow of the Victoria Nile and outflow of the Albert Nile. We aimed to study ecological patterns across the lake, focusing on sequence variant richness and community composition, testing for differences among locations and between shoreline and pelagic zones. Consistent with previous morphology-based observations, our results revealed differences in community composition among the three sites, with cyclopoid copepods dominating the communities. Distance from shore was a significant factor influencing community composition, confirming expectations about the effects of nutrient and oxygen availability gradients. However, the lack of comprehensive reference sequence data limited accurate taxonomic assignments. Despite these limitations, our study demonstrates that eDNA metabarcoding is highly useful for assessing biodiversity in underexplored tropical freshwater ecosystems. We advocate for urgent efforts to generate reference sequences from tropical regions to enhance the utility of eDNA for biodiversity monitoring and conservation. Our findings underscore the potential of eDNA in providing insights into ecological patterns of entire communities and emphasize the need for comprehensive studies addressing the full taxonomic spectrum in tropical freshwater ecosystems.}, }
@article {pmid39519959, year = {2024}, author = {Pun, TB and Thapa Magar, R and Koech, R and Owen, KJ and Adorada, DL}, title = {Emerging Trends and Technologies Used for the Identification, Detection, and Characterisation of Plant-Parasitic Nematode Infestation in Crops.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {21}, pages = {}, pmid = {39519959}, issn = {2223-7747}, abstract = {Accurate identification and estimation of the population densities of microscopic, soil-dwelling plant-parasitic nematodes (PPNs) are essential, as PPNs cause significant economic losses in agricultural production systems worldwide. This study presents a comprehensive review of emerging techniques used for the identification of PPNs, including morphological identification, molecular diagnostics such as polymerase chain reaction (PCR), high-throughput sequencing, meta barcoding, remote sensing, hyperspectral analysis, and image processing. Classical morphological methods require a microscope and nematode taxonomist to identify species, which is laborious and time-consuming. Alternatively, quantitative polymerase chain reaction (qPCR) has emerged as a reliable and efficient approach for PPN identification and quantification; however, the cost associated with the reagents, instrumentation, and careful optimisation of reaction conditions can be prohibitive. High-throughput sequencing and meta-barcoding are used to study the biodiversity of all tropical groups of nematodes, not just PPNs, and are useful for describing changes in soil ecology. Convolutional neural network (CNN) methods are necessary to automate the detection and counting of PPNs from microscopic images, including complex cases like tangled nematodes. Remote sensing and hyperspectral methods offer non-invasive approaches to estimate nematode infestations and facilitate early diagnosis of plant stress caused by nematodes and rapid management of PPNs. This review provides a valuable resource for researchers, practitioners, and policymakers involved in nematology and plant protection. It highlights the importance of fast, efficient, and robust identification protocols and decision-support tools in mitigating the impact of PPNs on global agriculture and food security.}, }
@article {pmid39519254, year = {2024}, author = {Tshiabuila, D and Choga, W and San, JE and Maponga, T and Van Zyl, G and Giandhari, J and Pillay, S and Preiser, W and Naidoo, Y and Baxter, C and Martin, DP and de Oliveira, T}, title = {An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings.}, journal = {International journal of molecular sciences}, volume = {25}, number = {21}, pages = {}, pmid = {39519254}, issn = {1422-0067}, support = {U01 AI151698/AI/NIAID NIH HHS/United States ; }, mesh = {*Hepatitis B virus/genetics ; Humans ; *Genome, Viral ; *Genotype ; Nanopore Sequencing/methods ; Hepatitis B, Chronic/virology/diagnosis/epidemiology ; Phylogeny ; High-Throughput Nucleotide Sequencing/methods ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Genomics/methods ; Nanopores ; Drug Resistance, Viral/genetics ; Hepatitis B/diagnosis/virology/epidemiology ; Genetic Variation ; }, abstract = {Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A-J). Tests to determine HBV genotypes are based on full-genome sequencing or reverse hybridization. In practice, both approaches have limitations. Whereas diagnostic sequencing, generally using the Sanger approach, tends to focus only on the S-gene and yields little or no information on intra-patient HBV genetic diversity, reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV diagnostic sequencing protocol suitable for clinical virology that yields both complete genome sequences and extensive intra-patient HBV diversity data. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit (Oxford nanopore Technologies, Oxford, OX4 4DQ, UK), ONT GridION sequencing, genotyping using genome detective software v1.132/1.133, a recombination analysis using jpHMM (26 October 2011 version) and RDP5.61 software, and drug resistance profiling using Geno2pheno v2.0 software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 residual diagnostic samples from HBV-infected patients in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.}, }
@article {pmid39516507, year = {2024}, author = {Rodrigues, BL and de Oliveira, AG and da Silva, LEH and Vasconcelos Dos Santos, T and de Oliveira, LNC and Rêgo, FD and de Andrade, AJ and Maia, GB and de Souza Pinto, I and Andrade Filho, JD and Galati, EAB}, title = {Hidden diversity in anthropophilic sand flies of the Monticola Series (Diptera, Psychodidae).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27215}, pmid = {39516507}, issn = {2045-2322}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 314260/2023-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2023/03715-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Animals ; *Phylogeny ; *Psychodidae/genetics/classification/anatomy &amp; histology ; *Electron Transport Complex IV/genetics ; *Haplotypes ; Brazil ; *Genetic Variation ; }, abstract = {The Monticola series comprises two anthropophilic and widely distributed species in Brazil: Pintomyia (Pifanomyia) monticola (Costa Lima, 1932) and Pintomyia (Pifanomyia) misionensis (Castro, 1959). They mainly occur in the Atlantic Rainforest, and it is known that Pi. monticola comprises at least two well-structured genetic lineages regarding a fragment of the cytochrome c oxidase subunit I (COI) gene. Here, we aim to elucidate the taxonomic status of this group using integrative taxonomy tools. Collections were performed in nine localities of four Brazilian states, and COI fragments were sequenced and merged with publicly available data. Several single-locus species delimitation algorithms, genetic distance metrics, phylogenetic trees, and haplotype networks were used to uncover cryptic diversity and population structure within Pi. monticola and Pi. misionensis. The resulting genetic clusters were then tested for morphological differences through linear and geometric morphometry of several characters. We analyzed 152 COI sequences, comprising 48 haplotypes. The maximum intraspecific p distances were 8.21% (mean 4.17%) and 9.12% (mean 4.4%) for Pi. monticola and Pi. misionensis, respectively, while interspecific ones ranged from 10.94 to 14.09% (mean 12.33%). Phylogenetic gene trees showed well-supported clades for both species, with clear structuring patterns within them. Species-delimitation algorithms split our dataset into at least three putative species for each taxon. Moreover, population structure analysis showed a strong correlation between Atlantic Forest areas of endemism as sources of molecular variation in Pi. monticola. Morphometric analyses were significant for wing shape variation and some linear measurements (mainly of the head) when comparing specimens of different genetic clusters for both taxa. These results indicate strong genetic structuring of Monticola series species, confirmed by morphometry, indicating two possible cryptic species complexes.}, }
@article {pmid39514381, year = {2024}, author = {Barone, ML and Wilson, JD and Zapata, L and Soto, EM and Haddad, CR and Grismado, C and Izquierdo, M and Arias, E and Pizarro-Araya, J and Briones, R and Barriga, JE and Peralta, L and Ramírez, MJ}, title = {Genetic barcodes for species identification and phylogenetic estimation in ghost spiders (Araneae: Anyphaenidae: Amaurobioidinae).}, journal = {Invertebrate systematics}, volume = {38}, number = {}, pages = {}, doi = {10.1071/IS24053}, pmid = {39514381}, issn = {1447-2600}, mesh = {*Spiders/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Electron Transport Complex IV/genetics ; Species Specificity ; Algorithms ; }, abstract = {The identification of spider species presents many challenges, since in most cases the characters used are from genital structures that are only fully developed in the adult stage, hence the identification of immatures is most often not possible. Additionally, these structures usually also present some intra-specific variability, which in some cases makes the identification of closely related species difficult. The genetic barcode technique (DNA barcodes), based on sequencing of the mitochondrial marker cytochrome c oxidase subunit I (COI), has proven a useful, complementary tool to overcome these limitations. In this work, the contribution of DNA barcoding to the taxonomy of the subfamily Amaurobioidinae is explored using the refined single linkage analysis (RESL) algorithm for the delimitation of operational taxonomic units (OTUs), in comparison with the assemble species by automatic partitioning (ASAP) algorithm, and presented in conjunction with an updated molecular phylogenetic analysis of three other markers (28S rRNA, 16S rRNA, Histone H3), in addition to COI . Of a total of 97 included species identified by morphology, 82 species were concordant with the operational taxonomic units obtained from RESL, representing an 85% correspondence between the two methods. Similar results were obtained using the ASAP algorithm. Previous observations of morphological variation within the same species are supported, and this technique provides new information on genetic structure and potentially cryptic species. Most of the discrepancies between DNA barcoding and morphological identification are explained by low geographic sampling or by divergent or geographically structured lineages. After the addition of many specimens with only COI data, the multi-marker phylogenetic analysis is consistent with previous results and the support is improved. The markers COI , closely followed by 28S , are the most phylogenetically informative. We conclude that the barcode DNA technique is a valuable source of data for the delimitation of species of Amaurobioidinae, in conjunction with morphological and geographic data, and it is also useful for the detection of cases that require a more detailed and meticulous study.}, }
@article {pmid39512489, year = {2024}, author = {Rodrigues, IVB and de Souza, PGC and Nunes, RC and Nunes Godeiro, N and Bellini, BC}, title = {A century later: a new species of Mastigoceras Handschin, 1924 (Collembola, Orchesellidae), with morphological and systematic updates on the genus.}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {79-100}, pmid = {39512489}, issn = {1313-2989}, abstract = {Mastigocerascamponoti Handschin, the sole member of its genus and the Mastigocerini tribe, exhibits unusual dorsal chaetotaxy compared to other Orchesellidae. This includes a reduction in dorsal macrochaetotaxy and a secondary covering of fusiform scales intermixed with ciliate microchaetae. Despite three redescriptions, Mastigoceras chaetotaxy remains poorly understood, with no data on tergal sensilla patterns or dorsal macrochaetae homology. Here, the genus is revisited by describing a new Brazilian species a century after the original description of M.camponoti, based on morphological depiction combined with the use of DNA barcoding, Mastigocerashandschini Rodrigues, Souza &amp; Bellini, sp. nov. The two species are differentiated by a few and unusual aspects of the dorsal chaetotaxy, especially scales distribution, and may be considered as pseudocryptic taxa. Our study of tergal sensilla formula, scales morphology, and distribution in Mastigoceras reveals no clear morphological support for placing Mastigocerini within Heteromurinae.}, }
@article {pmid39512488, year = {2024}, author = {Lewis, JH and Kojima, H and Suenaga, M and Petsopoulos, D and Fujisawa, Y and Truong, XL and Warren, DL}, title = {The era of cybertaxonomy: X-ray microtomography reveals cryptic diversity and concealed cuticular sculpture in Aphanerostethus Voss, 1957 (Coleoptera, Curculionidae).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {1-45}, pmid = {39512488}, issn = {1313-2989}, abstract = {Weevils represent one of the most speciose and economically important animal clades, but remain poorly studied across much of the Oriental Region. Here, an integrative revision of the Oriental, flightless genus Aphanerostethus Voss, 1957 (Curculionidae: Molytinae) based on X-ray microtomography, multi-gene DNA barcoding (CO1, Cytb, 16S), and traditional morphological techniques (light microscopy, dissections) is presented. Twelve new species, namely, A.armatus Lewis &amp; Kojima, sp. nov., A.bifidus Kojima &amp; Lewis, sp. nov., A.darlingi Lewis, sp. nov., A.decoratus Lewis &amp; Kojima, sp. nov., A.falcatus Kojima, Lewis &amp; Fujisawa, sp. nov., A.incurvatus Kojima &amp; Lewis, sp. nov., A.japonicus Lewis &amp; Kojima, sp. nov., A.magnus Lewis &amp; Kojima, sp. nov., A.morimotoi Kojima &amp; Lewis, sp. nov., A.nudus Lewis &amp; Kojima, sp. nov., A.spinosus Lewis &amp; Kojima, sp. nov., and A.taiwanus Lewis, Fujisawa &amp; Kojima, sp. nov. are described from Japan, Taiwan, Vietnam, and Malaysia. A neotype is designated for A.vannideki Voss, 1957. The hitherto monotypic genus Darumazo Morimoto &amp; Miyakawa, 1985, syn. nov. is synonymized under Aphanerostethus based on new morphological data and Aphanerostethusdistinctus (Morimoto &amp; Miyakawa, 1985), comb. nov. is transferred accordingly. X-ray microtomography is successfully used to explore for stable interspecific differences in cuticular, internal and micro morphology. Remarkable species-specific sexual dimorphism in the metatibial uncus is described in seven of the newly described Aphanerostethus species and the evolution of this character is discussed.}, }
@article {pmid39502327, year = {2024}, author = {Mao, H and Wang, Z and Shan, Y and Cheng, X and Yu, J}, title = {The complete genome sequence of the chloroplast of Bidens aurea.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {9}, number = {11}, pages = {1487-1491}, pmid = {39502327}, issn = {2380-2359}, abstract = {Bidens aurea (Asteraceae), a native of tropical America is now widespread in Asia and the Americas. We explored the B. aurea chloroplast genome and conducted a phylogenetic analysis. The chloroplast genome was circular, consisting of a large single copy (LSC) of 83,909 base pairs (bp), a small single copy (SSC) of 18,407 bp, and two inverted repeat regions (IR) of 24,729 bp each. Phylogenetic analysis showed that the 19 Bidens taxa were divided into five major clades, and B. aurea was most closely related to two species. Our findings offer a high-quality B. aurea chloroplast genome, aiding DNA barcode development and evolutionary history reconstruction.}, }
@article {pmid39501899, year = {2024}, author = {Zhang, T and Dong, B and Wang, H and Zhang, S}, title = {An innovative electrohydrodynamics-driven SERS platform for molecular stratification and treatment monitoring of lung cancer.}, journal = {Journal of materials chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4tb01434k}, pmid = {39501899}, issn = {2050-7518}, abstract = {The advancement of molecular diagnostics for lung cancer stratification and monitoring is essential for the strategic planning and prompt modification of treatments, aiming to enhance clinical results. To address this need, we suggest a nanocavity structure designed to sensitively analyze the protein signature on small extracellular vesicles (sEVs). This approach facilitates precise, noninvasive staging and treatment monitoring of lung cancer. The nanocavity is created through molecular recognition, involving the interaction of sEVs with nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and asymmetric, mirrorlike gold microelectrodes. By applying an alternating current to the gold microelectrodes, a nanofluidic shear force was generated, promoting the binding of sEVs and the effective assembly of the nanoboxes. This interaction induced a nanocavity between the nanobox and the gold microelectrode, which significantly amplified the electromagnetic field. This amplification enhanced Raman signals from four SERS barcodes simultaneously, allowing the generation of patient-specific molecular sEV signatures. When tested on a cohort of clinical samples (n = 76) using the nanocavity architecture, these patient-specific sEV molecular signatures accurately identified, stratified, and monitored lung cancer patients' treatment, demonstrating its potential for clinical application.}, }
@article {pmid39497575, year = {2024}, author = {Velázquez-Urrieta, Y and García-Varela, M and Pérez-Ponce de León, G}, title = {Assessing the diversity of freshwater fish trematodes from Laguna Escondida, Los Tuxtlas tropical rainforest, Mexico, using morphology and 28S rDNA sequences as barcodes.}, journal = {Journal of helminthology}, volume = {98}, number = {}, pages = {e67}, doi = {10.1017/S0022149X2400049X}, pmid = {39497575}, issn = {1475-2697}, mesh = {Animals ; *Trematoda/genetics/classification/isolation &amp; purification/anatomy &amp; histology ; Mexico ; *Fishes/parasitology ; *RNA, Ribosomal, 28S/genetics ; *Phylogeny ; *DNA Barcoding, Taxonomic ; *Fresh Water/parasitology ; *DNA, Ribosomal/genetics ; *Rainforest ; Fish Diseases/parasitology ; Biodiversity ; Trematode Infections/parasitology/veterinary ; DNA, Helminth/genetics ; Lakes/parasitology ; }, abstract = {Despite a great effort made for almost 90 years, the diversity of freshwater fish trematodes in Mexico is still far from being fully known. The addition of molecular data to the description of trematode diversity in the last two decades added the potential to establish more robust species limits and a more accurate biodiversity estimation, but also led in some instances to the recognition of cryptic species complexes. Here, we used sequences of the large subunit of the nuclear ribosomal gene (28S rRNA) as barcodes, and morphological data, to assess the diversity of freshwater fish trematodes from a lake within a tropical rainforest. Eighty freshwater fish specimens of eight species were studied, and 120 trematode specimens were collected. Morphologically, specimens were allocated into nine genera; molecular phylogenetic analyses along with sequence divergence data provided evidence for recognising 11 trematode taxa, six adults and five metacercariae; six of them were identified to species level. Geographical distribution and host association patterns are briefly discussed for each trematode taxa.}, }
@article {pmid39497202, year = {2024}, author = {Benallal, KE and Mefissel, M and Dib, Y and Depaquit, J and Kavan, D and Harrat, Z and Dvořák, V and Volf, P and Halada, P}, title = {Phlebotomine sand fly survey, blood meal source identification, and description of Sergentomyia imihra n. sp. in the central Sahara of Algeria.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {449}, pmid = {39497202}, issn = {1756-3305}, mesh = {Animals ; Algeria ; *Psychodidae/classification/physiology/anatomy &amp; histology ; Female ; Humans ; *Insect Vectors/classification/physiology/parasitology/anatomy &amp; histology ; *Feeding Behavior ; Phlebotomus/classification/anatomy &amp; histology/physiology/genetics ; Male ; Leishmaniasis/transmission ; Leishmania/genetics/physiology/classification ; Goats/parasitology ; }, abstract = {BACKGROUND: Phlebotomine sand flies (Diptera: Psychodidae) are important vectors of various pathogens, mainly Leishmania parasites. In the Old World, the most important genus in term of pathogens transmission is the genus Phlebotomus, which includes many proven or suspected vectors of several Leishmania species, while the genus Sergentomyia remains so far unproven as a vector of human pathogens. Algeria is one of the most affected countries by human leishmaniasis.<br><br>METHODS: In the present study, an entomological survey was carried out in two provinces, Gharda&#xef;a and Illizi, located in the north and central Sahara, respectively, where cases of human leishmaniasis are recorded. Our goal was to understand the role of the local sand fly species in the transmission of Leishmania parasites and to analyze their blood meal preferences. Collected sand flies were identified by a combination of morphological and molecular approaches that included DNA-barcoding and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein profiling. In addition, female blood meals were analyzed by peptide mass mapping using MALDI-TOF MS.<br><br>RESULTS: In total, 640 sand fly specimens belonging to Phlebotomus and Sergentomyia genera were collected in the two provinces. Sergentomyia antennata and Se.&#xa0;fallax were most abundant species in Gharda&#xef;a, and Ph.&#xa0;papatasi and Ph.&#xa0;alexandri in Illizi. In addition, a new sand fly species was described in Illizi named Sergentomyia (Sergentomyia) imihra n. sp. Blood meal analysis of the engorged females revealed various mammalian hosts, especially goats, but also humans for Phlebotomus papatasi and Ph.&#xa0;alexandri, suggesting that these vector species are opportunistic feeders.<br><br>CONCLUSIONS: Integrative approach that combined morphological analysis, sequencing of DNA markers, and protein profiling enabled the recognition and description of a new Sergentomyia species, raising the number of the Algerian sand fly fauna to 27 species. Further sand fly surveillance in the central Sahara is recommended to identify the thus-far unknown males of Se.&#xa0;imihra n. sp.}, }
@article {pmid39497190, year = {2024}, author = {Qi, J and Li, Z and Zhang, YZ and Li, G and Gao, X and Han, R}, title = {TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {285}, pmid = {39497190}, issn = {1474-760X}, mesh = {*Nanopore Sequencing/methods ; *Software ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Nanopores ; }, abstract = {Oxford Nanopore Technologies (ONT) offers ultrahigh-throughput multi-sample sequencing but only provides barcode kits that enable up to 96-sample multiplexing. We present TDFPS-Designer, a new toolkit for nanopore sequencing barcode design, which creates significantly more barcodes: 137 with a length of 20 base pairs, 410 at 24 bp, and 1779 at 30 bp, far surpassing ONT's offerings. It includes GPU-based acceleration for ultra-fast demultiplexing and designs robust barcodes suitable for high-error ONT data. TDFPS-Designer outperforms current methods, improving the demultiplexing recall rate by 20% relative to Guppy, without a reduction in precision.}, }
@article {pmid39497089, year = {2024}, author = {Zhang, J and Zhou, D and Chen, W and Lin, P and Zhao, S and Wang, M and Wang, H and Shi, S and Mehmood, F and Ye, X and Meng, J and Zhuang, W}, title = {Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1046}, pmid = {39497089}, issn = {1471-2229}, mesh = {*Phylogeny ; *Genome, Chloroplast ; *Endangered Species ; *Orchidaceae/genetics/classification ; Genomics ; Microsatellite Repeats/genetics ; Chloroplasts/genetics ; }, abstract = {BACKGROUND: Habenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear.<br><br>RESULTS: We sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259-155,269&#xa0;bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections.<br><br>CONCLUSIONS: The results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.}, }
@article {pmid39494514, year = {2024}, author = {Pradhan, R and Chimene, D and Ko, BS and Goncharov, A and Ozcan, A and McShane, MJ}, title = {Insertable Biomaterial-Based Multianalyte Barcode Sensor toward Continuous Monitoring of Glucose and Oxygen.}, journal = {ACS sensors}, volume = {9}, number = {11}, pages = {6060-6070}, doi = {10.1021/acssensors.4c01926}, pmid = {39494514}, issn = {2379-3694}, mesh = {*Oxygen/chemistry ; *Biosensing Techniques/methods/instrumentation ; *Hydrogels/chemistry ; *Biocompatible Materials/chemistry ; Animals ; Glucose/analysis ; Polyethylene Glycols/chemistry ; Blood Glucose/analysis ; Humans ; }, abstract = {Chronic diseases, including diabetes, cardiovascular diseases, and microvascular complications, contribute significantly to global morbidity and mortality. Current monitoring tools such as glucometers and continuous glucose monitors only measure one analyte; multiplexing technologies offer a promising approach for monitoring multiple biomarkers, enabling the management of comorbidities and providing more comprehensive disease insights. In this work, we describe a miniaturized optical "barcode" sensor with high biocompatibility for the continuous monitoring of glucose and oxygen. This enzymatic sensor relies on oxygen consumption in proportion to local glucose levels and the phosphorescence reporting of tissue oxygen with a lifetime-based probe. The sensor was specifically designed to operate in a tissue environment with low levels of dissolved oxygen. The barcode sensor consists of a poly(ethylene glycol) diacrylate (PEGDA) hydrogel with four discrete compartments separately filled with glucose- or oxygen-sensing phosphorescent microparticles. We evaluated the response of the barcode hydrogels to fluctuating glucose levels over the physiological range under low oxygen conditions, demonstrating the controlled tuning of dynamic range and sensitivity. Moreover, the barcode sensor exhibited remarkable storage stability over 12 weeks, along with full reversibility and excellent reproducibility (∼6% variability in the phosphorescence lifetime) over nearly 50 devices. Electron beam sterilization had a negligible effect on the glucose response of the barcode sensors. Furthermore, our investigation revealed minimal phosphorescence lifetime changes in oxygen compartments while exhibiting increased lifetime in glucose-responsive compartments when subjected to alternating glucose concentrations (0 and 200 mg/dL), showcasing the sensor's multianalyte sensing capabilities without crosstalk between compartments. Additionally, the evaluation of chronic tissue response to sensors inserted in pigs revealed the appropriate biocompatibility of the barcodes as well as excellent material stability over many months. These findings support further development of similar technologies for introducing optical assays for multiple biomarkers that can provide continuous or on-demand feedback to individuals to manage chronic conditions.}, }
@article {pmid39494108, year = {2024}, author = {Yetchom Fondjo, JA and Nzoko Fiemapong, AR and Tindo, M and Duressa, TF and Ivković, S and Husemann, M}, title = {Taxonomic review of the grasshopper genus Pteropera Karsch, 1891 (Orthoptera, Acrididea, Catantopinae) with description of three new species and a preliminary phylogeny of the Cameroonian species.}, journal = {ZooKeys}, volume = {1216}, number = {}, pages = {219-264}, pmid = {39494108}, issn = {1313-2989}, abstract = {The Afrotropical grasshopper genus Pteropera Karsch, 1891, is reviewed. Some species present in Cameroon are described, Pteroperaaugustini Donskoff, 1981, is recorded for the first time in the country, and three new species are described from Cameroon, Pteroperakennei Yetchom &amp; Husemann, sp. nov., Pteroperamatzkei Yetchom &amp; Husemann, sp. nov. and Pteroperamissoupi Yetchom &amp; Husemann, sp. nov., increasing the number of Pteropera species in Cameroon from eight to 12, and overall to 30 species in Central Africa. An updated key of Pteropera is provided. Photographs with data on the distributions of all known species are given. In addition, a phylogenetic tree was constructed using maximum likelihood and Bayesian inference on the basis of a concatenated dataset of COI, 16S, and 12S markers of available Cameroonian species. The maximum likelihood and Bayesian inference analyses of the concatenated datasets resulted in a well-resolved phylogeny of the group and species of Pteropera were recovered as monophyletic, largely with high support. In all cases, the discrimination of all studied species based on barcode information was congruent with the species limits determined by traditional taxonomy. Our findings show the potential of integrative taxonomy to resolve the relationships among grasshoppers below the family level. Further analyses, including more comprehensive taxon sampling and additional nuclear markers, are needed, and the occurrence of several taxa still needs to be confirmed in African rainforests.}, }
@article {pmid39490742, year = {2024}, author = {Surwase, SS and Zhou, XMM and Luly, KM and Zhu, Q and Anders, RA and Green, JJ and Tzeng, SY and Sunshine, JC}, title = {Highly Multiplexed Immunofluorescence PhenoCycler Panel for Murine Formalin-Fixed Paraffin-Embedded Tissues Yields Insight Into Tumor Microenvironment Immunoengineering.}, journal = {Laboratory investigation; a journal of technical methods and pathology}, volume = {105}, number = {1}, pages = {102165}, doi = {10.1016/j.labinv.2024.102165}, pmid = {39490742}, issn = {1530-0307}, abstract = {Spatial proteomics profiling is an emerging set of technologies that has the potential to elucidate the cell types, interactions, and molecular signatures that make up complex tissue microenvironments, with applications in the study of cancer, immunity, and much more. An emerging technique in the field is CoDetection by indEXing, recently renamed as the PhenoCycler system. This is a highly multiplexed immunofluorescence imaging technology that relies on oligonucleotide-barcoded antibodies and cyclic immunofluorescence to visualize many antibody markers in a single specimen while preserving tissue architecture. Existing PhenoCycler panels are primarily designed for fresh frozen tissues. Formalin-fixed paraffin-embedded blocks offer several advantages in preclinical research, but few antibody clones have been identified in this setting for PhenoCycler imaging. Here, we present a novel PhenoCycler panel of 28 validated antibodies for murine formalin-fixed paraffin-embedded tissues. We describe our workflow for selecting and validating clones, barcoding antibodies, designing our panel, and performing multiplex imaging. We further detail our analysis pipeline for comparing marker expressions, clustering and phenotyping single-cell proteomics data, and quantifying spatial relationships. We then apply our panel and analysis protocol to profile the effects of 3 gene delivery nanoparticle formulations, in combination with systemic anti-PD1, on the murine melanoma tumor immune microenvironment. Intralesional delivery of genes expressing the costimulatory molecule 4-1BBL and the cytokine IL-12 led to a shift toward intratumoral M1 macrophage polarization and promoted closer associations between intratumoral CD8 T cells and macrophages. Delivery of interferon gamma, in addition to 4-1BBL and IL-12, not only further increased markers of antigen presentation on tumor cells and intratumoral antigen-presenting cells but also promoted greater expression of checkpoint marker PD-L1 and closer associations between intratumoral CD8 T cells and PD-L1-expressing tumor cells. These findings help explain the benefits of 4-1BBL and IL-12 delivery while offering additional mechanistic insights into the limitations of interferon gamma therapeutic efficacy.}, }
@article {pmid39484616, year = {2024}, author = {Lu, X and Pritko, DJ and Abravanel, ME and Huggins, JR and Ogunleye, F and Biswas, T and Ashy, KC and Woods, SK and Livingston, MWT and Blenner, MA and Birtwistle, MR}, title = {Genetically-Encoded Fluorescence Barcodes for Single-Cell Analysis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39484616}, issn = {2692-8205}, support = {R35 GM141891/GM/NIGMS NIH HHS/United States ; }, abstract = {Genetically-encoded, single-cell barcodes are broadly useful for experimental tasks such as lineage tracing or genetic screens. For such applications, a barcode library would ideally have high diversity (many unique barcodes), non-destructive identification (repeated measurements in the same cells or population), and fast, inexpensive readout (many cells and conditions). Current nucleic acid barcoding methods generate high diversity but require destructive and slow/expensive readout, and current fluorescence barcoding methods are non-destructive, fast, and inexpensive to readout but lack high diversity. We recently proposed theory for how fluorescent protein combinations may generate a high-diversity barcode library with non-destructive, fast and inexpensive identification. Here, we present an initial experimental proof-of-concept by generating a library of ~150 barcodes from two-way combinations of 18 fluorescent proteins. We use a pooled cloning strategy to generate a barcode library that is validated to contain every possible combination of the 18 fluorescent proteins. Experimental results using single mammalian cells and spectral flow cytometry demonstrate excellent classification performance of individual fluorescent proteins, with the exception of mTFP1, and of most evaluated barcodes, with many true positive rates >99%. The library is compatible with genetic screening for hundreds of genes (or gene pairs) and lineage tracing hundreds of clones. This work lays a foundation for greater diversity libraries (potentially ~10[5] and more) generated from hundreds of spectrally-resolvable tandem fluorescent protein probes.}, }
@article {pmid39483244, year = {2024}, author = {Dockerill, M and Sabale, PM and Russo, F and Barluenga, S and Winssinger, N}, title = {Translation of Deoxyribonucleic Acid into Synthetic Alpha Helical Peptides for Darwinian Evolution.}, journal = {JACS Au}, volume = {4}, number = {10}, pages = {4013-4022}, pmid = {39483244}, issn = {2691-3704}, abstract = {DNA-encoded libraries connect the phenotypes of synthetic molecules to a DNA barcode; however, most libraries do not tap into the potential of Darwinian evolution. Herein, we report a DNA-templated synthesis (DTS) architecture to make peptides that are stabilized into α-helical conformations via head-to-tail supramolecular cyclization. Using a pilot library targeting MDM2, we show that repeated screening can amplify a binder from the lowest abundance in the library to a ranking that correlates to binding affinity. The study also highlights the need to design libraries such that the chemistry avoids biases from the heterogeneous yield in DTS.}, }
@article {pmid39480818, year = {2024}, author = {Ramesh, S and Rapp, S and Tapias Gomez, J and Levine, B and Tapias-Gomez, D and Chung, D and Truong, Z}, title = {Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0309707}, pmid = {39480818}, issn = {1932-6203}, mesh = {*User-Computer Interface ; *Software ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Databases, Nucleic Acid ; Web Browser ; }, abstract = {Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.}, }
@article {pmid39485438, year = {2024}, author = {Pham, NV and Nguyen, QN and Nguyen, TV and Nguyen, TA and Ta, VD}, title = {High quality factor, monodisperse micron-sized random lasers based on porous PLGA spheres.}, journal = {Optics letters}, volume = {49}, number = {21}, pages = {6165-6168}, doi = {10.1364/OL.538543}, pmid = {39485438}, issn = {1539-4794}, abstract = {Miniature random lasers with high quality factor are crucial for applications in barcoding, bioimaging, and on-chip technologies. However, achieving monodisperse and size-tunable biocompatible random lasers has been a significant challenge. In this study, we employed poly(lactic-co-glycolic) acid (PLGA), a biocompatible material approved for medical use, as the base material for random lasers. By integrating a dye-doped PLGA solution with a microfluidic system, we successfully fabricated monodisperse and miniature dye-doped PLGA spheres with tunable sizes ranging from 25 to 52 µm. Upon optical pulse excitation, these spheres exhibited strong random lasing emission at 610-640 nm with a threshold of approximately 22 µJ·mm[-2]. The lasing modes demonstrated a spectral linewidth of 0.2 nm, corresponding to a quality factor of 3100. Fourier transform analysis of the lasing emission revealed fundamental cavity lengths, providing insights into the properties of the random lasers.}, }
@article {pmid39482470, year = {2024}, author = {Dini, A and Barker, H and Piki, E and Sharma, S and Raivola, J and Murumägi, A and Ungureanu, D}, title = {A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery.}, journal = {Nature chemical biology}, volume = {}, number = {}, pages = {}, pmid = {39482470}, issn = {1552-4469}, support = {336449//Academy of Finland (Suomen Akatemia)/ ; 333583//Academy of Finland (Suomen Akatemia)/ ; 288475//Academy of Finland (Suomen Akatemia)/ ; 271845//Academy of Finland (Suomen Akatemia)/ ; 349787//Academy of Finland (Suomen Akatemia)/ ; }, abstract = {The gene-regulatory dynamics governing drug responses in cancer are yet to be fully understood. Here, we report a pipeline capable of producing high-throughput pharmacotranscriptomic profiling through live-cell barcoding using antibody-oligonucleotide conjugates. This pipeline combines drug screening with 96-plex single-cell RNA sequencing. We show the potential of this approach by exploring the heterogeneous transcriptional landscape of primary high-grade serous ovarian cancer (HGSOC) cells after treatment with 45 drugs, with 13 distinct classes of mechanisms of action. A subset of phosphatidylinositol 3-OH kinase (PI3K), protein kinase B (AKT) and mammalian target of rapamycin (mTOR) inhibitors induced the activation of receptor tyrosine kinases, such as the epithelial growth factor receptor (EGFR), and this was mediated by the upregulation of caveolin 1 (CAV1). This drug resistance feedback loop could be mitigated by the synergistic action of agents targeting PI3K-AKT-mTOR and EGFR for HGSOC with CAV1 and EGFR expression. Using this workflow could enable the personalized testing of patient-derived tumor samples at single-cell resolution.}, }
@article {pmid39480094, year = {2024}, author = {Alexander, LM and Khalid, S and Gallego-Lopez, GM and Astmann, TJ and Oh, J-H and Heggen, M and Huss, P and Fisher, R and Mukherjee, A and Raman, S and Choi, IY and Smith, MN and Rogers, CJ and Epperly, MW and Knoll, LJ and Greenberger, JS and van Pijkeren, J-P}, title = {Development of a Limosilactobacillus reuteri therapeutic delivery platform with reduced colonization potential.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {11}, pages = {e0031224}, pmid = {39480094}, issn = {1098-5336}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; 75N93021C00008/AI/NIAID NIH HHS/United States ; R01 GM135483/GM/NIGMS NIH HHS/United States ; //SciMed Graduate Research Scholars Program at UW-Madison/ ; 2021-67015-34316//U.S. Department of Agriculture (USDA)/ ; R01GM135483//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; U01 AI172885/AI/NIAID NIH HHS/United States ; //Louis and Elsa Thomsen Wisconsin Distinguished Graduate Fellowship from the UW-Madison College of Agricultural &amp; Life Sciences/ ; //Dissertation Completion Fellowship from the UW-Madison Graduate School/ ; U01-AI172885//HHS | National Institutes of Health (NIH)/ ; R41 AI157357/AI/NIAID NIH HHS/United States ; 1R41AI157357-01//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; MSN1856150//UW-Madison Food Research Institute/ ; }, mesh = {*Limosilactobacillus reuteri/genetics/physiology ; Animals ; Mice ; Humans ; Bacterial Adhesion ; HT29 Cells ; Adhesins, Bacterial/genetics ; Drug Delivery Systems ; Female ; }, abstract = {Bacterial biotherapeutic delivery vehicles have the potential to treat a variety of diseases. This approach obviates the need to purify the recombinant effector molecule, allows delivery of therapeutics in situ via oral or intranasal administration, and protects the effector molecule during gastrointestinal transit. Lactic acid bacteria have been broadly developed as therapeutic delivery vehicles though risks associated with the colonization of a genetically modified microorganism have so-far not been addressed. Here, we present an engineered Limosilactobacillus reuteri strain with reduced colonization potential. We applied a dual-recombineering scheme for efficient barcoding and generated mutants in genes encoding five previously characterized and four uncharacterized putative adhesins. Compared with the wild type, none of the mutants were reduced in their ability to survive gastrointestinal transit in mice. CmbA was identified as a key protein in L. reuteri adhesion to HT-29 and enteroid cells. The nonuple mutant, a single strain with all nine genes encoding adhesins inactivated, had reduced capacity to adhere to enteroid monolayers. The nonuple mutant producing murine IFN-β was equally effective as its wild-type counterpart in mitigating radiation toxicity in mice. Thus, this work established a novel therapeutic delivery platform that lays a foundation for its application in other microbial therapeutic delivery candidates and furthers the progress of the L. reuteri delivery system towards human use.IMPORTANCEOne major advantage to leverage gut microbes that have co-evolved with the vertebrate host is that evolution already has taken care of the difficult task to optimize survival within a complex ecosystem. The availability of the ecological niche will support colonization. However, long-term colonization of a recombinant microbe may not be desirable. Therefore, strategies need to be developed to overcome this potential safety concern. In this work, we developed a single strain in which we inactivated the encoding sortase, and eight genes encoding characterized/putative adhesins. Each individual mutant was characterized for growth and adhesion to epithelial cells. On enteroid cells, the nonuple mutant has a reduced adhesion potential compared with the wild-type strain. In a model of total-body irradiation, the nonuple strain engineered to release murine interferon-β performed comparable to a derivative of the wild-type strain that releases interferon-β. This work is an important step toward the application of recombinant L. reuteri in humans.}, }
