@article {pmid38761946,
year = {2024},
author = {Múrria, C and Wangensteen, OS and Somma, S and Väisänen, L and Fortuño, P and Arnedo, MA and Prat, N},
title = {Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {173243},
doi = {10.1016/j.scitotenv.2024.173243},
pmid = {38761946},
issn = {1879-1026},
abstract = {Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.},
}

@article {pmid38757413,
year = {2024},
author = {Tiono, YV and Prasetyo, AH and Wulanjati, MP and Wink, M and Nurcahyanti, ADR},
title = {Inhibition of oxidative stress of Biancaea sappan (L) Tod. from Java.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/14786419.2024.2355585},
pmid = {38757413},
issn = {1478-6427},
abstract = {Increased reactive oxygen species and advanced glycation end products are often associated with human ageing and degenerative diseases. Biancaea sappan L serves as a medicinal plant and a healthy drinks ingredient in Java. However, the pharmacological investigation of the plant native to this island is still lacking in depth. In the current study, DNA barcoding using the marker gene maturase K (matK), evaluation of the chemical composition, total phenolic content (TPC) and antioxidant properties, antiglycation, anti-β-amyloid, anti-inflammatory, and selective cytotoxic activities were performed. B. sappan shares well-known phytoconstituents with other members of the genus Biancaea. The heartwood ethanol extract possesses the most prominent antioxidant, anti-inflammatory, and anti-β-amyloid effects. The aqueous extract demonstrated a most substantial anti-glycation activity and was rich in phenolics. The ethanol extract from heartwood exhibited the highest cytotoxicity against SW-48, indicating B. sappan heartwood from Java holds promise as antioxidants and may selectively inhibit colorectal cancer.},
}

@article {pmid38756345,
year = {2024},
author = {Crabo, LG},
title = {A new noctuid genus and species (Lepidoptera, Noctuidae, Amphipyrinae, Psaphidini, Triocnemidina) from New Mexico and Texas, United States of America.},
journal = {ZooKeys},
volume = {1200},
number = {},
pages = {199-213},
pmid = {38756345},
issn = {1313-2989},
abstract = {Pooleagen. nov. is described for two noctuid species from southwestern United States: Pooleagrandimacula Barnes & McDunnough, comb. nov., previously in Oxycnemis Grote, and Pooleapsaphidoidessp. nov.Poolea is compared to Oxycnemis (Amphipyrinae, Psaphidini, Triocnemidina) and is retained in the same subtribe. Adult moths and male and female genitalia of Poolea species are illustrated along with those of Oxycnemisadvena Grote, the genus type species. Pertinent recent taxonomic changes to Amphipyrinae classification are reviewed.},
}

@article {pmid38751964,
year = {2024},
author = {Li, Z and Zhang, F},
title = {Two new species of the genus Cheiracanthium C. L. Koch, 1839 (Araneae, Cheiracanthiidae) from China.},
journal = {ZooKeys},
volume = {1200},
number = {},
pages = {145-157},
pmid = {38751964},
issn = {1313-2989},
abstract = {Two species of the long-legged sac spider genus Cheiracanthium C. L. Koch, 1839 collected from China are diagnosed and described as new to science: Cheiracanthiumbannaensissp. nov. (♂♀) from Yunnan Province and C.bifurcatumsp. nov. (♂♀) from Xinjiang Uyger Autonomous Region. Photos of the habitus and copulatory organs are given. In addition, DNA barcode information of the two new species is provided.},
}

@article {pmid38750233,
year = {2024},
author = {Karras, P and Black, JRM and McGranahan, N and Marine, JC},
title = {Decoding the interplay between genetic and non-genetic drivers of metastasis.},
journal = {Nature},
volume = {629},
number = {8012},
pages = {543-554},
pmid = {38750233},
issn = {1476-4687},
mesh = {Humans ; *Neoplasm Metastasis/genetics ; *Neoplasms/genetics/pathology ; Animals ; Single-Cell Analysis ; },
abstract = {Metastasis is a multistep process by which cancer cells break away from their original location and spread to distant organs, and is responsible for the vast majority of cancer-related deaths. Preventing early metastatic dissemination would revolutionize the ability to fight cancer. Unfortunately, the relatively poor understanding of the molecular underpinnings of metastasis has hampered the development of effective anti-metastatic drugs. Although it is now accepted that disseminating tumour cells need to acquire multiple competencies to face the many obstacles they encounter before reaching their metastatic site(s), whether these competencies are acquired through an accumulation of metastasis-specific genetic alterations and/or non-genetic events is often debated. Here we review a growing body of literature highlighting the importance of both genetic and non-genetic reprogramming events during the metastatic cascade, and discuss how genetic and non-genetic processes act in concert to confer metastatic competencies. We also describe how recent technological advances, and in particular the advent of single-cell multi-omics and barcoding approaches, will help to better elucidate the cross-talk between genetic and non-genetic mechanisms of metastasis and ultimately inform innovative paths for the early detection and interception of this lethal process.},
}

Humans
*Neoplasm Metastasis/genetics
*Neoplasms/genetics/pathology
Animals
Single-Cell Analysis

@article {pmid38746545,
year = {2024},
author = {Quattrini, AM and McCartin, LJ and Easton, EE and Horowitz, J and Wirshing, HH and Bowers, H and Mitchell, K and González-García, MDP and Sei, M and McFadden, CS and Herrera, S},
title = {Skimming genomes for systematics and DNA barcodes of corals.},
journal = {Ecology and evolution},
volume = {14},
number = {5},
pages = {e11254},
pmid = {38746545},
issn = {2045-7758},
abstract = {Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.},
}

@article {pmid38746196,
year = {2024},
author = {Andriienko, V and Buczek, M and Meier, R and Srivathsan, A and Łukasik, P and Kolasa, MR},
title = {Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.30.591865},
pmid = {38746196},
abstract = {BACKGROUND: Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.

METHODS: High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.

RESULTS: We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.

