@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 {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.},
}

*DNA Barcoding, Taxonomic
*Ferns/genetics/classification
*Biodiversity
*Phylogeny
DNA, Plant/genetics

@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 & 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 {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.},
}

*Electron Transport Complex IV/genetics
*Leishmania/genetics/enzymology/classification
*DNA Barcoding, Taxonomic/methods
*Phylogeny
Species Specificity

@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, Ž 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.

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.},
}

*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

@article {pmid39616387,
year = {2024},
author = {Huang, G and Peng, X},
title = {Genus Bithynia: morphological classification to molecular identification.},
journal = {Parasites & 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.},
}

Animals
*Snails/parasitology
Trematode Infections/parasitology/veterinary
Phylogeny
Humans

@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 & 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.},
}

Animals
*Goats/microbiology
Thailand/epidemiology
*Mycoplasma/genetics/isolation & purification
*Siphonaptera/microbiology
Goat Diseases/microbiology/epidemiology
Mycoplasma Infections/veterinary/epidemiology/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny

@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 & Peng, 2023 were recognised, based on the morphological characteristics and molecular evidence.

NEW INFORMATION: A new species of Phintella Strand, 1906 is described: P.hongkan sp. nov. (♂♀) from Hainan, China. The unknown female of P.liae Wang, Mi & 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.

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 bp for C. bicornutum and 156,905 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 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.

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.},
}

*Phylogeny
Animals
*Orchidaceae/genetics/classification
Genome, Plastid
Ants/genetics/classification
Plastids/genetics
Symbiosis
Gryllidae

@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.

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.

RESULTS: Our findings revealed only two haplotypes, suggesting low genetic variability in a parasite that arrived in the Americas with the Spanish colonization.

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 Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_179125//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_159709//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 316030_150817//Schweizerischer Nationalfonds zur Förderung 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.},
}

*Foraminifera/genetics/classification
*DNA Barcoding, Taxonomic
RNA, Ribosomal, 18S/genetics
DNA, Ribosomal/genetics

@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 Förderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics/isolation & purification ; Humans ; Bacteria/genetics/isolation & 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.},
}

*Metagenomics/methods
*Nanopore Sequencing/methods
*Drug Resistance, Bacterial/genetics
DNA, Bacterial/genetics/isolation & purification
Humans
Bacteria/genetics/isolation & purification/classification

@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.},
}

*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

@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 {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 {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.

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.

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.

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).

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 & 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.

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.

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.

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.},
}

*Phylogeny
*Genome, Plastid
Kazakhstan
*Tulipa/genetics
Microsatellite Repeats/genetics
Plastids/genetics
RNA, Transfer/genetics
Whole Genome Sequencing/methods

@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.},
}

*Juglans/genetics/classification
*Phylogeny
*Genotype
Genetic Markers/genetics
DNA Barcoding, Taxonomic/methods
Pakistan

@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.},
}

*Genome, Mitochondrial
*Phylogeny
*Trichoderma/genetics
*Molecular Sequence Annotation
RNA, Transfer/genetics
Base Composition/genetics
Evolution, Molecular
Introns/genetics

@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 & 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.},
}

*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 & purification
Escherichia coli Infections/microbiology/epidemiology/diagnosis
Sequence Analysis, DNA/methods
Pilot Projects

@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 & 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 & 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 Tecnologías/ ; 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 Investigación 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.},
}

*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

@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.},
}

Humans
*Neurosciences
*Brain/metabolism
Proteomics
Transcriptome
High-Throughput Nucleotide Sequencing
Animals
Genomics
In Situ Hybridization, Fluorescence
Neurons/metabolism
Epigenomics

@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//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; code 406489/2023-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
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.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Brazil
*Electron Transport Complex IV/genetics
*Phylogeny
Biodiversity
RNA, Ribosomal, 16S/genetics
Caribbean Region
Genetic Variation
Fishes/genetics/classification

@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.

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 > 40 × 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).

RESULTS: Comparison of wgMLST profiles based on long-read and short-read WGS data revealed > 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.

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.},
}

*Drug Resistance, Multiple, Bacterial/genetics
Humans
*Genome, Bacterial
Genomics/methods
High-Throughput Nucleotide Sequencing/methods
Bacteria/genetics/drug effects/classification
Whole Genome Sequencing/methods

@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 & 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.},
}

Animals
*Anura/genetics/physiology
*Hybridization, Genetic
Reproductive Isolation
Vocalization, Animal/physiology
Polymorphism, Single Nucleotide
Genomics/methods
Gene Flow
France

@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.},
}

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

@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.