@article {pmid39478489, year = {2024}, author = {Jiang, LQ and Drew, BT and Arthan, W and Yu, GY and Wu, H and Zhao, Y and Peng, H and Xiang, CL}, title = {Comparative plastome analysis of Arundinelleae (Poaceae, Panicoideae), with implications for phylogenetic relationships and plastome evolution.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1016}, pmid = {39478489}, issn = {1471-2164}, support = {31110103911//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *Poaceae/genetics/classification ; *Evolution, Molecular ; Genome, Plastid ; Base Composition ; }, abstract = {BACKGROUND: Arundinelleae is a small tribe within the Poaceae (grass family) possessing a widespread distribution that includes Asia, the Americas, and Africa. Several species of Arundinelleae are used as natural forage, feed, and raw materials for paper. The tribe is taxonomically cumbersome due to a paucity of clear diagnostic morphological characters. There has been scant genetic and genomic research conducted for this group, and as a result the phylogenetic relationships and species boundaries within Arundinelleae are poorly understood.<br><br>RESULTS: We compared and analyzed 11 plastomes of Arundinelleae, of which seven plastomes were newly sequenced. The plastomes range from 139,629 base pairs (bp) (Garnotia tenella) to 140,943&#xa0;bp (Arundinella barbinodis), with a standard four-part structure. The average GC content was 38.39%, but varied in different regions of the plastome. In all, 110 genes were annotated, comprising 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Furthermore, 539 simple sequence repeats, 519 long repeats, and 10 hyper-variable regions were identified from the 11 plastomes of Arundinelleae. A phylogenetic reconstruction of Panicoideae based on 98 plastomes demonstrated the monophyly of Arundinella and Garnotia, but the circumscription of Arundinelleae remains unresolved.<br><br>CONCLUSION: Complete chloroplast genome sequences can improve phylogenetic resolution relative to single marker approaches, particularly within taxonomically challenging groups. All phylogenetic analyses strongly support the monophyly of Arundinella and Garnotia, respectively, but the monophylly of Arundinelleae was not well supported. The intergeneric phylogenetic relationships within Arundinelleae require clarification, indicating that more data is necessary to resolve generic boundaries and evaluate the monophyly of Arundinelleae. A comprehensive taxonomic revision for the tribe is necessary. In addition, the identified hyper-variable regions could function as molecular markers for clarifying phylogenetic relationships and potentially as barcoding markers for species identification in the future.}, }
@article {pmid39478225, year = {2024}, author = {Lu, Z and Mo, S and Xie, D and Zhai, X and Deng, S and Zhou, K and Wang, K and Kang, X and Zhang, H and Tong, J and Hou, L and Hu, H and Li, X and Zhou, D and Lee, LTO and Liu, L and Zhu, Y and Yu, J and Lan, P and Wang, J and He, Z and He, X and Hu, Z}, title = {Polyclonal-to-monoclonal transition in colorectal precancerous evolution.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39478225}, issn = {1476-4687}, abstract = {Unravelling the origin and evolution of precancerous lesions is crucial for effectively preventing malignant transformation, yet our current knowledge remains limited[1-3]. Here we used a base editor-enabled DNA barcoding system[4] to comprehensively map single-cell phylogenies in mouse models of intestinal tumorigenesis induced by inflammation or loss of the Apc gene. Through quantitative analysis of high-resolution phylogenies including 260,922 single cells from normal, inflamed and neoplastic intestinal tissues, we identified tens of independent cell lineages undergoing parallel clonal expansions within each lesion. We also found polyclonal origins of human sporadic colorectal polyps through bulk whole-exome sequencing and single-gland whole-genome sequencing. Genomic and clinical data support a model of polyclonal-to-monoclonal transition, with monoclonal lesions representing a more advanced stage. Single-cell RNA sequencing revealed extensive intercellular interactions in early polyclonal lesions, but there was significant loss of interactions during monoclonal transition. Therefore, our data suggest that colorectal precancer is often founded by many different lineages and highlight their cooperative interactions in the earliest stages of cancer formation. These findings provide insights into opportunities for earlier intervention in colorectal cancer.}, }
@article {pmid39472907, year = {2024}, author = {Nguyen, TT and Nugraheni, YR and Nguyen, HLA and Arnuphapprasert, A and Pengsakul, T and Thong, LQ and Ampol, R and Siriyasatien, P and Kaewthamasorn, M}, title = {Survey of sand fly fauna in six provinces of Southern Vietnam with species identification using DNA barcoding.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {443}, pmid = {39472907}, issn = {1756-3305}, mesh = {Animals ; Vietnam/epidemiology ; *DNA Barcoding, Taxonomic ; *Psychodidae/classification/genetics ; *Phylogeny ; *Biodiversity ; Electron Transport Complex IV/genetics ; Cytochromes b/genetics ; Insect Vectors/classification/genetics ; Female ; Haplotypes ; Genetic Variation ; }, abstract = {BACKGROUND: Sand flies, belonging to the Psychodidae family, represent small, hairy insects that serve as significant vectors in various important medical and veterinary diseases. Despite being recognized by the World Health Organization as an endemic area for leishmaniasis, Southeast Asia lacks comprehensive information on the species composition and biology of sand flies. To address this, the current study aimed to survey sand fly biodiversity.<br><br>METHODS: Sand flies from six provinces in Southern Vietnam were collected using CDC light traps. Sand flies were subsequently identified morphologically and confirmed molecularly using mitochondrial cytochrome oxidase c subunit I (COI) and cytochrome b (cytb) sequences. BLASTN searches were conducted, and the species identity of sand flies was further confirmed through a Barcode of Life Database (BOLD) search utilizing COI sequences. Subsequently, nucleotide sequences were subjected to a panel of analyses including intraspecific variation, phylogenetic relationships and haplotype network. The average densities of collected sand flies (sand flies/trap/night) and species richness were also recorded.<br><br>RESULTS: A total of 753 sand flies were collected. After excluding damaged specimens, six sand fly species, namely Phlebotomus stantoni, Sergentomyia khawi, Se. silvatica, Se. barraudi, Se. bailyi and Grassomyia indica, were identified. All conspecific sand fly sequences, including Ph. stantoni, Se. barraudi, Gr. indica, Se. bailyi, Se. khawi and Se. silvatica, clustered with their reference sequences, corroborating the results of morphology-based identification, BLASTN analysis and BOLD search. For intraspecific variation of sand flies obtained from the current study, COI diversity indices were consistently higher than those of cytb.<br><br>CONCLUSIONS: This study provides the first updates on morphological and molecular characterization of sand flies in Southern Vietnam. This acquired knowledge on sand fly species composition is essential for controlling sand fly-borne diseases in this potentially endemic region.}, }
@article {pmid39470724, year = {2024}, author = {Jiang, J and Ye, X and Kong, Y and Guo, C and Zhang, M and Cao, F and Zhang, Y and Pei, W}, title = {scLTdb: a comprehensive single-cell lineage tracing database.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae913}, pmid = {39470724}, issn = {1362-4962}, support = {2022YFA1105700//National Key R&amp;D Program of China/ ; 82270123//National Natural Science Foundation of China/ ; 2024SSYS0034 to W.P.//Key R&amp;D Program of Zhejiang Province/ ; //Westlake Education Foundation/ ; }, abstract = {Single-cell lineage tracing (scLT) is a powerful technique that integrates cellular barcoding with single-cell sequencing technologies. This new approach enables the simultaneous measurement of cell fate and molecular profiles at single-cell resolution, uncovering the gene regulatory program of cell fate determination. However, a comprehensive scLT database is not yet available. Here, we present the single-cell lineage tracing database (scLTdb, https://scltdb.com) containing 109 datasets that are manually curated and analyzed through a standard pipeline. The scLTdb provides interactive analysis modules for visualizing and re-analyzing scLT datasets, especially the comprehensive cell fate analysis and lineage relationship analysis. Importantly, scLTdb also allows users to identify fate-related gene signatures. In conclusion, scLTdb provides an interactive interface of scLT data exploration and analysis, and will facilitate the understanding of cell fate decision and lineage commitment in development and diseases.}, }
@article {pmid39468463, year = {2024}, author = {Jiang, C and Liu, F and Qin, J and Hubert, N and Kang, B and Huang, L and Yan, Y}, title = {DNA barcode reference library of the fish larvae and eggs of the South China Sea: taxonomic effectiveness and geographic structure.}, journal = {BMC ecology and evolution}, volume = {24}, number = {1}, pages = {132}, pmid = {39468463}, issn = {2730-7182}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Larva/genetics/anatomy &amp; histology ; China ; Ovum ; Electron Transport Complex IV/genetics ; Gene Library ; }, abstract = {Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.}, }
@article {pmid39467896, year = {2024}, author = {Thakur, P and Khanal, S and Tapwal, A and Kumar, D and Verma, R and Chauhan, P and Sharma, N}, title = {Exploring Ganoderma lucidum: morphology, cultivation and market potential.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {11}, pages = {369}, pmid = {39467896}, issn = {1573-0972}, support = {CRG/2021/001815//DST, New Delhi/ ; CRG/2021/001815//DST, New Delhi/ ; CRG/2021/001815//DST, New Delhi/ ; }, mesh = {*Reishi/growth &amp; development/metabolism/genetics ; *Fermentation ; *Wood/microbiology ; *Phylogeny ; Biomass ; DNA Barcoding, Taxonomic ; }, abstract = {Ganoderma lucidum, known as the "mushroom of immortality," is a white rot fungus renowned for its medicinal properties, attributed to its bioactive compounds. Although species with similar morphological traits to G. lucidum are found across the globe, precise identification is made possible through DNA barcoding and molecular phylogenetic analysis. Global cultivation and wild harvesting of G. lucidum are both done in response to the growing market needs. Artificial cultivation is typically performed on sawdust, but other woody substrates and the wood log method are also employed. This cultivation leverages the fungus's ecological role in converting industrial and agricultural solid wastes into biomass, thereby producing functional food and potential pharmaceutical sources. The review consolidates research on various aspects of, including cultivation methods (sawdust, agricultural waste, wood logs, and submerged fermentation), and the current global market conditions.}, }
@article {pmid39467031, year = {2024}, author = {Fahlberg, MD and Forward, S and Assita, ER and Mazzola, M and Kiem, A and Handley, M and Yun, SH and Kwok, SJJ}, title = {Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {105}, number = {11}, pages = {838-848}, doi = {10.1002/cyto.a.24904}, pmid = {39467031}, issn = {1552-4930}, support = {R44-GM139504/NH/NIH HHS/United States ; R43-GM140527/NH/NIH HHS/United States ; R01-EB033155/NH/NIH HHS/United States ; F31HL158020-03/NH/NIH HHS/United States ; T32GM132089-01/NH/NIH HHS/United States ; 5T32GM007226-43/NH/NIH HHS/United States ; R44-GM139504/NH/NIH HHS/United States ; R43-GM140527/NH/NIH HHS/United States ; R01-EB033155/NH/NIH HHS/United States ; F31HL158020-03/NH/NIH HHS/United States ; T32GM132089-01/NH/NIH HHS/United States ; 5T32GM007226-43/NH/NIH HHS/United States ; }, mesh = {*Flow Cytometry/methods ; Humans ; *Fluorescent Dyes/chemistry ; Tissue Fixation/methods ; Biomarkers/metabolism ; Cell Line, Tumor ; }, abstract = {The fixation and permeabilization of cells are essential for labeling intracellular biomarkers in flow cytometry. However, these chemical treatments often alter fragile targets, such as cell surface and fluorescent proteins (FPs), and can destroy chemically-sensitive fluorescent labels. This reduces measurement accuracy and introduces compromises into sample workflows, leading to losses in data quality. Here, we demonstrate a novel multi-pass flow cytometry approach to address this long-standing problem. Our technique utilizes individual cell barcoding with laser particles, enabling sequential analysis of the same cells with single-cell resolution maintained. Chemically-fragile protein markers and their fluorochrome conjugates are measured prior to destructive sample processing and adjoined to subsequent measurements of intracellular markers after fixation and permeabilization. We demonstrate the effectiveness of our technique in accurately measuring intracellular FPs and methanol-sensitive antigens and fluorophores, along with various surface and intracellular markers. This approach significantly enhances assay flexibility, enabling accurate and comprehensive cellular analysis without the constraints of conventional one-time measurement flow cytometry. This innovation paves new avenues in flow cytometry for a wide range of applications in immuno-oncology, stem cell research, and cell biology.}, }
@article {pmid39466839, year = {2024}, author = {Dlauchy, D and Álvarez-Pérez, S and Tóbiás, A and Péter, G}, title = {Vishniacozyma floricola sp. nov., a flower-related tremellomycetous yeast species from Europe.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {10}, pages = {}, doi = {10.1099/ijsem.0.006555}, pmid = {39466839}, issn = {1466-5034}, mesh = {*Phylogeny ; *DNA, Fungal/genetics ; *Flowers/microbiology ; *Sequence Analysis, DNA ; *DNA, Ribosomal Spacer/genetics ; *Basidiomycota/genetics/classification/isolation &amp; purification ; Hungary ; Spain ; Mycological Typing Techniques ; }, abstract = {During the course of two independent studies conducted in Hungary and Spain, four conspecific yeast strains were isolated from flowers of different plant species. DNA sequences of two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2), revealed that the four strains represent an undescribed Vishniacozyma (family Bulleribasidiaceae, Basidiomycota) species. In terms of pairwise sequence similarities and according to our phylogenetic analyses of the concatenated DNA sequences of the ITS region and the D1/D2 domain of the LSU rRNA gene, the undescribed species is most closely related to Vishniacozyma melezitolytica, a yeast species of phylloplane origin. The novel species differs from the type strain of V. melezitolytica by 8 substitutions and 3 insertion/deletion (indels) and 11 substitutions and 5 indels along the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. In addition to the DNA sequence divergences, the two species differ in some physiological characters as well. We propose the species Vishniacozyma floricola sp. nov. to accommodate the above-noted strains (holotype, NCAIM Y.02320; isotype, CBS 18939; MycoBank number, 856028).}, }
@article {pmid39466790, year = {2024}, author = {Reyes Hueros, RA and Gier, RA and Shaffer, SM}, title = {Non-genetic differences underlie variability in proliferation among esophageal epithelial clones.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012360}, pmid = {39466790}, issn = {1553-7358}, support = {DP5 OD028144/OD/NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Cell Proliferation/genetics ; *Epithelial Cells/cytology ; *Esophagus/cytology ; Clone Cells/cytology ; Cell Line ; Single-Cell Analysis/methods ; Computational Biology ; }, abstract = {Individual cells grown in culture exhibit remarkable differences in their growth, with some cells capable of forming large clusters, while others are limited or fail to grow at all. While these differences have been observed across cell lines and human samples, the growth dynamics and associated cell states remain poorly understood. In this study, we performed clonal tracing through imaging and cellular barcoding of an in vitro model of esophageal epithelial cells (EPC2-hTERT). We found that about 10% of clones grow exponentially, while the remaining have cells that become non-proliferative leading to a halt in the growth rate. Using mathematical models, we demonstrate two distinct growth behaviors: exponential and logistic. Further, we discovered that the propensity to grow exponentially is largely heritable through four doublings and that the less proliferative clones can become highly proliferative through increasing plating density. Combining barcoding with single-cell RNA-sequencing (scRNA-seq), we identified the cellular states associated with the highly proliferative clones, which include genes in the WNT and PI3K pathways. Finally, we identified an enrichment of cells resembling the highly proliferative cell state in the proliferating healthy human esophageal epithelium.}, }
@article {pmid39465511, year = {2024}, author = {White, OW and Hall, A and Price, BW and Williams, ST and Clark, MD}, title = {A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14036}, doi = {10.1111/1755-0998.14036}, pmid = {39465511}, issn = {1755-0998}, abstract = {Low coverage 'genome-skims' are often used to assemble organelle genomes and ribosomal gene sequences for cost-effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction-based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome-skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, skim2mito and skim2rrna perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low-coverage genome skims. The third pipeline gene2phylo takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet.}, }
@article {pmid39463700, year = {2024}, author = {Recuero, E and Etzler, FE and Caterino, MS}, title = {Most soil and litter arthropods are unidentifiable based on current DNA barcode reference libraries.}, journal = {Current zoology}, volume = {70}, number = {5}, pages = {637-646}, pmid = {39463700}, issn = {1674-5507}, abstract = {We are far from knowing all species living on the planet. Understanding biodiversity is demanding and requires time and expertise. Most groups are understudied given problems of identifying and delimiting species. DNA barcoding emerged to overcome some of the difficulties in identifying species. Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups. Here, we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the southern Appalachian Mountains (USA). We used 3 reference databases and several automated classification methods on a data set including several arthropod groups. Acari, Araneae, Collembola, Coleoptera, Diptera, and Hymenoptera were well represented, showing different performances across methods and databases. Spiders performed the best, with correct identification rates to species and genus levels of ~50% across databases. Springtails performed poorly, no barcodes were identified to species or genus. Other groups showed poor to mediocre performance, from around 3% (mites) to 20% (beetles) correctly identified barcodes to species, but also with some false identifications. In general, BOLD-based identification offered the best identification results but, in all cases except spiders, performance is poor, with less than a fifth of specimens correctly identified to genus or species. Our results indicate that the soil arthropod fauna is still insufficiently documented, with many species unrepresented in DNA barcode libraries. More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNA barcoding as a universally applicable identification method.}, }
@article {pmid39460611, year = {2024}, author = {Burgos, HL and Mandel, MJ}, title = {Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions.}, journal = {Current protocols}, volume = {4}, number = {10}, pages = {e70024}, doi = {10.1002/cpz1.70024}, pmid = {39460611}, issn = {2691-1299}, support = {F32 GM140673/GM/NIGMS NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {*Aliivibrio fischeri/genetics ; *DNA Barcoding, Taxonomic/methods ; Gene Deletion ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Gene Library ; }, abstract = {Vibrio fischeri is a model mutualist for studying molecular processes affecting microbial colonization of animal hosts. We present a detailed protocol for a barcode sequencing (BarSeq) approach that combines targeted gene deletion with short-read sequencing technology to enable studies of mixed bacterial populations. This protocol includes wet lab steps to plan and produce the deletions, approaches to scale up mutant generation, protocols to prepare and conduct the strain competition, library preparation for sequencing on an Illumina iSeq 100 instrument, and data analysis with the barseq python package. Aspects of this protocol could be readily adapted for tagging wild-type V. fischeri strains with a neutral barcode for examination of population dynamics or BarSeq analyses in other species. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Production of the erm-bar DNA Basic Protocol 2: Generation of a targeted and barcoded deletion strain of V. fischeri Alternate Protocol: Parallel generation of multiple barcode-tagged V. fischeri deletion strains Basic Protocol 3: Setting up mixed populations of barcode-tagged strains Basic Protocol 4: Performing a competitive growth assay Basic Protocol 5: Amplicon library preparation and equimolar pooling Basic Protocol 6: Sequencing on Illumina iSeq 100 Basic Protocol 7: BarSeq data analysis.}, }
@article {pmid39460509, year = {2024}, author = {Yang, M and Wang, Y and Dai, P and Feng, D and Hughes, AC and Li, H and Zhang, A}, title = {Sympatric diversity pattern driven by the secondary contact of two deeply divergent lineages of the soybean pod borer Leguminivora glycinivorella.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12917}, pmid = {39460509}, issn = {1749-4877}, abstract = {The soybean pod borer, Leguminivora glycinivorella (Matsumura), is an important tortricid pest species widely distributed in most parts of China and its adjacent regions. Here, we analyzed the genetic diversity and population differentiation of L. glycinivorella using diverse genetic information including the standard cox1 barcode sequences, mitochondrial genomes (mitogenomes), and single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Based on a comprehensive sampling (including adults or larvae of L. glycinivorella newly collected at 22 of the total 30 localities examined) that covers most of the known distribution range of this pest, analyses of 543 cox1 barcode sequences and 60 mitogenomes revealed that the traditionally recognized and widely distributed L. glycinivorella contains two sympatric and widely distributed genetic lineages (A and B) that were estimated to have diverged ∼1.14 million years ago during the middle Pleistocene. Moreover, low but statistically significant correlations were recognized between genetic differentiation and geographic or environmental distances, indicating the existence of local adaptation to some extent. Based on SNPs, phylogenetic inference, principal component analysis, fixation index, and admixture analysis all confirm the two divergent sympatric lineages. Compared with the stable demographic history of Lineage B, the expansion of Lineage A had possibly made the secondary contact of the two lineages probable, and this process may be driven by the climate fluctuation during the late Pleistocene as revealed by ecological niche modeling.}, }
@article {pmid39459593, year = {2024}, author = {Xia, X}, title = {Phylogeographic Analysis for Understanding Origin, Speciation, and Biogeographic Expansion of Invasive Asian Hornet, Vespa velutina Lepeletier, 1836 (Hymenoptera, Vespidae).}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, pmid = {39459593}, issn = {2075-1729}, support = {RGPIN-2024-05641//Natural Sciences and Engineering Research Council/ ; }, abstract = {The Asian hornet, Vespa velutina, is an invasive species that has not only expanded its range in Asia but has also invaded European countries, and it incurs significant costs on local apiculture. This phylogeographic study aims to trace the evolutionary trajectory of V. velutina and its close relatives; it aims to identify features that characterize an invasive species. The last successful invasion of Vespa velutina into France occurred in late May, 2002, and into South Korea in early October, 2002, which were estimated by fitting a logistic equation to the number of observations over time. The instantaneous rate of increase is 1.3667 for V. velutina in France and 0.2812 in South Korea, which are consistent with the interpretation of little competition in France and strong competition from local hornet species in South Korea. The invasive potential of two sister lineages can be compared by their distribution area when proper statistical adjustments are made to account for differences in sample size. V. velutina has a greater invasive potential than its sister lineage. The ancestor of V. velutina split into two lineages, one found in Indonesia/Malaysia and the other colonizing the Asian continent. The second lineage split into a sedentary clade inhabiting Pakistan and India and an invasive lineage colonizing much of Southeast Asia. This latter lineage gave rise to the subspecies V. v. nigrithorax, which invaded France, South Korea, and Japan. My software PGT version 1.5, which generates geophylogenies and computes geographic areas for individual taxa, is useful for understanding biogeography in general and invasive species in particular. I discussed the conceptual formulation of an index of invasiveness for a comparison between sister lineages.}, }
@article {pmid39458823, year = {2024}, author = {Tahir, S and Hassan, SS and Yang, L and Ma, M and Li, C}, title = {Detection Methods for Pine Wilt Disease: A Comprehensive Review.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {20}, pages = {}, pmid = {39458823}, issn = {2223-7747}, support = {2022ZD0401602//Biological Breeding-Major Projects/ ; }, abstract = {Pine wilt disease (PWD), caused by the nematode Bursaphelenchus xylophilus, is a highly destructive forest disease that necessitates rapid and precise identification for effective management and control. This study evaluates various detection methods for PWD, including morphological diagnosis, molecular techniques, and remote sensing. While traditional methods are economical, they are limited by their inability to detect subtle or early changes and require considerable time and expertise. To overcome these challenges, this study emphasizes advanced molecular approaches such as real-time polymerase chain reaction (RT-PCR), droplet digital PCR (ddPCR), and loop-mediated isothermal amplification (LAMP) coupled with CRISPR/Cas12a, which offer fast and accurate pathogen detection. Additionally, DNA barcoding and microarrays facilitate species identification, and proteomics can provide insights into infection-specific protein signatures. The study also highlights remote sensing technologies, including satellite imagery and unmanned aerial vehicle (UAV)-based hyperspectral analysis, for their capability to monitor PWD by detecting asymptomatic diseases through changes in the spectral signatures of trees. Future research should focus on combining traditional and innovative techniques, refining visual inspection processes, developing rapid and portable diagnostic tools for field application, and exploring the potential of volatile organic compound analysis and machine learning algorithms for early disease detection. Integrating diverse methods and adopting innovative technologies are crucial to effectively control this lethal forest disease.}, }
@article {pmid39455411, year = {2024}, author = {He, M and Zhu, X and Chen, Z and Wang, C and Mi, L and Shang, Y and Zheng, J and Xiang, C and Song, H and Liu, X}, title = {Epitaxial Growth of Multicolor Lanthanide MOFs by Ultrasound for Photonic Barcodes.}, journal = {ACS applied materials &amp; interfaces}, volume = {16}, number = {44}, pages = {60884-60889}, doi = {10.1021/acsami.4c16625}, pmid = {39455411}, issn = {1944-8252}, abstract = {Epitaxially grown lanthanide metal-organic frameworks (Ln MOFs) exhibit multicolor and characteristic Ln emission with sharp emission bands, which are of great value in the field of information security and anti-counterfeiting. Epitaxial growth of Ln MOFs is generally achieved by solvothermal or hydrothermal methods, which suffer from challenges such as high reaction temperature and long growth time. Here, we report the fast epitaxial growth of multicolor lanthanide MOFs by an ultrasonic method at room temperature. The TbSmSQ shows a core-shell type structure with the Tb ion in the core and Sm in the shell within one crystal and exhibits the characteristic emission lines of Tb and Sm, respectively. The nonporous structure and large distance between lanthanide ions effectively avoid the influence of solvent vapor on the intensity and color of luminescence emission. Its application as photonic barcodes has been studied. This work demonstrates the feasibility of epitaxial growth of multicolor Ln MOFs by the ultrasonic method and its value for anti-counterfeiting and information security applications.}, }
@article {pmid39454580, year = {2024}, author = {Lima, GM and Jame-Chenarboo, Z and Sojitra, M and Sarkar, S and Carpenter, EJ and Yang, CY and Schmidt, E and Lai, J and Atrazhev, A and Yazdan, D and Peng, C and Volker, EA and Ho, R and Monteiro, G and Lai, R and Mahal, LK and Macauley, MS and Derda, R}, title = {The liquid lectin array detects compositional glycocalyx differences using multivalent DNA-encoded lectins on phage.}, journal = {Cell chemical biology}, volume = {31}, number = {11}, pages = {1986-2001.e9}, doi = {10.1016/j.chembiol.2024.09.010}, pmid = {39454580}, issn = {2451-9448}, mesh = {*Glycocalyx/metabolism/chemistry ; *Lectins/chemistry/metabolism ; Humans ; Bacteriophages/chemistry/metabolism ; Animals ; DNA/chemistry/metabolism ; Mice ; Polysaccharides/chemistry/metabolism ; }, abstract = {Selective detection of disease-associated changes in the glycocalyx is an emerging field in modern targeted therapies. Detecting minor glycan changes on the cell surface is a challenge exacerbated by the lack of correspondence between cellular DNA/RNA and glycan structures. We demonstrate that multivalent displays of lectins on DNA-barcoded phages-liquid lectin array (LiLA)-detect subtle differences in density of glycans on cells. LiLA constructs displaying 73 copies of diCBM40 (CBM) lectin per virion (φ-CBM73) exhibit non-linear ON/OFF-like recognition of sialoglycans on the surface of normal and cancer cells. A high-valency φ-CBM290 display, or soluble CBM protein, cannot amplify the subtle differences detected by φ-CBM73. Similarly, multivalent displays of CBM and Siglec-7 detect differences in the glycocalyx between stem-like and non-stem populations in cancer. Multivalent display of lectins offer in situ detection of minor differences in glycocalyx in cells both in vitro and in vivo not feasible to currently available technologies.}, }
@article {pmid39453698, year = {2024}, author = {Rodger, G and Lipworth, S and Barrett, L and Oakley, S and Crook, DW and Eyre, DW and Stoesser, N}, title = {Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from Escherichia coli isolates.}, journal = {Microbial genomics}, volume = {10}, number = {10}, pages = {}, pmid = {39453698}, issn = {2057-5858}, mesh = {*Escherichia coli/genetics ; *Nanopore Sequencing/methods ; *DNA, Complementary/genetics ; Polymerase Chain Reaction/methods ; Humans ; Escherichia coli Infections/microbiology ; Sequence Analysis, RNA/methods ; RNA, Bacterial/genetics ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods ; Transcriptome ; }, abstract = {Whole-transcriptome (long-read) RNA sequencing (Oxford Nanopore Technologies, ONT) holds promise for reference-agnostic analysis of differential gene expression in pathogenic bacteria, including for antimicrobial resistance genes (ARGs). However, direct cDNA ONT sequencing requires large concentrations of polyadenylated mRNA, and amplification protocols may introduce technical bias. Here we evaluated the impact of direct cDNA- and cDNA PCR-based ONT sequencing on transcriptomic analysis of clinical Escherichia coli. Four E. coli bloodstream infection-associated isolates (n=2 biological replicates per isolate) were sequenced using the ONT Direct cDNA Sequencing SQK-DCS109 and PCR-cDNA Barcoding SQK-PCB111.24 kits. Biological and technical replicates were distributed over eight flow cells using 16 barcodes to minimize batch/barcoding bias. Reads were mapped to a transcript reference and transcript abundance was quantified after in silico depletion of low-abundance and rRNA genes. We found there were strong correlations between read counts using both kits and when restricting the analysis to include only ARGs. We highlighted that correlations were weaker for genes with a higher GC content. Read lengths were longer for the direct cDNA kit compared to the PCR-cDNA kit whereas total yield was higher for the PCR-cDNA kit. In this small but methodologically rigorous evaluation of biological and technical replicates of isolates sequenced with the direct cDNA and PCR-cDNA ONT sequencing kits, we demonstrated that PCR-based amplification substantially improves yield with largely unbiased assessment of core gene and ARG expression. However, users of PCR-based kits should be aware of a small risk of technical bias which appears greater for genes with an unusually high (>52%)/low (<44%) GC content.}, }
@article {pmid39452649, year = {2024}, author = {Yang, J and Reyes Loaiciga, C and Yue, HR and Hou, YJ and Li, J and Li, CX and Li, J and Zou, Y and Zhao, S and Zhang, FL and Zhao, XQ}, title = {Genomic Characterization and Establishment of a Genetic Manipulation System for Trichoderma sp. (Harzianum Clade) LZ117.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {10}, pages = {}, pmid = {39452649}, issn = {2309-608X}, support = {No. 2022YFE0108500//the State Key Research and Development Program of China/ ; }, abstract = {Trichoderma species have been reported as masters in producing cellulolytic enzymes for the biodegradation of lignocellulolytic biomass and biocontrol agents against plant pathogens and pests. In our previous study, a novel Trichoderma strain LZ117, which shows potent capability in cellulase production, was isolated. Herein, we conducted multilocus phylogenetic analyses based on DNA barcodes and performed time-scaled phylogenomic analyses using the whole genome sequences of the strain, annotated by integrating transcriptome data. Our results suggest that this strain represents a new species closely related to T. atrobrunneum (Harzianum clade). Genes encoding carbohydrate-active enzymes (CAZymes), transporters, and secondary metabolites were annotated and predicted secretome in Trichoderma sp. LZ117 was also presented. Furthermore, genetic manipulation of this strain was successfully achieved using PEG-mediated protoplast transformation. A putative transporter gene encoding maltose permease (Mal1) was overexpressed, which proved that this transporter does not affect cellulase production. Moreover, overexpressing the native Cre1 homolog in LZ117 demonstrated a more pronounced impact of glucose-caused carbon catabolite repression (CCR), suggesting the importance of Cre1-mediated CCR in cellulase production of Trichoderma sp. LZ117. The results of this study will benefit further exploration of the strain LZ117 and related species for their applications in bioproduction.}, }
@article {pmid39450195, year = {2024}, author = {Lee, HE and Lee, GH and Min, GS}, title = {A new species of Thoracophelia (Annelida, Opheliidae) from the Yellow Sea of South Korea.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e129526}, pmid = {39450195}, issn = {1314-2828}, abstract = {BACKGROUND: Thoracophelia Ehlers, 1897 is a genus of Opheliidae characterised by the body divided into three distinct regions, modified parapodia in chaetiger 10 and a ventral groove restricted to the posterior half of the body. To date, 18 species have been described in the genus. Amongst them, six species have been recorded in northeast Asia.<br><br>NEW INFORMATION: A new species, Thoracopheliafoliformis sp. nov., was discovered in the intertidal zone of the Yellow Sea, South Korea. This is the first Thoracophelia species report from the Yellow Sea. This new species is closely related to T.dillonensis (Hartman, 1938) from California and T.ezoensis Okuda, 1936 from Japan in having pectinate branchiae. However, the new species can be distinguished from the two species by the unique combination of the following characteristics: 15 pairs of wrinkled pectinate branchiae with 12-15 filaments at best development and a foliaceous mid-ventral plate in the pygidium instead of one or two thick ventral cirri. Detailed descriptions and illustrations of T.foliformis sp. nov. are provided. Sequences of the mitochondrial cytochrome c oxidase subunit I (COI), nuclear 18S ribosomal DNA (rDNA) and 28S rDNA of the new species were determined and analysed.}, }
@article {pmid39450043, year = {2024}, author = {Likhitrakarn, N and Golovatch, SI and Srisonchai, R and Jirapatrasilp, P and Sapparojpattana, P and Jeratthitikul, E and Panha, S and Sutcharit, C}, title = {A new species of the pill millipede genus Rhopalomeris Verhoeff, 1906 (Diplopoda, Glomerida, Glomeridae) from Myanmar, and notes on Rhopalomeriscarnifex (Pocock, 1889).}, journal = {ZooKeys}, volume = {1215}, number = {}, pages = {235-257}, pmid = {39450043}, issn = {1313-2989}, abstract = {The taxonomy of the pill millipede genus Rhopalomeris Verhoeff, 1906, which is restricted to Indochina and currently comprises six described species, is refined and updated. An integrative taxonomic approach was employed that combines morphological examination with DNA barcoding using the cytochrome c oxidase subunit I (COI) gene for species identification and delineation. The first objective was to confirm the identity of Rhopalomeriscarnifex (Pocock, 1889), a charismatic species known as the "candy pill millipede" due to its vivid coloration, based on specimens collected near the type locality in Myanmar. The second objective was to describe a new species, Rhopalomerisnigroflava Likhitrakarn, sp. nov., discovered in Linno Gu, Kayin State, Myanmar. This new species is distinguished by its small body size (5.1-9.7 mm long) and yellow body with contrasting brown to blackish markings on certain terga. In addition, the position of the telopod syncoxital lobe relative to the lateral syncoxite horns separates it from other Rhopalomeris species. The interspecific divergence between R.nigroflava Likhitrakarn, sp. nov. and other congeners ranges from 10.85% to 16.13%, based on uncorrected COI p-distances, while the intraspecific divergence was 0%-7.44%. A distribution map of and a revised identification key to all known species of Rhopalomeris are also provided.}, }
@article {pmid39444847, year = {2024}, author = {Mwamula, AO and Kim, YS and Lee, DW}, title = {Morphological and molecular characterization of Paractinolaimus uljinensis n. sp. (Nematoda: Actinolaimidae) from Korea, with an updated compendium of the genus.}, journal = {Journal of nematology}, volume = {56}, number = {1}, pages = {20240040}, pmid = {39444847}, issn = {0022-300X}, abstract = {A new species of the genus Paractinolaimus isolated from the bark of a dead red pine tree was characterized using morphometric data and molecular DNA barcodes. Paractinolaimus uljinensis n. sp. was characterized by its medium sized body 2.50 to 2.98 mm long; lip region truncate, angular and offset by a depression; odontostyle 23.5 to 27.0 μm long; basal shield of pharynx present; vulval opening wide and longitudinal, positioned slightly anteriorly (V = 42.5-47.7); several advulval papillae; female tail long and filiform (324.0-435.0 μm long, c' = 10.1-14.2); a clearly visible copulatory hump; spicules 60.0 to 70.5 μm long; 12 to 15 (mostly 12-14) large contiguous ventromedian supplements, and male tail conoid to broadly rounded. The new species was morphologically compared with P. intermedius, P. sahandi, P. decraemerae, P. acutus, P. macrolaimus, and P. tuberculatus. The phylogenetic relationships among species were reconstructed using 18S- and 28S-rRNA gene sequences. The phylogenies showed well-supported sister relations of Paractinolaimus uljinensis n. sp. with P. sahandi, P. macrolaimus, and P. decraemerae. In addition, the ITS-rRNA gene sequences of Paractinolaimus uljinensis n. sp. were supplied, representing the first characterization of the gene for the genus.}, }