CONCLUSION: Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.},
}

@article {pmid38746155,
year = {2024},
author = {Su, C and Chandradoss, KR and Malachowski, T and Boya, R and Ryu, HS and Brennand, KJ and Phillips-Cremins, JE},
title = {MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.29.591790},
pmid = {38746155},
abstract = {UNLABELLED: More than 60 human disorders have been linked to unstable expansion of short tandem repeat (STR) tracts. STR length and the extent of DNA methylation is linked to disease pathology and can be mosaic in a cell type-specific manner in several repeat expansion disorders. Mosaic phenomenon have been difficult to study to date due to technical bias intrinsic to repeat sequences and the need for multi-modal measurements at single-allele resolution. Nanopore long-read sequencing accurately measures STR length and DNA methylation in the same single molecule but is cost prohibitive for studies assessing a target locus across multiple experimental conditions or patient samples. Here, we describe MASTR-seq, M ultiplexed A nalysis of S hort T andem R epeats, for cost-effective, high-throughput, accurate, multi-modal measurements of DNA methylation and STR genotype at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, and PCR-free multiplexed barcoding to achieve a >ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses.

KEY POINTS: We provide a protocol for MASTR-seq: M ultiplexed A nalysis of S hort T andem R epeats using Cas9-mediated target enrichment and PCR-free, multiplexed nanopore sequencing. MASTR-seq achieves a >10-fold increase in on-target read proportion for highly repetitive, technically inaccessible regions of the genome relevant for human health and disease.MASTR-seq allows for high-throughput, efficient, accurate, and cost-effective measurement of STR length and DNA methylation in the same single allele for up to 8-12 samples in parallel in one Nanopore MinION flow cell.},
}

@article {pmid38744526,
year = {2024},
author = {Dreyer, N and Olesen, J and Grygier, MJ and Eibye-Jacobsen, D and Savchenko, AS and Fujita, Y and Kolbasov, GA and Machida, RJ and Chan, BKK and Palero, F},
title = {Novel molecular resources for single-specimen barcoding of enigmatic crustacean y-larvae.},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS23018},
pmid = {38744526},
issn = {1447-2600},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Larva/genetics/anatomy & histology/growth & development ; Crustacea/genetics/classification/anatomy & histology ; Species Specificity ; Phylogeny ; },
abstract = {Despite discovery more than 100years ago and documented global occurrence from shallow waters to the deep sea, the life cycle of the enigmatic crustacean y-larvae isincompletely understood and adult forms remain unknown. To date, only 2 of the 17 formally described species, all based on larval stages, have been investigated using an integrative taxonomic approach. This approach provided descriptions of the morphology of the naupliar and cyprid stages, and made use of exuvial voucher material and DNA barcodes. To improve our knowledge about the evolutionary history and ecological importance of y-larvae, we developed a novel protocol that maximises the amount of morpho-ecological and molecular data that can be harvested from single larval specimens. This includes single-specimen DNA barcoding and daily imaging of y-nauplii reared in culture dishes, mounting of the last naupliar exuviae on a slide as a reference voucher, live imaging of the y-cyprid instar that follows, and fixation, DNA extraction, amplification and sequencing of the y-cyprid specimen. Through development and testing of a suite of new primers for both nuclear and mitochondrial protein-coding and ribosomal genes, we showcase how new sequence data can be used to estimate the phylogeny of Facetotecta. We expect that our novel procedure will help to unravel the complex systematics of y-larvae and show how these fascinating larval forms have evolved. Moreover, we posit that our protocols should work on larval specimens from a diverse array of moulting marine invertebrate taxa.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Larva/genetics/anatomy & histology/growth & development
Crustacea/genetics/classification/anatomy & histology
Species Specificity
Phylogeny

@article {pmid38742850,
year = {2024},
author = {Neven, LG and Walker, WB and Gowton, C and Carrillo, J},
title = {Using eDNA to play whack-a-mole with invasive species in green yard waste.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toae090},
pmid = {38742850},
issn = {1938-291X},
support = {K2530//Washington State Department of Agriculture/ ; },
abstract = {As large cities begin to overrun their landfill capacities, they begin to look for alternative locations to handle the waste stream. Seeing an opportunity to bring in revenue, rural communities offer to handle municipal waste in their landfills. However, many rural communities are also places of agricultural production, which are vulnerable to attacks by invasive insect species, which could be present in green yard waste, the component of municipal waste most likely to contain agriculturally harmful insect species. We used environmental DNA (eDNA) to determine whether green yard waste could be a pathway for invasive insect species to enter and establish in the landfill-receiving agricultural community. We identified several target species that could be in green yard waste coming from Vancouver, BC, Canada, to Central Washington State, USA. We sampled green yard waste from 3 sites every 2 weeks from June to October in 2019 and 2020. DNA was extracted from the nearly 400 samples and subjected to amplification with COI barcoding primers followed by sequencing to identify target insects in the samples. Sequence analyses identified 3 species from the target list: 2 species that are pests of deciduous tree fruits and a generalist root-feeding crop pest. This eDNA technique was useful in identifying potential invasive species in green yard waste and may prove to be an important tool informing policy on the movement of biological material across borders and stemming the spread of invasive species.},
}

@article {pmid38742184,
year = {2024},
author = {Tarkhnishvili, D and Seropian, A and Erhardt, C and Kachlishvili, N and Krammer, HJ and Hein, N},
title = {How dispersal rates depend on the prey capture strategy: A case study of Georgia's spiders.},
journal = {Ecology and evolution},
volume = {14},
number = {5},
pages = {e11372},
pmid = {38742184},
issn = {2045-7758},
abstract = {Large-scale barcoding projects help to aggregate information on genetic variability of multiple species throughout their ranges. Comparing DNA sequences of both non-conspecific and conspecific individuals from distant parts of their ranges helps to compare level of genetic isolation-by-distance patterns in different species and adaptive types. We compared mitochondrial CO1 gene sequences of 223 spiders from Georgia (Caucasus), representing 124 species and eight families, with 3097 homological sequences from spiders mostly from Europe, but also from other parts of the World. In most families, a significant isolation-by distance pattern was observed on family level. On species level, a significant isolation-by-distance was observed in 40 species, although this low proportion is most likely related to a lack of data. Simultaneously, remarkable differences in spatial structure were shown for different species. Although the majority of the studied species have a broad western Palearctic range, web-building spiders from families Araneidae, Theridiidae, and Linyphiidae are less isolated spatially than flower spiders (Thomisidae), jumping spiders (Salticidae), wolf spiders (Lycosidae), sac spiders (Clubionidae), and ground spiders (Gnaphosidae). This pattern is related with more common ballooning in web building than in actively hunting spiders, which commonly remain isolated since preglacial time. Ground spiders build the most isolated populations in the Caucasus.},
}