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.},
}

Sri Lanka
*Environmental Monitoring/methods
*Ecosystem
*Fungi
*Biodiversity
Lichens
Climate Change
Bryophyta

@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.},
}

Animals
Brazil
*DNA Barcoding, Taxonomic
*Genetic Variation/genetics
*Characidae/genetics/classification
*Haplotypes/genetics
Phylogeny
Bayes Theorem
DNA, Mitochondrial/genetics

@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 & 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 & nanoengineering},
volume = {10},
number = {1},
pages = {172},
pmid = {39567484},
issn = {2055-7434},
support = {UH3TR002978//U.S. Department of Health & 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 & Human Services | National Institutes of Health (NIH)/ ; R01GM141055//U.S. Department of Health & 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.},
}

Animals
*Butterflies/genetics
Taiwan
*Earthquakes
DNA Barcoding, Taxonomic
Haplotypes
Phylogeny
DNA, Mitochondrial/genetics
Electron Transport Complex IV/genetics
Female
Male

@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 & 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 & 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.

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.

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' = 3.044) than in the S. asakoae complex (H' = 1.920). Regression analysis revealed that Leucocytozoon diversity was positively related to black fly abundance and negatively related to maximum air temperature.

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.},
}

Animals
Thailand/epidemiology
*Simuliidae/parasitology/classification
*Haemosporida/isolation & 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

@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 & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U01-AI160418//U.S. Department of Health & 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.},
}

*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

@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.

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.},
}

*Single-Cell Analysis/methods
Humans
Sequence Analysis, RNA/methods
Genotype
Genotyping Techniques/methods
Computational Biology/methods
Mitochondria/genetics/metabolism

@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 & 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 & control/transmission ; *Leishmania donovani/genetics/isolation & 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.},
}

Animals
*Leishmaniasis, Visceral/epidemiology/parasitology/prevention & control/transmission
*Leishmania donovani/genetics/isolation & purification
India/epidemiology
Cross-Sectional Studies
*Insect Vectors/parasitology
Psychodidae/parasitology
Phlebotomus/parasitology
Humans
Disease Eradication/methods

@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.},
}

*DNA Barcoding, Taxonomic/methods
*Plants, Medicinal/genetics/classification
*DNA, Plant/genetics

@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.

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 & 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 & DeLong, 1917) is redescribed, and a lectotype is designated to clarify the application of the name. Deltocephalusplagus Ball & DeLong, 1926 and Laevicephalusshingwauki Beamer & 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 & 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.},
}

Animals
*Heteroptera/genetics/classification/anatomy & histology
*Phylogeny
Europe
Male
Genome, Mitochondrial
DNA Barcoding, Taxonomic
Female

@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.

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.

RESULTS: The reading times for RFID-tagged surgical instruments in the skilled and unskilled groups were 64.0 ± 9.0s and 79.4 ± 17.0 s, respectively, whereas those for barcode-engraved surgical instruments were 190.4 ± 28.1 s and 212.3 ± 40.3 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 h/d for 250 d).

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.},
}

Humans
*Single-Cell Analysis/methods
*Gene Expression Profiling/methods
*Hematopoietic Stem Cells/metabolism/cytology
Cell Differentiation/genetics
Lentivirus/genetics
Single-Cell Gene Expression 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.

RESULTS: Urocystis heteropogonis was identified as a novel species, distinct from other Urocystis species. Morphologically, it is characterized by larger spore balls (14-69 × 11-45 μm) and central spores that are 14-28 × 11-20 μm in size, with each spore containing1-8 central spores. The spore walls measure 0.9-2.5 μm 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.

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.},
}

*Phylogeny
DNA, Fungal/genetics
Spores, Fungal/genetics
Pakistan
Animals

@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 & histology/classification ; Egypt ; Phylogeny ; DNA, Plant/genetics ; Plant Leaves/anatomy & 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.},
}

*DNA Barcoding, Taxonomic
*Ficus/genetics/anatomy & histology/classification
Egypt
Phylogeny
DNA, Plant/genetics
Plant Leaves/anatomy & histology/genetics/metabolism
Species Specificity

@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.},
}

Animals
*Larva/parasitology
*Triticum/parasitology
*Diptera/parasitology
*DNA Barcoding, Taxonomic/methods
Hymenoptera/genetics

@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 & 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.},
}

*Rosaceae/genetics
*Genotype
*Polymorphism, Genetic
*DNA Barcoding, Taxonomic/methods
Fruit/genetics/anatomy & histology
Pakistan
Phylogeny
DNA, Plant/genetics

@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.

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 and Parse techniques showed 10x data to have lower technical variability and more precise annotation of biological states in the thymus compared to Parse.

CONCLUSION: Our results provide a comprehensive comparison of the suitability of both single-cell platforms for immunological studies.},
}

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

@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.},
}

Humans
*Bias
Diagnostic Imaging/methods/standards
Image Processing, Computer-Assisted/methods/standards
Algorithms
Neural Networks, Computer
Radiology/methods/standards

@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.

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.

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.

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.

OBJECTIVE: The review evaluates DNA barcoding and common alternative testing in plant-related sectors to enhance quality assurance and accurate authentication.

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.

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.

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&M Triads for transformation/ ; //Texas A&M University Galveston/ ; //Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; //CONACYT- Texas A&M University/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //National Science Foundation/ ; //Texas A&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.},
}

*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