@article {pmid39443484, year = {2024}, author = {Wu, B and Bennett, HM and Ye, X and Sridhar, A and Eidenschenk, C and Everett, C and Nazarova, EV and Chen, HH and Kim, IK and Deangelis, M and Owen, LA and Chen, C and Lau, J and Shi, M and Lund, JM and Xavier-Magalhães, A and Patel, N and Liang, Y and Modrusan, Z and Darmanis, S}, title = {Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9146}, pmid = {39443484}, issn = {2041-1723}, support = {R01 EY031209/EY/NEI NIH HHS/United States ; }, mesh = {*Single-Cell Analysis/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Cell Line, Tumor ; Melanoma/genetics/drug therapy/pathology ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Transcriptome ; }, abstract = {Multiomic profiling of single cells by sequencing is a powerful technique for investigating cellular diversity. Existing droplet-based microfluidic methods produce many cell-free droplets, underutilizing bead barcodes and reagents. Combinatorial indexing on microplates is more efficient for barcoding but labor-intensive. Here we present Overloading And unpacKing (OAK), which uses a droplet-based barcoding system for initial compartmentalization followed by a second aliquoting round to achieve combinatorial indexing. We demonstrate OAK's versatility with single-cell RNA sequencing as well as paired single-nucleus RNA sequencing and accessible chromatin profiling. We further showcase OAK's performance on complex samples, including differentiated bronchial epithelial cells and primary retinal tissue. Finally, we examine transcriptomic responses of over 400,000 melanoma cells to a RAF inhibitor, belvarafenib, discovering a rare resistant cell population (0.12%). OAK's ultra-high throughput, broad compatibility, high sensitivity, and simplified procedures make it a powerful tool for large-scale molecular analysis, even for rare cells.}, }
@article {pmid39443100, year = {2024}, author = {Oshiro, A and Sumi, T and Imai, H}, title = {[Identification of Fish Species Involved with Ciguatera Food Poisoning in Okinawan Waters by Using PCR-RFLP analysis].}, journal = {Shokuhin eiseigaku zasshi. Journal of the Food Hygienic Society of Japan}, volume = {65}, number = {4}, pages = {79-83}, doi = {10.3358/shokueishi.65.79}, pmid = {39443100}, issn = {0015-6426}, mesh = {Animals ; *Polymorphism, Restriction Fragment Length ; *Ciguatera Poisoning ; Japan ; *Polymerase Chain Reaction ; *RNA, Ribosomal, 16S/genetics ; *Fishes/genetics ; DNA, Mitochondrial/genetics/analysis ; Phylogeny ; }, abstract = {Ciguatera fish poisoning (CFP), known as a seafood-borne disease, is caused by consumption of fish contaminated with ciguatoxins in tropical and subtropical sea. The ciguatera fishes, Variola louti, Lutjanus monostigma and L. bohar have an absolute majority in the Ryukyu Archipelago, southwestern Japan. We developed the cluster analysis of phylogenetic tree by using mitochondrial (mt) DNA 16S rRNA sequences of V. louti, L. monostigma and L. bohar and differentiate them from morphologically similar species (L. fulviflamma, L. russellii, L. argentimaculatus, Plectropomus leopardus and V. albimarginata) in our previous study. The fish were acquired from the coastal waters of the Ryukyu Archipelago, and a polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) marker of the mtDNA 16S rRNA region was used, employing the restriction enzymes BmgT120 I, Dde I, and SnaB I, to identify the fish species responsible for CFP. These results showed that a PCR-RFLP marker can be obtained more easily than a nucleotide sequence.}, }
@article {pmid39441940, year = {2024}, author = {Smitha Pillai, K and Laxton, O and Li, G and Lin, J and Karginova, O and Nanda, R and Olopade, OI and Tay, S and Moellering, RE}, title = {Single-cell chemoproteomics identifies metastatic activity signatures in breast cancer.}, journal = {Science advances}, volume = {10}, number = {43}, pages = {eadp2622}, pmid = {39441940}, issn = {2375-2548}, support = {T32 GM144290/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Breast Neoplasms/metabolism/pathology/genetics ; *Single-Cell Analysis/methods ; Female ; *Proteomics/methods ; Cell Line, Tumor ; *Neoplasm Metastasis ; }, abstract = {Protein activity state, rather than protein or mRNA abundance, is a biologically regulated and relevant input to many processes in signaling, differentiation, development, and diseases such as cancer. While there are numerous methods to detect and quantify mRNA and protein abundance in biological samples, there are no general approaches to detect and quantify endogenous protein activity with single-cell resolution. Here, we report the development of a chemoproteomic platform, single-cell activity-dependent proximity ligation, which uses automated, microfluidics-based single-cell capture and nanoliter volume manipulations to convert the interactions of family-wide chemical activity probes with native protein targets into multiplexed, amplifiable oligonucleotide barcodes. We demonstrate accurate, reproducible, and multiplexed quantitation of a six-enzyme (Ag-6) panel with known ties to cancer cell aggressiveness directly in single cells. We further identified increased Ag-6 enzyme activity across breast cancer cell lines of increasing metastatic potential, as well as in primary patient-derived tumor cells and organoids from patients with breast cancer.}, }
@article {pmid39438815, year = {2024}, author = {Bastidas-Caldes, C and Hernández-Alomía, F and Almeida, M and Ormaza, M and Boada, J and Graham, J and Calvopiña, M and Castillejo, P}, title = {Molecular identification and antimicrobial resistance patterns of enterobacterales in community urinary tract infections among indigenous women in Ecuador: addressing microbiological misidentification.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1195}, pmid = {39438815}, issn = {1471-2334}, mesh = {Humans ; *Urinary Tract Infections/microbiology/drug therapy/epidemiology ; Female ; Ecuador/epidemiology ; Cross-Sectional Studies ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Adult ; Microbial Sensitivity Tests ; Indigenous Peoples ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Enterobacteriaceae/drug effects/genetics/isolation &amp; purification ; Young Adult ; Enterobacteriaceae Infections/microbiology/epidemiology/drug therapy ; Community-Acquired Infections/microbiology ; }, abstract = {BACKGROUND: Antibiotic resistance of Enterobacterales poses a major challenge in the treatment of urinary tract infections (UTIs). In low- and middle-income countries (LMICs), standard microbiological (i.e. urine culture and simple disk diffusion test) methods are considered the "gold standard" for bacterial identification and drug susceptibility testing, while PCR and DNA sequencing are less commonly used. In this study, we aimed to re-identifying Enterobacterales as the primary bacterial agents responsible for urinary tract infections (UTIs) by comparing the sensitivity and specificity of traditional microbiological methods with advanced molecular techniques for the detection of uropathogens in indigenous women from Otavalo, Ecuador.<br><br>METHODS: A facility-based cross-sectional study was conducted from October 2021 to February 2022 among Kichwa-Otavalo women. Pathogens from urine samples were identified using culture and biochemical typing. Morphological identification was doble-checked through PCR and DNA sequencing of 16S, recA, and rpoB molecular barcodes. The isolates were subjected to antimicrobial susceptibility-testing using disk diffusion test.<br><br>RESULTS: This study highlighted a 32% misidentification rate between biochemical and molecular identification. Using traditional methods, E. coli was 26.19% underrepresented meanwhile Klebsiella oxytoca was overrepresented by 92.86%. Furthermore, the genera Pseudomonas, Proteus, and Serratia were confirmed to be E. coli and Klebsiella spp. by molecular method, and one Klebsiella spp. was reidentified as Enterobacter spp. The susceptibility profile showed that 59% of the isolates were multidrug resistant strains and 31% produced extended spectrum beta-lactamases (ESBLs). Co-trimoxazole was the least effective antibiotic with 61% of the isolates resistant. Compared to previous reports, resistance to nitrofurantoin and fosfomycin showed an increase in resistance by 25% and 15%, respectively.<br><br>CONCLUSIONS: Community-acquired UTIs in indigenous women in Otavalo were primarily caused by E. coli and Klebsiella spp. Molecular identification (16S/rpoB/recA) revealed a high rate of misidentification by standard biochemical and microbiological techniques, which could lead to incorrect antibiotic prescriptions. UTI isolates in this population displayed higher levels of resistance to commonly used antibiotics compared with non-indigenous groups. Accurate identification of pathogens causing UTIs and their antibiotic susceptibility in local populations is important for local antibiotic prescribing guidelines.}, }
@article {pmid39434349, year = {2024}, author = {Hamdan, NT}, title = {Molecular identification of Hypomyces chrysospermus mycoparasitic fungus isolated from mushrooms in a local market of Iraq.}, journal = {JPMA. The Journal of the Pakistan Medical Association}, volume = {74}, number = {10 (Supple-8)}, pages = {S398-S401}, doi = {10.47391/JPMA-BAGH-16-90}, pmid = {39434349}, issn = {0030-9982}, mesh = {Iraq ; *Phylogeny ; Agaricales/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; }, abstract = {In this study, mycoparasitic fungus was identified by using the rDNA internal transcribed spacer barcode marker, i.e. ITS rDNA gene. Amplicons were sequenced and identified by NCBI - BLAST (Basic local alignment search tool). The BLAST results revealed that NOOR strain matched 100% with accession numbers [MH854754.1]. The phylogenetic tree shows close relationship between NOOR strain and H. chrysospermus [MH854754-1], H. chrysospermus [MZ389105-1], H. chrysospermus [MK605327- 1], H. chrysospermus [MT595227-1], H. [EU816370-1], H. chrysospermus [MG685885-1]. The Iraqi isolate was recorded as NOOR strain in the National Centre for Biotechnology Information for the first time in Iraq.}, }
@article {pmid39434133, year = {2024}, author = {Gąsiorek, P and Sørensen, MV and Lillemark, MR and Leerhøi, F and Tøttrup, AP}, title = {Massive citizen science sampling and integrated taxonomic approach unravel Danish cryptogam-dwelling tardigrade fauna.}, journal = {Frontiers in zoology}, volume = {21}, number = {1}, pages = {27}, pmid = {39434133}, issn = {1742-9994}, abstract = {Tardigrade diversity and distribution are enigmatic in most parts of the globe, and only some European countries can boast of a relatively well-studied water bear fauna. However, even these suffer from the lack of genetic data, which would substantiate faunistic data and make biogeographic comparisons easier. Denmark has never been intensively and systematically researched in this regard, thus a citizen science sampling of cryptogams (mosses, liverworts, and lichens) was launched in spring 2023, aiming at a comprehensive biodiversity survey across this insular country. Nearly 700 samples were selected out of 8.000 sent to NHMD, based on the quality of samples, representativeness of various regions of Denmark, and the type of substrate to allow unravelling of potential ecological associations between tardigrades and cryptogams. Importantly, a large fraction of morphological identifications was backed up by DNA barcode data based on ITS-2 (1001 sequences), and in some cases also on COI (93 sequences) and ITS-1 (22 sequences) molecular markers, which are recognised DNA fragments used in species delimitation. We quadruple the number of known Danish limno-terrestrial tardigrade species (55 spp. reported in this paper vs. 14 spp. reported in literature so far, most of which were contentious due to the insufficient knowledge on tardigrade taxonomy), demonstrating the power of integrative taxonomy. No fewer than nine spp. are new to science. This is the first case where tardigrade fauna of an entire country is examined both from morphological and DNA barcoding data perspective.}, }
@article {pmid39433876, year = {2024}, author = {Simon, JJ and Fowler, DM and Maly, DJ}, title = {Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq.}, journal = {Nature methods}, volume = {21}, number = {11}, pages = {2094-2106}, pmid = {39433876}, issn = {1548-7105}, support = {R01GM145011//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; RM1HG010461//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Proto-Oncogene Proteins B-raf/genetics/metabolism ; Mutation ; Cell Line, Tumor ; Cell Proliferation/drug effects ; }, abstract = {Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein-protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability.}, }
@article {pmid39432187, year = {2024}, author = {Ben Ahmed, R and Gajda, &#x141; and Świątek, P}, title = {Morphological data and DNA barcoding reveal the presence of the alien freshwater leech Helobdella octatestisaca (Hirudinida: Glossiphoniformes) in North Africa (Tunisia).}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {1081}, pmid = {39432187}, issn = {1573-4978}, mesh = {Animals ; *Phylogeny ; *Leeches/genetics/anatomy &amp; histology/classification ; *DNA Barcoding, Taxonomic/methods ; Tunisia ; Fresh Water ; Introduced Species ; Electron Transport Complex IV/genetics ; }, abstract = {BACKGROUND: We hereby report the first occurrence of Helobdella octatestisaca in North Africa, specifically in Tunisia, as a likely introduced species from the Neotropical Region. Historically, leeches bearing a prominent chitinous scute on their dorsal surface were commonly diagnosed as H. stagnalis. Most probably, H. octatestisaca had previously been misidentified as H. stagnalis in Tunisia.<br><br>METHODS AND RESULTS: The identification was primarily based on morphological evidence, supplemented by genetic data obtained from COI DNA barcoding. The morphology of the examined specimens was consistent with the original species description, notably characterized by the presence of four pairs of testisacs. To support our findings, we conducted a phylogenetic analysis using the Maximum Likelihood method based on COI alignment constructed with the newly obtained sequence from Tunisian specimens and complete or nearly complete 'Folmer fragment' sequences of congeners sourced from the GenBank database.<br><br>CONCLUSIONS: This study highlights the first identification of H. octatestisaca in North Africa and suggests that previous records of H. stagnalis in Tunisia likely misidentified this species.}, }
@article {pmid39431921, year = {2024}, author = {Sun, F and Liu, J and Su, Z and Wu, D and Qu, S and Wu, Y and Li, L and Li, G}, title = {Encodable DNA Hairpin Probes for Nanopore Multiplexed Target Detection.}, journal = {Analytical chemistry}, volume = {96}, number = {44}, pages = {17612-17619}, doi = {10.1021/acs.analchem.4c03469}, pmid = {39431921}, issn = {1520-6882}, mesh = {*Nanopores ; *DNA Probes/chemistry/genetics ; *Hemolysin Proteins/chemistry/genetics ; MicroRNAs/analysis ; Biosensing Techniques/methods ; Nucleic Acid Conformation ; Inverted Repeat Sequences ; DNA/chemistry/analysis ; }, abstract = {Owing to the co-occurrence of hazardous compounds, it is crucial to build multiple highly discriminative probe libraries for simultaneous determination. Drawing inspiration from nucleic acid barcodes, we developed a probe system that is exclusively based on the nucleic acid secondary structure's hairpin structure, which can be directly read by nanopores. The highly distinguishable hairpin probes were constructed, and a detailed explanation of the possible patterns in their design was provided. These probe-representative events measured through the α-hemolysin (α-HL) nanopores were both distinguished, either through visual observation or comparison of the nanopore parameters. Besides, the potential design pattern for probes with unique telegraphic switching between the two levels was also unveiled. Finally, these probes were utilized to realize simultaneous, ultrasensitive mycotoxin multiple-detection, and their prospective applications for the detection of proteins and microRNAs were presented, indicating their suitability for a wide range of sensing applications.}, }
@article {pmid39424732, year = {2025}, author = {Holmes, AB and Corinaldesi, C and Basso, K}, title = {Single-Cell Transcriptomic Analysis of Normal and Malignant B Cells.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2865}, number = {}, pages = {347-374}, pmid = {39424732}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; Humans ; *Gene Expression Profiling/methods ; *B-Lymphocytes/metabolism/immunology ; *Transcriptome ; Software ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {In the past decade, single-cell (sc) transcriptomics has overcome the limitations of bulk analysis by measuring gene expression in individual cells, not just a population average. This can identify diverse cell types and states within a sample with high resolution, even without prior purification. Various technologies exist, each with its own capture, barcoding, and library preparation methods. This chapter focuses on the analysis of normal and malignant mature B cells using the 10× Genomics 5' sc-gene expression in parallel with B cell immune repertoire profiling. By integrating the gene expression data from similar cells, the complete transcriptome for each population can be reconstructed, while the identification of the expressed immunoglobulin genes allows investigating clonotype evolution and the detection of tumor clones that share the same clonally rearranged B cell receptor sequence. Researchers are guided through both the experimental protocols and data analysis with a comprehensive, step-by-step walkthrough of how to use some of the more popular single-cell software tools.}, }
@article {pmid39422558, year = {2024}, author = {Zhang, SJ and Wu, C and Walt, DR}, title = {A Multiplexed Digital Platform Enables Detection of Attomolar Protein Levels with Minimal Cross-Reactivity.}, journal = {ACS nano}, volume = {18}, number = {43}, pages = {29891-29901}, doi = {10.1021/acsnano.4c10340}, pmid = {39422558}, issn = {1936-086X}, support = {R01 EB032826/EB/NIBIB NIH HHS/United States ; R56 EB032826/EB/NIBIB NIH HHS/United States ; }, mesh = {Humans ; *Enzyme-Linked Immunosorbent Assay ; Cross Reactions ; Antibodies/immunology/chemistry ; }, abstract = {Protein-based biomarkers are essential for disease diagnostics, yet their low abundance in biofluids often presents significant detection challenges for traditional enzyme-linked immunosorbent assay (ELISA) techniques. While various ultrasensitive methods such as digital ELISA have improved sensitivity, multiplex assays still suffer from considerable cross-reactivities that can compromise result accuracies. To address this challenge, we have developed barcoded Molecular On-bead Signal Amplification for Individual Counting (barcoded MOSAIC), a multiplexed digital ELISA technology that markedly reduces cross-reactivity by pairing barcoded detection antibodies with specific bead types. This approach enables the simultaneous detection of eight analytes from less than 9 μL of blood, with sensitivities ranging from midpicomolar to low-attomolar levels and a collective dynamic range exceeding seven logs across multiple analytes within a single multiplex assay. Additionally, barcoded MOSAIC is compatible with standard immunoassay reagents and workflows, utilizing a rapid, automatable flow cytometric readout for quantification, which makes it a highly accessible benchtop platform that is readily adoptable by both research and clinical laboratories, setting the stage for future translation into point-of-care applications.}, }
@article {pmid39421424, year = {2024}, author = {Subbiah, VK and Gomez, CR and Robben, DM and Subramaniam, R and Hearn, AJ}, title = {Characterization of the complete mitochondrial genome of the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18190}, pmid = {39421424}, issn = {2167-8359}, mesh = {*Genome, Mitochondrial/genetics ; Borneo ; Animals ; *Phylogeny ; *Mustelidae/genetics ; Sequence Analysis, DNA ; RNA, Transfer/genetics ; }, abstract = {BACKGROUND: The Mephitidae is a family of skunks and stink-badgers that includes 12 extant species in four genera, namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only genus within Mephitidae found outside the American continent, with its distribution limited to the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e., javanensis and marchei. Currently, complete mitogenomes are unavailable for either species. Here, we present the characterization of the first complete mitogenome for the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.<br><br>METHODS: Muscle tissue was obtained and the DNA was sequenced using a combination of Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome was annotated with MITOS and manually checked for accuracy. A circular map of the mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were aligned with reference sequences from GenBank and used for the construction of phylogenetic trees (maximum liklihood (ML) and Bayesian inference (BI)). Additionally, due to the lack of available complete genomes in public databases, we constructed another tree with the cyt b gene.<br><br>RESULTS: The complete circular mitogenome was 16,391 base pairs in length. It comprises the typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR) and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly clustered the species with other members of the Mephitidae family but were unique enough to set it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the species.}, }
@article {pmid39418234, year = {2024}, author = {Cherie, N and Berta, DM and Tamir, M and Yiheyis, Z and Angelo, AA and Mekuanint Tarekegn, A and Chane, E and Nigus, M and Teketelew, BB}, title = {Improving laboratory turnaround times in clinical settings: A systematic review of the impact of lean methodology application.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0312033}, pmid = {39418234}, issn = {1932-6203}, mesh = {Humans ; *Laboratories, Clinical ; Efficiency, Organizational ; Laboratories/standards ; Time Factors ; Workflow ; }, abstract = {BACKGROUND: Lean methodology, originally developed in the manufacturing sector, is a process management philosophy focused on maximizing value by eliminating waste. Its application in laboratory settings, particularly concerning laboratory turnaround times (TAT), involves a systematic approach to identifying inefficiencies and optimizing processes to enhance value for end customers.<br><br>METHODS: This systematic review was registered in PROSPERO with identification number (CRD42024552350) and reported based on the 2020 PRISMA checklist. An extensive search strategy was performed using PubMed, Scopus, and Embase databases and gray literatures. Advanced searching was used using Boolean operators (AND &amp; OR). After articles were exported to endnote x8, duplications were removed and articles were selected based on titles, abstracts, and full texts. The illegibility of the articles was independently assessed by the three authors (NC, DMB, and BBT), and the disagreements were settled through scientific consensus. Methodological quality was assessed using JBI critical appraisal checklist.<br><br>DISCUSSION: In this review, electronic databases search yielded 1261 articles, of which 7 met the inclusion criteria. The review demonstrated, implementation of lean principle into the routine laboratory testing had an overall impact 76.1% on reducing laboratory TAT. Transportation, manual data processing, inefficient workflow, and the heavy workload were identified as the main wasteful procedures. To eliminate these non-value-added steps, several intervention techniques were implemented, including the use of a barcoding system, process redesign, workflow optimization, hiring additional staff, and relocating the sample collection room closer to the result distribution center. Lean implementation is crucial in the medical laboratory industry for optimizing processes, reducing TAT, and ultimately enhancing customer satisfaction. As a result, all clinical laboratories should adopt and implement lean principles in their routine testing processes. The medical laboratory industry should also proactively look for and apply lean tools, provide ongoing training, and foster awareness among laboratory staffs.}, }
@article {pmid39417120, year = {2024}, author = {Sadler, JM and Simkin, A and Tchuenkam, VPK and Gyuricza, IG and Fola, AA and Wamae, K and Assefa, A and Niaré, K and Thwai, K and White, SJ and Moss, WJ and Dinglasan, RR and Nsango, S and Tume, CB and Parr, JB and Ali, IM and Bailey, JA and Juliano, JJ}, title = {Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39417120}, support = {R01 AI165537/AI/NIAID NIH HHS/United States ; R01 AI177791/AI/NIAID NIH HHS/United States ; U19 AI089680/AI/NIAID NIH HHS/United States ; R01 AI155730/AI/NIAID NIH HHS/United States ; R01 AI156267/AI/NIAID NIH HHS/United States ; K24 AI134990/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing.<br><br>METHODS: P lasmodium f alciparum Streamlined Multiplex Antimalarial Resistance and Relatedness Testing (Pf-SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach.<br><br>RESULTS: We evaluated Pf-SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf-SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf-SMARRT's hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed.<br><br>CONCLUSION: Overall, Pf-SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible.}, }
@article {pmid39416120, year = {2024}, author = {Richardson, M and Zhao, S and Sheth, RU and Lin, L and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416120}, issn = {2692-8205}, support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 EB031935/EB/NIBIB NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; }, abstract = {The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or "spatial hubs" dominated by Bacteroideceae, Ruminococceae, and Lachnospiraceae families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.}, }
@article {pmid39416107, year = {2024}, author = {Chen, J and Nilsen, ED and Chitboonthavisuk, C and Mo, CY and Raman, S}, title = {Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416107}, issn = {2692-8205}, support = {R21 AI156785/AI/NIAID NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; }, abstract = {Understanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries for systematically assessing gene essentiality in bacteriophages. Using PhageMaP, we generate gene essentiality maps across hundreds of genes in the model phage T7 and the non-model phage Bas63, on diverse hosts. These maps provide fundamental insights into genome organization, gene function, and host-specific conditional essentiality. By applying PhageMaP to a collection of anti-phage defense systems, we uncover phage genes that either inhibit or activate eight defenses and offer novel mechanistic hypotheses. Furthermore, we engineer synthetic phages with enhanced infectivity by modular transfer of a PhageMaP-discovered defense inhibitor from Bas63 to T7. PhageMaP is generalizable, as it leverages homologous recombination, a universal cellular process, for locus-specific barcoding. This versatile tool advances bacteriophage functional genomics and accelerates rational phage design for therapy.}, }
@article {pmid39416026, year = {2024}, author = {Sendinc, E and Yu, H and Hwang Fu, YH and Santos, J and Johnson, Z and Kirstein, JR and Niu, J and Chabot, MB and Cantu, VA and Džakula, &#x17d; and Lam, Q and Anmangandla, A and Burcham, TS and Davis, EM and Miles, ZD and Price, AD and Purse, BW and Gregory, RI and Stengel, G}, title = {Mapping multiple RNA modifications simultaneously by proximity barcode sequencing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416026}, issn = {2692-8205}, support = {R35 CA232115/CA/NCI NIH HHS/United States ; R44 HG012170/HG/NHGRI NIH HHS/United States ; }, abstract = {RNA is subject to a multitude of different chemical modifications that collectively represent the epitranscriptome. Individual RNA modifications including N6-methyladenosine (m[6]A) on mRNA play essential roles in the posttranscriptional control of gene expression. Recent technological advances have enabled the transcriptome-wide mapping of certain RNA modifications, to reveal their broad relevance and characteristic distribution patterns. However, convenient methods that enable the simultaneous mapping of multiple different RNA marks within the same sample are generally lacking. Here we present EpiPlex RNA modification profiling, a bead-based proximity barcoding assay with sequencing readout that expands the scope of molecular recognition-based RNA modification detection to multiple targets, while providing relative quantification and enabling low RNA input. Measuring signal intensity against spike-in controls provides relative quantification, indicative of the RNA mod abundance at each locus. We report on changes in the modification status of HEK293T cells upon treatment with pharmacological inhibitors separately targeting METTL3, the dominant m[6]A writer enzyme, and the EIF4A3 component of the exon junction complex (EJC). The treatments resulted in decreased or increased m[6]A levels, respectively, without effect on inosine levels. Inhibiting the helicase activity of EIF4A3 and EIF4A3 knockdown both cause a significant increase of m[6]A sites near exon junctions, consistent with the previously reported role of EIF4A3 in shaping the m[6]A landscape. Thus, EpiPlex offers a reliable and convenient method for simultaneous mapping of multiple RNA modifications to facilitate epitranscriptome studies.}, }
@article {pmid39415074, year = {2024}, author = {Sojitra, M and Schmidt, EN and Lima, GM and Carpenter, EJ and McCord, KA and Atrazhev, A and Macauley, MS and Derda, R}, title = {Measuring carbohydrate recognition profile of lectins on live cells using liquid glycan array (LiGA).}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {39415074}, issn = {1750-2799}, support = {RGPIN-2016-402511//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; RGPIN-2018-03815//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; CR-29//UAlberta | Canadian Glycomics Network (GlycoNet)/ ; TP-22//UAlberta | Canadian Glycomics Network (GlycoNet)/ ; }, abstract = {Glycans constitute a significant fraction of biomolecular diversity on cellular surfaces across all kingdoms of life. As the structure of glycans is not directly encoded by the organism's DNA, it is impossible to use high-throughput DNA technologies to study the role of cellular glycosylation or to understand how glycocalyx is recognized by glycan-binding proteins (GBPs). To address this gap, we recently described a liquid glycan array (LiGA) platform that allows profiling of glycan-GBP interactions on the surface of live cells in vitro and in vivo using next-generation sequencing. LiGA is a library of DNA-barcoded bacteriophages, where each clonal bacteriophage displays 5-1,500 copies of a glycan and the distinct DNA barcode inside each bacteriophage clone encodes the structure and density of the displayed glycans. Deep sequencing of the glycophages associated with live cells yields a glycan-binding profile of GBPs expressed on the surface of cells. This protocol provides detailed instructions for how to use LiGA to probe cell surface receptors and includes information on the preparation of glycophages, analysis by MALDI-TOF mass spectrometry, the assembly of a LiGA library and its deep sequencing. Using this protocol, we measure glycan-binding profiles of the immunomodulatory sialic acid-binding immunoglobulin-like lectins‑1, -2, -6, -7 and -9 expressed on the surface of different cell types. Compared with existing methods that require complex specialist equipment, this method allows users with basic molecular biology expertise to measure the precise glycan-binding profile of GBPs on the surface of any cell type expressing exogenous GBP within 2-3 d.}, }
@article {pmid39411212, year = {2024}, author = {Sasaki, M and Fukumoto, N and Fukumoto, S}, title = {DNA barcoding of Anoplocephala perfoliata derived from a draft horse (Ban'ei horse) in Hokkaido, Japan.}, journal = {Journal of equine science}, volume = {35}, number = {3}, pages = {43-46}, pmid = {39411212}, issn = {1340-3516}, abstract = {A two-year-old male Japanese draft horse (known as a "Ban'ei horse") excreted eight cestodes. Based on their morphological features, they were identified as Anoplocephala perfoliata. The partial mitochondrial cytochrome c oxidase subunit 1 (COI) sequences of the worms were nearly identical to A. perfoliata isolated from horses in Europe. The results of phylogenetic analyses of COI revealed that our samples and the European isolates formed the same clade, which was separate from Chinese and Australian isolates. Ban'ei horses were developed by crossbreeding draft horses imported from European countries in the 1900s. Our results suggest that A. perfoliata was transported to Hokkaido with horses from Europe. To our knowledge, this is the first report of A. perfoliata infection in a Japanese draft horse.}, }
@article {pmid39410130, year = {2024}, author = {Liu, J and Sun, J and He, R and Xia, J and He, P}, title = {The Situation of Counterfeited and Mislabeled Commercialized Edible Mushrooms in China and the Development of Possible Controls.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {19}, pages = {}, pmid = {39410130}, issn = {2304-8158}, abstract = {Edible mushroom products, encompassing both cultivated and wild varieties, are highly favored by consumers due to their rich nutritional profiles, including significant levels of proteins and amino acids. These mushrooms have extensive applications across the food, pharmaceutical, and cosmetic industries, making the edible mushroom industry a vital component of global poverty alleviation efforts. Taking China as an example, the country produces over 45 million tons of edible mushrooms annually, accounting for 94.01% of the world's total production, thereby establishing itself as the leading global producer of edible mushrooms. However, alongside the rapid expansion of this industry, concerns have emerged regarding counterfeit products and incidents of poisoning resulting from the consumption of toxic wild mushrooms. As follows, to advance the development and integrity of the mushroom production and processing industry: (1) This study presents the situation of counterfeit edible mushrooms and elucidates the factors contributing to the production of fraudulent products from both subjective and non-subjective perspectives. (2) We provide a detailed introduction to 22 varieties of freshly cultivated edible mushrooms and commonly encountered wild edible mushrooms in the Chinese consumer market, proposing the application of DNA barcoding, environmental DNA analysis, and other technologies for the future authentication of counterfeit mushroom products. (3) Concurrently, we present an overview of mushroom poisoning incidents in China from 2010 to 2023, emphasizing the challenges in mitigating the risks associated with wild mushroom consumption and preventing food poisoning, thereby necessitating heightened consumer caution. (4) Finally, we offer four recommendations aimed at ensuring the healthy, stable, and sustainable growth of the edible mushroom industry.}, }
@article {pmid39409790, year = {2024}, author = {Altvater-Hughes, TE and Hodgins, HP and Hodgins, DC and Bauman, CA and Paibomesai, MA and Mallard, BA}, title = {Investigating the IgM and IgG B Cell Receptor Repertoires and Expression of Ultralong Complementarity Determining Region 3 in Colostrum and Blood from Holstein-Friesian Cows at Calving.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {19}, pages = {}, pmid = {39409790}, issn = {2076-2615}, support = {RGPIN04638//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {In cattle, colostral maternal immunoglobulins and lymphocytes transfer across the neonate's intestinal epithelium to provide protection against pathogens. This study aimed to compare repertoires of B cell populations in blood and colostrum in cows for the first time, with an emphasis on ultralong complementarity determining region 3 (CDR3, ≥40 amino acids). Blood mononuclear cells (BMCs, n= 7) and colostral cells (n = 7) were isolated from Holstein-Friesian dairy cows. Magnetic-activated cell sorting was used to capture IgM and IgG B cells from BMCs. Colostral cells were harvested by centrifugation. RNA was extracted and cDNA was produced; IgM and IgG transcripts were amplified using polymerase chain reactions. Amplicons were sequenced using the Nanopore Native barcoding kit 24 V14 and MinION with R10.4 flow cells. In colostrum, there was a significantly greater percentage of IgM B cells with ultralong CDR3s (8.09% ± 1.73 standard error of the mean) compared to blood (4.22% ± 0.70, p = 0.05). There was a significantly greater percentage of IgG B cells in colostrum with ultralong CDR3s (12.98% ± 1.98) compared to blood (6.61% ± 1.11, p = 0.05). A higher percentage of IgM and IgG B cells with ultralong CDR3s in colostrum may be indicative of a potential role in protecting the neonate.}, }
@article {pmid39409782, year = {2024}, author = {Dinh-Hung, N and Mwamburi, SM and Dong, HT and Rodkhum, C and Meemetta, W and Linh, NV and Mai, HN and Dhar, AK and Hirono, I and Senapin, S and Chatchaiphan, S}, title = {Unveiling Insights into the Whole Genome Sequencing of Mycobacterium spp. Isolated from Siamese Fighting Fish (Betta splendens).}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {19}, pages = {}, pmid = {39409782}, issn = {2076-2615}, abstract = {This study aims to genomically elucidate six isolates of rapidly growing non-tuberculous mycobacteria (RGM) derived from Siamese fighting fish (Betta splendens). These isolates had previously undergone phenotypic and biochemical characterization, antibiotic susceptibility testing, and in vivo virulence assessment. Initial DNA barcoding using the 16S rRNA sequence assigned these six isolates to five different species, namely Mycobacterium chelonae (BN1983), M. cosmeticum (BN1984 and N041), M. farcinogenes (SNSK5), M. mucogenicum (BN1956), and M. senegalense (BN1985). However, the identification relied solely on the highest percent identity of the 16S rRNA gene, raising concerns about the taxonomic ambiguity of these species. Comprehensive whole genome sequencing (WGS) and extended genomic comparisons using multilocus sequence typing (MLST), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) led to the reclassification of BN1985 and SNSK5 as M. conceptionense while confirming BN1983 as M. chelonae and BN1984 and N041 as M. cosmeticum. Notably, the analysis of the BN1956 isolate revealed a potential new species that is proposed here as M. mucogenicum subsp. phocaicum sp. nov. Common genes encoding "mycobacterial" virulence proteins, such as PE and PPE family proteins, MCE, and YrbE proteins, were detected in all six isolates. Two species, namely M. chelonae and M. cosmeticum, appear to have horizontally acquired T6SS-II (clpB), catalase (katA), GroEL (groel), and capsule (rmlb) from distantly related environmental bacteria such as Klebsiella sp., Neisseria sp., Clostridium sp., and Streptococcus sp. This study provides the first draft genome sequence of RGM isolates currently circulating in B. splendens and underscores the necessity of WGS for the identification and classification of mycobacterial species.}, }
@article {pmid39409767, year = {2024}, author = {Mezzasalma, M and Odierna, G and Macirella, R and Brunelli, E}, title = {New Insights on Chromosome Diversification in Malagasy Chameleons.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {19}, pages = {}, pmid = {39409767}, issn = {2076-2615}, abstract = {In this work, we performed a preliminary molecular analysis and a comparative cytogenetic study on 5 different species of Malagasy chameleons of the genus Brookesia (B. superciliaris) and Furcifer (F. balteautus, F. petteri, F. major and F. minor). A DNA barcoding analysis was first carried out on the study samples using a fragment of the mitochondrial gene coding for the cytochrome oxidase subunit 1 (COI) in order to assess the taxonomic identity of the available biological material. Subsequently, we performed on the studied individuals a chromosome analysis with standard karyotyping (5% Giemsa solution at pH 7) and sequential C-banding + Giemsa, + CMA3, and + DAPI. The results obtained indicate that the studied species are characterized by a different chromosome number and a variable heterochromatin content and distribution, with or without differentiated sex chromosomes. In particular, B. superciliaris (2n = 36) and F. balteatus (2n = 34) showed a similar karyotype with 6 macro- and 12-11 microchromosome pairs, without differentiated sex chromosomes. In turn, F. petteri, F. major, and F. minor showed a karyotype with a reduced chromosome number (2n = 22-24) and a differentiated sex chromosome system with female heterogamety (ZZ/ZW). Adding our newly generated data to those available from the literature, we highlight that the remarkable chromosomal diversification of the genus Furcifer was likely driven by non-homologous chromosome fusions, including autosome-autosome, Z-autosome, and W-autosome fusions. The results of this process resulted in a progressive reduction in the chromosome number and partially homologous sex chromosomes of different shapes and sizes.}, }
@article {pmid39409561, year = {2024}, author = {Mehmood, F and Li, M and Bertolli, A and Prosser, F and Varotto, C}, title = {Comparative Plastomics of Plantains (Plantago, Plantaginaceae) as a Tool for the Development of Species-Specific DNA Barcodes.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {19}, pages = {}, pmid = {39409561}, issn = {2223-7747}, support = {CN00000033, CUPD43C22001280006//European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1034 17/06/2022/ ; }, abstract = {Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species' adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products.}, }