@article {pmid38741893,
year = {2024},
author = {Musa, S and Hemberle, T and Bensch, S and Palinauskas, V and Baltrūnaitė, L and Woog, F and Mackenstedt, U},
title = {Raising the bar: genus-specific nested PCR improves detection and lineage identification of avian haemosporidian parasites.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1385599},
doi = {10.3389/fcimb.2024.1385599},
pmid = {38741893},
issn = {2235-2988},
mesh = {Animals ; *Haemosporida/genetics/isolation & purification/classification ; *Polymerase Chain Reaction/methods ; *Protozoan Infections, Animal/diagnosis/parasitology ; Bird Diseases/parasitology/diagnosis ; Birds/parasitology ; Phylogeny ; Sensitivity and Specificity ; Passeriformes/parasitology ; DNA, Protozoan/genetics ; },
abstract = {Avian haemosporidian parasites are useful model organisms to study the ecology and evolution of parasite-host interactions due to their global distribution and extensive biodiversity. Detection of these parasites has evolved from microscopic examination to PCR-based methods, with the mitochondrial cytochrome b gene serving as barcoding region. However, standard PCR protocols used for screening and identification purposes have limitations in detecting mixed infections and generating phylogenetically informative data due to short amplicon lengths. To address these issues, we developed a novel genus-specific nested PCR protocol targeting avian haemosporidian parasites. The protocol underwent rigorous testing utilizing a large dataset comprising blood samples from Malagasy birds of three distinct Passeriformes families. Furthermore, validation was done by examining smaller datasets in two other laboratories employing divergent master mixes and different bird species. Comparative analyses were conducted between the outcomes of the novel PCR protocol and those obtained through the widely used standard nested PCR method. The novel protocol enables specific identification of Plasmodium, Haemoproteus (Parahaemoproteus), and Leucocytozoon parasites. The analyses demonstrated comparable sensitivity to the standard nested PCR with notable improvements in detecting mixed infections. In addition, phylogenetic resolution is improved by amplification of longer fragments, leading to a better understanding of the haemosporidian biodiversity and evolution. Overall, the novel protocol represents a valuable addition to avian haemosporidian detection methodologies, facilitating comprehensive studies on parasite ecology, epidemiology, and evolution.},
}

Animals
*Haemosporida/genetics/isolation & purification/classification
*Polymerase Chain Reaction/methods
*Protozoan Infections, Animal/diagnosis/parasitology
Bird Diseases/parasitology/diagnosis
Birds/parasitology
Phylogeny
Sensitivity and Specificity
Passeriformes/parasitology
DNA, Protozoan/genetics

@article {pmid38740284,
year = {2024},
author = {Qin, T and Hernandez, SER and Shiers, J and Crittall, M and Novak, A and Smith, CS},
title = {A decentralized solid compound storage facility managed by a centralized electronic platform at a growing drug discovery company.},
journal = {SLAS technology},
volume = {},
number = {},
pages = {100143},
doi = {10.1016/j.slast.2024.100143},
pmid = {38740284},
issn = {2472-6311},
abstract = {Within a growing drug discovery company, scientists acquire (either through in house synthesis or purchase) then store, retrieve, and ship solid compound samples daily between multiple locations. The efficient management and tracking of this entire process to support drug discovery is a significant challenge. This article describes a decentralized and cost-effective inventory facility that simplifies the solid compound storage and retrieval process. Standardized storage cabinets from the market are utilized, providing a cost-effective physical infrastructure. The cabinets can be distributed across storage rooms at multiple sites and arranged into spaces with a variety of dimensions, allowing the system to be retrofitted into existing facilities and scaled up easily. We can provide storage close to work areas at each location, minimizing both unnecessary movement of staff and transportation of substances. We have applied a systematic barcoding method to the compound batch identifier that correlates with its compound location. This simplifies the compound registration process as well as the process of finding and returning compounds. Additionally, a centralized electronic platform has been employed to store, update and track solid compound information, such as properties, location and quantity. Compound shipment may be initiated from different sites, and a centralized electronic platform assists the information retrieval process, ensuring each location possesses up-to-date information. The electronic platform we present streamlines the management of compound registration, location tracking, weight updates and shipment information, facilitating seamless record sharing among all stakeholders. Every step of the process can be tracked in real time by the project team. The platform can be flexibly configured to adapt to an evolving set of storage locations, with all information and processes being audited.},
}

@article {pmid38739854,
year = {2024},
author = {Dos Santos, EL and Xavier, JKAM and Galvão, PLN and Carneiro, AR and Alegria, OVC and Moreira, EC and Maia, JGS and Setzer, WN and Figueiredo, PLB and DA Silva, JK},
title = {Volatile Profiles and DNA Barcodes of Myrtaceae species with Occurrence in the Brazilian Amazon.},
journal = {Chemistry & biodiversity},
volume = {},
number = {},
pages = {e202400388},
doi = {10.1002/cbdv.202400388},
pmid = {38739854},
issn = {1612-1880},
abstract = {Myrtaceae family includes many species with taxonomic challenges, making it one of the most complex families to identify. This study used DNA barcoding to find molecular markers for species authentication based on the Myrtaceae family's chemical composition and genetic diversity. Essential oils and genetic material were extracted from the leaves of six different species: Eugenia uniflora, E. patrisii, Myrcia splendens, Psidium guajava, P. guineense, and Psidium sp. The samples were analyzed based on compound classes and grouped into two categories. Group I included samples with high amounts of oxygenated sesquiterpenes (3.69-76.05%) and fatty acid derivatives (0.04-43.59%), such as E. uniflora, Myrcia splendens, and E. patrisii. Group II included samples P. guajava, P. guineense, and Psidium sp., which had a significant content of monoterpene hydrocarbons (0.69-72.35%), oxygenated sesquiterpenes (8.06-68.1%), phenylpropanoids (0.45-22.59%), and sesquiterpene hydrocarbons (0.27-21.84%). The PsbA-trnH gene sequences had a high genetic variability, allowing the species to be distinguished. A phylogenetic analysis showed two main clusters with high Bootstrap values corresponding to the subtribes Eugeniineae, Myrciinae, and Pimentinae. The results suggest a weak correlation between genetic and chemical data in these Myrtaceae species.},
}

@article {pmid38737823,
year = {2024},
author = {Wang, T and Shen, H and Xu, B and Yang, W and Chen, S and Chen, J},
title = {Genome Analysis of Plasmodium falciparum: A Preliminary Observation - Sierra Leone, 2022-2023.},
journal = {China CDC weekly},
volume = {6},
number = {17},
pages = {368-373},
pmid = {38737823},
issn = {2096-7071},
abstract = {Sierra Leone, with a gross domestic product (GDP) per capita below $300 and significant poverty, ranks among the world's least developed countries (LDCs). Despite its modest population of 8.6 million, the nation reports approximately 2.6 million malaria cases annually. Previously, there has been no reporting on the malaria genome data from this country.

WHAT IS ADDED BY THIS REPORT?: In this study, we present the first reported whole-genome sequence analysis of 19 high parasite-density Plasmodium falciparum isolates from Sierra Leone, providing insights into the genomic epidemiology of this high-prevalence area. We found a high degree of relatedness among infections and substantial genetic diversity, consistent with the gradual reduction in overall case numbers. Moreover, our whole-genome analysis revealed that, beyond drug-resistance genes, gene families related to blood cell invasion, immune evasion, and others are undergoing directional selection. This suggests that the population in Sierra Leone has developed a relatively strong acquired immunity.

The genomic data not only facilitate the creation of single nucleotide polymorphism barcodes for case tracking but also enable the analysis of evolving transmission dynamics and selection pressures. Additionally, the samples from Sierra Leone exhibited higher selective pressures on resistance genes compared to those from Asia, a trend not commonly observed in other African samples. This suggests that less stringent healthcare systems and inconsistent treatment strategies can subject parasites to increased drug pressure, thereby accelerating the development of resistant strains.},
}

@article {pmid38734639,
year = {2024},
author = {Bušić, N and Klobučar, A and Landeka, N and Žitko, T and Vignjević, G and Turić, N and Sudarić Bogojević, M and Merdić, E and Kučinić, M and Bruvo Mađarić, B},
title = {A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species.},
journal = {Parasites & vectors},
volume = {17},
number = {1},
pages = {216},
pmid = {38734639},
issn = {1756-3305},
support = {IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Croatia ; *Mosquito Vectors/genetics/classification/anatomy & histology ; *Culicidae/classification/genetics ; *Electron Transport Complex IV/genetics ; Anopheles/genetics/classification ; Phylogeny ; Gene Library ; },
abstract = {BACKGROUND: Mosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species.

METHODS: Sampling was carried out in three biogeographical regions of Croatia over six years (2017-2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs.

RESULTS: A total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna.

CONCLUSION: We present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.},
}

Animals
*DNA Barcoding, Taxonomic
Croatia
*Mosquito Vectors/genetics/classification/anatomy & histology
*Culicidae/classification/genetics
*Electron Transport Complex IV/genetics
Anopheles/genetics/classification
Phylogeny
Gene Library

@article {pmid38734030,
year = {2024},
author = {Stanley, S and Spaulding, CN and Liu, Q and Chase, MR and Ha, DTM and Thai, PVK and Lan, NH and Thu, DDA and Quang, NL and Brown, J and Hicks, ND and Wang, X and Marin, M and Howard, NC and Vickers, AJ and Karpinski, WM and Chao, MC and Farhat, MR and Caws, M and Dunstan, SJ and Thuong, NTT and Fortune, SM},
title = {Identification of bacterial determinants of tuberculosis infection and treatment outcomes: a phenogenomic analysis of clinical strains.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2666-5247(24)00022-3},
pmid = {38734030},
issn = {2666-5247},
abstract = {BACKGROUND: Bacterial diversity could contribute to the diversity of tuberculosis infection and treatment outcomes observed clinically, but the biological basis of this association is poorly understood. The aim of this study was to identify associations between phenogenomic variation in Mycobacterium tuberculosis and tuberculosis clinical features.

METHODS: We developed a high-throughput platform to define phenotype-genotype relationships in M tuberculosis clinical isolates, which we tested on a set of 158 drug-sensitive M tuberculosis strains sampled from a large tuberculosis clinical study in Ho Chi Minh City, Viet Nam. We tagged the strains with unique genetic barcodes in multiplicate, allowing us to pool the strains for in-vitro competitive fitness assays across 16 host-relevant antibiotic and metabolic conditions. Relative fitness was quantified by deep sequencing, enumerating output barcode read counts relative to input normalised values. We performed a genome-wide association study to identify phylogenetically linked and monogenic mutations associated with the in-vitro fitness phenotypes. These genetic determinants were further associated with relevant clinical outcomes (cavitary disease and treatment failure) by calculating odds ratios (ORs) with binomial logistic regressions. We also assessed the population-level transmission of strains associated with cavitary disease and treatment failure using terminal branch length analysis of the phylogenetic data.

FINDINGS: M tuberculosis clinical strains had diverse growth characteristics in host-like metabolic and drug conditions. These fitness phenotypes were highly heritable, and we identified monogenic and phylogenetically linked variants associated with the fitness phenotypes. These data enabled us to define two genetic features that were associated with clinical outcomes. First, mutations in Rv1339, a phosphodiesterase, which were associated with slow growth in glycerol, were further associated with treatment failure (OR 5·34, 95% CI 1·21-23·58, p=0·027). Second, we identified a phenotypically distinct slow-growing subclade of lineage 1 strains (L1.1.1.1) that was associated with cavitary disease (OR 2·49, 1·11-5·59, p=0·027) and treatment failure (OR 4·76, 1·53-14·78, p=0·0069), and which had shorter terminal branch lengths on the phylogenetic tree, suggesting increased transmission.

INTERPRETATION: Slow growth under various antibiotic and metabolic conditions served as in-vitro intermediate phenotypes underlying the association between M tuberculosis monogenic and phylogenetically linked mutations and outcomes such as cavitary disease, treatment failure, and transmission potential. These data suggest that M tuberculosis growth regulation is an adaptive advantage for bacterial success in human populations, at least in some circumstances. These data further suggest markers for the underlying bacterial processes that contribute to these clinical outcomes.