@article {pmid39406839, year = {2024}, author = {Shen, Y and Zhou, X and Zhang, Y and Zhang, J and Li, Q and Chen, Q and Liu, Z and Li, Y and Cheng, R and Luo, Y}, title = {Important fish diversity maintenance status of the tributaries in a hotspot fish conservation area in the upper Yangtze River revealed by eDNA metabarcoding.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24128}, pmid = {39406839}, issn = {2045-2322}, support = {No. 32202939//National Natural Science Foundation of China/ ; No. CSTB2022NSCQ-MSX0793//Natural Science Foundation of Chongqing, China/ ; }, mesh = {Animals ; *Rivers ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; China ; DNA, Environmental/genetics/analysis ; Conservation of Natural Resources ; Ecosystem ; Seasons ; }, abstract = {This study employed Environmental DNA (eDNA) barcoding technology to delve into the influence of the tributaries and mainstem on fish diversity and spatiotemporal distribution in a hotspot fish conservation area in the upper Yangtze River. A total of 123 fish species were detected, belonging to 7 orders, 19 families, and 77 genera. The composition of fish species in tributaries is similar to that in mainstem, with higher fish community diversity in tributaries during the spring and summer. Exploration of fish ecotypes revealed significant differences between mainstem and tributaries. The fish community is mainly influenced by key environmental factors such as water temperature, dissolved oxygen, electrical conductivity, and ammonia nitrogen, with a higher impact of these factors on tributaries than on mainstem. In conclusion, while tributaries and mainstem in the Jiangjin section exhibit similarities in fish community composition, there are notable differences in community structure and diversity. Therefore, the protection of not only mainstem but also tributaries and their associated fish habitats is crucial for promoting the overall health and sustainability.}, }
@article {pmid39406030, year = {2024}, author = {Hymus, CM and Cooper, PL and Rye, MS}, title = {Demonstration of potential DNA contamination introduced by laboratory consumables using Fluorescein.}, journal = {Forensic science international. Genetics}, volume = {74}, number = {}, pages = {103157}, doi = {10.1016/j.fsigen.2024.103157}, pmid = {39406030}, issn = {1878-0326}, abstract = {The development of increasingly efficient DNA extraction and profiling kits has increased the amount of allelic information obtained from trace DNA samples, but also inadvertently, increased the detection of DNA contamination. This study aimed to evaluate the potential of DNA transfer using fluorescein, fluorescent under an alternate light source, in the use of a range of forensically relevant DNA profiling consumables. An evaluation of two pre-lysis methods adopting three different sample tubes, some with deliberate seal damage, showed the PrepFiler™ Automated Forensic DNA Extraction Kit caused leakage and crusting when the rim of the PrepFiler™ LySep column was compromised, but no leakage was observed under the same conditions using the Investigator STAR Lyse&amp;Prep kit. The AutoLys tube showed minimal leakage using the PrepFiler™ chemistry. A DNA extract tube with an external thread, similar to the AutoLys tube, showed no leakage after fridge or freezer storage. However, it highlighted that a centrifugal spin does not guarantee all the DNA will pool at the base of the tube. A comparison of adhesive plate sealing films to 8-well strip caps for sealing 96-well PCR plates showed the adhesive plate sealing films presented a lower risk of DNA transfer, largely due to the adhesion of dispersed liquid on the sticky surface of the film. Overall, this study highlighted a number of variables that may be considered in the development of more refined contamination minimisation protocols in respect to increased sensitivities of DNA profiling.}, }
@article {pmid39405910, year = {2024}, author = {Popović, L and Brankatschk, B and Palladino, G and Rossner, MJ and Wehr, MC}, title = {Polypharmacological profiling across protein target families and cellular pathways using the multiplexed cell-based assay platform safetyProfiler reveals efficacy, potency and side effects of drugs.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {180}, number = {}, pages = {117523}, doi = {10.1016/j.biopha.2024.117523}, pmid = {39405910}, issn = {1950-6007}, mesh = {Humans ; *Polypharmacology ; HEK293 Cells ; Signal Transduction/drug effects ; Receptors, G-Protein-Coupled/metabolism/drug effects ; }, abstract = {Selectivity profiling is key for assessing the pharmacological properties of multi-target drugs. We have developed a cell-based and barcoded assay encompassing ten druggable targets, including G protein-coupled receptors (GPCRs), receptor tyrosine kinases (RTKs), nuclear receptors, a protease as well as their key downstream pathways and profiled 17 drugs in living cells for efficacy, potency, and side effects. Notably, this multiplex assay, termed safetyProfiler assay, enabled the simultaneous assessment of multiple target and pathway activities, shedding light on the polypharmacological profile of compounds. For example, the neuroleptics clozapine, paliperidone, and risperidone potently inhibited primary targets DRD2 and HTR2A as well as cAMP and calcium pathways. However, while paliperidone and risperidone also potently inhibited the secondary target ADRA1A and mitogen-activated protein kinase (MAPK) downstream pathways, clozapine only exhibited mild antagonistic effects on ADRA1A and lacked MAPK inhibition downstream of DRD2 and HTR2A. Furthermore, we present data on the selectivity for bazedoxifene, an estrogen receptor antagonist currently undergoing clinical phase 2 trials for breast cancer, on MAPK signaling. Additionally, precise potency data for LY2452473, an androgen receptor antagonist, that completed a phase 2 clinical trial for prostate cancer, are presented. The non-selective kinase inhibitor staurosporine was observed to potently inactivate the two RTKs EGFR and ERBB4 as well as MAPK signaling, while eliciting stress-related cAMP responses. Our findings underscore the value of comprehensive profiling in elucidating the pharmacological properties of established and novel therapeutics, thereby facilitating the development of novel multi-target drugs with enhanced efficacy and selectivity.}, }
@article {pmid39403482, year = {2024}, author = {Zhou, QR and Ma, YY and Lv, HQ and Lu, ZC and Wang, LS and Liang, JS and Li, JJ}, title = {Chloroplast mini-barcodes combined with high resolution melting analysis to identify herbal medicine Difengpi (Illicium difengpi).}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38700}, pmid = {39403482}, issn = {2405-8440}, abstract = {Difengpi, derived from the air-dried stem bark of Illicium difengpi and enlisted in the Chinese Pharmacopoeia for its therapeutic effect against common ailments, confronts challenges due to dwindling wild resources and intentional substitution with potentially harmful botanical relatives. The imperative need to authenticate this herbal remedy has led to the development of robust methods. Here, we integrated chloroplast mini-barcoding and high resolution melting (HRM) analysis to distinguish Difengpi from the reported adulterants. We assembled the complete chloroplast (cp) genomes of I. difengpi and substituted close relatives I. jiadifengpi and I. majus, and conducted an in-depth comparative analysis to screen divergent regions for exploiting as DNA mini-barcodes. Despite the conservativeness characterizing the whole cp genomes among these Illicium species, we identified some highly variable regions with promising potential as molecular markers for species identification. Subsequently, we designed DNA mini-barcodes and subjected them to HRM analysis to assess their efficacy in species discrimination. Melting profiles unveiled that mini-barcodes designed from four divergence regions trnL-trnF, trnF-ndhJ, ycf1-ndhF and rpl32-trnL exhibited substantial discriminatory power, distinctly differentiated I. difengpi from I. jiadifengpi, I. majus and I. verum. We tested ten commercially available Difengpi products from online stores and local traditional markets using these four mini-barcodes. All ten samples clustered closely with the reference I. difengpi with genotype confidence higher than 93 %, indicating the presence of the claimed species in these samples, sans any reported toxic adulterants. Consequently, we simulated Difengpi mimic samples utilizing I. jiadifengpi, I. majus and I. verum and subjected them to evaluate the practicability of these mini-barcodes. The outcomes confirmed the precision of the four mini-barcodes in accurately discerning the mimic samples. In conclusion, integrating taxon-specific DNA mini-barcodes with HRM analysis is an efficient strategy for the authentication of species identity within commercial herbal products.}, }
@article {pmid39402626, year = {2024}, author = {Liu, Y and Li, N and Qi, J and Xu, G and Zhao, J and Wang, N and Huang, X and Jiang, W and Wei, H and Justet, A and Adams, TS and Homer, R and Amei, A and Rosas, IO and Kaminski, N and Wang, Z and Yan, X}, title = {SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {271}, pmid = {39402626}, issn = {1474-760X}, support = {R01 LM014087/LM/NLM NIH HHS/United States ; R21LM012884//Foundation for the National Institutes of Health/ ; R01LM014087//Foundation for the National Institutes of Health/ ; DMS1916246//National Science Foundation/ ; }, mesh = {*Machine Learning ; *Single-Cell Analysis/methods ; *Transcriptome ; Humans ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Software ; Animals ; Regression Analysis ; RNA-Seq/methods ; }, abstract = {Spatial barcoding-based transcriptomic (ST) data require deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method to deconvolve ST data using reference single-cell RNA sequencing (scRNA-seq) data. SDePER tackles platform effects between ST and scRNA-seq data, ensuring a linear relationship between them while addressing sparsity and spatial correlations in cell types across capture spots. SDePER estimates cell-type proportions, enabling enhanced resolution tissue mapping by imputing cell-type compositions and gene expressions at unmeasured locations. Applications to simulated data and four real datasets showed SDePER's superior accuracy and robustness over existing methods.}, }
@article {pmid39400321, year = {2024}, author = {Castellanos-Labarcena, J and Steinke, D and Adamowicz, SJ}, title = {Anomalous latitudinal gradients in parasitoid wasp diversity-Hotspots in regions with larger temperature range.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.14196}, pmid = {39400321}, issn = {1365-2656}, support = {//Arrell Food Institute/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Genome Canada/ ; //Ontario Ministry of Economic Development, Job Creation and Trade/ ; //Canada First Research Excellence Fund/ ; }, abstract = {Knowledge of global patterns of genetic diversity is essential for biodiversity conservation as this parameter describes the ability of a species to respond to environmental changes. Ichneumonoids parasitoid wasps are among the few taxa showing an anomalous latitudinal diversity gradient. Using the largest georeferenced molecular dataset for this group, we used a macrogenetics approach to examine latitudinal patterns and predictors of intraspecific genetic diversity. We calculated the mean nucleotide diversity of mitochondrial DNA barcode sequences at three geographic levels: grid cells, latitudinal bands and climatic zones. Nucleotide diversity values were consistently higher at northern temperate latitudes, peaking at 50°. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra- and interspecific diversity, and a positive effect of the temperature range. Examining the spatial relationship between different levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary and geographical components when analysing the processes leading to species richness gradients.}, }
@article {pmid39395971, year = {2024}, author = {Li, Z and Ran, Z and Xiao, X and Yan, C and Xu, J and Tang, M and An, M}, title = {Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {955}, pmid = {39395971}, issn = {1471-2229}, support = {2022&#xff08;072&#xff09;//Guizhou Provincial Basic Research Program (Natural Science)/ ; 32360101//National Natural Science Foundation of China/ ; 31960043//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Mitochondrial ; China ; *Camellia/genetics ; Phylogeny ; RNA Editing ; Genome, Plant ; Base Composition ; }, abstract = {BACKGROUND: The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the "Queen of the Tea Family", most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.<br><br>RESULTS: In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836&#xa0;bp (C. nitidissima) to 1,098,121&#xa0;bp (C. tianeensis) with GC content of 45.71-45.78% and contained 48-58 genes, including 28-37 protein-coding genes, 17-20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.<br><br>CONCLUSIONS: In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.}, }
@article {pmid39387679, year = {2024}, author = {Hebert, PDN and Floyd, R and Jafarpour, S and Prosser, SWJ}, title = {Barcode 100K Specimens: In a Single Nanopore Run.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14028}, doi = {10.1111/1755-0998.14028}, pmid = {39387679}, issn = {1755-0998}, support = {OGI-208//Genome Canada/ ; OGI-233//Ontario Genomics/ ; //Canada Foundation for Innovation/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; }, abstract = {It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on the abundance and distribution of species. The acquisition of such information is currently constrained by high costs. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive sequencing protocols are critical as the census of all animal species is likely to require the analysis of a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By enabling the sequencing of highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until recently, constrained adoption. However, the improved performance of its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that a MinION flow cell can characterise an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow.}, }
@article {pmid39394065, year = {2024}, author = {Kan, S and Su, X and Yang, L and Zhou, H and Qian, M and Zhang, W and Li, C}, title = {From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {949}, pmid = {39394065}, issn = {1471-2229}, support = {32200187//National Natural Science Foundation of China/ ; 82173936//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Plastid ; *Phylogeny ; Light ; Plastids/genetics ; Adaptation, Physiological/genetics ; }, abstract = {BACKGROUND: Plastids originated from an ancient endosymbiotic event and evolved into the photosynthetic organelles in plant cells. They absorb light energy and carbon dioxide, converting them into chemical energy and oxygen, which are crucial for plant development and adaptation. However, little is known about the plastid genome to light adaptation. Petrocosmea, a member of the Gesneriaceae family, comprises approximately 70 species with diverse light environment, serve as an ideal subject for studying plastomes adapt to light.<br><br>RESULTS: In this study, we selected ten representative species of Petrocosmea from diverse light environments, assembled their plastid genomes, and conducted a comparative genomic analysis. We found that the plastid genome of Petrocosmea is highly conserved in both structure and gene content. The phylogenetic relationships reconstructed based on the plastid genes were divided into five clades, which is consistent with the results of previous studies. The vast majority of plastid protein-coding genes were under purifying selection, with only the rps8 and rps16 genes identified under positive selection in different light environments. Notably, significant differences of evolutionary rate were observed in NADH dehydrogenase, ATPase ribosome, and RNA polymerase between Clade A and the other clades. Additionally, we identified ycf1 and several intergenic regions (trnH-psbA, trnK-rps16, rpoB-trnC, petA-psbJ, ccsA-trnL, rps16-trnQ, and trnS-trnG) as candidate barcodes for this emerging ornamental horticulture.<br><br>CONCLUSION: We newly assembled ten plastid genomes of Petrocosmea and identified several hypervariable regions, providing genetic resources and candidate markers for this promising emerging ornamental horticulture. Furthermore, our study suggested that rps8 and rps16 were under positive selection and that the evolutionary patterns of NADH dehydrogenase, ATPase ribosome, and RNA polymerase were related to the diversity light environment in Petrocosmea. This revealed an evolutionary scenario for light adaptation of the plastid genome in plants.}, }
@article {pmid39391540, year = {2024}, author = {Selnekovič, D and Kodada, J and Gülperçin, N and Tezcan, S and Ruzzier, E}, title = {Morphological and molecular characterisation of Mordellistenapeloponnesensis Batten, 1980 (Coleoptera, Mordellidae), with first records from Italy and Turkey.}, journal = {ZooKeys}, volume = {1214}, number = {}, pages = {105-117}, pmid = {39391540}, issn = {1313-2989}, abstract = {Mordellistenapeloponnesensis Batten, 1980, previously known from Cyprus and Greece, is reported from Italy and Turkey for the first time. The species is redescribed based on type specimens and additional material from its entire known distributional range. Eighteen DNA barcoding sequences of M.peloponnesensis from Greece, Cyprus, and Italy were generated, and genetic variability across the sampling localities was examined. Three mitochondrial haplotypes were detected within M.peloponnesensis. Specimens from mainland Italy share the same haplotype as those from Rhodes and Cyprus, whereas Sardinian specimens exhibit a distinct haplotype. The third haplotype is represented by one specimen from Cyprus. The DNA barcoding sequences of M.peloponnesensis were compared with those of the morphologically allied M.gemellata Schilsky, 1898, and M.pyrenaea Ermisch, 1966, to reveal the phylogenetic relationships between the species.}, }
@article {pmid39388461, year = {2024}, author = {Martoni, F and Rako, L and Jaroslow, D and Selleck, C and Kant, P and Nancarrow, N and Blacket, MJ}, title = {Diversity and composition of the bacterial communities associated with the Australian spittlebugs Bathyllus albicinctus and Philagra parva (Hemiptera: Aphrophoridae).}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0311938}, pmid = {39388461}, issn = {1932-6203}, mesh = {Animals ; *Hemiptera/microbiology ; Australia ; Xylella/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Microbiota ; Nymph/microbiology ; Plant Diseases/microbiology/parasitology ; Insect Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Spittlebugs and froghoppers (Hemiptera: Cercopoidea) are insects feeding on xylem, which potentially can cause significant economic damage worldwide by transmitting plant pathogenic bacteria such as Xylella fastidiosa. Australia and New Zealand are currently free from X. fastidiosa, but they are home to at least 45 native spittlebug species. Among these, the Australian natives Bathyllus albicinctus (Erichson, 1842) and Philagra parva (Donovan, 1805) are particularly widespread and can be found across southern and eastern Australia, with B. albicinctus also in New Zealand. The potential that both species might be capable of vectoring Xylella fastidiosa poses a substantial biosecurity risk if the bacterium were to invade these regions. In this study, we examined 87 spittlebug nymphs collected across 12 different host plant species, in five locations in Victoria, Australia. Our objective was to explore the factors influencing bacterial communities within and between these widespread spittlebug species, considering geographic location, insect phylogenetics, and host plant associations. We employed COI barcoding to assess insect genetic variation and 16S high throughput sequencing (HTS) metabarcoding to analyse bacterial microbiome diversity across various host plants. Our findings revealed minimal genetic divergence among spittlebug individuals in the same species, highlighting conspecificity despite conspicuous morphological divergences. On the other hand, we recorded significant variation in bacterial communities harboured by Bathyllus albicinctus nymphs feeding on different plants, even when these were collected within close proximity to each other. Therefore, host plant association appeared to shape the bacterial communities of spittlebugs more than insect genetic divergence or geographical location. These diverse bacterial communities could potentially facilitate transmission of plant pathogenic bacteria, underscoring the risk of widespread transmission among numerous plant hosts through insect-plant interactions. This study emphasizes the critical need to understand these complex interactions, particularly in the context of biosecurity.}, }
@article {pmid39386966, year = {2024}, author = {Twyford, AD and Beasley, J and Barnes, I and Allen, H and Azzopardi, F and Bell, D and Blaxter, ML and Broad, G and Campos-Dominguez, L and Choonea, D and Crowley, L and Cuber, P and Cunliffe, M and Dombrowski, A and Douglas, B and Forrest, LL and Gaya, E and Greeves, C and Griffin, C and Harley, J and Hart, ML and Holland, PWH and Hollingsworth, PM and Januszczak, I and Jones, A and Kersey, P and Kilias, E and Lawniczak, MKN and Lewis, OT and Mian, S and Minotto, A and Misra, R and Mulhair, PO and Pereira da Conceicoa, L and Price, BW and Salatino, S and Shaw, F and Sivell, O and Sivess, L and Uhl, R and Woof, K and , }, title = {A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {339}, pmid = {39386966}, issn = {2398-502X}, abstract = {Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.}, }
@article {pmid39386620, year = {2024}, author = {Mays, JC and Mei, S and Kogenaru, M and Quysbertf, HM and Bosco, N and Zhao, X and Bianchi, JJ and Goldberg, A and Kidiyoor, GR and Holt, LJ and Fenyö, D and Davoli, T}, title = {KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39386620}, issn = {2692-8205}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 HG012590/HG/NHGRI NIH HHS/United States ; R37 CA240765/CA/NCI NIH HHS/United States ; R01 DK135089/DK/NIDDK NIH HHS/United States ; R37 CA248631/CA/NCI NIH HHS/United States ; }, abstract = {Investigating chromosomal instability and aneuploidy within tumors is essential for understanding tumorigenesis and developing diagnostic and therapeutic strategies. Single-cell DNA sequencing technologies have enabled such analyses, revealing aneuploidies specific to individual cells within the same tumor. However, it has been difficult to scale the throughput of these methods to detect rare aneuploidies while maintaining high sensitivity. To overcome this deficit, we developed KaryoTap, a method combining custom targeted DNA sequencing panels for the Tapestri platform with a computational framework to enable detection of chromosome- and chromosome arm-scale aneuploidy (gains or losses) and copy number neutral loss of heterozygosity in all human chromosomes across thousands of single cells simultaneously. KaryoTap allows detecting gains and losses with an average accuracy of 83% for arm events and 91% for chromosome events. Importantly, together with chromosomal copy number, our system allows us to detect barcodes and gRNAs integrated into the cells' genome, thus enabling pooled CRISPR- or ORF-based functional screens in single cells. As a proof of principle, we performed a small screen to expand the chromosomes that can be targeted by our recently described CRISPR-based KaryoCreate system for engineering aneuploidy in human cells. KaryoTap will prove a powerful and flexible approach for the study of aneuploidy and chromosomal instability in both tumors and normal tissues.}, }
@article {pmid39386543, year = {2024}, author = {Vong, KI and Alvarez, YD and Noel, G and Barton, ST and Chung, C and Howarth, R and Meave, N and Zhang, Q and Jiwani, F and Barrows, C and Patel, A and Wang, JX and Chi, N and Kingsmore, SF and White, MD and Yang, X and Gleeson, JG}, title = {Genomic mosaicism reveals developmental organization of trunk neural crest-derived ganglia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39386543}, issn = {2692-8205}, support = {U01 MH108898/MH/NIMH NIH HHS/United States ; R01 MH124890/MH/NIMH NIH HHS/United States ; P01 HD104436/HD/NICHD NIH HHS/United States ; K99 HD111686/HD/NICHD NIH HHS/United States ; R21 MH134401/MH/NIMH NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; S10 OD021644/OD/NIH HHS/United States ; }, abstract = {The neural crest generates numerous cell types, but conflicting results leave developmental origins unresolved. Here using somatic mosaic variants as cellular barcodes, we infer embryonic clonal dynamics of trunk neural crest, focusing on the sensory and sympathetic ganglia. From three independent adult neurotypical human donors, we identified 1,278 mosaic variants using deep whole-genome sequencing, then profiled allelic fractions in 187 anatomically dissected ganglia. We found a massive rostrocaudal spread of progenitor clones specific to sensory or sympathetic ganglia, which unlike in the brain, showed robust bilateral distributions. Computational modeling suggested neural crest progenitor fate specification preceded delamination from neural tube. Single-cell multiomic analysis suggested both neurons and glia contributed to the rostrocaudal clonal organization. CRISPR barcoding in mice and live imaging in quail embryos confirmed these clonal dynamics across multiple somite levels. Our findings reveal an evolutionarily conserved clonal spread of cells populating peripheral neural ganglia.}, }
@article {pmid39386478, year = {2024}, author = {Vaidya, K and Regan, MS and Lin, J and Houle, J and Stopka, SA and Agar, NYR and Hammond, PT and Boehnke, N}, title = {Pooled nanoparticle screening using a chemical barcoding approach.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.24.614746}, pmid = {39386478}, issn = {2692-8205}, abstract = {We report the development of a small molecule-based barcoding platform for pooled screening of nanoparticle delivery. Using aryl halide-based tags (halocodes), we achieve high-sensitivity detection via gas chromatography coupled with mass spectrometry or electron capture. This enables barcoding and tracking of nanoparticles with minimal halocode concentrations and without altering their physicochemical properties. To demonstrate the utility of our platform for pooled screening, we synthesized a halocoded library of polylactide-co-glycolide (PLGA) nanoparticles and quantified uptake in ovarian cancer cells in a pooled manner. Our findings correlate with conventional fluorescence-based assays. Additionally, we demonstrate the potential of halocodes for spatial mapping of nanoparticles using mass spectrometry imaging (MSI). Halocoding presents an accessible and modular nanoparticle screening platform capable of quantifying delivery of pooled nanocarrier libraries in a range of biological settings.}, }
@article {pmid39386005, year = {2024}, author = {Lin, X and Waring, K and Ghezzi, H and Tropini, C and Tyson, J and Ziels, RM}, title = {High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.}, journal = {PNAS nexus}, volume = {3}, number = {10}, pages = {pgae411}, pmid = {39386005}, issn = {2752-6542}, abstract = {Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.}, }
@article {pmid39385931, year = {2024}, author = {Da Silva, C and Mannise, N and Seguí, R and Iriarte, A and Bou, N and Bonifacino, JM and Mailhos, A and Anza, L and Chitaro, S and Ocampo, F and Gándaras, R and Arezo, F and Capurro, L and Iturburu, M and Nieto, N and Juan, H and Garrido, J and Platero, R and Gago, J and Lezama, F and Do Carmo, M and Cosse, M}, title = {Exploring biodiversity of Uruguayan vascular plants through DNA barcoding.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1435592}, pmid = {39385931}, issn = {1664-8021}, }
@article {pmid39385841, year = {2024}, author = {Siedlecki, I and Kochanowski, M and Pawłowska, J and Reszotnik, G and Okrasińska, A and Wrzosek, M}, title = {Ant's Nest as a microenvironment: Distinct Mucoromycota (Fungi) community of the red wood ants' (Formica polyctena) mounds.}, journal = {Ecology and evolution}, volume = {14}, number = {10}, pages = {e70333}, pmid = {39385841}, issn = {2045-7758}, abstract = {Many social insect species build nests, which differ from the surrounding environment and are often occupied by specific organismal communities. These organisms may interact mutualistically or parasitically with the nest-builders, or simply co-occur, being able to survive in these microenvironments. In temperate forests, red wood ants (e.g. Formica polyctena) are known to create distinct, highly developed nests, which consist of large, above-ground mounds, built primarily out of plant matter collected from the forest litter. The microorganismal communities of such mounds remain understudied. As representatives of Mucoromycota fungi commonly engage in the decomposition process of the forest litter, they would be expected to occur in the mounds. However, it is still not known whether the Mucoromycota community of these ants' nests differ from the one of the surrounding forest litter. In order to distinguish mound-associated taxa, we characterized Mucoromycota communities of Formica polyctena mounds and the surrounding forest litter. We sampled four sites, twice in a season. Sampled material was plated on agar media and emerging Mucoromycota colonies were identified based on their morphology. Fungal identification was further confirmed using DNA barcoding. In order to compare described communities, PERMANOVA test and non-metric multidimensional scaling ordinations were used. To distinguish taxa associated with the mounds, multilevel pattern analysis was performed. Our results show that the Mucoromycota community of Formica polyctena's mound differs from the community of the surrounding forest litter. While representatives of Entomortierella lignicola and Absidia cylindrospora clade were found to be associated with the mound environment, representatives of Umbelopsis curvata and Podila verticillata-humilis clade were associated with forest litter, and were rarely present in the mounds. Our findings strongly suggest that the red wood ants' nest is a specific microenvironment in the temperate forest floor, which is a preferred microhabitat for the mound-associated Mucoromycota, possibly adapted to live in proximity to ants.}, }
@article {pmid39385531, year = {2024}, author = {Nirchio, M and Oliveira, C and de Bello Cioffi, M and Sassi, FMC and Rizzi, FP and Benavides, SWN and Berrones, AJC and Romero, JFR and Deon, GA and Kuranaka, M and Valdiviezo-Rivera, JS and Carrión Olmedo, JC and Rossi, AR}, title = {Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae).}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.15924}, pmid = {39385531}, issn = {1095-8649}, support = {2020/UTMACH-GPR-155//Universidad T&#xe9;cnica de Machala/ ; DI-CONV-2017-009//Universidad Central del Ecuador/ ; 2020/13433-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/00955-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/08116-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; proc. 306054/2006-0//Consejo de Desarrollo Cient&#xed;fico, Human&#xed;stico, Tecnol&#xf3;gico y de las Artes, Universidad de Los Andes Venezuela/ ; 441128/2020-3//Consejo de Desarrollo Cient&#xed;fico, Human&#xed;stico, Tecnol&#xf3;gico y de las Artes, Universidad de Los Andes Venezuela/ ; RP12117A6764463C//Sapienza Universit&#xe0; di Roma/ ; }, abstract = {Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.}, }
@article {pmid39384703, year = {2024}, author = {Araújo, KS and Alves, JL and Pereira, OL and de Queiroz, MV}, title = {Five new species of endophytic Penicillium from rubber trees in the Brazilian Amazon.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39384703}, issn = {1678-4405}, support = {Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {The Amazon rainforest is the world's most diverse ecosystem, full of fauna and flora. Among the trees that make up the forest are the rubber trees of the genus Hevea (H. brasiliensis and H. guianensis), which stand out for the industrial use of latex. It was previously shown that endophytic fungi colonize the leaves, stems, and roots of Hevea spp. In this study, 47 Penicillium spp. and three Talaromyces spp. isolates were analyzed using specific DNA barcodes: internal transcribed spacers region (ITS), β-tubulin (BenA), calmodulin (CaM), and the DNA-dependent RNA polymerase II second largest subunit (RPB2) genes and additionally, for species delimitation, the genealogical concordance phylogenetic species recognition (GCPSR) criteria were applied. The phylogenetic analyses placed the Penicillium isolates into four sections Lanata-Divaricata, Sclerotiora, Citrina, and Fasciculata. The morphological and molecular characteristics resulted in the discovery of five new species (P. heveae sp. nov., P. acrean sp. nov., P. aquiri sp. nov., P. amazonense sp. nov., and P. pseudomellis sp. nov.). The five new species were also compared to closely related species, with observations on morphologically distinguishing features and colony appearances. Bayesian inference and maximum likelihood analysis have supported the placement of P. heveae sp. nov. as a sister group to P. globosum; P. acrean sp. nov. and P. aquiri sp. nov. as sister groups to P. sumatrense; P. amazonense sp. nov. closely related to isolates of P. rolfsii, and P. pseudomellis sp. nov. closely related to P. mellis. The study of endophytic Penicillium species of rubber trees and the description of five new taxa of Penicillium sect. Citrina, Lanata-Divaricata, and Sclerotiora as endophytes add to the fungal biodiversity knowledge in native rubber trees. Reports of fungi in native tropical plants may reveal taxonomic novelties, potential pathogen control agents, and producers of molecular bioactive compounds of medical and agronomic interest.}, }
@article {pmid39384034, year = {2024}, author = {Martínez Del Río, J and Frutos-Beltrán, E and Sebastián-Martín, A and Lasala, F and Yasukawa, K and Delgado, R and Menéndez-Arias, L}, title = {HIV-1 Reverse Transcriptase Error Rates and Transcriptional Thresholds Based on Single-strand Consensus Sequencing of Target RNA Derived From In Vitro-transcription and HIV-infected Cells.}, journal = {Journal of molecular biology}, volume = {436}, number = {22}, pages = {168815}, doi = {10.1016/j.jmb.2024.168815}, pmid = {39384034}, issn = {1089-8638}, mesh = {*HIV Reverse Transcriptase/genetics/metabolism ; Humans ; *HIV-1/genetics ; *RNA, Viral/genetics ; Reverse Transcription/genetics ; High-Throughput Nucleotide Sequencing/methods ; HIV Infections/virology/genetics ; Transcription, Genetic ; }, abstract = {Nucleotide incorporation and lacZ-based forward mutation assays have been widely used to determine the accuracy of reverse transcriptases (RTs) in RNA-dependent DNA polymerization reactions. However, they involve quite complex and laborious procedures, and cannot provide accurate error rates. Recently, NGS-based methods using barcodes opened the possibility of detecting all errors introduced by the RT, although their widespread use is limited by cost, due to the large size of libraries to be sequenced. In this study, we describe a novel and relatively simple NGS assay based on single-strand consensus sequencing that provides robust results with a relatively small number of raw sequences (around 60 Mb). The method has been validated by determining the error rate of HIV-1 (BH10 strain) RT using the HIV-1 protease-coding sequence as target. HIV-1 reverse transcription error rates in standard conditions (37 °C/3 mM Mg[2+]) using an in vitro-transcribed RNA were around 7.3 × 10[-5]. In agreement with previous reports, an 8-fold increase in RT's accuracy was observed after reducing Mg[2+] concentration to 0.5 mM. The fidelity of HIV-1 RT was also higher at 50 °C than at 37 °C (error rate 1.5 × 10[-5]). Interestingly, error rates obtained with HIV-1 RNA from infected cells as template of the reverse transcription at 3 mM Mg[2+] (7.4 × 10[-5]) were similar to those determined with the in vitro-transcribed RNA, and were reduced to 1.8 × 10[-5] in the presence of 0.5 mM Mg[2+]. Values obtained at low magnesium concentrations were modestly higher than the transcription error rates calculated for human cells, thereby suggesting a realistic transcriptional threshold for our NGS-based error rate determinations.}, }
@article {pmid39383837, year = {2024}, author = {Mansfield, KL and González, E and McKay, S and Apaa, T and Kent, AJ and Cropper, P and Berry, N and Hernández-Triana, LM and Johnson, N}, title = {Short Communication: Anaplasma phagocytophilum and Babesia spp. in ixodid ticks infesting red foxes (Vulpes vulpes) in Great Britain.}, journal = {Ticks and tick-borne diseases}, volume = {15}, number = {6}, pages = {102401}, doi = {10.1016/j.ttbdis.2024.102401}, pmid = {39383837}, issn = {1877-9603}, abstract = {Red foxes (Vulpes vulpes) are found throughout the United Kingdom (UK), and can reach high population densities in urban areas. They are often infested with ticks which may carry tick-borne pathogens, leading to a risk of transmission to domestic animals and humans. This study investigated the prevalence of tick-borne pathogens in ticks sourced from red fox carcasses across Great Britain between 2018 and 2022. Tick species were identified using morphological keys and molecular barcoding, followed by specific pathogen testing using PCR. In total, 227 ticks were collected from 93 foxes. Pooling (n = 2) was undertaken for unengorged nymphs from the same tick species and fox host, with 203 homogenates tested in total (24 pools and 179 individual ticks). Ixodes hexagonus was the most abundant tick species sampled (73 %), of which 59 % were nymphs and 41 % were females. Less common were Ixodes ricinus (12 %) and Ixodes canisuga (15 %), the majority of which were females (73 % and 91 %, respectively). One Ixodes sp. larva was identified. Babesia DNA was identified in seven individual ticks and once in pooled ticks (n = 2); seven detections were in I. hexagonus and one in I. canisuga, with an overall detection rate of 7 % (95 % CI: 6 - 8 %). Sequence analysis confirmed that all Babesia detections in I. hexagonus were Babesia vulpes, with detection of Babesia Badger Type A in I. canisuga. Screening for Anaplasma phagocytophilum DNA through amplification of the msp2 gene yielded an overall detection rate of 4 % (detected in I. hexagonus only). Louping ill virus was not detected by qRT-PCR in any tick RNA tested. The majority of pathogen detections were in ticks from red foxes in rural areas of the UK, although a small number of Babesia detections were in ticks collected from semi-rural or urban red foxes. Additionally, B. vulpes was detected in GB red fox tissues, suggesting a potential role as a reservoir host. This study confirms the detection of tick-borne pathogens in ticks infesting UK red foxes and highlights the involvement of GB tick species in animal or human disease transmission.}, }
@article {pmid39380764, year = {2023}, author = {Kartiganer, Z and Rojas, G and Riccio, M and Tyree, A and Noronha, K and Wetzel, M and Barnett, J and McGann, J and Garbarino, J and Massucci, D and Chafi, NS and Decker, S and McDaniels, A and Sabina, J and Levchenko, D and Perez, J and Ng, C and Wang, K}, title = {Improved cell-type identification and comprehensive mapping of regulatory features with spatial epigenomics 96-channel microfluidic platform.}, journal = {GEN biotechnology}, volume = {2}, number = {6}, pages = {503-514}, pmid = {39380764}, issn = {2768-1556}, support = {R44 CA287890/CA/NCI NIH HHS/United States ; }, abstract = {Gene expression is subject to epigenetic regulation and is dependent upon cellular context. Spatial omics tools can provide insight into cellular context; however, development has centered on spatial transcriptomics and proteomics. Deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq) was the first spatial epigenomics platform at the cellular level. Here we present a comparison of spatial epigenomic profiling on both 50-channel and 96-channel platforms. The new 96-channel microfluidics chip design greatly improved precision in cell typing and identification of regulatory elements by spatial-ATAC-seq. Spatial mapping reveals complexity of glial cell and neuronal localization within brain structures as well as cis-regulatory elements controlling cellular function. This technology streamlines spatial analysis of the epigenome and contributes a new layer of spatial omics to uncover the context dependent regulatory mechanisms underpinning development, disease, and normal cellular function.}, }
@article {pmid39380274, year = {2024}, author = {Abdulrahman Ismael, K and Abdul-Qadir Ali, L}, title = {Morphological and molecular identification of freshwater eutardigrade Dactylobiotus parthenogeneticus (Bertolani, 1982) in the Greater Zab River of Kurdistan Region - Iraq.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {70}, number = {9}, pages = {86-90}, doi = {10.14715/cmb/2024.70.9.12}, pmid = {39380274}, issn = {1165-158X}, mesh = {Animals ; Iraq ; *Tardigrada/genetics/classification/anatomy &amp; histology ; *Rivers ; *Electron Transport Complex IV/genetics ; *Phylogeny ; DNA Barcoding, Taxonomic/methods ; Fresh Water ; }, abstract = {Dactylobiotus parthenogeneticus is one of the widespread species of tardigrade all over the world. Tardigrades of this species were collected from the Greater Zab River in Erbil City-Iraq by filtering water of the river through a plankton net with a mesh of 45 µm pore. The samples were mounted on a slide with a cover slip and examined under the microscope to determine morphological characteristics and measurements. Based on these characters the species identified to be D. parthenogeneticus. To support this diagnosis, DNA barcoding techniques were applied to do molecular analysis and sequencing on the cytochrome oxidase subunit I (COI) gene. The sequence was subjected to the GenBank database of NCBI and recorded with the accession number PP140905. The result of the sequencing and molecular analysis of the cytochrome oxidase subunit I (COI) gene confirmed to be the same species diagnosed by relying upon morphological characters. This study represents one of the pioneer researches and documents on tardigrades and found D. parthenogeneticus for the first time in the Greater Zab River in Kurdistan, North of Iraq. Tardigrades play a magnificent role in different trophic levels and can be utilized as an indicator of ecosystem health.}, }