FUNDING: National Health and Medical Research Council/A∗STAR, National Institutes of Allergy and Infectious Diseases, National Institute of Child Health and Human Development, and the Wellcome Trust Fellowship in Public Health and Tropical Medicine.},
}

@article {pmid38732467,
year = {2024},
author = {Kim, JH and Doh, EJ and Kim, HY and Lee, G},
title = {Chemical Relationship among Genetically Authenticated Medicinal Species of Genus Angelica.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/plants13091252},
pmid = {38732467},
issn = {2223-7747},
support = {NRF-2021R1A2C1095558//the National Research Foundation of Korea/ ; },
abstract = {The genus Angelica comprises various species utilized for diverse medicinal purposes, with differences attributed to the varying levels or types of inherent chemical components in each species. This study employed DNA barcode analysis and HPLC analysis to genetically authenticate and chemically classify eight medicinal Angelica species (n = 106) as well as two non-medicinal species (n = 14) that have been misused. Nucleotide sequence analysis of the nuclear internal transcribed spacer (ITS) region revealed differences ranging from 11 to 117 bp, while psbA-trnH showed variances of 3 to 95 bp, respectively. Phylogenetic analysis grouped all samples except Angelica sinensis into the same cluster, with some counterfeits forming separate clusters. Verification using the NCBI database confirmed the feasibility of species identification. For chemical identification, a robust quantitative HPLC analysis method was developed for 46 marker compounds. Subsequently, two A. reflexa-specific and seven A. biserrata-specific marker compounds were identified, alongside non-specific markers. Moreover, chemometric clustering analysis reflecting differences in chemical content between species revealed that most samples formed distinct clusters according to the plant species. However, some samples formed mixed clusters containing different species. These findings offer crucial insights for the standardization and quality control of medicinal Angelica species.},
}

@article {pmid38731365,
year = {2024},
author = {Ricardo, F and Lopes, ML and Mamede, R and Domingues, MR and Ferreira da Silva, E and Patinha, C and Calado, R},
title = {Combined Use of Fatty Acid Profiles and Elemental Fingerprints to Trace the Geographic Origin of Live Baits for Sports Fishing: The Solitary Tube Worm (Diopatra neapolitana, Annelida, Onuphidae) as a Case Study.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/ani14091361},
pmid = {38731365},
issn = {2076-2615},
support = {TC-C10-i01//Desenvolvimento do Projeto de Reforço do Polo de Aveiro (H4)", framed within Measure 10 of Investment TC-C10-i01 - Hub Azul - Rede de Infraestruturas para a Economia Azul, financed by the Recovery and Resilience Plan (PRR) and supported by Fundo Azul of t/ ; + UIDB/50017/2020+ LA/P/0094/2020 + UIDB/50006/2020//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Diopatra neapolitana Delle Chiaje, 1841 (Annelida, Onuphidae) is one of the most exploited polychaete species in European waters, particularly in Ria de Aveiro, a coastal lagoon in mainland Portugal, where the overexploitation of this resource has led to a generalized decline of local populations. In an attempt to reduce the impact of harvesting, several management actions were implemented, but illegal poaching still fuels a parallel economy that threatens the sustainable use of this marine resource. The present study evaluated the combination of fatty acid profiles and elemental fingerprints of the whole body and jaws, respectively, of D. neapolitana collected from four harvesting locations within Ria de Aveiro in order to determine if their geographic origin could be correctly assigned post-harvesting. Results showed that both fatty acid profiles and elemental fingerprints differ significantly among locations, discriminating the geographic origin with higher accuracy when combining these two natural barcodes than when employing each individually. The present work can, therefore, contribute to the implementation of an effective management plan for the sustainable use of this marine resource, making it possible to detect if D. neapolitana was sourced from no-take zones and if it was collected from the place of origin claimed by live bait traders.},
}

@article {pmid38729950,
year = {2024},
author = {Cheng, C and Wang, G and Zhu, Y and Wu, H and Zhang, L and Liu, Z and Huang, Y and Zhang, J},
title = {Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3946},
pmid = {38729950},
issn = {2041-1723},
support = {31871453//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Organoids/metabolism ; *Single-Cell Analysis/methods ; *Induced Pluripotent Stem Cells/metabolism/cytology ; Humans ; *Cell Differentiation/genetics ; *RNA-Seq/methods ; Sequence Analysis, RNA/methods ; Macrophages/metabolism/cytology ; Animals ; Single-Cell Gene Expression Analysis ; },
abstract = {Disease modeling with isogenic Induced Pluripotent Stem Cell (iPSC)-differentiated organoids serves as a powerful technique for studying disease mechanisms. Multiplexed coculture is crucial to mitigate batch effects when studying the genetic effects of disease-causing variants in differentiated iPSCs or organoids, and demultiplexing at the single-cell level can be conveniently achieved by assessing natural genetic barcodes. Here, to enable cost-efficient time-series experimental designs via multiplexed bulk and single-cell RNA-seq of hybrids, we introduce a computational method in our Vireo Suite, Vireo-bulk, to effectively deconvolve pooled bulk RNA-seq data by genotype reference, and thereby quantify donor abundance over the course of differentiation and identify differentially expressed genes among donors. Furthermore, with multiplexed scRNA-seq and bulk RNA-seq, we demonstrate the usefulness and necessity of a pooled design to reveal donor iPSC line heterogeneity during macrophage cell differentiation and to model rare WT1 mutation-driven kidney disease with chimeric organoids. Our work provides an experimental and analytic pipeline for dissecting disease mechanisms with chimeric organoids.},
}

*Organoids/metabolism
*Single-Cell Analysis/methods
*Induced Pluripotent Stem Cells/metabolism/cytology
Humans
*Cell Differentiation/genetics
*RNA-Seq/methods
Sequence Analysis, RNA/methods
Macrophages/metabolism/cytology
Animals
Single-Cell Gene Expression Analysis

@article {pmid38729384,
year = {2024},
author = {Dufresnes, C and Ghielmi, S and Halpern, B and Martínez-Freiría, F and Mebert, K and Jelić, D and Crnobrnja-Isailović, J and Gippner, S and Jablonski, D and Joger, U and Laddaga, L and Petrovan, S and Tomović, L and Vörös, J and İğci, N and Kariş, M and Zinenko, O and Ursenbacher, S},
title = {Phylogenomic insights into the diversity and evolution of Palearctic vipers.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108095},
doi = {10.1016/j.ympev.2024.108095},
pmid = {38729384},
issn = {1095-9513},
abstract = {Despite decades of molecular research, phylogenetic relationships in Palearctic vipers (genus Vipera) still essentially rely on a few loci, such as mitochondrial barcoding genes. Here we examined the diversity and evolution of Vipera with ddRAD-seq data from 33 representative species and subspecies. Phylogenomic analyses of ∼ 1.1 Mb recovered nine major clades corresponding to known species/species complexes which are generally consistent with the mitochondrial phylogeny, albeit with a few deep discrepancies that highlight past hybridization events. The most spectacular case is the Italian-endemic V. walser, which is grouped with the alpine genetic diversity of V. berus in the nuclear tree despite carrying a divergent mitogenome related to the Caucasian V. kaznakovi complex. Clustering analyses of SNPs suggest potential admixture between diverged Iberian taxa (V. aspis zinnikeri and V. seoanei), and confirm that the Anatolian V. pontica corresponds to occasional hybrids between V. (ammodytes) meridionalis and V. kaznakovi. Finally, all analyzed lineages of the V. berus complex (including V. walser and V. barani) form vast areas of admixture and may be delimited as subspecies. Our study sets grounds for future taxonomic and phylogeographic surveys on Palearctic vipers, a group of prime interest for toxinological, ecological, biogeographic and conservation research.},
}

@article {pmid38728918,
year = {2024},
author = {Luo, Y and Yang, H and Tao, G},
title = {Systematic review on fingerprinting development to determine adulteration of Chinese herbal medicines.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {129},
number = {},
pages = {155667},
doi = {10.1016/j.phymed.2024.155667},
pmid = {38728918},
issn = {1618-095X},
abstract = {BACKGROUND: It has been a current research hospots using fingerprinting technology for quality control of Chinese herbal medicines (CHMs), which provides a scientific basis for establishment of overall quality control in accordance with the characteristics of CHMs. The fingerprinting technology for CHMs is diverse, and the research field covers many disciplines, such as analytical chemistry, pharmacology, pharmaceutics, biochemistry, and molecular biology.

PURPOSE: To effectively understand the key areas and future directions of research regarding the fingerprint and adulteration of CHMs.

METHODS/RESULTS: this paper analyzed 879 articles in this field in the Web of Science Core Collection from 2000 to 2023 with CiteSpace and VOSviewer, and systematically assessed the research process, hotspots, topic distribution among disciplines, etc. The most prominent contributors of fingerprint and adulteration of CHMs research are mainly from China, India, the United States, England, and Brazil. The knowledge domains of fingerprint and adulteration of CHMs research focus mainly on the topics of molecular authentication, DNA barcoding, HPLC, near-infrared spectroscopy, manage data, chemometrics, and electrochemical fingerprinting. Most countries have recognized the pharmaceutical potential of natural products, and have paid more attention to the fingerprint and adulteration of CHMs in the past decade. Future the research tends to focus more on molecular identification and authentication, and electrochemical and chromatographic fingerprinting in controlling the adulteration of CHMs.

CONCLUSION: This research provides a valuable reference for scholars in related fields to analyze existing research results, understand the development trend, and explore new research directions.},
}

@article {pmid38727924,
year = {2024},
author = {Niu, J and Wang, X and Zhou, S and Yue, J and Liu, Z and Zhou, J},
title = {Molecular authentication of commercial "Qian-hu" through the integration of nrDNA internal transcribed spacer 2 and nucleotide signature.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {639},
pmid = {38727924},
issn = {1573-4978},
support = {202205AM070006//Gaoligong Mountain, Forest Ecosystem, Observation and Research Station of Yunnan Province/ ; 31960048//National Natural Science Foundation of China/ ; YNWRQNBJ-2019-208//Ten Thousand Talents Program of Yunnan/ ; 202201AT070118//Department of Science and Technology of Yunnan Province/ ; },
mesh = {*DNA, Plant/genetics ; *DNA Barcoding, Taxonomic/methods ; Drugs, Chinese Herbal/standards ; Apiaceae/genetics/classification ; Medicine, Chinese Traditional/standards ; DNA, Ribosomal Spacer/genetics ; Drug Contamination ; Plants, Medicinal/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Polymerase Chain Reaction/methods ; Nucleotides/genetics/analysis ; },
abstract = {BACKGROUND: Peucedani Radix, also known as "Qian-hu" is a traditional Chinese medicine derived from Peucedanum praeruptorum Dunn. It is widely utilized for treating wind-heat colds and coughs accompanied by excessive phlegm. However, due to morphological similarities, limited resources, and heightened market demand, numerous substitutes and adulterants of Peucedani Radix have emerged within the herbal medicine market. Moreover, Peucedani Radix is typically dried and sliced for sale, rendering traditional identification methods challenging.

MATERIALS AND METHODS: We initially examined and compared 104 commercial "Qian-hu" samples from various Chinese medicinal markets and 44 species representing genuine, adulterants or substitutes, utilizing the mini barcode ITS2 region to elucidate the botanical origins of the commercial "Qian-hu". The nucleotide signature specific to Peucedani Radix was subsequently developed by analyzing the polymorphic sites within the aligned ITS2 sequences.

RESULTS: The results demonstrated a success rate of 100% and 93.3% for DNA extraction and PCR amplification, respectively. Forty-five samples were authentic "Qian-hu", while the remaining samples were all adulterants, originating from nine distinct species. Peucedani Radix, its substitutes, and adulterants were successfully identified based on the neighbor-joining tree. The 24-bp nucleotide signature (5'-ATTGTCGTACGAATCCTCGTCGTC-3') revealed distinct differences between Peucedani Radix and its common substitutes and adulterants. The newly designed specific primers (PR-F/PR-R) can amplify the nucleotide signature region from commercial samples and processed materials with severe DNA degradation.

CONCLUSIONS: We advocate for the utilization of ITS2 and nucleotide signature for the rapid and precise identification of herbal medicines and their adulterants to regulate the Chinese herbal medicine industry.},
}

*DNA, Plant/genetics
*DNA Barcoding, Taxonomic/methods
Drugs, Chinese Herbal/standards
Apiaceae/genetics/classification
Medicine, Chinese Traditional/standards
DNA, Ribosomal Spacer/genetics
Drug Contamination
Plants, Medicinal/genetics
Phylogeny
Sequence Analysis, DNA/methods
Polymerase Chain Reaction/methods
Nucleotides/genetics/analysis