@article {pmid39380264, year = {2024}, author = {Khawaja Ghulam, R and Husain, M and Sharaf, MR and Muhammad Tufail,  and Sutanto, KD and Alwaneen, WS and Aldawood, AS}, title = {Mitochondrial DNA sequence-based identification of two subterranean termite species, from Riyadh Province, Kingdom of Saudi Arabia.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {70}, number = {9}, pages = {189-197}, doi = {10.14715/cmb/2024.70.9.26}, pmid = {39380264}, issn = {1165-158X}, mesh = {Animals ; *Isoptera/genetics/classification ; *Phylogeny ; Saudi Arabia ; *DNA, Mitochondrial/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; Base Sequence ; }, abstract = {Termites are economically important wood-destroying and agricultural pests. The termite fauna almost consists of 2900 described species in 286 genera worldwide. In the present study, hundreds of termite samples from 42 different locations in the Riyadh province were collected. These samples were previously used for morphometric identification and reported two subterranean termite species, Coptotermes heimi and Psammotermes hypostoma, in the family Rhinotermitidae. In the present study, these samples were analysed using DNA barcoding with the mitochondrial cytochrome c oxidase subunit 1 gene to confirm the conventional taxonomical identification on a molecular basis. The obtained COI gene sequences of all 42 termite specimens were submitted to GenBank (accession numbers: ON529959-ON529969, OP825131-OP825132, and OP890882-OP890910). Eleven of the 42 samples were thus identified as C. heimi and the remaining 31 samples as P. hypostoma, which were phylogenetically analysed. All the 11 C. heimi sequences were grouped in a single clade, indicating close relatedness. While 31 sequences of P. hypostoma constituted two clades in the phylogenetic tree. Pairwise nucleotide sequence identity and divergence analysis showed that C. heimi sequences showed high nucleotide identities of 87.6-99.5% and less divergence ranging from 0.5% to 13.6%. Similarly, sequences of P. hypostoma also showed high nucleotide identity of 78.6-100% and low divergence among them ranging from 0-10.7%. A further application, significance, and shortcomings of COI-based DNA barcoding have been discussed. DNA barcoding using the COI gene is a reliable tool to distinguish C. heimi and P. hypostoma genotypes.}, }
@article {pmid39380090, year = {2024}, author = {Amstler, S and Streiter, G and Pfurtscheller, C and Forer, L and Di Maio, S and Weissensteiner, H and Paulweber, B and Schönherr, S and Kronenberg, F and Coassin, S}, title = {Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex lipoprotein(a) KIV-2 VNTR.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {117}, pmid = {39380090}, issn = {1756-994X}, mesh = {Humans ; *Haplotypes ; *Minisatellite Repeats ; *Lipoprotein(a)/genetics ; *Nanopore Sequencing/methods ; DNA Mutational Analysis/methods ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Repetitive genome regions, such as variable number of tandem repeats (VNTR) or short tandem repeats (STR), are major constituents of the uncharted dark genome and evade conventional sequencing approaches. The protein-coding LPA kringle IV type-2 (KIV-2) VNTR (5.6 kb per unit, 1-40 units per allele) is a medically highly relevant example with a particularly intricate structure, multiple haplotypes, intragenic homologies, and an intra-VNTR STR. It is the primary regulator of plasma lipoprotein(a) [Lp(a)] concentrations, an important cardiovascular risk factor. Lp(a) concentrations vary widely between individuals and ancestries. Multiple variants and functional haplotypes in the LPA gene and especially in the KIV-2 VNTR strongly contribute to this variance.<br><br>METHODS: We evaluated the performance of amplicon-based nanopore sequencing with unique molecular identifiers (UMI-ONT-Seq) for SNP detection, haplotype mapping, VNTR unit consensus sequence generation, and copy number estimation via coverage-corrected haplotypes quantification in the KIV-2 VNTR. We used 15 human samples and low-level mixtures (0.5 to 5%) of KIV-2 plasmids as a validation set. We then applied UMI-ONT-Seq to extract KIV-2 VNTR haplotypes in 48 multi-ancestry 1000 Genome samples and analyzed at scale a poorly characterized STR within the KIV-2 VNTR.<br><br>RESULTS: UMI-ONT-Seq detected KIV-2 SNPs down to 1% variant level with high sensitivity, specificity, and precision (0.977&#x2009;&#xb1;&#x2009;0.018; 1.000&#x2009;&#xb1;&#x2009;0.0005; 0.993&#x2009;&#xb1;&#x2009;0.02) and accurately retrieved the full-length haplotype of each VNTR unit. Human variant levels were highly correlated with next-generation sequencing (R[2]&#x2009;=&#x2009;0.983) without bias across the whole variant level range. Six reads per UMI produced sequences of each KIV-2 unit with Q40 quality. The KIV-2 repeat number determined by coverage-corrected unique haplotype counting was in close agreement with droplet digital PCR (ddPCR), with 70% of the samples falling even within the narrow confidence interval of ddPCR. We then analyzed 62,679 intra-KIV-2 STR sequences and explored KIV-2 SNP haplotype patterns across five ancestries.<br><br>CONCLUSIONS: UMI-ONT-Seq accurately retrieves the SNP haplotype and precisely quantifies the VNTR copy number of each repeat unit of the complex KIV-2 VNTR region across multiple ancestries. This study utilizes the KIV-2 VNTR, presenting a novel and potent tool for comprehensive characterization of medically relevant complex genome regions at scale.}, }
@article {pmid39380014, year = {2024}, author = {Liu, Z and Pei, Y and Chen, T and Yang, Z and Jiang, W and Feng, X and Li, X}, title = {Molecular quantification of fritillariae cirrhosae bulbus and its adulterants.}, journal = {Chinese medicine}, volume = {19}, number = {1}, pages = {138}, pmid = {39380014}, issn = {1749-8546}, support = {7244492//Beijing Natural Science Foundation/ ; 2019YFC1710600//National Key Research and Development Program of China/ ; CI2021A04106//The Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; ZZ15-YQ-033//Fundamental Research Funds for the Central public welfare research institutes of China/ ; ZXKT23004//Fundamental Research Funds for the Central public welfare research institutes of China/ ; CI2024C003YN//The Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; }, abstract = {BACKGROUND: Fritillariae Cirrhosae Bulbus (FCB) is frequently adulterated with its closely related species due to personal or non-man made factors, leading to alterations in the composition of its constituents and compromising the efficacy of its products.<br><br>METHODS: The specific single nucleotide polymorphisms (SNPs) were screened by comparing candidate barcodes of Fritillaria and verified by amplification and sequencing. Herb molecular quantification (Herb-Q) was established by detecting specific SNPs, and the methodological validation was performed. Quantitative standard curves were established for FCB mixed with each adulterated species, and the quantitative validity of this method was verified based on external standard substance. In addition, eight commercial Shedan Chuanbei capsules (SDCBs) randomly selected were detected.<br><br>RESULTS: FCB and its five adulterants can be distinguished based on the ITS 341 site. The methodological investigation of Herb-Q shows optimal accuracy, and repeatability, which exhibited good linearity with an R[2] of 0.9997 (>&#x2009;0.99). An average bias in quantitative validity was 5.973% between the measured and actual values. Four of eight commercial SDCBs were adulterated with F. ussuriensis or F. thunbergia with adulteration levels ranging from 9 to 15% of the total weight.<br><br>CONCLUSION: This study confirmed that Herb-Q can quantitatively detect both the mixed herbs and Chinese patent medicines (CPMs) containing FCB with high reproducibility and accuracy. This method provides technical support for market regulation and helps safeguard patient rights.}, }
@article {pmid39375852, year = {2024}, author = {Morales-Pulido, JM and Galindo-Sánchez, CE and Jiménez-Rosenberg, SPA and Batta-Lona, PG and Herzka, SZ and Arteaga, MC}, title = {A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.15921}, pmid = {39375852}, issn = {1095-8649}, support = {Fund Project 201441//Consejo Nacional de Ciencia y Tecnolog&#xed;a in Mexico (National Council for Science and Technology - Mexican Ministry of Energy - Hydrocarbon)/ ; 682136//Internal project: Environmental variations effects on mollusks: a genomic and transcriptomic approximation/ ; }, abstract = {Sparisoma species (parrotfish) comprise an important functional group contributing to coral-reef resilience. The morphological diagnostic characteristics for species identification are clearly described for adult forms but not for the early stages. Consequently, many taxonomical listings of Sparisoma larvae are restricted to the genus level. The aims of this study are to determine whether the morphological and molecular identification techniques are useful to assign the species taxonomic level to Sparisoma larvae occurring in the Gulf of Mexico and whether there is a set of diagnostic features that could be used to discriminate between species in larvae of different developmental stages. Morphological assignment of Sparisoma was performed based on morphological and meristic features for 30 larvae collected in the Gulf of Mexico from late August to mid-September 2015. To corroborate and complement the morphological assignments, molecular identification was carried out using DNA sequences from regions of two mitochondrial genes, mitochondrial cytochrome oxidase I (mtDNA COI) and mitochondrial 16S rRNA (mtDNA 16S rRNA). COI and 16S gene trees for Sparisoma and related fish taxa were constructed using sequences available in the NCBI (National Center for Biotechnology Information) GenBank and BOLD (Barcode of Life Data) databases. Two morphotypes were identified based on morphology, but no diagnostic characteristics for species discrimination were found. Molecular identification, in contrast, successfully discriminated four early development stages of Sparisoma atomarium, three stages of Sparisoma radians, and two stages of Sparisoma chrysopterum and Sparisoma aurofrenatum, therefore demonstrating the successful and necessary application of molecular taxonomic approaches for species-level identifications of Sparisoma larvae.}, }
@article {pmid39375541, year = {2024}, author = {Biggs, BW and Price, MN and Lai, D and Escobedo, J and Fortanel, Y and Huang, YY and Kim, K and Trotter, VV and Kuehl, JV and Lui, LM and Chakraborty, R and Deutschbauer, AM and Arkin, AP}, title = {High-throughput protein characterization by complementation using DNA barcoded fragment libraries.}, journal = {Molecular systems biology}, volume = {20}, number = {11}, pages = {1207-1229}, pmid = {39375541}, issn = {1744-4292}, support = {S10 OD018174/OD/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; NIH S10 OD018174//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Escherichia coli/genetics/metabolism ; *Gene Library ; *DNA Barcoding, Taxonomic ; Bacillus subtilis/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genetic Complementation Test ; High-Throughput Nucleotide Sequencing ; Escherichia coli Proteins/genetics/metabolism ; }, abstract = {Our ability to predict, control, or design biological function is fundamentally limited by poorly annotated gene function. This can be particularly challenging in non-model systems. Accordingly, there is motivation for new high-throughput methods for accurate functional annotation. Here, we used complementation of auxotrophs and DNA barcode sequencing (Coaux-Seq) to enable high-throughput characterization of protein function. Fragment libraries from eleven genetically diverse bacteria were tested in twenty different auxotrophic strains of Escherichia coli to identify genes that complement missing biochemical activity. We recovered 41% of expected hits, with effectiveness ranging per source genome, and observed success even with distant E. coli relatives like Bacillus subtilis and Bacteroides thetaiotaomicron. Coaux-Seq provided the first experimental validation for 53 proteins, of which 11 are less than 40% identical to an experimentally characterized protein. Among the unexpected function identified was a sulfate uptake transporter, an O-succinylhomoserine sulfhydrylase for methionine synthesis, and an aminotransferase. We also identified instances of cross-feeding wherein protein overexpression and nearby non-auxotrophic strains enabled growth. Altogether, Coaux-Seq's utility is demonstrated, with future applications in ecology, health, and engineering.}, }
@article {pmid39375449, year = {2024}, author = {Kudo, T and Meireles, AM and Moncada, R and Chen, Y and Wu, P and Gould, J and Hu, X and Kornfeld, O and Jesudason, R and Foo, C and Höckendorf, B and Corrada Bravo, H and Town, JP and Wei, R and Rios, A and Chandrasekar, V and Heinlein, M and Chuong, AS and Cai, S and Lu, CS and Coelho, P and Mis, M and Celen, C and Kljavin, N and Jiang, J and Richmond, D and Thakore, P and Benito-Gutiérrez, E and Geiger-Schuller, K and Hleap, JS and Kayagaki, N and de Sousa E Melo, F and McGinnis, L and Li, B and Singh, A and Garraway, L and Rozenblatt-Rosen, O and Regev, A and Lubeck, E}, title = {Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39375449}, issn = {1546-1696}, abstract = {Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture due to limitations associated with in situ sequencing of perturbation barcodes. Here, we develop PerturbView, an OPS technology that leverages in vitro transcription to amplify barcodes before in situ sequencing, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in induced pluripotent stem cell-derived neurons, primary immune cells and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NF-κB signaling. Furthermore, we combine PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way to in situ screens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.}, }
@article {pmid39375448, year = {2024}, author = {Gu, J and Iyer, A and Wesley, B and Taglialatela, A and Leuzzi, G and Hangai, S and Decker, A and Gu, R and Klickstein, N and Shuai, Y and Jankovic, K and Parker-Burns, L and Jin, Y and Zhang, JY and Hong, J and Niu, X and Costa, JA and Pezet, MG and Chou, J and Snoeck, HW and Landau, DA and Azizi, E and Chan, EM and Ciccia, A and Gaublomme, JT}, title = {Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39375448}, issn = {1546-1696}, support = {1DP2CA281605//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA197774-04//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA227450-04//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 1R21HG012639-01A1//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; 1R01HG012875-01//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; Lloyd J. Old STAR award//Cancer Research Institute (CRI)/ ; }, abstract = {Unlike sequencing-based methods, which require cell lysis, optical pooled genetic screens enable investigation of spatial phenotypes, including cell morphology, protein subcellular localization, cell-cell interactions and tissue organization, in response to targeted CRISPR perturbations. Here we report a multimodal optical pooled CRISPR screening method, which we call CRISPRmap. CRISPRmap combines in situ CRISPR guide-identifying barcode readout with multiplexed immunofluorescence and RNA detection. Barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency. CRISPRmap enables in situ barcode readout in cell types and contexts that were elusive to conventional optical pooled screening, including cultured primary cells, embryonic stem cells, induced pluripotent stem cells, derived neurons and in vivo cells in a tissue context. We conducted a screen in a breast cancer cell line of the effects of DNA damage repair gene variants on cellular responses to commonly used cancer therapies, and we show that optical phenotyping pinpoints likely pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance.}, }
@article {pmid39372282, year = {2024}, author = {Huber, BA and Meng, G}, title = {Old World Micropholcus spiders, with first records of acrocerid parasitoids in Pholcidae (Araneae).}, journal = {ZooKeys}, volume = {1213}, number = {}, pages = {95-182}, pmid = {39372282}, issn = {1313-2989}, abstract = {Micropholcus Deeleman-Reinhold &amp; Prinsen, 1987 is one of only two Pholcidae genera known to occur both in the Old and New Worlds. However, there are major morphological and ecological differences among geographically separate groups of species, and it was mainly molecular data that have resulted in our current view of uniting all these species into a single genus. In the Old World, only four species have previously been described. Here, current knowledge about Old World Micropholcus is reviewed, redescribing three of the four previously known species, and describing twelve new species, originating from Saudi Arabia (M.dhahran Huber, sp. nov., M.harajah Huber, sp. nov., M.alfara Huber, sp. nov., M.abha Huber, sp. nov., M.tanomah Huber, sp. nov., M.bashayer Huber, sp. nov., M.maysaan Huber, sp. nov.), Oman (M.darbat Huber, sp. nov., M.shaat Huber, sp. nov.), Morocco (M.ghar Huber, sp. nov., M.khenifra Huber, Lecigne &amp; Lips, sp. nov.), and the Philippines (M.bukidnon Huber, sp. nov.). We provide an exploratory species delimitation analysis based on CO1 barcodes, extensive SEM data, and first records of Acroceridae (Diptera) larvae in Pholcidae, extracted from book lungs.}, }
@article {pmid39371081, year = {2024}, author = {Ward, DF}, title = {Building a DNA barcode reference collection of Hymenoptera in New Zealand.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e131701}, pmid = {39371081}, issn = {1314-2828}, abstract = {Molecular tools used for the identification of species are heavily reliant on reference DNA sequences and taxonomic annotation. Despite this, there are large gaps in the availability of DNA sequences for many taxonomic groups and for different parts of the globe. Here, a DNA barcode library for the Hymenoptera of New Zealand is presented, based on the COI region for 3,145 sequences assigned to 837 BINs and which represent 231 genera and 236 species. This study provides a DNA barcode for approximately 25% of species and 42% of genera of Hymenoptera in New Zealand. However, when combined with sequences previously deposited in BOLD (a further 170 genera), DNA barcodes are available for 73% of New Zealand Hymenopteran genera. To further increase coverage, future efforts need to focus predominantly on taxa from seven families (Encyrtidae, Pteromalidae s.l., Mymaridae, Eulophidae, Diapriidae, Braconidae and Platygastridae). This database facilitates DNA-based identification of taxa for use in both taxonomic revisions and biodiversity monitoring.}, }
@article {pmid39370741, year = {2024}, author = {Mayo Ilodiri, W and Huyghe, CET and da Costa, LM and Mambo Baba, T and Danadu Mizani, C and Vreven, EJWMN}, title = {Hidden species diversity in the Enteromius Cope, 1867 (Teleostei: Cyprinidae) from the Aruwimi basin (Middle Congo) in the Okapi Wildlife Reserve (Democratic Republic of the Congo).}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.15883}, pmid = {39370741}, issn = {1095-8649}, support = {//DEA scholarship/ ; //Mbisa Congo II/ ; //BICS project/ ; //Royal Museum for Central Africa (RMCA)/ ; //Directorate-General for Development Cooperation and Humanitarian Aid (DGD)/ ; }, abstract = {Two new African minnow species, Enteromius cerinus sp. nov. and Enteromius ruforum sp. nov., are described for science from the Angadiko River, a left-bank sub-affluent of first order of the Nepoko River, draining the north-eastern part of the Okapi Wildlife Reserve (OWR). Both new species belong to the group of Enteromius for which the last unbranched dorsal-fin ray is flexible and underrated. Within this morphological group, both are most similar to Enteromius kamolondoensis, especially in life colour pattern characteristics. However, Enteromius cerinus sp. nov. differs from E. kamolondoensis by its low number of circumpeduncular scales, 10-11 (vs. 12), low maximum body depth, 22.8%-25.7% standard length (Ls) (vs. 26.1%-30.0%), and long anterior and posterior barbel lengths, 32.6%-35.3% head length (LH) (vs. 23.6%-27.2%) and 41.6%-43.9% LH (vs. 30.3%-34.9%), respectively. Further, E. ruforum sp. nov. is also easily distinguished from E. kamolondoensis by its high maximum body depth, 30.6%-33.3% Ls (vs. 26.1%-30.0%), and small, isometric, eye diameter, 26.2%-28.0% LH (vs. 29.1%-31.9%). A barcoding study (mtDNA, cytochrome oxidase subunit I [COI]) revealed that specimens of both new species form lineages well differentiated from those of other available species. As such, (i) E. cerinus sp. nov. diverges from E. kamolondoensis by a K2P genetic distance (GD) of 10.3% and (ii) E. ruforum sp. nov. by a K2P GD of 11.2%. To the present day, the fish fauna of the left-bank sub-affluents of the Nepoko River, in general, remains poorly known or undocumented. Unfortunately, at the same time, multiple anthropogenic impacts are affecting this fauna, such as (i) the destruction of habitats along the river banks for agriculture and fishing and (ii) the use of illegal fishing practices, such as fishing with plant-based ichthyotoxins during ecopage, which is combined with dam building. As a result of the demographic growth, this ecopage results in overfishing and thus is threatening both new species in particular, but all other co-occurring fish species as well. Both new species, E. cerinus sp. nov. and E. ruforum sp. nov., should thus be considered Vulnerable (VU) according to IUCN criterion D2. It is therefore hoped that their discovery highlights the urgent need for a better protection and further in situ exploration of the reserve's freshwater (fish) biodiversity, in general, and that of those small sub-affluents, in particular.}, }
@article {pmid39369928, year = {2024}, author = {Chomphuphuang, N and Leamyongyai, C and Songsangchote, C and Piraonapicha, K and Pojprasat, N and Piyatrakulchai, P}, title = {Phylogenetics and species delimitation of the recluse spider, Loxosceles rufescens (Araneae: Sicariidae) populations invading Bangkok, Thailand.}, journal = {Acta tropica}, volume = {260}, number = {}, pages = {107424}, doi = {10.1016/j.actatropica.2024.107424}, pmid = {39369928}, issn = {1873-6254}, abstract = {The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8-9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.}, }
@article {pmid39369756, year = {2025}, author = {Li, H and Shangqing, Z and Yae, Z and Fan, Y and Xinyue, Z and Shirui, L and Tianyi, Z and Dongling, N}, title = {Classification, identification, and DNA barcoding study for common cockroach species (Dictyoptera: Blattaria) from China.}, journal = {Gene}, volume = {933}, number = {}, pages = {148981}, doi = {10.1016/j.gene.2024.148981}, pmid = {39369756}, issn = {1879-0038}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; China ; *Phylogeny ; *Cockroaches/genetics/classification ; DNA, Mitochondrial/genetics ; Periplaneta/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Cockroaches are well-known pests and quarantined organisms worldwide. Due to morphological diversity and a lack of molecular data, their classification and identification are facing challenges. This study performed classification, identification, and DNA barcoding for cockroaches collected from China. Seventy-six samples were morphologically identified as seven species of two superfamilies that included Blattella germanica, Eublaberus posticus and Blaptica dubia belonging to the superfamily Blaberoidea, and Periplaneta americana, Periplaneta lateralis, Periplaneta fuliginosa and Periplaneta australasiae belonging to the superfamily Blattoidea. Based on sequence alignments of nine ribosomal and mitochondrial genes across the order Blattaria retrieved from GenBank, rDNA ITS2-517 bp and mtDNA 16S-327 bp were screened as candidates for molecular identification. Universal primers were designed for PCR amplification, cloning, and sequencing of the 37 representative samples. Sequence alignments and phylogeny analysis showed that both ITS2 and 16S confirmed samples 1-9, 20-24, and 25-29 as B. germanica, P. americana, and P. lateralis, respectively; only 16S (not ITS2) confirmed samples 10-14, 15-19, 30-34, and 35-37 as E. posticus, Blap. dubia, P. fuliginosa, and P. australasiae, respectively, indicating that 16S was a better target than ITS2 for molecular identification of cockroaches. Conservative motif and divergence analysis further revealed that ITS2 sequences vary significantly among different taxa, whereas 16S sequences are relatively conserved. There is an obvious barcoding gap between maximum intraspecific divergence and minimum interspecific divergence (2.57 % vs. 5.62 %) for ITS2, but not for 16S (6.15 % vs. 2.63 %). Therefore, it was confirmed that ITS2 is an ideal DNA barcode for molecular identification of cockroaches at lower category.}, }
@article {pmid39365069, year = {2024}, author = {Biggel, M and Cernela, N and Horlbog, JA and Stephan, R}, title = {Oxford Nanopore's 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges.}, journal = {Journal of clinical microbiology}, volume = {62}, number = {11}, pages = {e0108324}, pmid = {39365069}, issn = {1098-660X}, mesh = {*Listeria monocytogenes/genetics/classification/isolation &amp; purification ; *Listeriosis/microbiology/epidemiology/diagnosis ; *Disease Outbreaks ; Humans ; *Whole Genome Sequencing ; Genome, Bacterial/genetics ; Nanopore Sequencing/methods ; Nanopores ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements. To evaluate its readiness for outbreak detection, we selected 78 Listeria monocytogenes isolates from diverse lineages or known epidemiological clusters for sequencing with ONT's V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, the cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality, with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5'-GAAG6mAC-3'/5'-GT4mCTTC-3'). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that most L. monocytogenes genomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations.}, }
@article {pmid39364681, year = {2024}, author = {Stancheva, R and Cantonati, M and Manoylov, K and Furey, PC and Cahoon, AB and Jones, RC and Gillevet, P and Amsler, CD and Wehr, JD and Salerno, JL and Krueger-Hadfield, SA}, title = {The importance of integrating phycological research, teaching, outreach, and engagement in a changing world.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.13507}, pmid = {39364681}, issn = {1529-8817}, support = {DEB-2141971//National Science Foundation/ ; DEB-2436117//National Science Foundation/ ; }, abstract = {The ecological, evolutionary, economic, and cultural importance of algae necessitates a continued integration of phycological research, education, outreach, and engagement. Here, we comment on several topics discussed during a networking workshop-Algae and the Environment-that brought together phycological researchers from a variety of institutions and career stages. We share some of our perspectives on the state of phycology by examining gaps in teaching and research. We identify action areas where we urge the phycological community to prepare itself to embrace the rapidly changing world. We emphasize the need for more trained taxonomists as well as integration with molecular techniques, which may be expensive and complicated but are important. An essential benefit of these integrative studies is the creation of high-quality algal reference barcoding libraries augmented with morphological, physiological, and ecological data that are important for studies of systematics and crucial for the accuracy of the metabarcoding bioassessment. We highlight different teaching approaches for engaging undergraduate students in algal studies and the importance of algal field courses, forays, and professional phycological societies in supporting the algal training of students, professionals, and citizen scientists.}, }
@article {pmid39364584, year = {2024}, author = {Buchner, D and Sinclair, JS and Ayasse, M and Beermann, AJ and Buse, J and Dziock, F and Enss, J and Frenzel, M and Hörren, T and Li, Y and Monaghan, MT and Morkel, C and Müller, J and Pauls, SU and Richter, R and Scharnweber, T and Sorg, M and Stoll, S and Twietmeyer, S and Weisser, WW and Wiggering, B and Wilmking, M and Zotz, G and Gessner, MO and Haase, P and Leese, F}, title = {Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14023}, doi = {10.1111/1755-0998.14023}, pmid = {39364584}, issn = {1755-0998}, support = {//Hessisches Landesamt f&#xfc;r Naturschutz, Umwelt und Geologie/ ; 871128//EU Horizon 2020 project eLTER PLUS/ ; //Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz of the German federal State of Hesse/ ; }, abstract = {Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.}, }
@article {pmid39364448, year = {2024}, author = {Zhou, R and Huang, L and Ma, YT}, title = {Smooth post-labial chaetae in Homidia (Collembola, Entomobryidae) and the description of four new species from China with the aid of DNA barcoding.}, journal = {ZooKeys}, volume = {1213}, number = {}, pages = {41-73}, pmid = {39364448}, issn = {1313-2989}, abstract = {Four new species of Homidia are described from the Guangxi Zhuang Autonomous Region, China. Homidialongiantenna sp. nov. is characterised by its long antenna and slightly expanded post-labial chaetae; H.guangxiensis sp. nov. by the presence of smooth chaetae on the post-labium and posterior face of the ventral tube; H.huapingensis sp. nov. by the presence of smooth post-labial chaetae and pointed tenent hairs; and H.oligoseta sp. nov. by the pointed tenent hairs and fewer macrochaetae on Abdomen IV. Additions to the original description of Homidiaacutus Jing &amp; Ma, 2022 are also provided.}, }
@article {pmid39364039, year = {2024}, author = {Zheng, LL and Yu, D and Sun, N and Wang, C and Chen, WJ and Ding, ZF and He, SP and Yang, LD}, title = {DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang.}, journal = {Ecology and evolution}, volume = {14}, number = {10}, pages = {e70352}, pmid = {39364039}, issn = {2045-7758}, abstract = {The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor-Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.}, }
@article {pmid39363107, year = {2024}, author = {Kumar, B and Navarro, C and Yung, PYK and Lyu, J and Salazar Mantero, A and Katsori, AM and Schwämmle, H and Martin, M and Elsässer, SJ}, title = {Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {39363107}, issn = {1750-2799}, support = {2020-04313//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, abstract = {ChIP-seq is a widely used technique for studying histone post-translational modifications and DNA-binding proteins. DNA fragments associated with a specific protein or histone modification epitope are captured by using antibodies, sequenced and mapped to a reference genome. Albeit versatile and popular, performing many parallel ChIP-seq experiments to compare different conditions, replicates and epitopes is laborious, is prone to experimental variation and does not allow quantitative comparisons unless adequate spike-in chromatin is included. We present a detailed protocol for performing and analyzing a multiplexed quantitative chromatin immunoprecipitation-sequencing experiment (MINUTE-ChIP), in which multiple samples are profiled against multiple epitopes in a single workflow. Multiplexing not only dramatically increases the throughput of ChIP-seq experiments (e.g., profiling 12 samples against multiple histone modifications or DNA-binding proteins in a single experiment), but also enables accurate quantitative comparisons. The protocol consists of four parts: sample preparation (i.e., lysis, chromatin fragmentation and barcoding of native or formaldehyde-fixed material), pooling and splitting of the barcoded chromatin into parallel immunoprecipitation reactions, preparation of next-generation sequencing libraries from input and immunoprecipitated DNA and data analysis using our dedicated analysis pipeline. This pipeline autonomously generates quantitatively scaled ChIP-seq tracks for downstream analysis and visualization, alongside necessary quality control indicators. The entire workflow requires basic knowledge in molecular biology and bioinformatics and can be completed in 1 week. MINUTE-ChIP empowers biologists to perform every ChIP-seq experiment with an appropriate number of replicates and control conditions, delivering more statistically robust, exquisitely quantitative and biologically meaningful results.}, }
@article {pmid39363072, year = {2025}, author = {Ramírez Rojas, AA and Brinkmann, CK and Schindler, D}, title = {Validation of Golden Gate Assemblies Using Highly Multiplexed Nanopore Amplicon Sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2850}, number = {}, pages = {171-196}, pmid = {39363072}, issn = {1940-6029}, mesh = {*Nanopore Sequencing/methods ; *Synthetic Biology/methods ; Cloning, Molecular/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Polymerase Chain Reaction/methods ; Nanopores ; Workflow ; }, abstract = {Golden Gate cloning has revolutionized synthetic biology. Its concept of modular, highly characterized libraries of parts that can be combined into higher order assemblies allows engineering principles to be applied to biological systems. The basic parts, typically stored in Level 0 plasmids, are sequence validated by the method of choice and can be combined into higher order assemblies on demand. Higher order assemblies are typically transcriptional units, and multiple transcriptional units can be assembled into multi-gene constructs. Higher order Golden Gate assembly based on defined and validated parts usually does not introduce sequence changes. Therefore, simple validation of the assemblies, e.g., by colony polymerase chain reaction (PCR) or restriction digest pattern analysis is sufficient. However, in many experimental setups, researchers do not use defined parts, but rather part libraries, resulting in assemblies of high combinatorial complexity where sequencing again becomes mandatory. Here, we present a detailed protocol for the use of a highly multiplexed dual barcode amplicon sequencing using the Nanopore sequencing platform for in-house sequence validation. The workflow, called DuBA.flow, is a start-to-finish procedure that provides all necessary steps from a single colony to the final easy-to-interpret sequencing report.}, }
@article {pmid39360178, year = {2024}, author = {Fahldieck, M and Rulik, B and Thormann, J and Mengual, X}, title = {A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e127190}, pmid = {39360178}, issn = {1314-2828}, abstract = {Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination. In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. Our DNA barcode library comprises 824 high-quality cytochrome c oxidase I (COI) barcodes encompassing 76 crane fly species, counting for ca. 54% of the German tipulid fauna. Our results significantly increased the number of European tipulid species available in the Barcode of Life Data System (BOLD) by 14%. Additionally, the number of barcodes from European tipulid specimens more than doubled, with an increase of 118%, bolstering the DNA resource for future identification inquiries. Employing diverse species delimitation algorithms - including the multi-rate Poisson tree processes model (mPTP), Barcode Index Number assignments (BIN), Assemble Species by Automatic Partitioning (ASAP), and the TaxCI R-script - we successfully match 76-86% of the morphologically identified species. Further validation through neighbor-joining tree topology analysis and comparison with 712 additional European tipulid barcodes yield a remarkable 89% success rate for the species identification of German tipulids based on COI barcodes. This comprehensive DNA barcode dataset not only enhances species identification accuracy but also serves as a pivotal resource for ecological and biomonitoring studies, fostering a deeper understanding of crane fly diversity and distribution across terrestrial landscapes.}, }
@article {pmid39353738, year = {2024}, author = {Tek, AL and Nagaki, K and Yıldız Akkamış, H and Tanaka, K and Kobayashi, H}, title = {Chromosome-specific barcode system with centromeric repeat in cultivated soybean and wild progenitor.}, journal = {Life science alliance}, volume = {7}, number = {12}, pages = {}, pmid = {39353738}, issn = {2575-1077}, mesh = {*Glycine max/genetics ; *Centromere/genetics ; *Chromosomes, Plant/genetics ; DNA Barcoding, Taxonomic/methods ; Domestication ; Genome, Plant/genetics ; Histones/genetics/metabolism ; Plant Breeding/methods ; DNA, Plant/genetics ; }, abstract = {Wild soybean Glycine soja is the progenitor of cultivated soybean Glycine max Information on soybean functional centromeres is limited despite extensive genome analysis. These species are an ideal model for studying centromere dynamics for domestication and breeding. We performed a detailed chromatin immunoprecipitation analysis using centromere-specific histone H3 protein to delineate two distinct centromeric DNA sequences with unusual repeating units with monomer sizes of 90-92 bp (CentGm-1) and 413-bp (CentGm-4) shorter and longer than standard nucleosomes. These two unrelated DNA sequences with no sequence similarity are part of functional centromeres in both species. Our results provide a comparison of centromere properties between a cultivated and a wild species under the effect of the same kinetochore protein. Possible sequence homogenization specific to each chromosome could highlight the mechanism for evolutionary conservation of centromeric properties independent of domestication and breeding. Moreover, a unique barcode system to track each chromosome is developed using CentGm-4 units. Our results with a unifying centromere composition model using CentGm-1 and CentGm-4 superfamilies could have far-reaching implications for comparative and evolutionary genome research.}, }
@article {pmid39353436, year = {2024}, author = {Bai, Z and Zhang, D and Gao, Y and Tao, B and Zhang, D and Bao, S and Enninful, A and Wang, Y and Li, H and Su, G and Tian, X and Zhang, N and Xiao, Y and Liu, Y and Gerstein, M and Li, M and Xing, Y and Lu, J and Xu, ML and Fan, R}, title = {Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues.}, journal = {Cell}, volume = {187}, number = {23}, pages = {6760-6779.e24}, pmid = {39353436}, issn = {1097-4172}, support = {R01 GM138856/GM/NIGMS NIH HHS/United States ; R56 HG012310/HG/NHGRI NIH HHS/United States ; R33 CA246711/CA/NCI NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; U54 CA268083/CA/NCI NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U54 DK106857/DK/NIDDK NIH HHS/United States ; U01 CA294514/CA/NCI NIH HHS/United States ; R01 HG013185/HG/NHGRI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; U54 AG079759/AG/NIA NIH HHS/United States ; UM1 MH130991/MH/NIMH NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; RM1 MH132648/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Paraffin Embedding ; *Formaldehyde/chemistry ; *Tissue Fixation ; MicroRNAs/genetics/metabolism ; RNA/metabolism/genetics ; Transcriptome/genetics ; RNA Splicing/genetics ; Lymphoma/genetics/pathology ; Gene Expression Profiling/methods ; Polyadenylation ; }, abstract = {The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years. Furthermore, genome-wide single-nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Single-cell level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.}, }
@article {pmid39353093, year = {2024}, author = {Meier, R and Lawniczak, MKN and Srivathsan, A}, title = {Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics.}, journal = {Annual review of entomology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-ento-040124-014001}, pmid = {39353093}, issn = {1545-4487}, abstract = {Most insects encountered in the field are initially entomological dark matter in that they cannot be identified to species while alive. This explains the enduring quest for efficient ways to identify collected specimens. Morphological tools came first but are now routinely replaced or complemented with DNA barcodes. Initially too expensive for widespread use, these barcodes have since evolved into powerful tools for specimen identification and sorting, given that the evolution of sequencing approaches has dramatically reduced the cost of barcodes, thus enabling decentralized deployment across the planet. In this article, we review how DNA barcodes have become a key tool for accelerating biodiversity discovery and analyzing insect communities through both megabarcoding and metabarcoding in an era of insect decline. We predict that DNA barcodes will be particularly important for assembling image training sets for deep learning algorithms, global biodiversity genomics, and functional analysis of insect communities.Review in Advance first posted online on October 1, 2024. Updated on November 5, 2024. Changes may still occur before final publication.}, }
@article {pmid39355103, year = {2024}, author = {Truong, C and Gabbarini, LA and Moretto, A and Escobar, JM and Smith, ME}, title = {Ectomycorrhizal fungi and the nitrogen economy of Nothofagus in southern Patagonia.}, journal = {Ecology and evolution}, volume = {14}, number = {10}, pages = {e70299}, pmid = {39355103}, issn = {2045-7758}, abstract = {Subantarctic Nothofagus forests are the southernmost forests in the world, with negligible atmospheric nitrogen (N) deposition. Most paradigms about the role of ectomycorrhizal (ECM) fungi in N cycling and plant N uptake at high latitudes have been tested in boreal coniferous forests, while in the southern hemisphere, ECM hosts are primarily angiosperms. Using ITS1 meta-barcoding, we characterized ECM and saprotrophic fungal communities in evergreen and deciduous Nothofagus forests forming monodominant and mixed stands in the archipelago of Tierra del Fuego (Chile and Argentina). We assessed the N economy of Nothofagus by correlating host species with fungal relative abundances, edaphic variables, net N mineralization, microbial biomass N and the activity of eight extracellular soil enzymes activities. The N economy of deciduous N. pumilio forests was strikingly similar to boreal coniferous forests, with the lowest inorganic N availability and net N mineralization, in correlation to higher relative abundances of ECM fungi with enzymatic capacity for organic N mobilization (genus Cortinarius). In contrast, the N economy of evergreen N. betuloides forests was predominantly inorganic and correlated with ECM lineages from the family Clavulinaceae, in acidic soils with poor drainage. Grassy understory vegetation in deciduous N. antarctica forests likely promoted saprotrophic fungi (i.e., genus Mortierella) in correlation with higher activities of carbon-degrading enzymes. Differences between Nothofagus hosts did not persist in mixed forests, illustrating the range of soil fertility of these ECM angiosperms and the underlying effects of soil and climate on Nothofagus distribution and N cycling in southern Patagonia.}, }
@article {pmid39354174, year = {2024}, author = {Ali, M and Dey, R and Das, M and Kumar, V and Chandra, K and Uniyal, VP and Gupta, SK}, title = {Unique among high passes: Insights into the genetic uniqueness among butterflies of Ladakh Trans-Himalaya through DNA barcoding.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {1033}, pmid = {39354174}, issn = {1573-4978}, mesh = {Animals ; *Butterflies/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Bayes Theorem ; Genetic Variation/genetics ; Genetics, Population ; }, abstract = {BACKGROUND: The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a COI barcode reference library of 60 specimens representing 23 species.<br><br>METHODS AND RESULTS: Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani. Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species.<br><br>CONCLUSIONS: Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.}, }
@article {pmid39351591, year = {2024}, author = {Bigirimana, A and Kisekelwa, T and da Costa, LM and Huyghe, CET and Banyankimbona, G and Vreven, EJWMN}, title = {Description of a new endemic Enteromius (Teleostei: Cyprinidae) from the upper Malagarazi in Burundi: Lessons for a protected area under implementation.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.15652}, pmid = {39351591}, issn = {1095-8649}, abstract = {Recent collecting efforts in the upper Malagarazi basin (2013-2022) allowed for an integrative study based on qualitative (colour), quantitative (meristic and metric), and barcoding gene [mtDNA, cytochrome c oxidase (COI)] data of specimens similar to Enteromius sp. 'ascutelatus', being a previously identified, potentially, new species. Based on these data, the present study confirms its identification as a new species for science, which is here formally described as Enteromius nzigidaherai sp. nov. This new species belongs to the group of Enteromius species for which the last unbranched ray of the dorsal fin is flexible and devoid of serrations along its posterior edge. This species has a horizontal series of black spots at the midlateral level of the sides. Three congeneric species, known from the Congo basin sensu lato, with two of them also found in the upper Malagarazi basin, are most similar to it. However, E. nzigidaherai sp. nov. is distinguished from the two sympatric upper Malagarazi species, that is, E. quadrilineatus and E. lineomaculatus, at least by two meristics and two morphometrics. It is also distinguished from E. urostigma, known from the upper Congo basin, by two meristics and one, apparently related, morphometric. In addition, a barcoding (mtDNA, COI) study revealed that the specimens of E. nzigidaherai sp. nov. form a well-supported, separate lineage, with a K2P genetic distance of more than 10% with specimens identified as E. quadrilineatus and E. lineomaculatus, both originating from the upper Malagarazi basin and for which tissue samples were available. Finally, the new species was found to be endemic to the upper reaches of two left bank affluents of the upper Malagarazi basin: the Muyovozi and the Kinwa. However, both affluents are threatened by human activities, which seem to have resulted in its local disappearance as recent intensive collecting efforts in the latter affluent have remained unsuccessful. The species should thus be considered Critically Endangered (CR) according to IUCN criteria B1ab(ii,iv)c(i,iii). Therefore, it is hoped that the present description draws renewed attention to the importance of aquatic protection in the region by highlighting the need for the effective establishment of the Malagarazi Nature Reserve and concern for its optimal delimitation to efficiently protect the entire ichthyofauna of the upper Malagarazi, without excluding the fish species confined to its affluent rivers.}, }
@article {pmid39351291, year = {2024}, author = {Mwamula, AO and Lee, SM and Jung, YH and Kim, YS and Lee, DW}, title = {Description and Molecular Characterization of a New Dorylaimid Nematode, Mesodorylaimus pini n. sp. (Nematoda: Dorylaimidae) from Korea.}, journal = {Journal of nematology}, volume = {56}, number = {1}, pages = {20240028}, pmid = {39351291}, issn = {0022-300X}, abstract = {Mesodorylaimus pini n. sp., a new species isolated from the bark and cambium layer of a dead black pine tree is characterized herein using integrative taxonomy, considering both morphological and molecular phylogenetic analyses of the 18S- and 28S-rRNA genes. Mesodorylaimus pini n. sp. is characterized by having a medium-sized body 1.50-1.89 mm long; lip region angular and offset by a depression; a relatively long odontostyle (17.0-19.0 μm); vulval opening a transverse slit, positioned slightly posteriorly; pars refringens vaginae with two elongated drop-shaped to spindle-shaped sclerotizations; an intestine-prerectum junction with a long anteriorly directed conical or tongue-like projection; a relatively long female tail (115-187 μm); spicules 48.0-57.0 μm long; and regularly spaced 7-8 ventromedian supplements. It is closest to M. subtilis, especially in having similar body length and number of ventromedian supplements but can be differentiated from M. subtilis by the longer odontostyle, tongue-like projection, and longer spicules. The phylogenies based on the 18S- and 28S-rRNA sequences showed a well-supported sister relation of M. pini n. sp. with M. subtilis, M. japonicus, M. bastiani, M. pseudobastiani, Calcaridorylaimus castaneae, C. heynsi, and other member species of the group.}, }
@article {pmid39349515, year = {2024}, author = {Zhang, S and Liao, A and Wang, Y and Liu, Q and Ouyang, L and Peng, H and Yuan, L and Zhao, L and Yang, X and Chen, X and He, Y and Li, Z}, title = {Profiling expressing features of surface proteins on single-exosome in first-episode Schizophrenia patients: a preliminary study.}, journal = {Schizophrenia (Heidelberg, Germany)}, volume = {10}, number = {1}, pages = {84}, pmid = {39349515}, issn = {2754-6993}, support = {82101576//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Proximity barcoding assay, a high-throughput method for single-exosome analysis, was employed to profile surface proteins on individual exosomes of SCZ patients. This analysis identified five differentially expressed proteins (DEPs) between SCZ patients and healthy controls (HC) and six DEPs between antipsychotic responders and non-responders. Furthermore, two exosome clusters were found to be associated with SCZ, and certain DEPs were correlated with cognitive functions.}, }
@article {pmid39349404, year = {2024}, author = {Villa, S and Magoga, G and Montagna, M and Pierce, S}, title = {Elevational shifts in reproductive ecology indicate the climate response of a model chasmophyte, Rainer's bellflower (Campanula raineri).}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcae164}, pmid = {39349404}, issn = {1095-8290}, support = {PSR2019_DIP_014SPIER//Department of Agricultural and Environmental Sciences (DiSAA), University of Milan, Italy/ ; //Department of Agricultural and Environmental Sciences/ ; //Doctoral School of Agriculture, Environment and Bioenergy/ ; }, abstract = {BACKGROUND AND AIMS: Elevation gradients provide 'natural experiments' for investigating plant climate change responses, advantageous for the study of protected species and life forms for which transplantation experiments are illegal or unfeasible, such as chasmophytes with perennial rhizomes pervading rock fissures. Elevational climatic differences impact mountain plant reproductive traits (pollen and seed quality, sexual vs. vegetative investment) and pollinator community composition; we investigated the reproductive ecology of a model chasmophyte, Campanula raineri Perp. (Campanulaceae), throughout its current elevational/climatic range to understand where sub-optimal conditions jeopardise survival. We hypothesised that: 1) reproductive fitness measures are positively correlated with elevation, indicative of the relationship between fitness and climate; 2) C. raineri, like other campanulas, is pollinated mainly by Hymenoptera; 3) potential pollinators shift with elevation.<br><br>METHODS: We measured pollen and seed quality, seed production, the relative investment in sexual vs. vegetative structures and vegetative (Grime's CSR) strategies at different elevations. Potential pollinators were assessed by combining molecular and morphological identification.<br><br>KEY RESULTS: Whereas CSR strategies were not linked to elevation, pollen and seed quality were positively correlated, as was seed production per fruit (Hypothesis 1 is supported). The main pollinators of C. raineri were Apidae, Andrenidae, Halictidae (Hymenoptera) and Syrphidae (Diptera), probably complemented by a range of occasional pollinators and visitors (Hypothesis 2 partially supported). Potential pollinator communities showed a taxonomic shift towards Diptera with elevation (particularly Anthomyiidae and Muscidae) and away from Hymenoptera (Hypothesis 3 was supported).<br><br>CONCLUSIONS: Pollinator availability is maintained at all elevations by taxon replacement. However, reduced pollen quality and seed production at lower elevations suggest an impact of climate change on reproduction (especially <1200 m a.s.l., where seed germination was limited). Aside from guiding targeted conservation actions for C. raineri, our results highlight problems that may be common to mountain chasmophytes worldwide.}, }
@article {pmid39348735, year = {2025}, author = {Wang, S and Zhou, Y and Ding, K and Ding, ZQ and Zhang, W and Liu, Y}, title = {High-throughput and multimodal profiling of antigen-specific T cells with a droplet-based cell-cell interaction screening platform.}, journal = {Biosensors &amp; bioelectronics}, volume = {267}, number = {}, pages = {116815}, doi = {10.1016/j.bios.2024.116815}, pmid = {39348735}, issn = {1873-4235}, mesh = {Humans ; *Cell Communication ; *Biosensing Techniques/methods ; *T-Lymphocytes/immunology/cytology ; Antigen-Presenting Cells/immunology ; Single-Cell Analysis/methods ; High-Throughput Screening Assays/methods ; Animals ; Antigens/immunology/chemistry ; Click Chemistry ; }, abstract = {Identifying antigen-specific T cells from tumor-infiltrating lymphocytes is essential for designing effective T cell immunotherapies. Traditional methods can detect antigen-specific T cells but struggle with high-throughput screening and multimodal profiling simultaneously. To address this issue, we developed DropCCI, a new strategy that transfers antigen information to co-incubated T cells for high-throughput, non-contaminated multimodal profiling. In DropCCI, droplets encapsulated DNA barcodes and antigen-loaded antigen-presenting cells (APCs), while click chemistry-modified T cells were injected into these droplets to capture free barcodes and acquire the corresponding antigen information. Following cell-cell interaction, APCs were removed via streptavidin-biotin conjugation, to prevent contamination. The resulting T cells underwent single-cell omics sequencing for comprehensive profiling of their antigen specificity, transcriptome, and genomics accurately. This click-chemistry method allowed detection of antigen-specific T cells without lysing APCs, avoiding cross-cell contamination and enabling low-noise multimodal profiling of primary T cells. With a completion time within 12 h and no requirement for complex equipment, DropCCI provides unbiased single-cell sequencing results that offer a comprehensive understanding of anti-tumor T cell responses. The concept of DropCCI holds great promise not only for advancing the field of T cell immunotherapy but also for its potential application in studying other cell-cell interactions.}, }
@article {pmid39348593, year = {2024}, author = {Ren, J and Zhang, R}, title = {Delimiting species, revealing cryptic diversity in Molytinae (Coleoptera: Curculionidae) weevil through DNA barcoding.}, journal = {Journal of insect science (Online)}, volume = {24}, number = {4}, pages = {}, pmid = {39348593}, issn = {1536-2442}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Weevils/genetics/classification ; *Electron Transport Complex IV/genetics ; Genetic Variation ; Phylogeny ; }, abstract = {The subfamily Molytinae (Coleoptera: Curculionidae), being the second largest group within the family Curculionidae, exhibits a diverse range of hosts and poses a serious threat to agricultural and forestry industries. We used 1,290 cytochrome c oxidase subunit I (COI) barcodes to assess the efficiency of COI barcodes in species differentiation and uncover cryptic species diversity within weevils of Molytinae. The average Kimura 2-parameter distances within species, genus, and subfamily were 2.90%, 11.0%, and 22.26%, respectively, indicating significant genetic differentiation at both levels. Moreover, there exists a considerable degree of overlap between intraspecific (0%-27.50%) and interspecific genetic distances (GDs; 0%-39.30%). The application of Automatic barcode gap discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP), and jMOTU resulted in the identification of 279, 275, 494, 322, 320, and 279 molecular operational taxonomic units, respectively. The integration of 6 methods successfully delimited species of Molytinae in 86.6% of all examined morphospecies, surpassing a threshold value of 3% GD (73.0%). A total of 28 morphospecies exhibiting significant intraspecific divergences were assigned to multiple MOTUs, respectively, suggesting the presence of cryptic diversity or population divergence. The identification of cryptic species within certain morphological species in this study necessitates further investigation through comprehensive taxonomic practices in the future.}, }
@article {pmid39347602, year = {2024}, author = {Kamata, K and Birkholz, N and Ceelen, M and Fagerlund, RD and Jackson, SA and Fineran, PC}, title = {Repurposing an Endogenous CRISPR-Cas System to Generate and Study Subtle Mutations in Bacteriophages.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1089/crispr.2024.0047}, pmid = {39347602}, issn = {2573-1602}, abstract = {While bacteriophage applications benefit from effective phage engineering, selecting the desired genotype after subtle modifications remains challenging. Here, we describe a two-phase endogenous CRISPR-Cas-based phage engineering approach that enables selection of small defined edits in Pectobacterium carotovorum phage ZF40. We designed plasmids containing sequences homologous to ZF40 and a mini-CRISPR array. The plasmids allowed genome editing through homologous recombination and counter-selection against non-recombinant phage genomes using an endogenous type I-E CRISPR-Cas system. With this technique, we first deleted target genes and subsequently restored loci with modifications. This two-phase approach circumvented major challenges in subtle phage modifications, including inadequate sequence distinction for CRISPR-Cas counter-selection and the requirement of a protospacer-adjacent motif, limiting sequences that can be modified. Distinct 20-bp barcodes were incorporated through engineering as differential target sites for programmed CRISPR-Cas activity, which allowed quantification of phage variants in mixed populations. This method aids studies and applications that require mixtures of similar phages.}, }
@article {pmid39345550, year = {2024}, author = {Carlos, AJ and Yang, D and Thomas, DM and Huang, S and Harter, KI and Moellering, RE}, title = {Family-Wide Photoproximity Profiling of Integrin Protein Social Networks in Cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345550}, issn = {2692-8205}, support = {DP2 GM128199/GM/NIGMS NIH HHS/United States ; R01 GM145852/GM/NIGMS NIH HHS/United States ; T32 CA009594/CA/NCI NIH HHS/United States ; }, abstract = {Integrin family transmembrane receptors mediate dynamic interactions between cells and their extracellular microenvironment. The heterogeneous interaction partners of integrins directly regulate cell adhesion, motility, proliferation, and intracellular signaling. Despite the recognized importance of protein-protein interactions and the formation of signaling hubs around integrins, the ability to detect and quantify these dynamic binding partners with high spatial and temporal resolution remains challenging. Here, we developed an integrin-family-directed quantitative photoproximity protein interaction (PhotoPPI) profiling method to detect and quantify native integrin-centered protein social networks on live cells and tissues without the need for genetic manipulation, antibodies, or non-physiologic cell culture conditions. We drafted quantitative maps of integrin-centered protein social networks, highlighting conserved and unique binding partners between different cell types and cellular microenvironments. Comparison of integrin social networks in cancer cell lines of diverse tissue of origin and disease state identified specific AND-gate binding partners involved cell migration, microenvironmental interactions and proliferation that serve as markers of tumor cell metastatic state. Finally, we identified unique combinations - or barcodes - of integrin-proximal proteins on the surface of pre- and post-metastatic triple negative breast cancer (TNBC) cells whose expression strongly correlate with both positive and negative disease progression and outcomes in TNBC patients. Taken together, these data provide the first family-wide high-resolution maps of native protein interactors on live cells and identify dynamic integrin-centered social networks as potential AND-gate markers of cell identity, microenvironmental context and disease state.}, }
@article {pmid39345539, year = {2024}, author = {Ashkin, EL and Tang, YJ and Xu, H and Hung, KL and Belk, J and Cai, H and Lopez, S and Dolcen, DN and Hebert, JD and Li, R and Ruiz, PA and Keal, T and Andrejka, L and Chang, HY and Petrov, DA and Dixon, JR and Xu, Z and Winslow, MM}, title = {A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.14.613043}, pmid = {39345539}, issn = {2692-8205}, abstract = {UNLABELLED: The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and show that STAG2 is uniquely tumor suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo , and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo . STAG2 inactivation elicits changes in gene expression, chromatin accessibility and 3D genome conformation that impact cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relates STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin mediated mechanisms of lung tumor suppression.<br><br>SUMMARY: STAG2 is a frequently mutated cohesin subunit across several cancers and one of the most important functional suppressors of lung adenocarcinoma. Our findings underscore important roles of STAG2 in suppressing lung tumorigenesis and highlight a STAG2-PAXIP1/PAGR1 tumor-suppressive program that may transcend cancer type.}, }
@article {pmid39345444, year = {2024}, author = {Boutelle, AM and Mabene, AR and Yao, D and Xu, H and Wang, M and Tang, YJ and Lopez, SS and Sinha, S and Demeter, J and Cheng, R and Benard, BA and Valente, LJ and Drainas, AP and Fischer, M and Majeti, R and Petrov, DA and Jackson, PK and Yang, F and Winslow, MM and Bassik, MC and Attardi, LD}, title = {Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.17.612743}, pmid = {39345444}, issn = {2692-8205}, abstract = {TP53 , the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seq [Ultra] somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3 - Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.}, }
@article {pmid39345427, year = {2024}, author = {Fang, C and Lindsey, J and Abbott, LF and Aronov, D and Chettih, S}, title = {Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345427}, issn = {2692-8205}, support = {DP2 AG071918/AG/NIA NIH HHS/United States ; K99 NS136846/NS/NINDS NIH HHS/United States ; }, abstract = {Forming an episodic memory requires binding together disparate elements that co-occur in a single experience. One model of this process is that neurons representing different components of a memory bind to an "index" - a subset of neurons unique to that memory. Evidence for this model has recently been found in chickadees, which use hippocampal memory to store and recall locations of cached food. Chickadee hippocampus produces sparse, high-dimensional patterns ("barcodes") that uniquely specify each caching event. Unexpectedly, the same neurons that participate in barcodes also exhibit conventional place tuning. It is unknown how barcode activity is generated, and what role it plays in memory formation and retrieval. It is also unclear how a memory index (e.g. barcodes) could function in the same neural population that represents memory content (e.g. place). Here, we design a biologically plausible model that generates barcodes and uses them to bind experiential content. Our model generates barcodes from place inputs through the chaotic dynamics of a recurrent neural network and uses Hebbian plasticity to store barcodes as attractor states. The model matches experimental observations that memory indices (barcodes) and content signals (place tuning) are randomly intermixed in the activity of single neurons. We demonstrate that barcodes reduce memory interference between correlated experiences. We also show that place tuning plays a complementary role to barcodes, enabling flexible, contextually-appropriate memory retrieval. Finally, our model is compatible with previous models of the hippocampus as generating a predictive map. Distinct predictive and indexing functions of the network are achieved via an adjustment of global recurrent gain. Our results suggest how the hippocampus may use barcodes to resolve fundamental tensions between memory specificity (pattern separation) and flexible recall (pattern completion) in general memory systems.}, }
@article {pmid39342262, year = {2024}, author = {Bisaglia, B and Castelli, M and Soresinetti, L and Negri, A and Arnoldi, I and Montarsi, F and Gobbo, F and Defilippo, F and Callegari, E and Di Luca, M and Calzolari, M and Mastrantonio, V and Porretta, D and Ficetola, GF and Sassera, D and Gabrieli, P and Bandi, C and Epis, S}, title = {Barcoding of Italian mosquitoes (BITMO): generation and validation of DNA barcoding reference libraries for native and alien species of Culicidae.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {407}, pmid = {39342262}, issn = {1756-3305}, support = {MUSA - Multilayered Urban Sustainability Action - project, funded by the European Union - NextGenerationEU, under the National Recovery and Resilience Plan (NRRP) Mission 4 Component 2 Investment Line 1.5: Strengthening of research structures and creation of R&amp;D "innovation ecosystems", set up of "territorial leaders in R&amp;D".//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; PNRR Project title "National Biodiversity Future Center - NBFC" Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; PNRR project PE-13, INF-ACT "One Health Basic and Translational Research Actions addressing Unmet Needs on Emerging Infectious Diseases"//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; MUSA - Multilayered Urban Sustainability Action - project, funded by the European Union - NextGenerationEU, under the National Recovery and Resilience Plan (NRRP) Mission 4 Component 2 Investment Line 1.5: Strengthening of research structures and creation of R&amp;D "innovation ecosystems", set up of "territorial leaders in R&amp;D".//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *RNA, Ribosomal, 16S/genetics ; *Culicidae/genetics/classification ; Italy ; *Introduced Species ; *Mosquito Vectors/genetics/classification ; *Phylogeny ; Gene Library ; Electron Transport Complex IV/genetics ; }, abstract = {BACKGROUND: Mosquitoes (Culicidae), as disease vectors, represent a risk for human health worldwide. Repeated introductions of alien mosquito species and the spread of invasive species have been recorded in different countries. Traditionally, identification of mosquitoes relies on morphological observation. However, morphology-based identification is associated with a number of potential disadvantages, such as the high level of specialisation of the operator and its limited applicability to damaged samples. In these cases, species identification is achieved through molecular methods based on DNA amplification. Molecular-based taxonomy has also enabled the development of techniques for the study of environmental DNA (eDNA). Previous studies indicated the 16S mitochondrial ribosomal RNA (rRNA) gene as a promising target for this application; however, 16S rRNA sequences are available for only a limited number of mosquito species. In addition, although primers for the 16S rRNA gene were designed years ago, they are based on limited numbers of mosquito sequences. Thus, the aims of this study were to: (i) design pan-mosquito 16S rRNA gene primers; (ii) using these primers, generate a 16S rRNA gene mosquito reference library (with a focus on mosquitoes present in Italy); and (iii) compare the discriminatory power of the 16S rRNA gene with two widely used molecular markers, cytochrome c oxidase subunit 1 mitochondrial gene (COI) and internal transcribed spacer 2 (ITS2).<br><br>METHODS: A total of six mosquito genera (28 mosquito species) were included in this study: Aedes (n = 16 species), Anopheles (5 species), Coquillettidia (1 species), Culex (3 species), Culiseta (2 species) and Uranotaenia (1 species). DNA was extracted from the whole mosquito body, and more than one specimen for each species was included in the analysis. Sanger sequencing was used to generate DNA sequences that were then analysed through the Barcode of Life Data Systems (BOLD). Phylogenetic analyses were also performed.<br><br>RESULTS: Novel 16S rDNA gene, COI and ITS2 sequences were generated. The 16S rRNA gene was shown to possess sufficient informativeness for the identification of mosquito species, with a discriminatory power equivalent to that of COI.<br><br>CONCLUSIONS: This study contributes to the generation of DNA barcode libraries, focussed on Italian mosquitoes, with a significant increase in the number of 16S rRNA gene sequences. We hope that these novel sequences will provide a resource for studies on the biodiversity, monitoring and metabarcoding of mosquitoes, including eDNA-based approaches.}, }
@article {pmid39339949, year = {2024}, author = {Sartingen, N and Stürmer, V and Kaltenböck, M and Müller, TG and Schnitzler, P and Kreshuk, A and Kräusslich, HG and Merle, U and Mücksch, F and Müller, B and Pape, C and Laketa, V}, title = {Multiplex Microscopy Assay for Assessment of Therapeutic and Serum Antibodies against Emerging Pathogens.}, journal = {Viruses}, volume = {16}, number = {9}, pages = {}, pmid = {39339949}, issn = {1999-4915}, support = {TTU 04.710//German Center for Infection Research/ ; EXC 2067/1- 390729940//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *SARS-CoV-2/immunology ; *COVID-19/diagnosis/immunology/virology ; *Antibodies, Viral/blood/immunology ; *Spike Glycoprotein, Coronavirus/immunology ; HeLa Cells ; Antigens, Viral/immunology ; Microscopy/methods ; Coronavirus Nucleocapsid Proteins/immunology ; Machine Learning ; Phosphoproteins ; }, abstract = {The emergence of novel pathogens, exemplified recently by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need for rapidly deployable and adaptable diagnostic assays to assess their impact on human health and guide public health responses in future pandemics. In this study, we developed an automated multiplex microscopy assay coupled with machine learning-based analysis for antibody detection. To achieve multiplexing and simultaneous detection of multiple viral antigens, we devised a barcoding strategy utilizing a panel of HeLa-based cell lines. Each cell line expressed a distinct viral antigen, along with a fluorescent protein exhibiting a unique subcellular localization pattern for cell classification. Our robust, cell segmentation and classification algorithm, combined with automated image acquisition, ensured compatibility with a high-throughput approach. As a proof of concept, we successfully applied this approach for quantitation of immunoreactivity against different variants of SARS-CoV-2 spike and nucleocapsid proteins in sera of patients or vaccinees, as well as for the study of selective reactivity of monoclonal antibodies. Importantly, our system can be rapidly adapted to accommodate other SARS-CoV-2 variants as well as any antigen of a newly emerging pathogen, thereby representing an important resource in the context of pandemic preparedness.}, }
@article {pmid39339575, year = {2024}, author = {Heo, JH and Yeon, J and Jung, JK and Shin, IS and Sim, SC}, title = {Development of Cost-Effective SNP Markers for Genetic Variation Analysis and Variety Identification in Cultivated Pears (Pyrus spp.).}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {18}, pages = {}, pmid = {39339575}, issn = {2223-7747}, support = {320040052HD060//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET)/ ; }, abstract = {Pear (Pyrus spp.) is a major fruit crop in the Rosaceae family, and extensive efforts have been undertaken to develop elite varieties. With advances in genome sequencing technologies, single-nucleotide polymorphisms (SNPs) are commonly used as DNA markers in crop species. In this study, a large-scale discovery of SNPs was conducted using genotyping by sequencing in a collection of 48 cultivated pear accessions. A total of 256,538 confident SNPs were found on 17 chromosomes, and 288 SNPs were filtered based on polymorphic information content, heterozygosity rate, and genome distribution. This subset of SNPs was used to genotype an additional 144 accessions, consisting of P. pyrifolia (53), P. ussuriensis (27), P. bretschneideri (19), P. communis (26), interspecific hybrids (14), and others (5). The 232 SNPs with reliable polymorphisms revealed genetic variations between and within species in the 192 pear accessions. The Asian species (P. pyrifolia, P. ussuriensis, and P. bretschneideri) and interspecific hybrids were genetically differentiated from the European species (P. communis). Furthermore, the P. pyrifolia population showed higher genetic diversity relative to the other populations. The 232 SNPs and four subsets (192, 96, 48, and 24 SNPs) were assessed for variety identification. The 192 SNP subset identified 173 (90.1%) of 192 accessions, which was comparable to 175 (91.1%) from the 232 SNPs. The other three subsets showed 81.8% (24 SNPs) to 87.5% (96 SNPs) identification rates. The resulting SNPs will be a useful resource to investigate genetic variations and develop an efficient DNA barcoding system for variety identification in cultivated pears.}, }
@article {pmid39338960, year = {2024}, author = {Olszak-Przybyś, H and Korbecka-Glinka, G}, title = {The Diversity of Seed-Borne Fungi Associated with Soybean Grown in Southern Poland.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39338960}, issn = {2076-0817}, abstract = {Fungi have the potential to colonize soybean seeds in the field, during their maturation in the pods and after harvest, during storage. The aim of this study was to identify fungi inhabiting soybean seeds after storage with varying germination capacity and to evaluate their chemical composition. The research material consisted of twelve soybean seed lots collected from the fields in southern Poland and stored over winter. The germination percentage of these lots ranged between 20.67% and 81.33%. The seeds were subjected to analyses of the main chemical components and mycological analysis. Fungal isolates were subjected to taxonomic identification using microscopic methods and DNA sequencing (using internal transcribed spacer region and secondary barcoding regions). A total number of 355 fungal isolates from 16 genera were identified, with Aspergillus, Alternaria, and Fusarium being the most common. Species were successfully identified in 94% of isolates. Twelve examined seed lots varied significantly in the number of isolated fungal species (from 1 to 17). Moreover, they also differed in the isolated species composition. Highly significant positive correlation was found between the number of Aspergillus psedudoglaucus isolates and the content of free fatty acids. In turn, the number of Fusarium spp. isolates correlated negatively with protein and nitrogen content. Similarly, highly significant negative correlation was found between the number of all fungal isolates and the 1000-seed weight, indicating that smaller seeds are more vulnerable to fungal infection. The results obtained in this study identify species of fungi which may be responsible for lowering quality of the seeds obtained in southern Poland.}, }
@article {pmid39337711, year = {2024}, author = {Noh, S and Kim, WJ and Cha, JM and Choi, G and Yang, S and Song, JH and Moon, BC}, title = {Rapid Diagnostic PCR Assay Method for Species Identification of Mantidis Ootheca (Sangpiaoxiao) Based on Cytochrom C Oxidase I (COI) Barcode Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, pmid = {39337711}, issn = {1422-0067}, support = {KSN1823320//Korea Institute of Oriental Medicine/ ; }, mesh = {*Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Animals ; Polymerase Chain Reaction/methods ; Species Specificity ; Mantodea/genetics/classification ; Rapid Diagnostic Tests ; }, abstract = {Mantidis Ootheca (sangpiaoxiao), the egg case of the mantis, is a type of insect-derived traditional medicine widely used in East Asia. However, species identification based on egg morphology is challenging, leading to the distribution of counterfeit and adulterated products. The use of inauthentic ingredients can pose serious health risks to consumers. This study aimed to develop PCR markers that can rapidly and accurately differentiate between authentic and counterfeit Mantidis Ootheca. The mitochondrial cytochrome c oxidase I (COI) region was sequenced in thirteen samples from four mantis species: Tenodera angustipennis, Statilia maculata, Hierodula patellifera, and T. sinensis. Four sets of SCAR primers were designed based on species-specific nucleotide polymorphisms, and a multiplex SCAR assay was developed by combining all sets of the primers. The sequence-characterized amplified region (SCAR) primers successfully produced amplicons for each target species, even with low-DNA templates or templates containing DNA from multiple samples. No amplification was observed for nontarget species. This study presents a novel approach for identifying authentic Mantidis Ootheca species using DNA-based diagnostic marker assays, which enable rapid and precise species identification. The SCAR assays developed in this study will aid in maintaining quality control and promoting the standardization of commercial Mantidis Ootheca products.}, }
@article {pmid39337663, year = {2024}, author = {Sikora, J and Celiński, K}, title = {Exploring Taxonomic and Genetic Relationships in the Pinus mugo Complex Using Genome Skimming Data.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, pmid = {39337663}, issn = {1422-0067}, support = {"Diamond Grant" program No. DI2017003147//Ministry of Science and Higher Education of the Republic of Poland./ ; }, mesh = {*Pinus/genetics/classification ; *Phylogeny ; *Genome, Plant ; *Genetic Variation ; DNA Barcoding, Taxonomic/methods ; Haplotypes/genetics ; Genomics/methods ; }, abstract = {Genome skimming is a novel approach that enables obtaining large-scale genomic information based on high-copy DNA fractions from shallow whole-genome sequencing. The simplicity of this method, low analysis costs, and large amounts of generated data have made it widely used in plant research, including species identification, especially in the case of protected or endangered taxa. This task is particularly difficult in the case of closely related taxa. The Pinus mugo complex includes several dozen closely related taxa occurring in the most important mountain ranges in Europe. The taxonomic rank, origin, or distribution of many of these taxa have been debated for years. In this study, we used genome skimming and multilocus DNA barcoding approaches to obtain different sequence data sets and also to determine their genetic diversity and suitability for distinguishing closely related taxa in the Pinus mugo complex. We generated seven different data sets, which were then analyzed using three discrimination methods, i.e., tree based, distance based, and assembling species by automatic partitioning. Genetic diversity among populations and taxa was also investigated using haplotype network analysis and principal coordinate analysis. The proposed data set based on divergence hotspots is even twenty-times more variable than the other analyzed sets and improves the phylogenetic resolution of the Pinus mugo complex. In light of the obtained results, Pinus × rhaetica does not belong to the Pinus mugo complex and should not be identified with either Pinus uliginosa or Pinus rotundata. It seems to represent a fixed hybrid or introgressant between Pinus sylvestris and Pinus mugo. In turn, Pinus mugo and Pinus uncinata apparently played an important role in the origins of Pinus uliginosa and Pinus rotundata.}, }
@article {pmid39336651, year = {2024}, author = {Pramatarova, M and Burckhardt, D and Malenovský, I and Gjonov, I and Schuler, H and Štarhová Serbina, L}, title = {Unravelling the Molecular Identity of Bulgarian Jumping Plant Lice of the Family Aphalaridae (Hemiptera: Psylloidea).}, journal = {Insects}, volume = {15}, number = {9}, pages = {}, pmid = {39336651}, issn = {2075-4450}, support = {80-10-5/2024//Scientific Research Fund of SU "St. Kliment Ohridski", FWF Austrian Science Fund, Province of Bolzano-Bozen/ ; }, abstract = {Psyllids (Hemiptera: Psylloidea) are plant sap-sucking insects whose identification is often difficult for non-experts. Despite the rapid development of DNA barcoding techniques and their widespread use, only a limited number of sequences of psyllids are available in the public databases, and those that are available are often misidentified. Here, we provide 80 sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and cytochrome b (Cytb), for 25 species of Aphalaridae, mainly from Bulgaria. The DNA barcodes for 15 of these species are published for the first time. In cases where standard primers failed to amplify the target gene fragment, we designed new primers that can be used in future studies. The distance-based thresholds for the analysed species were between 0.0015 and 0.3415 for COI and 0.0771 and 0.4721 for Cytb, indicating that the Cytb gene has a higher interspecific divergence, compared to COI, and therefore allows for more accurate species identification. The species delimitation based on DNA barcodes is largely consistent with the differences resulting from morphological and host plant data, demonstrating that the use of DNA barcodes is suitable for successful identification of most aphalarid species studied. The phylogenetic reconstruction based on maximum likelihood and Bayesian inference analyses, while showing similar results at high taxonomic levels to previously published phylogenies, provides additional information on the placement of aphalarids at the species level. The following five species represent new records for Bulgaria: Agonoscena targionii, Aphalara affinis, Colposcenia aliena, Co. bidentata, and Craspedolepta malachitica. Craspedolepta conspersa is reported for the first time from the Czech Republic, while Agonoscena cisti is reported for the first time from Albania.}, }
@article {pmid39336619, year = {2024}, author = {Costa, MM and Corbel, V and Ben Hamouda, R and Almeras, L}, title = {MALDI-TOF MS Profiling and Its Contribution to Mosquito-Borne Diseases: A Systematic Review.}, journal = {Insects}, volume = {15}, number = {9}, pages = {}, pmid = {39336619}, issn = {2075-4450}, support = {Grant no PDH-2-NBC 2-B-2201//Direction G&#xe9;n&#xe9;rale de l'Armement/ ; }, abstract = {Mosquito-borne diseases are responsible for hundreds of thousands of deaths per year. The identification and control of the vectors that transmit pathogens to humans are crucial for disease prevention and management. Currently, morphological classification and molecular analyses via DNA barcoding are the standard methods used for vector identification. However, these approaches have several limitations. In the last decade, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as an innovative technology in biological sciences and is now considered as a relevant tool for the identification of pathogens and arthropods. Beyond species identification, this tool is also valuable for determining various life traits of arthropod vectors. The purpose of the present systematic review was to highlight the contribution of MALDI-TOF MS to the surveillance and control of mosquito-borne diseases. Published articles from January 2003 to August 2024 were retrieved, focusing on different aspects of mosquito life traits that could be determinants in disease transmission and vector management. The screening of the scientific literature resulted in the selection of 54 published articles that assessed MALDI-TOF MS profiling to study various mosquito biological factors, such species identification, life expectancy, gender, trophic preferences, microbiota, and insecticide resistance. Although a large majority of the selected articles focused on species identification, the present review shows that MALDI-TOF MS profiling is promising for rapidly identifying various mosquito life traits, with high-throughput capacity, reliability, and low cost. The strengths and weaknesses of this proteomic tool for vector control and surveillance are discussed.}, }