@article {pmid38722810,
year = {2024},
author = {Marshall, WF and Fung, JC},
title = {Modeling homologous chromosome recognition via nonspecific interactions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {20},
pages = {e2317373121},
doi = {10.1073/pnas.2317373121},
pmid = {38722810},
issn = {1091-6490},
support = {R35 GM130327/GM/NIGMS NIH HHS/United States ; R01 GM137126/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Models, Genetic ; Chromosome Pairing ; Drosophila melanogaster/genetics ; Chromosomes ; Drosophila/genetics ; Computer Simulation ; Chromosomes, Insect/genetics/metabolism ; },
abstract = {In many organisms, most notably Drosophila, homologous chromosomes associate in somatic cells, a phenomenon known as somatic pairing, which takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, mediated by different proteins that bind to these different regions. Here, we use computational modeling to evaluate an alternative "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. In this model, buttons are nonuniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a nonhomolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. By simulating randomly generated nonuniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.},
}

Animals
*Models, Genetic
Chromosome Pairing
Drosophila melanogaster/genetics
Chromosomes
Drosophila/genetics
Computer Simulation
Chromosomes, Insect/genetics/metabolism

@article {pmid38721629,
year = {2024},
author = {Waki, T and Kumagai, T and Nishino, Y},
title = {Identification of Lepidapedon oregonense as the current world's deepest trematode.},
journal = {Journal of helminthology},
volume = {98},
number = {},
pages = {e38},
doi = {10.1017/S0022149X24000269},
pmid = {38721629},
issn = {1475-2697},
mesh = {Animals ; *Trematoda/classification/genetics/isolation & purification ; *RNA, Ribosomal, 28S/genetics ; *Phylogeny ; *DNA, Helminth/genetics ; *DNA, Ribosomal/genetics ; Gastropoda/parasitology ; Sequence Analysis, DNA ; Fishes/parasitology ; Fish Diseases/parasitology ; Trematode Infections/parasitology/veterinary ; },
abstract = {The deepest recorded depth for trematodes currently stands at approximately 6200 m. This depth record was achieved solely through sequence datasets of Lepidapedon sp. obtained from a gastropod. Given that trematodes of this genus typically use fish as definitive hosts, the origin of the trematode sequence was thought to be larval stages. However, the specific species remained unclear owing to the absence of reported adult-stage sequences. In the present study, we definitively identified the deepest trematode as Lepidapedon oregonense by comparing 28S ribosomal DNA sequences from adult worms from the macrourid fish Coelorinchus gilberti with data from the gastropod in the previous study.},
}

Animals
*Trematoda/classification/genetics/isolation & purification
*RNA, Ribosomal, 28S/genetics
*Phylogeny
*DNA, Helminth/genetics
*DNA, Ribosomal/genetics
Gastropoda/parasitology
Sequence Analysis, DNA
Fishes/parasitology
Fish Diseases/parasitology
Trematode Infections/parasitology/veterinary

@article {pmid38718049,
year = {2024},
author = {Lokken-Toyli, KL and Aggarwal, SD and Bee, GCW and de Steenhuijsen Piters, WAA and Wu, C and Chen, KZM and Loomis, C and Bogaert, D and Weiser, JN},
title = {Impaired upper respiratory tract barrier function during postnatal development predisposes to invasive pneumococcal disease.},
journal = {PLoS pathogens},
volume = {20},
number = {5},
pages = {e1012111},
pmid = {38718049},
issn = {1553-7374},
mesh = {Animals ; *Pneumococcal Infections/microbiology/immunology ; Mice ; *Streptococcus pneumoniae ; Humans ; Animals, Newborn ; Disease Models, Animal ; Mice, Inbred C57BL ; Respiratory Mucosa/microbiology/metabolism ; Female ; Nasopharynx/microbiology ; },
abstract = {Infants are highly susceptible to invasive respiratory and gastrointestinal infections. To elucidate the age-dependent mechanism(s) that drive bacterial spread from the mucosa, we developed an infant mouse model using the prevalent pediatric respiratory pathogen, Streptococcus pneumoniae (Spn). Despite similar upper respiratory tract (URT) colonization levels, the survival rate of Spn-infected infant mice was significantly decreased compared to adults and corresponded with Spn dissemination to the bloodstream. An increased rate of pneumococcal bacteremia in early life beyond the newborn period was attributed to increased bacterial translocation across the URT barrier. Bacterial dissemination in infant mice was independent of URT monocyte or neutrophil infiltration, phagocyte-derived ROS or RNS, inflammation mediated by toll-like receptor 2 or interleukin 1 receptor signaling, or the pore-forming toxin pneumolysin. Using molecular barcoding of Spn, we found that only a minority of bacterial clones in the nasopharynx disseminated to the blood in infant mice, indicating the absence of robust URT barrier breakdown. Rather, transcriptional profiling of the URT epithelium revealed a failure of infant mice to upregulate genes involved in the tight junction pathway. Expression of many such genes was also decreased in early life in humans. Infant mice also showed increased URT barrier permeability and delayed mucociliary clearance during the first two weeks of life, which corresponded with tighter attachment of bacteria to the respiratory epithelium. Together, these results demonstrate a window of vulnerability during postnatal development when altered mucosal barrier function facilitates bacterial dissemination.},
}

Animals
*Pneumococcal Infections/microbiology/immunology
Mice
*Streptococcus pneumoniae
Humans
Animals, Newborn
Disease Models, Animal
Mice, Inbred C57BL
Respiratory Mucosa/microbiology/metabolism
Female
Nasopharynx/microbiology