@article {pmid39336609, year = {2024}, author = {Stonis, JR and Remeikis, A and Diškus, A and Dobrynina, V and Orlovskytė, S}, title = {A Phenomenon: What Are the Minuscule Grey Moths Abundant in the Dry Season in the Tropical Dry Forests of the Pacific Coast of Honduras?.}, journal = {Insects}, volume = {15}, number = {9}, pages = {}, pmid = {39336609}, issn = {2075-4450}, abstract = {Our investigation centered on the tropical dry forests along the Pacific coast of Honduras, aiming to elucidate the presence and abundance of minuscule grey moths during the dry season. Through specimen dissections and the taxonomic identification of the collected material, we have described three new species: Acalyptris podenasi sp. nov., A. palpiformis sp. nov., and A. tortoris sp. nov. Additionally, we documented two species previously known from neighboring countries, A. lascuevella Puplesis &amp; Robinson and A. basicornis Remeikis &amp; Stonis. The females of A. lascuevella were previously unknown and are documented here for the first time. Morphological examinations were complemented by DNA barcoding, particularly highlighting variation in A. lascuevella. The paper's primary significance lies not only in the description of new species but also in uncovering their taxonomic, morphological, and molecular importance. We found that these species are unique and indicative of the previously unstudied dry forests as a distinct ecosystem. Our findings revealed several novel atypical morphological traits within the studied Nepticulidae, including unusually large signum cells in the female genitalia, a dorso-ventrally divided uncus, and asymmetrical valvae in the male genitalia. These discoveries underscore the morphological diversity of Acalyptris Meyrick and their significance in evolutionary biology. Consequently, the paper addresses a previously unknown phenomenon of the occurrence and astonishing abundance of minuscule plant-mining micromoths in dry deciduous forests during the peak of the dry season. We hope that this paper will encourage Lepidoptera taxonomists to explore micromoths in other tropical dry forests, which, while limited in distribution, hold global importance. The paper is extensively illustrated with photographs of Acalyptris adults and their genitalia, along with maps, habitats, and molecular phylogenetic trees.}, }
@article {pmid39335263, year = {2024}, author = {Poonlaphdecha, S and Ribas, A and Chaisiri, K and Morand, S and Chan, AHE and Thaenkham, U}, title = {Genetic Characterization of the Co-Invasive Rodent Parasite Heterakis spumosa (Nematoda, Heterakidae).}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {18}, pages = {}, pmid = {39335263}, issn = {2076-2615}, support = {ANR BiodivHealthSEA , ANR-17-CE35-0003-02//Agence nationale de la recherche/ ; }, abstract = {Heterakis spumosa, a parasitic worm infecting rodents, is globally prevalent in black rats, brown rats, and house mice. It is hypothesized to originate from Asia due to its widespread presence in Southeast Asia in various Murinae. Previous molecular studies focused on European, African, and Japanese specimens, but none included samples from the putative native range. Rodents were collected between 2008 and 2015 across various localities in Southeast Asia and Europe, identified by morphology or genetic barcoding. Viscera were examined or preserved for later inspection. DNA was extracted from H. spumosa. PCR amplification targeting the mtCOI gene and ITS1 region was conducted in this study using newly designed primers (based on Heterakis reference sequences). PCR amplicons were subsequently sequenced and analyzed. In this study, the phylogenetic analysis using ITS1 sequences revealed that Heterakis samples from Thai and Laotian rodents belong to the species H. spumosa, exhibiting low genetic variation compared to samples from other regions. Genetic distance calculations using mtCOI sequences confirmed the marked distinction of H. spumosa from other Heterakis species. Our phylogenetic analyses using partial mtCOI and ITS1 sequences have significantly enhanced our comprehension of the genetic diversity and evolutionary history of the nematode H. spumosa.}, }
@article {pmid39334308, year = {2024}, author = {Hartop, E and Lee, L and Srivathsan, A and Jones, M and Peña-Aguilera, P and Ovaskainen, O and Roslin, T and Meier, R}, title = {Resolving biology's dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {215}, pmid = {39334308}, issn = {1741-7007}, support = {2016-203 4.3//Swedish Taxonomy Initiative/ ; ERC-synergy grant 856506-LIFEPLAN//H2020 European Research Council/ ; ERC-synergy grant 856506-LIFEPLAN//H2020 European Research Council/ ; 336212 and 345110//Academy of Finland/ ; }, mesh = {Animals ; *Diptera/physiology/genetics ; *Biodiversity ; Sweden ; *DNA Barcoding, Taxonomic ; Seasons ; Climate Change ; Animal Distribution ; }, abstract = {BACKGROUND: Zoology's dark matter comprises hyperdiverse, poorly known taxa that are numerically dominant but largely unstudied, even in temperate regions where charismatic taxa are well understood. Dark taxa are everywhere, but high diversity, abundance, and small size have historically stymied their study. We demonstrate how entomological dark matter can be elucidated using high-throughput DNA barcoding ("megabarcoding"). We reveal the high abundance and diversity of scuttle flies (Diptera: Phoridae) in Sweden using 31,800 specimens from 37 sites across four seasonal periods. We investigate the number of scuttle fly species in Sweden and the environmental factors driving community changes across time and space.<br><br>RESULTS: Swedish scuttle fly diversity is much higher than previously known, with 549 putative specie) detected, compared to 374 previously recorded species. Hierarchical Modelling of Species Communities reveals that scuttle fly communities are highly structured by latitude and strongly driven by climatic factors. Large dissimilarities between sites and seasons are driven by turnover rather than nestedness. Climate change is predicted to significantly affect the 47% of species that show significant responses to mean annual temperature. Results were robust regardless of&#xa0;whether haplotype diversity or species-proxies were used&#xa0;as response variables. Additionally, species-level models of common taxa adequately predict overall species richness.<br><br>CONCLUSIONS: Understanding the bulk of the diversity around us is imperative during an era of biodiversity change. We show that dark insect taxa can be efficiently characterised and surveyed with megabarcoding. Undersampling of rare taxa and choice of operational taxonomic units do not alter the main ecological inferences, making it an opportune time to tackle zoology's dark matter.}, }
@article {pmid39333158, year = {2024}, author = {Yuan, L and Chen, X and Zhan, H and Henry, GL and Zador, AM}, title = {Massive multiplexing of spatially resolved single neuron projections with axonal BARseq.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8371}, pmid = {39333158}, issn = {2041-1723}, support = {RF1MH123403//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RF1 MH123403/MH/NIMH NIH HHS/United States ; U19NS123716//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U19 NS123716/NS/NINDS NIH HHS/United States ; D16PC0008//ODNI | Intelligence Advanced Research Projects Activity (IARPA)/ ; }, mesh = {Animals ; *Axons/metabolism ; *Neurons/cytology ; Mice ; Male ; *Auditory Cortex/cytology/physiology ; Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Mice, Inbred C57BL ; }, abstract = {Neurons in the cortex are heterogeneous, sending diverse axonal projections to multiple brain regions. Unraveling the logic of these projections requires single-neuron resolution. Although a growing number of techniques have enabled high-throughput reconstruction, these techniques are typically limited to dozens or at most hundreds of neurons per brain, requiring that statistical analyses combine data from different specimens. Here we present axonal BARseq, a high-throughput approach based on reading out nucleic acid barcodes using in situ RNA sequencing, which enables analysis of even densely labeled neurons. As a proof of principle, we have mapped the long-range projections of >8000 primary auditory cortex neurons from a single male mouse. We identified major cell types based on projection targets and axonal trajectory. The large sample size enabled us to systematically quantify the projections of intratelencephalic (IT) neurons, and revealed that individual IT neurons project to different layers in an area-dependent fashion. Axonal BARseq is a powerful technique for studying the heterogeneity of single neuronal projections at high throughput within individual brains.}, }
@article {pmid39333091, year = {2024}, author = {O'Neill, MJ and Yang, T and Laudeman, J and Calandranis, ME and Harvey, ML and Solus, JF and Roden, DM and Glazer, AM}, title = {ParSE-seq: a calibrated multiplexed assay to facilitate the clinical classification of putative splice-altering variants.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8320}, pmid = {39333091}, issn = {2041-1723}, support = {R35 GM150465/GM/NIGMS NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; F30 HL163923/HL/NHLBI NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 HL164675/HL/NHLBI NIH HHS/United States ; R00 HG010904/HG/NHGRI NIH HHS/United States ; S10 OD025281/OD/NIH HHS/United States ; R01 HL149826/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Induced Pluripotent Stem Cells/metabolism ; *Myocytes, Cardiac/metabolism/cytology ; *RNA Splicing/genetics ; *NAV1.5 Voltage-Gated Sodium Channel/genetics/metabolism ; Arrhythmias, Cardiac/genetics ; RNA Splice Sites/genetics ; CRISPR-Cas Systems/genetics ; Calibration ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; Introns/genetics ; HEK293 Cells ; }, abstract = {Interpreting the clinical significance of putative splice-altering variants outside canonical splice sites remains difficult without time-intensive experimental studies. To address this, we introduce Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed assay to quantify variant effects on RNA splicing. We first apply this technique to study hundreds of variants in the arrhythmia-associated gene SCN5A. Variants are studied in 'minigene' plasmids with molecular barcodes to allow pooled variant effect quantification. We perform experiments in two cell types, including disease-relevant induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). The assay strongly separates known control variants from ClinVar, enabling quantitative calibration of the ParSE-seq assay. Using these evidence strengths and experimental data, we reclassify 29 of 34 variants with conflicting interpretations and 11 of 42 variants of uncertain significance. In addition to intronic variants, we show that many synonymous and missense variants disrupted RNA splicing. Two splice-altering variants in the assay also disrupt splicing and sodium current when introduced into iPSC-CMs by CRISPR-Cas9 editing. ParSE-seq provides high-throughput experimental data for RNA-splicing to support precision medicine efforts and can be readily adopted to study other loss-of-function genotype-phenotype relationships.}, }
@article {pmid39332616, year = {2025}, author = {Lone, S and Narayan, S and Hussain, K and Malik, M and Yadav, SK and Khan, FA and Safa, A and Ahmad, A and Masoodi, KZ}, title = {Investigating the antioxidant and anticancer potential of Daucus spp. extracts against human prostate cancer cell line C4-2, and lung cancer cell line A549.}, journal = {Journal of ethnopharmacology}, volume = {337}, number = {Pt 2}, pages = {118855}, doi = {10.1016/j.jep.2024.118855}, pmid = {39332616}, issn = {1872-7573}, mesh = {Humans ; *Antioxidants/pharmacology/isolation &amp; purification ; *Plant Extracts/pharmacology/chemistry ; Male ; *Daucus carota/chemistry ; *Prostatic Neoplasms/drug therapy ; *Lung Neoplasms/drug therapy ; *Antineoplastic Agents, Phytogenic/pharmacology/isolation &amp; purification ; A549 Cells ; Cell Line, Tumor ; Cell Proliferation/drug effects ; }, abstract = {The study evaluated 297 carrot germplasm lines, focusing on 52 cultivars to explore their therapeutic potential and address challenges related to the accessibility and affordability of nutraceuticals and health promoting foods. The investigation explores the application of DNA barcoding using the ITS region for precise species identification, highlighting genetic diversity among the examined cultivars. Through ITS sequence-based analysis and phylogenetic examination, six diverse Daucus spp. genotypes were differentiated and classified into distinct groups, indicating the presence of vast genetic variation. Evaluation of antioxidant activities using the DPPH radical scavenging assay revealed varying degrees of scavenging ability among genotypes with SKAU-C-15, SKAU-C-17, and SKAU-C-16 exhibiting the highest activity, suggesting their potential for antioxidant-rich products. Thin Layer Chromatography (TLC) bioautography confirmed the presence of bioactive compounds in carrot extracts responsible for their antioxidant properties. In cell culture studies, specific carrot genotype extracts demonstrated potential anti-proliferative and anti-invasive effects on recurrent prostate cancer cell line - C4-2 (SKAU-C-30, SKAU-C-10, and SKAU-C-42) and non-small cell lung cancer cell line - A549 (SKAU-C-18 and SKAU-C-11) cancer cells, as indicated by MTT assay, wound healing assay, and Colony Forming Unit assay. These findings suggest the promising therapeutic potential of carrot genotypes for developing anti-cancer functional foods, nutraceuticals and health supplements.Therefore, the study contributes to the nutrition security, paving the way for advancements in functional foods and health applications, particularly in cancer treatment and prevention.}, }
@article {pmid39331360, year = {2024}, author = {Foote, NE and Foote, GG and Comai, N and Ibarra Caballero, JR and Stewart, JE and Ambrose, AR and Baxter, WL and Davis, TS}, title = {Patterns of occurrence, phenology, and phylogeny of Phloeosinus punctatus LeConte (Coleoptera: Curculionidae, Scolytinae) in giant sequoia.}, journal = {Environmental entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/ee/nvae089}, pmid = {39331360}, issn = {1938-2936}, support = {//Save the Redwoods League/ ; //National Park Service/ ; P21AC12281//Colorado Plateau Cooperative Ecosystem Studies Unit, Northern Arizona University/ ; }, abstract = {Here, we describe patterns of reproduction and flight phenology of putative Phloeosinus punctatus in giant sequoia groves and compare morphology and genotypes of beetles from sympatric giant sequoia (Sequoiadendron giganteum) and California incense-cedar (Calocedrus decurrens). Surveys conducted in 2022 revealed that numerous branches fall from giant sequoia crowns (on average ~30 branches/tree), with 20%-50% of trees per site shedding branches, depositing breeding material for beetles on the forest floor that subsequently becomes colonized. When noninfested branches cut from mature giant sequoias were placed at the ground surface, they were colonized by P. punctatus and produced an average of 28 beetles/kg branch. Climbing and examination of sequoia crowns in 2023 showed that 75% of mature trees across 11 groves showed evidence of adult beetle entrance holes in their crowns. In 2021, tests with sticky traps showed that beetles alighted on fallen branches from 20th May to 20th August (peak landing: 2nd July); a logistic model developed from emergence data in 2021 and 2022 predicts the emergence of F1 offspring from branches between 10th July and 1st September (peak emergence: 8th August). Beetles emerging from giant sequoia preferred to settle on giant sequoia, did not reproduce in incense-cedar, and diverged morphologically from beetles emerging from incense-cedar. However, phylogenetic analysis of three genes (28S, CAD, and COI) revealed no clear pattern of sequence divergence, suggesting a single species (P. punctatus) that colonizes both hosts, though cryptic speciation may not be detectable with standard barcoding genes. Ecological and potential management implications are discussed.}, }
@article {pmid39329134, year = {2024}, author = {Andriienko, V and Buczek, M and Meier, R and Srivathsan, A and Łukasik, P and Kolasa, MR}, title = {Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18025}, pmid = {39329134}, issn = {2167-8359}, support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Microbiota/genetics ; *Insecta/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/isolation &amp; purification/classification ; Polymerase Chain Reaction/methods ; Biodiversity ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.<br><br>METHODS: High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.<br><br>RESULTS: We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.<br><br>CONCLUSION: Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.}, }
@article {pmid39329133, year = {2024}, author = {Morris, MRJ and Summers, MM and Kwan, M and Mee, JA and Rogers, SM}, title = {Mislabeled and ambiguous market names in invertebrate and finfish seafood conceal species of conservation concern in Calgary, Alberta, Canada.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18113}, pmid = {39329133}, issn = {2167-8359}, mesh = {Animals ; Alberta ; *Seafood/analysis ; *DNA Barcoding, Taxonomic ; Food Labeling/legislation &amp; jurisprudence ; Invertebrates/classification ; Conservation of Natural Resources ; Fishes/genetics ; Endangered Species ; }, abstract = {BACKGROUND: The mislabeling of seafood, wherein a food product's marketed name does not match its contents, has the potential to mask species of conservation concern. Less discussed is the role of legally ambiguous market names, wherein a single name could be used to sell multiple species. Here we report the first study in Canada to examine mislabeling and ambiguous market names in both invertebrate (e.g., bivalve, cephalopod, shrimp) and finfish products.<br><br>METHODS: A total of 109 invertebrate and 347 finfish products were sampled in Calgary between 2014 and 2020. Market names were documented from the label or equivalent and determined to be precise (the name could apply to only one species) or ambiguous (multiple species could be sold under that name). A region of the cytochrome c oxidase I gene was sequenced and compared to reference sequences from boldsystems.org. Samples were considered mislabeled if the species identified through DNA barcoding did not correspond to the market name, as determined through the Canadian Food Inspection Agency Fish List. Mislabeling was further differentiated between semantic mislabeling, wherein the market name was not found on the Fish List but the barcode identity was in line with what a consumer could reasonably have expected to have purchased; invalid market names, wherein the market name was so unusual that no legitimate inferences as to the product's identity could be made; and product substitution, wherein the DNA barcode identified the product as a species distinct from that associated with the market name. Invalid market names and product substitutions were used to provide conservative estimates of mislabeling. The global conservation status of the DNA-identified invertebrate or finfish was determined through the International Union for the Conservation of Nature Red List. A logistic regression was used to determine the relationship between precision and accuracy in predicting conservation status of the sampled species.<br><br>RESULTS: There was no significant difference in mislabeling occurrence between invertebrates (33.9% total mislabeling occurrence, 20.2% product substitution) and finfish (32.3% total mislabeling occurrence, 21.3% product substitution/invalid market names). Product substitutions sometimes involved species of conservation concern, such as foods marketed as freshwater eel (Anguilla rostrata) that were determined through DNA barcoding to be European eel (Anguilla anguilla), or cuttlefish balls putatively identified as the Endangered threadfin porgy (Evynnis cardinalis). Product substitutions and ambiguous market names were significantly associated with the sale of species of conservation concern, but ambiguity was a more important predictor. Although preventing the mislabeling of seafoods can and must remain a priority in Canada, our work suggests that moving towards precise names for all seafood products will better support sustainable fisheries goals.}, }
@article {pmid39326961, year = {2024}, author = {Khumalo, N and Ledwaba, MB and Labuschagne, K and Voster, I and Oosthuizen, M and Mwale, M and Chaisi, M}, title = {Identification of ticks and tick-borne pathogens of wildlife necropsy cases submitted to the SANBI National Zoological Gardens, South Africa.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {55}, number = {}, pages = {101105}, doi = {10.1016/j.vprsr.2024.101105}, pmid = {39326961}, issn = {2405-9390}, mesh = {Animals ; South Africa/epidemiology ; *Animals, Wild/parasitology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Tick-Borne Diseases/veterinary/parasitology/epidemiology/microbiology ; *RNA, Ribosomal, 16S/analysis ; *Ticks/parasitology/microbiology ; Phylogeny ; Female ; DNA Barcoding, Taxonomic/veterinary ; Animals, Zoo/parasitology ; }, abstract = {Ticks are arachnid blood-feeding parasites, which infest livestock, wildlife, and humans, transmitting medically and veterinary significant pathogens. Their biodiversity and distribution in wild animals remains complex. This study analysed archived tick samples (n = 48) from the South African Biodiversity Institute (SANBI) Wildlife Biobank utilizing morphology and genetic analyses of the 16S rRNA and COI (DNA barcoding) mitochondrial genes to identify ticks collected among 13 vertebratesavian, reptilian, and mammalian host species. The specimens came from nine localities including nature reserves and captive facilities (zoological garden) in South Africa, Namibia, and Botswana. These ticks were also assessed for associated pathogens with the reverse line blot (RLB) hybridization assay. Seven tick genera, Amblyomma, Hyalomma, Haemaphysalis, Ixodes, Rhipicephalus, Rhipicentor, and Otobius were identified, with Amblyomma being the most prevalent (22.9 %) in our sample set. Obtained sequences were 95-100 % similar to published records of tick species collected from wild and domestic animals, as well as those collected from vegetation, from different southern African areas. However, tick specimens (n = 3) identified morphologically as Hyalomma truncatum, Rhipicephalus e. evertsi, and R. simus, were, on a molecularly level, more closely related to their sister taxa (H. glabrum, R. e. mimeticus, and R. gertrudae, respectively) suggesting a need for taxonomic verification. With the RLB hybridization assay, six samples reacted with the Ehrlichia/Anaplasma genus-specific probe, while two reacted with the Theileria/Babesia genus-specific probe. Sequencing of the RLB amplicons targeting the 18S rRNA gene (n = 2) indicated 100 % similarity to Hepatozoon fitzsimonsi, while one was closely related to He. ingwe with 99.39 % similarity. The results show that wildlife harbour different tick species, and pathogen detection identified novel genotypes, indicating wildlife as potential pathogens reservoirs. This study enhances our understanding of tick biodiversity, distribution and highlights wildlife's role in harbouring diverse tick species and novel pathogens.}, }
@article {pmid39326113, year = {2025}, author = {Zhao, R and Niu, Q and Murtaza, G and Zhang, G and Yang, Y}, title = {Integrated identification and detection of hydration state and its evolution using terahertz technology.}, journal = {Talanta}, volume = {281}, number = {}, pages = {126943}, doi = {10.1016/j.talanta.2024.126943}, pmid = {39326113}, issn = {1873-3573}, abstract = {The accurate detection of dehydration processes in hydrated drugs can reveal various intermolecular vibration modes mediated by hydrogen bonds between water molecules and other components, which underpin the further development of pharmaceutical science, food safety and biophysics. Herein, terahertz (THz) technology is utilized to investigate the dehydration state of d(+)-Raffinose pentahydrate (Rf·5H2O), in conjunction with imaging-based point by point scanning data acquisition and barcodes methods, to establish an innovative platform integrated identification, trace detection, and application capabilities. Our study demonstrates that the dehydration process of Rf·5H2O can be dynamically monitored through the evolution of its THz absorption peaks, offering more precise results compared to XRD and Raman spectroscopies. Moreover, the absorbance spectra data collected at each individual pixel is utilized to build visualized THz images, achieving an ultralow minimum content required for detection of 0.032 μg/(50 μm)[2]. Additionally, we introduce a THz spectra-barcode conversion system that not only ensures efficient electronic recordkeeping but also enhances user readability, thereby facilitating the practical applications of THz technology.}, }
@article {pmid39323091, year = {2024}, author = {Zhang, Y and Shen, C and Xia, K}, title = {Multi-Cover Persistence (MCP)-based machine learning for polymer property prediction.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39323091}, issn = {1477-4054}, support = {//Nanyang Technological University SPMS Collaborative Research Award 2022/ ; MOE-T2EP20220-0010//Singapore Ministry of Education Academic Research/ ; }, mesh = {*Polymers/chemistry ; *Machine Learning ; Algorithms ; }, abstract = {Accurate and efficient prediction of polymers properties is crucial for polymer design. Recently, data-driven artificial intelligence (AI) models have demonstrated great promise in polymers property analysis. Even with the great progresses, a pivotal challenge in all the AI-driven models remains to be the effective representation of molecules. Here we introduce Multi-Cover Persistence (MCP)-based molecular representation and featurization for the first time. Our MCP-based polymer descriptors are combined with machine learning models, in particular, Gradient Boosting Tree (GBT) models, for polymers property prediction. Different from all previous molecular representation, polymer molecular structure and interactions are represented as MCP, which utilizes Delaunay slices at different dimensions and Rhomboid tiling to characterize the complicated geometric and topological information within the data. Statistic features from the generated persistent barcodes are used as polymer descriptors, and further combined with GBT model. Our model has been extensively validated on polymer benchmark datasets. It has been found that our models can outperform traditional fingerprint-based models and has similar accuracy with geometric deep learning models. In particular, our model tends to be more effective on large-sized monomer structures, demonstrating the great potential of MCP in characterizing more complicated polymer data. This work underscores the potential of MCP in polymer informatics, presenting a novel perspective on molecular representation and its application in polymer science.}, }
@article {pmid39322294, year = {2024}, author = {Wang, D and He, Z and Yang, C and Lu, D and Sun, Y and Kou, Y and Qian, D and Zhang, H and Liu, Y}, title = {[Genetic polymorphisms of common sandflies in selected areas of Henan Province based on DNA barcoding].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {36}, number = {4}, pages = {352-360}, doi = {10.16250/j.32.1374.2024036}, pmid = {39322294}, issn = {1005-6661}, support = {222102310722//Henan Provincial Science and Technology Research Project/ ; LHGJ20220171//Henan Provincial Medical Science and Technology Research Project/ ; LHGJ20230640//Henan Provincial Medical Science and Technology Research Project/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Polymorphism, Genetic ; China ; *Phylogeny ; *Psychodidae/genetics/classification ; *Electron Transport Complex IV/genetics ; }, abstract = {OBJECTIVE: To characterize the species of common sandflies in Henan Province using DNA barcoding with cytochrome c oxidase subunit I (COI) gene as the molecular marker, and to analyze the genetic polymorphisms of sandflies, so as to provide insights into visceral leishmaniasis prevention and control in Henan Province.<br><br>METHODS: Sandfly specimens were sampled from 13 sandflies surveillance sites from 2021 to 2023 in Anyang City, Zhengzhou, Luoyang and Xuchang cities (Zhengzhou-Luoyang-Xuchang areas) where visceral leishmaniasis cases were reported and in Jiaozuo and Xinxiang cities (Jiaozuo-Xinxiang areas) without visceral leishmaniasis cases reported. Genomic DNA was extracted from a single sandfly, and COI gene was amplified. The amplification product was subjected to bidirectional sequencing. Following sequence assembly, the species of sandflies was characterized through sequence alignment using the BLAST tool. The intra-specific and inter-specific genetic distances of sandflies were estimated among different areas using the software Mega 11, and phylogenetic trees were created. The polymorphisms of nucleotide sequences in the sandflies COI gene were estimated using the software DnaSP. The fixation index (FST) of different geographical isolates of sandflies was calculated using the Arlequin software, and the gene flow value (Nm) was used to measure the gene flow in the sandflies populations. In addition, the population genetic structure of different geographical populations of Phlebotomus chinensis was analyzed using the STRUCTURE software.<br><br>RESULTS: A total of 978 sandflies were collected from 13 sandflies surveillance sites in Zhengzhou-Luoyang-Xuchang areas, Jiaozuo-Xinxiang areas and Anyang City of Henan Province from 2021 to 2023, and 475 sandflies were randomly sampled for subsequent detections. A total of 304 Ph. chinensis, 162 Se. squamirostris and 9 Se. bailyi were identified based on molecular biological detection of the COI gene, and Se. bailyi was reported for the first time in Henan Province. The intraspecific genetic distances of sandflies were 0.000 to 0.040, and the inter-specific genetic distances ranged from 0.133 to 0.161. Phylogenetic analysis revealed that each of the three sandfly species was clustered into a clade. The genetic polymorphisms of Ph. chinensis populations varied among different areas, with the highest haplotype diversity (0.966 &#xb1; 0.007) and the greatest nucleotide diversity (0.011) in Zhengzhou-Luoyang-Xuchang areas, and the lowest haplotype diversity (0.720 &#xb1; 0.091) and nucleotide diversity (0.004) in Anyang City. The dominant haplotype of Ph. chinensis populations was Pch_Hap_2 in Anyang City and Jiaozuo-Xinxiang areas, with moderate genetic differentiation (0.05 < FST < 0.15) and frequent gene exchange (Nm value > 1) between Ph. chinensis populations sampled from Anyang City, and Jiaozuo-Xinxiang areas. Population genetic structure analysis showed that the dominant component of Ph. chinensis populations was K5 in Anyang City and Jiaozuo-Xinxiang areas. No obvious dominant haplotype was observed in Ph. chinensis populations sampled from Zhengzhou-Luoyang-Xuchang areas, which had very high genetic differentiation (FST > 0.25) and little gene exchange (Nm value < 1) with Ph. chinensis populations from Anyang City, and Jiaozuo-Xinxiang areas, with K3 as the dominant component. In addition, there was no significant difference in the genetic polymorphism level among Se. squamirostris populations from the three areas.<br><br>CONCLUSIONS: There are Ph. chinensis, Se. squamirostris and Se. bailyi in Henan Province, and S. bailyi is recorded for the first time in Henan Province by molecular biological assays. There are different levels of genetic differentiation and gene exchange among P. chinensis populations in different areas of Henan Province.}, }
@article {pmid39318677, year = {2024}, author = {Kaila, L and Huemer, P}, title = {Elachistadimicatella sensu auctt.-a complex of neglected species diversity (Lepidoptera, Elachistidae) from European mountain systems.}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {179-194}, pmid = {39318677}, issn = {1313-2989}, abstract = {Elachistadimicatella Rebel, 1903, has so far been considered a species in Europe with restricted distribution from Ukraine to western France. The species occurs on mountainous regions. However, the in-depth analysis of a taxonomically uncertain species of Elachista from the Cottian Alps (Italy), especially through DNA barcoding and subsequent morphological studies, led to the realization that individuals previously identified as E.dimicatella from the Cottian Alps and the Pyrenees were misidentified. According to our research, a total of three species can be differentiated: E.dimicatella from Carpathians and its former junior synonym E.niphadophanes Meyrick, 1937, sp. rev., from the Pyrenees, as well as the newly described E.cottiella sp. nov. from southwestern Alps, hitherto incorrectly identified as E.dimicatella. Diagnostic features of the three species are discussed and illustrated. Elachistadimicatella and E.niphadophanes are redescribed.}, }
@article {pmid39318675, year = {2024}, author = {Dettner, K and Kovács, Z and Rewicz, T and Csabai, Z}, title = {Age-dependent variation of aedeagal morphology in Agabusuliginosus and the status of A.lotti (Coleoptera, Dytiscidae).}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {153-177}, pmid = {39318675}, issn = {1313-2989}, abstract = {A doubt has arisen about the taxonomic status of Agabuslotti within the Agabusuliginosus species group due to morphological similarities and lack of molecular data. In this study, a comprehensive morphological and molecular analysis of specimens from Central Europe was conducted, focusing on the Hungarian population. Morphological comparisons of genital structures revealed age-dependent variations, suggesting a gradual transition from A.lotti to A.uliginosus. Molecular analysis of COI sequences further supported this hypothesis, showing minimal genetic differences among most specimens, with only one individual exhibiting distinctiveness. Therefore, A.lotti syn. nov. must be regarded as a junior synonym of A.uliginosus. Our findings also highlight the need for additional multi-marker studies covering a broader geographic range and including both molecular and morphological approaches to elucidate the taxonomic and phylogenetic relationships within this species group. The inclusion of Hungarian samples notably enriched the diversity of haplotypes, emphasizing the importance of expanding sampling efforts in future research.}, }
@article {pmid39318674, year = {2024}, author = {Qian, X and Tang, C and Wang, N and Yang, D}, title = {Syntormon Loew (Diptera, Dolichopodidae) from Inner Mongolia, China, with the description of a new species.}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {143-152}, pmid = {39318674}, issn = {1313-2989}, abstract = {Previously, no records of Syntormon Loew, 1857 species were known from Inner Mongolia (China). The genus is reported here from Inner Mongolia for the first time, with the description of a new species, S.sinicum sp. nov., along with two previously described species, S.dukha Hollis, 1964 and S.henanense Yang &amp; Saigusa, 2000. Syntormonsinicum sp. nov. and S.dukha Hollis, 1964 are barcoded for the first time to support the species delimitation. A key to Syntormon species in China is provided.}, }
@article {pmid39318673, year = {2024}, author = {Silva-Segundo, CA and Funes-Rodríguez, R and Anaya-Godínez, E and Gómez-Gutiérrez, J}, title = {Molecular and morphological identification of larvae of Carangidae (Teleostei, Carangiformes) species from southern Gulf of California.}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {195-215}, pmid = {39318673}, issn = {1313-2989}, abstract = {The description of diagnostic morphological characters and DNA barcoding of fish larvae from nine species of the carangid family are provided from specimens collected during a weekly zooplankton time-series (2016-2017) at Cabo Pulmo National Park, Gulf of California, Mexico. Five nominal species (Caranxsexfasciatus, C.caballus, Naucratesductor, Selarcrumenophthalmus, and Seleneperuviana) and three morphotypes of Decapterus spp. and one of Caranx spp. were identified and separated based on morphological, meristic, and pigmentary diagnostic characters. All larvae were genetically sequenced for a fragment of the cytochrome c oxidase subunit I mitochondrial gene. Sequences of larval Caranx and Decapterus showed high genetic similarity (> 99%), low intraspecific divergence (< 1%), and an interspecific divergence between 6% and 11%, allowing the discrimination of diagnostic pigmentation patterns of fish larvae among three sibling species from each genus: Caranx (C.caballus, C.caninus, and C.sexfasciatus) and Decapterus (D.macarellus, D.macrosoma, and D.muroadsi). DNA barcoding supported the presence of Caranxcaballus, C.caninus, C.sexfasciatus, Decapterusmacarellus, D.muroadsi, Selarcrumenophthalmus, and Seleneperuviana, and for the first time Naucratesductor and D.macrosoma at the CPNP. Abundance of these nine species (confirmed molecularly) was estimated throughout the 2016-2017 weekly time series. Decapterusmacarellus and Caranxcaninus were the most abundant species. The morphological and molecular taxonomic methods allowed us to infer the species number and abundance of these commercial species at the CPNP to improve conservation in protected areas and fishery management.}, }
@article {pmid39315963, year = {2024}, author = {George, FM and Venkatesan, S and Srinivasan, V and Semalaiyappan, J and Kuttiatt, VS}, title = {DNA barcoding and phylogenetic analysis of the vector Culex gelidus and its global and public health significance.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {49}, number = {2}, pages = {S5-S9}, doi = {10.52707/1081-1710-49.2.S5}, pmid = {39315963}, issn = {1948-7134}, mesh = {Animals ; *Culex/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Public Health ; Mosquito Vectors/genetics ; }, }
@article {pmid39315814, year = {2024}, author = {Loes, AN and Tarabi, RAL and Huddleston, J and Touyon, L and Wong, SS and Cheng, SMS and Leung, NHL and Hannon, WW and Bedford, T and Cobey, S and Cowling, BJ and Bloom, JD}, title = {High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains.}, journal = {Journal of virology}, volume = {98}, number = {10}, pages = {e0068924}, pmid = {39315814}, issn = {1098-5514}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; S10 OD028685/OD/NIH HHS/United States ; T11-712/19-N//Research Grants Council, University Grants Committee ()/ ; U01AI153700//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U01 AI153700/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; R01AI165821//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; Investigator Support//Howard Hughes Medical Institute (HHMI)/ ; R01 AI165821/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Antibodies, Neutralizing/immunology/blood ; *Influenza A Virus, H1N1 Subtype/immunology/genetics ; *Influenza Vaccines/immunology/administration &amp; dosage ; *Antibodies, Viral/blood/immunology ; *Influenza, Human/prevention &amp; control/immunology/virology ; *Neutralization Tests/methods ; *Vaccination ; *Hemagglutinin Glycoproteins, Influenza Virus/immunology/genetics ; Adult ; Female ; }, abstract = {UNLABELLED: The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes using a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify the infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately 1 month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers 6 months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. We provide an experimental protocol (dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.<br><br>IMPORTANCE: We describe a new approach that can rapidly measure how the antibodies in human serum inhibit infection by many different influenza strains. This new approach is useful for understanding how viral evolution affects antibody immunity. We apply the approach to study the effect of repeated influenza vaccination.}, }
@article {pmid39314939, year = {2024}, author = {Shao, F and Hu, J and Zhang, P and Akarapipad, P and Park, JS and Lei, H and Hsieh, K and Wang, TH}, title = {Enhanced CRISPR/Cas-Based Immunoassay through Magnetic Proximity Extension and Detection.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.06.24313206}, pmid = {39314939}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-associated systems have recently emerged as a focal point for developing next-generation molecular diagnosis, particularly for nucleic acid detection. However, the detection of proteins is equally critical across diverse applications in biology, medicine, and the food industry, especially for diagnosing and prognosing diseases like cancer, Alzheimer's and cardiovascular conditions. Despite recent efforts to adapt CRISPR/Cas systems for protein detection with immunoassays, these methods typically achieved sensitivity only in the femtomolar to picomolar range, underscoring the need for enhanced detection capabilities. To address this, we developed CRISPR-AMPED, an innovative CRISPR/Cas-based immunoassay enhanced by magnetic proximity extension and detection. This approach combines proximity extension assay (PEA) with magnetic beads that converts protein into DNA barcodes for quantification with effective washing steps to minimize non-specific binding and hybridization, therefore reducing background noise and increasing detection sensitivity. The resulting DNA barcodes are then detected through isothermal nucleic acid amplification testing (NAAT) using recombinase polymerase amplification (RPA) coupled with the CRISPR/Cas12a system, replacing the traditional PCR. This integration eliminates the need for thermocycling and bulky equipment, reduces amplification time, and provides simultaneous target and signal amplification, thereby significantly boosting detection sensitivity. CRISPR-AMPED achieves attomolar level sensitivity, surpassing ELISA by over three orders of magnitude and outperforming existing CRISPR/Cas-based detection systems. Additionally, our smartphone-based detection device demonstrates potential for point-of-care applications, and the digital format extends dynamic range and enhances quantitation precision. We believe CRISPR-AMPED represents a significant advancement in the field of protein detection.}, }
@article {pmid39314390, year = {2024}, author = {Cabrera-Sosa, L and Safarpour, M and Kattenberg, JH and Ramirez, R and Vinetz, J and Rosanas-Urgell, A and Gamboa, D and Delgado-Ratto, C}, title = {Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.09.611954}, pmid = {39314390}, issn = {2692-8205}, abstract = {Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv &amp; 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs &amp; Pf: 28 SNPs) and MS panels (Pv: 16 MS &amp; Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He) was similar across the subpopulations for both makers: He MS = 0.68 - 0.78 (p = 0.23) and He SNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, F ST) was also comparable: F ST-MS = 0.04 - 0.14 and F ST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends (He MS = 0 - 0.48 p = 0.03 - 1; He SNP = 0 - 0.09, p = 0.03 - 1) and pairwise F ST comparisons (F ST-MS = 0.14 - 0.65, F ST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.}, }
@article {pmid39314385, year = {2024}, author = {Baron, CS and Mitchell, O and Avagyan, S and Menard, R and Yang, S and Robertson, AL and Potluri, R and Shendure, J and Madelaine, R and McKenna, A and Zon, LI}, title = {Leukemia-derived apelin selects endothelial niche clones to promote tumorigenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.09.612077}, pmid = {39314385}, issn = {2692-8205}, abstract = {Hematopoietic stem cells are regulated by endothelial and mesenchymal stromal cells in the marrow niche1-3. Leukemogenesis was long believed to be solely driven by genetic perturbations in hematopoietic cells but introduction of genetic mutations in the microenvironment demonstrated the ability of niche cells to drive disease progression4-8. The mechanisms by which the stem cell niche induces leukemia remain poorly understood. Here, using cellular barcoding in zebrafish, we found that clones of niche endothelial and stromal cells are significantly expanded in leukemic marrows. The pro-angiogenic peptide apelin secreted by leukemic cells induced sinusoidal endothelial cell clonal selection and transcriptional reprogramming towards an angiogenic state to promote leukemogenesis in vivo. Overexpression of apelin in normal hematopoietic stem cells led to clonal amplification of the niche endothelial cells and promotes clonal dominance of blood cells. Knock-out of apelin in leukemic zebrafish resulted in a significant reduction in disease progression. Our results demonstrate that leukemic cells remodel the clonal and transcriptional landscape of the marrow niche to promote leukemogenesis and provide a potential therapeutic opportunity for anti-apelin treatment.}, }
@article {pmid39310847, year = {2024}, author = {Böning, S and Schneider, F and Huber, AK and Langhoff, D and Lin, H and Kaczorowski, A and Stenzinger, A and Hohenfellner, M and Duensing, S and Duensing, A}, title = {Region of interest localization, tissue storage time, and antibody binding density-a technical note on the GeoMx® Digital Spatial Profiler.}, journal = {Immuno-oncology technology}, volume = {23}, number = {}, pages = {100727}, pmid = {39310847}, issn = {2590-0188}, abstract = {BACKGROUND: Spatial biology is an emerging concept to interrogate tumor heterogeneity. The NanoString GeoMx® Digital Spatial Profiling (DSP) platform has become increasingly available. It combines high-plex analysis of protein or messenger RNA expression using barcoded antibodies or oligonucleotide probes with investigator-driven selection of regions of interest. Cell populations, e.g. immune cells, can be selectively analyzed via segmentation. A key advantage is the use of archived formalin-fixed, paraffin-embedded tissue, however, begging the question whether and to what extent tissue fixation and storage time affect the results.<br><br>MATERIALS AND METHODS: Antibody binding density (ABD), i.e. the number of barcodes/&#x3bc;m[2], is a key quality control measure for DSP spatial proteomics. To assess whether regional differences in tissue fixation have an influence on ABD, we compared 652 regions of interest selected from tumor center and periphery of 49 prostate cancer and 25 renal cell carcinoma (RCC) specimens. Moreover, the effect of tissue storage time on ABD was examined. Finally, we tested whether regional differences have an influence on ABD of segmented CD45+ or CD8+ cells.<br><br>RESULTS: No significant differences in ABD between tumor center and periphery were found in prostate cancer or RCC. However, ABD was significantly higher in recent specimens (&#x2264;5 years) when compared with those that were older (>5&#xa0;years; P&#xa0;= 0.027). There was a trend towards higher ABD in the tumor periphery of RCC specimens after segmentation for immune cells, albeit without reaching statistical significance.<br><br>CONCLUSIONS: The NanoString GeoMx&#xae; DSP platform delivers robust data to interrogate tumor heterogeneity, but tissue storage time should be considered when interpreting the results.}, }
@article {pmid39309168, year = {2024}, author = {Mitchueachart, B and Sutcharit, C and Tongkerd, P and Panha, S}, title = {Morphological and molecular evidence uncovers hidden species diversity in the leatherleaf slug genus Valiguna (Systellommatophora, Veronicellidae) from Thailand.}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {79-107}, pmid = {39309168}, issn = {1313-2989}, abstract = {The poorly studied leatherleaf slug genus Valiguna in Thailand was carefully investigated. Members of this genus are phenotypically similar, making their identification very challenging. This study clarifies the taxonomic status of all Valiguna species in Thailand by combining morphological and anatomical studies with DNA barcoding. Monophyly of all Valiguna species was confirmed by analysis of the mitochondrial COI data and that all Valiguna species have the acropleurocaulis type of penis. Currently, three Valiguna species are recognised: V.siamensis, V.semicerina Mitchueachart &amp; Panha, sp. nov., and V.crispa Mitchueachart &amp; Panha, sp. nov. that are new to science. For distinct characteristics, V.siamensis is characterised by having a cylindrical penis and honeycomb-like glans, V.semicerina sp. nov. has a lanceolate penis with half honeycomb-like glans, and V.crispa sp. nov. has a cylindrical penis with wavy-like glans. In addition, more detailed descriptions of the radula and genitalia of all three species and their distribution are also carefully presented, enhancing the understanding of this leatherleaf slug genus in Thailand.}, }
@article {pmid39309166, year = {2024}, author = {Srisonchai, R and Likhitrakarn, N and Sutcharit, C and Wesener, T}, title = {Integrative taxonomy reveals two new giant pill-millipedes of the genus Zephronia Gray, 1832 from eastern Thailand (Diplopoda, Sphaerotheriida, Zephroniidae).}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {29-64}, pmid = {39309166}, issn = {1313-2989}, abstract = {A large amount of material of the millipede genus Zephronia Gray, 1832 was collected during 2014-2023 from many parts of eastern Thailand. An integrative study of morphological characters and genetic data (COI gene) revealed two new species: Z.chantaburiensis Srisonchai &amp; Wesener, sp. nov. and Z.macula Srisonchai &amp; Wesener, sp. nov. The two new species clearly differ from other congeners by their unique characteristics, especially in their colour pattern and telopod shape. The interspecific genetic distances of the 658 bp COI gene barcoding fragment between these new species and all other species of giant pill-millipede from Thailand, Laos and Cambodia are 12.01-23.49% for Z.chantaburiensis sp. nov. and 17.93-25.13% for Z.macula sp. nov. While relationships among species remain preliminary, the phylogenetic tree shows that species of Zephronia are interspersed with species of Sphaerobelum Verhoeff, 1924 and Prionobelum Verhoeff, 1924. Phylogenetic analyses place both new species in a clade termed Zephronia s.s., which receives support also from morphological data, showing a unique position of the organ of Tömösváry. Z.macula sp. nov. appears to occur over a broad distribution whereas Z.chantaburiensis sp. nov. was found only at the type locality. Given that all known records are in the eastern part of Thailand, we thus regard both species as endemic. Morphological illustrations based on SEM micrographs and a distribution map are also provided.}, }
@article {pmid39308990, year = {2024}, author = {Nocella, E and Fassio, G and Zuccon, D and Puillandre, N and Modica, MV and Oliverio, M}, title = {From coral reefs into the abyss: the evolution of corallivory in the Coralliophilinae (Neogastropoda, Muricidae).}, journal = {Coral reefs (Online)}, volume = {43}, number = {5}, pages = {1285-1302}, pmid = {39308990}, issn = {1432-0975}, abstract = {UNLABELLED: In this study, we delved into the interaction between corallivorous marine gastropods, the muricid Coralliophilinae Chenu, 1859, and their cnidarian food targets. Coralliophilinae is a subfamily of specialised corallivorous caenogastropods that feed by browsing on octocorals or hexacorals. Only sparse information is available on the phylogenetic relationships and the degree of specificity of the trophic relationships within this corallivorous lineage. To address these gaps, we generated the largest molecular dataset to date, comprising two mitochondrial (cox1 and 16S rDNA) and one nuclear gene (ITS2 rDNA) from 586 specimens collected worldwide. The coral hosts of coralliophilines were identified through an integrative approach, combining literature data with new records, employing morphological and/or molecular markers, and incorporating data from DNA barcoding of the snail stomach content. Our comprehensive approach unveiled the existence of numerous cryptic species in Coralliophilinae, while the phylogeny showed that most of the currently accepted genera are not monophyletic. The molecular dating confirmed the origin of the Coralliophilinae in Middle Eocene, with diversification of most lineages during the Miocene. Our results indicate that the subfamily's ancestor evolved in shallow waters in association with Scleractinia. Through the evolutionary history of Coralliophilinae, multiple host shifts to other cnidarian orders were observed, not correlated with changes in the depth range. The results of diversification analyses within the subfamily further suggest that the association with the host has influenced the evolutionary patterns of Coralliophilinae, but not vice versa.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-024-02537-1.}, }
@article {pmid39306191, year = {2024}, author = {Seyedabadi, M and Gurevich, VV}, title = {Flavors of GPCR signaling bias.}, journal = {Neuropharmacology}, volume = {261}, number = {}, pages = {110167}, doi = {10.1016/j.neuropharm.2024.110167}, pmid = {39306191}, issn = {1873-7064}, mesh = {*Receptors, G-Protein-Coupled/metabolism ; Humans ; *Signal Transduction/physiology/drug effects ; Animals ; Ligands ; GTP-Binding Proteins/metabolism ; }, abstract = {GPCRs are inherently flexible molecules existing in an equilibrium of multiple conformations. Binding of GPCR agonists shifts this equilibrium. Certain agonists can increase the fraction of active-like conformations that predispose the receptor to coupling to a particular signal transducer or a select group of transducers. Such agonists are called biased, in contrast to balanced agonists that facilitate signaling via all transducers the receptor couples to. These biased agonists preferentially channel the signaling of a GPCR to particular G proteins, GRKs, or arrestins. Preferential activation of particular G protein or arrestin subtypes can be beneficial, as it would reduce unwanted on-target side effects, widening the therapeutic window. However, biasing GPCRs has two important limitations: a) complete bias is impossible due to inherent flexibility of GPCRs; b) receptor-independent functions of signal transducer proteins cannot be directly affected by GPCR ligands or differential receptor barcoding by GRK phosphorylation. This article is part of the Special Issue on "Ligand Bias".}, }
@article {pmid39303852, year = {2024}, author = {Yanar, A and Kamanli, SA and Sönmez, S and Hamdi, &#x130; and Özak, AA and Boxshall, GA}, title = {Caligus minimus Otto, 1821 (Copepoda: Caligidae): A commercially important but poorly described parasite of cultured European Sea Bass, Dicentrarchus labrax (Linnaeus, 1758).}, journal = {Parasitology international}, volume = {104}, number = {}, pages = {102964}, doi = {10.1016/j.parint.2024.102964}, pmid = {39303852}, issn = {1873-0329}, abstract = {Caligus minimus Otto, 1821 has been known for over two centuries and it is the second oldest of the approximately 275 species of Caligus O. F. Müller, 1985. Despite the numerous records of this species from European waters, it has never been fully described to modern standards. The lack of a comprehensive modern description has resulted in numerous misidentifications, even in recently published reports, and this is especially problematic for a species that is known to have a significant economic impact in aquaculture. This study presents a detailed description of both sexes and documents newly observed features of C. minimus collected from the buccal cavity of farmed European Sea Bass (ESB), Dicentrarchus labrax (Linnaeus, 1758). The morphology of C. minimus was examined using light microscope (LM), scanning electron microscope (SEM), and confocal laser scanning microscope (CLSM), and new details are revealed regarding the structure and ornamentation of the marginal membrane of the cephalothorax, maxilliped, antenna, sternal furca, abdomen, and legs 1, 3, 4, and 6. The ornamentation of the marginal membrane of the cephalothorax is unique and its impact on the functioning of the cephalothoracic sucker requires further investigation. Additionally, partial COI gene region sequences were obtained from four individuals of C. minimus and provided for future references. A phylogenetic analysis was conducted in conjunction with Caligus sequences available in the NCBI GenBank database.}, }
@article {pmid39302606, year = {2024}, author = {Krishnan, S and Ulagesan, S and Moon, JS and Choi, YH and Nam, TJ}, title = {Establishment, characterization, and sensory characteristics (taste and flavor) of an immortalized muscle cell line from the seven-band grouper Epinephelus septemfasciatus: implications for cultured seafood applications.}, journal = {In vitro cellular &amp; developmental biology. Animal}, volume = {}, number = {}, pages = {}, pmid = {39302606}, issn = {1543-706X}, support = {201803932//Future Fisheries Food Research Centre' funded by the Korea Institute of Marine Science and Technology (KIMST) promotions, Ministry of Oceans and Fisheries, Republic of Korea/ ; }, abstract = {Grouper muscle satellite cells (GMSCs) from the seven-band grouper (Epinephelus septemfasciatus) were isolated, and their growth conditions were optimized (10% fetal bovine serum, 24°C, 10 ng/mL bFGF). The cells were immortalized at passage 14 and designated as grouper immortalized muscle satellite cells (GIMSCs). DNA barcoding confirmed the grouper origin of both GMSC and GIMSC lines. GIMSCs exhibited enhanced proliferation, accelerated differentiation, and robust myotube formation compared to pre-crisis GMSCs. Western blot analysis showed upregulation of key myogenic factors (Pax7, MyoD, MyoG) and structural proteins (Desmin) in GIMSC, indicating the differentiation potential. The immortalized GIMSC line maintained consistent morphology, growth rates, and viability across multiple passages. Biocompatibility studies showed GIMSCs were compatible with bio-inks (sodium alginate, gelatin, κ-carrageenan) at 250 to 10,000 µg/mL, retaining ~ 80% viability at the highest concentration. Taste sensory analysis revealed GMSCs had the highest umami and lowest saltiness and sourness, contrasting with the muscle of the seven-band grouper, which had higher saltiness and sourness. Flavor analysis identified pronounced fishy, hot fat, and ethereal flavors in the cells at higher level than in the muscle. These findings suggest GMSCs and GIMSCs are promising for producing cultured meat with enhanced umami taste and flavors, advancing cellular agriculture and sustainable food production.}, }
@article {pmid39298427, year = {2024}, author = {Saiperaki, JL and Materu, SF and Mkenda, PA and Ligate, EJ and Rumisha, C}, title = {Field and DNA-barcode based surveys reveal evidence of rare endemic fishes in the Rufiji River Basin.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0310387}, pmid = {39298427}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Rivers ; *Fishes/genetics/classification ; Conservation of Natural Resources ; Fisheries ; Biodiversity ; }, abstract = {Endemic fish species have long supported the livelihoods of local communities in the Rufiji River Basin (RRB). However, destructive fishing practices have led to a concerning decline in endemic fish stocks. To assess these changes, this study employed key informant interviews, focus group discussions (FGDs), and fishery surveys to assess the historical and contemporary distribution of endemic fishes within the RRB. DNA barcoding was also used to verify species identities. Out of 37 reported fish species, 33 species (54.55% endemic and 45.45% exotic to RRB) were confirmed through DNA barcoding and morphological characteristics. About 5 species including, Heterobranchus longifilis, Citharinus congicus, Labeo congoro, Mormyrus longirostris, and Labeobarbus leleupanus were rarely found in the field, despite being classified as Least Concern by IUCN. Additionally, five species that were reported to be present in the RRB by experienced fishers were not captured during sampling. This highlights the need for validation of the existence of such species through eDNA metabarcoding. Moreover, due to the rarity of some species in the area, their IUCN assessment should be revisited.}, }
@article {pmid39296989, year = {2024}, author = {Caboňová, M and Vadkertiová, R and Adamčík, S and Bacigálová, K and Slovák, M and Zaib, S and Caboň, M}, title = {Taxonomic reintroduction of Taphrinaviridis (Taphrinales, Ascomycota) associated with Alnusalnobetula as one of five well defined European species colonizing alders.}, journal = {MycoKeys}, volume = {108}, number = {}, pages = {249-267}, pmid = {39296989}, issn = {1314-4049}, abstract = {Phylogenetic analysis of four DNA regions (ITS, LSU, mtSSU and tef1α) supported the existence of five European Taphrina species which colonise Alnus in Europe. In addition to previously well-defined species, T.viridis is, for the first time recognised, by molecular study as a species related to T.sadebeckii. Analysis of publicly available sequences of barcoding regions suggested that T.viridis is only associated with A.alnobetula and no other Taphrina species colonize this host tree. Symptomatic, morphological, and physiological characterisation of T.viridis are provided together with the key for identification of Alnus associated Taphrina species in Europe and North America.}, }
@article {pmid39293535, year = {2024}, author = {Rosenmai, AK and Svingen, T and Evrard, B and Nguyen, KH and Nielsen, C and Axelstad, M and Chalmel, F and Ramhøj, L}, title = {Distinct transcriptional profiles in rat thyroid glands after developmental exposure to three in vitro thyroperoxidase inhibiting chemicals.}, journal = {Genomics}, volume = {116}, number = {5}, pages = {110938}, doi = {10.1016/j.ygeno.2024.110938}, pmid = {39293535}, issn = {1089-8646}, mesh = {Animals ; *Thyroid Gland/metabolism/drug effects ; Rats ; *Iodide Peroxidase/genetics/metabolism ; Male ; *Transcriptome/drug effects ; Amitrole/pharmacology ; Enzyme Inhibitors/pharmacology ; Benzimidazoles/pharmacology ; }, abstract = {Thyroperoxidase (TPO) is central in thyroid hormone (TH) synthesis and inhibition can lead to TH deficiency. Many chemicals can inhibit TPO activity in vitro, but how this may manifest in the developing thyroid gland at the molecular level is unclear. Here, we characterized the thyroid gland transcriptome of male rats developmentally exposed to the in vitro TPO-inhibitors amitrole, 2-mercaptobenzimidazole (MBI), or cyanamide by use of Bulk-RNA-Barcoding (BRB) and sequencing. Amitrole exposure caused TH deficiency and 149 differentially expressed genes in the thyroid gland. The effects indicated an activated and growing thyroid gland. MBI caused intermittent changes to serum TH concentrations in a previous study and this was accompanied by 60 differentially expressed genes in the present study. More than half of these were also affected by amitrole, indicating that they could be early effect biomarkers of developmental TH system disruption due to TPO inhibition. Further work to validate the signature is needed, including assessment of substance independency and applicability domain.}, }
@article {pmid39293082, year = {2024}, author = {Liu, B and Klatt, D and Zhou, Y and Manis, JP and Sauvageau, G and Pellin, D and Brendel, C and Williams, DA}, title = {UM171 enhances fitness and engraftment of gene-modified hematopoietic stem cells from patients with sickle cell disease.}, journal = {Blood advances}, volume = {8}, number = {22}, pages = {5885-5895}, doi = {10.1182/bloodadvances.2024013932}, pmid = {39293082}, issn = {2473-9537}, mesh = {Humans ; *Hematopoietic Stem Cells/metabolism/cytology ; *Anemia, Sickle Cell/therapy ; Animals ; *Hematopoietic Stem Cell Transplantation/methods ; Mice ; Antigens, CD34/metabolism ; Lentivirus/genetics ; Transduction, Genetic ; Genetic Vectors ; Indoles ; Pyrimidines ; }, abstract = {Hematopoietic stem cell (HSC) transplantation with lentiviral vector (LVV)-transduced autologous cells has proven an effective therapeutic strategy for sickle cell disease (SCD). However, ex vivo culture or proliferative stress associated with in vivo reconstitution may amplify any underlying genetic risk of leukemia. We aimed to minimize culture-induced stress and reduce genomic damage during ex vivo culture and enhance stem cell fitness and reconstitution of SCD CD34+ cells transduced with BCL11A shmiR-encoding LVV. UM171, a pyrimidoindole derivative, can expand normal HSCs during in vitro culture and has been shown to be safe and effective using umbilical cord blood. We examined the effect of UM171 during ex vivo LVV transduction of SCD HSCs. Culture of SCD CD34+ HSCs with UM171 during transduction reduced DNA damage and reactive oxygen species, decreased apoptosis, and was associated with increased numbers of immunophenotypically defined long-term HSCs. UM171 increased the engraftment of LVV-transduced human HSCs in immunodeficient mice and barcode tracing revealed increased clonal diversity of engrafting cells. In competitive transplantation assays, analysis of bone marrow showed that cells transduced in the presence of UM171 consistently outcompeted those transduced under control conditions. In summary, exposure of SCD peripheral blood CD34+ cells to UM171 during LVV transduction enhances stem cell fitness. These findings suggest manufacturing of genetically modified HSCs in the presence of UM171 may improve efficacy, safety, and sustainability of gene therapy using ex vivo approaches. BCL11A shmiR-encoding LVV is in clinical trials to treat SCD (NCT03282656), UM171 is in clinical trials to culture umbilical cord blood (NCT02668315).}, }
@article {pmid39290075, year = {2024}, author = {Sato, H and Lain, A and Mizuno, T and Yamashita, S and Hassan, JB and Othman, KB and Itioka, T}, title = {Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest.}, journal = {Molecular ecology}, volume = {33}, number = {21}, pages = {e17529}, doi = {10.1111/mec.17529}, pmid = {39290075}, issn = {1365-294X}, support = {JPMJSA190//Science and Technology Research Partnership for Sustainable Development/ ; 20K06796//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/genetics/classification ; *Rainforest ; Malaysia ; Dipterocarpaceae/microbiology ; DNA Barcoding, Taxonomic ; Host Specificity ; Symbiosis/genetics ; Phylogeny ; Trees/microbiology ; }, abstract = {Ectomycorrhizal (ECM) fungi are important tree symbionts within forests. The biogeography of ECM fungi remains to be investigated because it is challenging to observe and identify species. Because most ECM plant taxa have a Holarctic distribution, it is difficult to evaluate the extent to which host preference restricts the global distribution of ECM fungi. To address this issue, we aimed to assess whether host preference enhances the endemism of ECM fungi that inhabit dipterocarp rainforests. Highly similar sequences of 175 operational taxonomic units (OTUs) for ECM fungi that were obtained from Lambir Hill's National Park, Sarawak, Malaysia, were searched for in a nucleotide sequence database. Using a two-step binomial model, the probability of presence for the query OTUs and the registration rate of barcode sequences in each country were simultaneously estimated. The results revealed that the probability of presence in the respective countries increased with increasing species richness of Dipterocarpaceae and decreasing geographical distance from the study site (i.e. Lambir). Furthermore, most of the ECM fungi were shown to be endemic to Malaysia and neighbouring countries. These findings suggest that not only dispersal limitation but also host preference are responsible for the high endemism of ECM fungi in dipterocarp rainforests. Moreover, host preference likely determines the areas where ECM fungi potentially expand and dispersal limitation creates distance-decay patterns within suitable habitats. Although host preference has received less attention than dispersal limitation, our findings support that host preference has a profound influence on the global distribution of ECM fungi.}, }
@article {pmid39287819, year = {2024}, author = {Pachalil, VT and Gupta, B and Maile, A and Sunish, IP}, title = {Molecular characterization of anopheline species diversity in the Andaman and Nicobar archipelago, with a particular emphasis on Anopheles barbirostris.}, journal = {Parasitology research}, volume = {123}, number = {9}, pages = {325}, pmid = {39287819}, issn = {1432-1955}, mesh = {Animals ; *Anopheles/genetics/classification ; *RNA, Ribosomal, 28S/genetics ; *DNA, Ribosomal Spacer/genetics ; *Electron Transport Complex IV/genetics ; *Phylogeny ; *Genetic Variation ; Biodiversity ; Sequence Analysis, DNA ; Cluster Analysis ; Molecular Sequence Data ; DNA, Ribosomal/genetics ; Islands ; }, abstract = {This study investigates anopheline species diversity in the Andaman and Nicobar Islands, employing morphological and molecular methods, focusing on the D3 domain of 28S rRNA (D3) and second internal spacer (ITS2). Ten Anopheline species were identified morphologically and confirmed with molecular markers. While the D3 region demonstrated low level of inter- and intra-specific genetic distance in all the species, ITS2 revealed clear barcoding gap. Among the ten species, A. barbirostris exhibited significant diversity when compared with the sequences from other countries available in GenBank. Further analyses of additional samples of A. barbirostris were carried out using ITS2 and cytochrome oxidase I (COI) markers. Limited variations among the sequences from the islands were observed, suggesting a prevalent single molecular form. However, when compared with the GenBank sequences, our samples formed a separate cluster closely related to the A3 species. The genetic distance between our samples and the A3 cluster was 0.02 for COI but very high (0.104) for ITS2, suggesting a potentially new molecular form or species in the island region. This warrants a more comprehensive and detailed analysis of A. barbirostris in these islands at both genetic and morphometric levels. Overall, these observations added-up the new knowledge in the understanding of anopheline diversity in the Andaman and Nicobar archipelago and highlight the necessity for continuous molecular investigations to unravel complexities within mosquito population dynamics.}, }
@article {pmid39285627, year = {2024}, author = {Salis, R and Sunde, J and Gubonin, N and Franzén, M and Forsman, A}, title = {Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity.}, journal = {Molecular ecology resources}, volume = {24}, number = {8}, pages = {e14018}, doi = {10.1111/1755-0998.14018}, pmid = {39285627}, issn = {1755-0998}, support = {//Crafoordska Stiftelsen/ ; 2020-03519//Vetenskapsr&#xe5;det/ ; 2018-02846//Svenska Forskningsr&#xe5;det Formas/ ; 2021-02142//Svenska Forskningsr&#xe5;det Formas/ ; }, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; *Insecta/genetics/classification/anatomy &amp; histology ; Wasps/genetics/classification/anatomy &amp; histology ; }, abstract = {For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.}, }
@article {pmid39285331, year = {2024}, author = {Zhang, Y and Song, M and Tang, D and Li, X and Xu, N and Li, H and Qu, L and Wang, Y and Yin, C and Zhang, L and Zhang, Z}, title = {Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {867}, pmid = {39285331}, issn = {1471-2229}, support = {2021-I2M-1-032//Yunnan "Xingdian Talent Support Program " young talents special project and CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; }, mesh = {*Genome, Chloroplast ; *Phylogeny ; Genetic Markers ; Base Composition ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Lasianthus species are widely used in traditional Chinese folk medicine with high medicinal value. However, source materials and herbarium specimens are often misidentified due to morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Lasianthus species. To improve the molecular methods for distinguishing among Lasianthus species, we report the complete chloroplast (CP) genomes of Lasianthus attenuatus, Lasianthus henryi, Lasianthus hookeri, Lasianthus sikkimensis, obtained via high-throughput Illumina sequencing.<br><br>RESULTS: These showed CP genomes size of 160164-160246&#xa0;bp and a typical quadripartite structure, including a large single-copy region (86675-86848&#xa0;bp), a small single-copy region (17177-17326&#xa0;bp), and a pair of inverted repeats (28089-28135&#xa0;bp). As a whole, the gene order, GC content and IR/SC boundary structure were remarkably similar among of the four Lasianthus CP genomes, the partial gene length and IR, LSC and SSC regions length are still different. The average GC content of the CP genomes was 36.71-36.75%, and a total of 129 genes were detected, including 83 different protein-coding genes, 8 different rRNA genes and 38 different tRNA genes. Furthermore, we compared our 4 complete CP genomes data with publicly available CP genome data from six other Lasianthus species, and we initially screened eleven highly variable region fragments were initially screened. We then evaluated the identification efficiency of eleven highly variable region fragments and 5 regular barcode fragments. Ultimately, we found that the optimal combination fragment' ITS2&#x2009;+&#x2009;psaI-ycf4' could authenticated the Lasianthus species well. Additionally, the results of genome comparison of Rubiaceae species showed that the coding region is more conservative than the non-coding region, and the ycf1 gene shows the most significant variation. Finally, 49 species of CP genome sequences belonging to 16 genera of the Rubiaceae family were used to construct phylogenetic trees.<br><br>CONCLUSIONS: Our research is the first to analyze the chloroplast genomes of four species of Lasianthus in detail and we ultimately determined that the combination fragment' ITS2&#x2009;+&#x2009;psaI-ycf4' is the optimal barcode combination for identifying the genus of Lasianthus. Meanwhile, we gathered the available CP genome sequences from the Rubiaceae and used them to construct the most comprehensive phylogenetic tree for the Rubiaceae family. These investigations provide an important reference point for further studies in the species identification, genetic diversity, and phylogenetic analyses of Rubiaceae species.}, }
@article {pmid39282932, year = {2024}, author = {Sun, L and Liu, M and Gong, Y and Zhai, K and Lv, F and He, L and Xue, X and Liu, X and Wang, H and Fan, D and You, Y and Fang, M and Sun, L and Xu, J and Zhang, J}, title = {Rapid Antimicrobial Susceptibility Test of Helicobacter pylori to Metronidazole via Single-Cell Raman Spectrometry.}, journal = {Helicobacter}, volume = {29}, number = {5}, pages = {e13136}, doi = {10.1111/hel.13136}, pmid = {39282932}, issn = {1523-5378}, support = {//Financial&#x2009;Special&#x2009;Fund/ ; //Project for software development and expansive application of Chinese Helicobacter pylori antimicrobial resistance dynamic map/ ; //Project for new techniques exploration for bacterial pathogens laboratory detection/ ; //National Natural Science Foundation of China/ ; //Project for collaborative research on analysis of Helicobacter pylori infection and gut flora changes/ ; }, mesh = {*Helicobacter pylori/drug effects ; *Metronidazole/pharmacology ; *Spectrum Analysis, Raman/methods ; *Microbial Sensitivity Tests/methods ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy/diagnosis ; Single-Cell Analysis/methods ; Drug Resistance, Bacterial ; }, abstract = {BACKGROUND: Metronidazole is a first-line antibiotic to treat Helicobacter pylori infections. However, the Clinical Laboratory Standards Institute guidelines recommend against using antimicrobial susceptibility test (AST) to test metronidazole resistance, due to the unreliable predictive power which can result in treatment failure.<br><br>OBJECTIVES: The aim of this study was to establish an 8-h, metabolic-phenotype based AST for H. pylori metronidazole susceptibility using D2O-probed Raman microspectroscopy.<br><br>METHODS: Minimal inhibitory concentration (MIC) measured by conventional AST (E-test) were compared with expedited MIC via metabolic activity (eMIC-MA) for 10 H. pylori isolates. Raman barcodes of cellular-response to stress (RBCS) incorporating protein and carbohydrate Raman bands, were utilized to identify a biomarker to distinguish metronidazole susceptibility.<br><br>RESULTS: Specifically, eMIC-MA produces metronidazole susceptibility results showing 100% agreement with E-test, and determines the bactericidal dosage for both high- and low-level resistant H. pylori strains. In addition, RBCS not just reliably distinguish between metronidazole-susceptible and -resistant strains, but reveal their distinct mechanisms in bacterial responses to metronidazole.<br><br>CONCLUSION: The speed, accuracy, low cost, and rich information content that reveals the mode-of-action of drugs suggest the method's value in guiding metronidazole prescriptions for H. pylori eradication and in rapid screening based on drug-resistance mechanism.}, }
@article {pmid39282286, year = {2024}, author = {Wu, JW and Yang, JM and Chen, CC and Au, G and Wang, S and Chern, GW and Huang, CH}, title = {Calibration of FRET-based biosensors using multiplexed biosensor barcoding.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.04.610346}, pmid = {39282286}, issn = {2692-8205}, support = {P50 CA098252/CA/NCI NIH HHS/United States ; R01 GM136711/GM/NIGMS NIH HHS/United States ; }, abstract = {Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) is widely used in the design of genetically encoded fluorescent biosensors, which are powerful tools for monitoring the dynamics of biochemical activities in live cells. FRET ratio, defined as the ratio between acceptor and donor signals, is often used as a proxy for the actual FRET efficiency, which must be corrected for signal crosstalk using donor-only and acceptor-only samples. However, the FRET ratio is highly sensitive to imaging conditions, making direct comparisons across different experiments and over time challenging. Inspired by a method for multiplexed biosensor imaging using barcoded cells, we reasoned that calibration standards with fixed FRET efficiency can be introduced into a subset of cells for normalization of biosensor signals. Our theoretical analysis indicated that the FRET ratio of high-FRET species relative to non-FRET species slightly decreases at high excitation intensity, suggesting the need for calibration using both high and low FRET standards. To test these predictions, we created FRET donor-acceptor pairs locked in "FRET-ON" and "FRET-OFF" conformations and introduced them into a subset of barcoded cells. Our results confirmed the theoretical predictions and showed that the calibrated FRET ratio is independent of imaging settings. We also provided a strategy for calculating the FRET efficiency. Together, our study presents a simple strategy for calibrated and highly multiplexed imaging of FRET biosensors, facilitating reliable comparisons across experiments and supporting long-term imaging applications.}, }
@article {pmid39281619, year = {2024}, author = {Lee, YJ and Phang, GJ and Chen, CC and Ou, JH and Fan, YH and Huang, YT}, title = {Optimal liquid-based DNA preservation for DNA barcoding of field-collected fungal specimens.}, journal = {Heliyon}, volume = {10}, number = {17}, pages = {e36829}, pmid = {39281619}, issn = {2405-8440}, abstract = {Preserving fungal tissue DNA in the field is essential for molecular ecological research, enabling the study of fungal biodiversity and community dynamics. This study systematically compares two liquid-based preservation solutions, RNAlater and DESS, for their effectiveness in maintaining macrofungi DNA integrity during field collection and storage. The research encompasses both controlled experiments and real-world field collections. In the controlled experiments, two fungal species were preserved in RNAlater and DESS at different temperatures and durations. DNA extraction success rates were high, but DNA quality and quantity metrics exhibited variations across samples. However, both preservation solutions demonstrated their viability for preserving fungal DNA, with no significant differences between them. In the field-collected macrofungi experiment, 160 paired fungal specimens were preserved in RNAlater and DESS, respectively. Including a drying process to facilitate tissue lysis for DNA extraction significantly impacted the outcomes. RNAlater showed a higher success rate and better DNA quality and quantity compared to DESS. Statistical analysis, including paired and independent t-tests, confirmed significant differences in DNA quality and quantity between the two preservation methods for field-collected samples. This study evaluates RNAlater and DESS for preserving macrofungi DNA in field conditions. Both methods are effective, but RNAlater is superior when a drying step is included in DNA extraction. Researchers can choose based on their specific needs without compromising DNA integrity. These findings advance fungal molecular ecology and DNA preservation strategies in ecological and environmental studies.}, }
@article {pmid39279612, year = {2024}, author = {Biswas, A and Cencillo-Abad, P and Chanda, D}, title = {Multispectral Molecular Chiral Barcoding.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {36}, number = {45}, pages = {e2409565}, doi = {10.1002/adma.202409565}, pmid = {39279612}, issn = {1521-4095}, support = {ECCS-1800845//National Science Foundation/ ; }, abstract = {More than half of pharmaceutical drugs in use are chiral, necessitating accurate techniques for their characterization. Enantiomers, molecules with mirrored symmetry, often exhibit similar physical traits but possess distinct chemical and biological implications. This study harnesses the strong light-matter interaction induced by "superchiral" light to perform Surface-Enhanced Infrared Absorption (SEIRA) induced vibrational circular dichroism measurements in the mid-infrared spectral region. Utilizing a nanopatterned pixelated array of achiral plasmonic nanostructures, the system allows unique identification of enantiomers and biomolecules. Tunability of plasmon resonance facilitates spectral variation of the optical chirality over a wide infrared range, enabling development of a unique chiral "barcoding" scheme to distinguish chiral molecules based on their infrared fingerprint. This simple, yet robust sensor presents a low-cost solution for chiral mapping of drugs and biomolecules.}, }
@article {pmid39278523, year = {2024}, author = {Hoxha, I and Trájer, AJ and Dvorak, V and Halada, P and Šupić, J and Obwaller, AG and Poeppl, W and Walochnik, J and Alić, A and Kniha, E}, title = {Phlebotomine sand flies (Diptera: Psychodidae) of Bosnia and Herzegovina: distribution, ecology and environmental preferences.}, journal = {Acta tropica}, volume = {260}, number = {}, pages = {107393}, doi = {10.1016/j.actatropica.2024.107393}, pmid = {39278523}, issn = {1873-6254}, abstract = {Sand flies (Diptera: Phlebotominae) are the principal vectors for the protozoan parasites Leishmania spp. and for phleboviruses. The sand fly fauna on the Balkan Peninsula, including Bosnia and Herzegovina (BIH), is diverse and the circulation of Leishmania infantum as well as phleboviruses has been proven. However, recent data on the sand fly fauna in BIH are scarce. In this study, we surveyed understudied regions in central and northeastern BIH to update the sand fly distribution and gain insights into the ecological and environmental factors shaping their appearance. CDC light trapping was conducted in 2022 and 2023 and a combination of morphological and molecular methods (cytochrome oxidase I barcoding) was performed for species identifications. We mapped the currently known distribution, modelled climatic suitability patterns and performed environmental analyses by applying machine learning methods. In addition, we analyzed blood meals by host gene sequencing and MALDI-TOF peptide mass mapping and screened for Leishmania spp. DNA and Phlebovirus RNA. Altogether, 591 sand