@article {pmid38715571,
year = {2024},
author = {Murwani, R and Anggraeni, R and Setiawan, GNA and Astari, PD and Cahyani, NKD and Sibero, MT and Ambariyanto, A},
title = {Lactic Acid Bacteria Isolates and the Microbiome of Cincalok, Tempoyak, and Mandai: A Traditional Fermented Food from Kalimantan Island, Indonesia.},
journal = {International journal of food science},
volume = {2024},
number = {},
pages = {6589766},
pmid = {38715571},
issn = {2314-5765},
abstract = {Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food and feed products. This research is aimed at (1) obtaining and identifying LAB isolates and (2) studying the microbiome (bacterial diversity and abundance) of spontaneously-fermented traditional foods of Kalimantan Island, Cincalok, Tempoyak, and Mandai. To obtain LAB isolates, food samples were serially diluted and inoculated on MRS agar that contained 1% CaCO3 (MRSA). Isolates forming clear zones were purified and identified by DNA barcoding. The microbiome was studied using genomic-sequencing techniques and analysed for taxonomic composition. Seven pure isolates were obtained from Cincalok, two Tempoyak, and one Mandai. DNA barcoding revealed that the Cincalok seven isolates were Staphylococcus carnosus (strain HSP-S16), Tetragenococcus halophilus (FSB201), Corynebacterium phoceense, Vagococcus vulneris (SS1995), Enterococcus faecalis (S11-6), Pisciglobus halotolerans (C01), and Priestia filamentosa (P3.1); two from Tempoyak, Levilactobacillus brevis (E1D3BL1) and Lactiplantibacillus plantarum (UMCC-2996); and one from Mandai, Staphylococcus cohnii (XAAS.x13; non-LAB). The T. halophilus, E. faecalis, P. halotolerans, L. brevis, and L. plantarum belong to LAB. The P. halotolerans from Cincalok and non-LAB in these three fermented foods were the first documented report. The microbiome revealed the dominance of Firmicutes phyla in the fermented foods, with 93% in Cincalok, 89.94% in Tempoyak, and 60.32% in Mandai. On the genus level, Cincalok was dominated by Tetragenococcus 40.33%, Anaerococcus 23.29%, Vagococcus 9.27%, and Lactobacillus 6.84%. Meanwhile, Tempoyak was dominated only by Lactobacillus 89.94%. Mandai were dominated by Lactobacillus 31.97%, Proteus 17.14%, Aerococcus 16.85%, Mangrovibacter 15.15%, and Vagococcus 6.2%. However, Mandai's microbiome LAB was not culturable/isolated on MRSA. The plausibility is that those unculturable LAB require coculturing with other bacteria and additional media components to grow on MRSA. This study is the first report regarding the microbiome of Cincalok, Tempoyak, and Mandai, along with their culturable LAB isolates.},
}

@article {pmid38714853,
year = {2024},
author = {Lindenhofer, D and Haendeler, S and Esk, C and Littleboy, JB and Brunet Avalos, C and Naas, J and Pflug, FG and van de Ven, EGP and Reumann, D and Baffet, AD and von Haeseler, A and Knoblich, JA},
title = {Cerebral organoids display dynamic clonal growth and tunable tissue replenishment.},
journal = {Nature cell biology},
volume = {},
number = {},
pages = {},
pmid = {38714853},
issn = {1476-4679},
abstract = {During brain development, neural progenitors expand through symmetric divisions before giving rise to differentiating cell types via asymmetric divisions. Transition between those modes varies among individual neural stem cells, resulting in clones of different sizes. Imaging-based lineage tracing allows for lineage analysis at high cellular resolution but systematic approaches to analyse clonal behaviour of entire tissues are currently lacking. Here we implement whole-tissue lineage tracing by genomic DNA barcoding in 3D human cerebral organoids, to show that individual stem cell clones produce progeny on a vastly variable scale. By using stochastic modelling we find that variable lineage sizes arise because a subpopulation of lineages retains symmetrically dividing cells. We show that lineage sizes can adjust to tissue demands after growth perturbation via chemical ablation or genetic restriction of a subset of cells in chimeric organoids. Our data suggest that adaptive plasticity of stem cell populations ensures robustness of development in human brain organoids.},
}

@article {pmid38714828,
year = {2024},
author = {Sipiczki, M and Czentye, K and Kállai, Z},
title = {High intragenomic, intergenomic, and phenotypic diversity in pulcherrimin-producing Metschnikowia yeasts indicates a special mode of genome evolution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10521},
pmid = {38714828},
issn = {2045-2322},
mesh = {*Metschnikowia/genetics ; *Genome, Fungal ; *Evolution, Molecular ; *Phylogeny ; Genetic Variation ; Phenotype ; DNA, Mitochondrial/genetics ; },
abstract = {In molecular systematics, the delimitation of yeast species is based on the notion that the barcode differences are smaller within species than between them. The most widely used barcodes are segments of the chromosomal repeats coding for ribosomal RNAs that are homogenised in yeasts. The analysis of these segments of the type strains of ten species recently merged in Metschnikowia pulcherrima and 37 new isolates demonstrated that this is not the case in this species. The intragenomic diversity significantly exceeded the threshold gaps used to differentiate related yeast species. Large segments of the D1/D2 domains were not diverse within the genomes and could therefore be used to determine the taxonomic affiliation of the isolates. The genome structures of the isolates were compared by RAPD and the RFLP of the mitochondrial DNA. Both patterns were highly heterogeneous. The sequence analysis of the PUL4 gene (a member of the PUL gene cluster involved in pulcherrimin production) revealed very high intragenomic differences, suggesting that the genomes may be chimerised. Three phenotypic traits related to the antimicrobial antagonism characteristic of the species were also highly diverse and prone to reversible segregation resembling epigenetic processes (silencing and reactivation of regulators) rather than mutations and back-mutations. These features make M. pulcherrima unique among yeasts and indicate that it evolves in a non-standard way.},
}

*Metschnikowia/genetics
*Genome, Fungal
*Evolution, Molecular
*Phylogeny
Genetic Variation
Phenotype
DNA, Mitochondrial/genetics

@article {pmid38712508,
year = {2024},
author = {Voorspoels, A and Gevers, J and Santermans, S and Akkan, N and Martens, K and Willems, K and Van Dorpe, P and Verhulst, AS},
title = {Design Principles of DNA-Barcodes for Nanopore-FET Readout, Based on Molecular Dynamics and TCAD Simulations.},
journal = {The journal of physical chemistry. A},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jpca.4c01772},
pmid = {38712508},
issn = {1520-5215},
abstract = {Nanopore field-effect transistor (NP-FET) devices hold great promise as sensitive single-molecule sensors, which provide CMOS-based on-chip readout and are also highly amenable to parallelization. A plethora of applications will therefore benefit from NP-FET technology, such as large-scale molecular analysis (e.g., proteomics). Due to its potential for parallelization, the NP-FET looks particularly well-suited for the high-throughput readout of DNA-based barcodes. However, to date, no study exists that unravels the bit-rate capabilities of NP-FET devices. In this paper, we design DNA-based barcodes by labeling a piece of double-stranded DNA with dumbbell-like DNA structures. We explore the impact of both the size of the dumbbells and their spacing on achievable bit-rates. The conformational fluctuations of this DNA-origami, as observed by molecular dynamics (MD) simulation, are accounted for when selecting label sizes. An experimentally informed 3D continuum nanofluidic-nanoelectronic device model subsequently predicts both the ionic current and FET signals. We present a barcode design for a conceptually generic NP-FET, with a 14 nm diameter pore, operating in conditions corresponding to experiments. By adjusting the spacing between the labels to half the length of the pore, we show that a bit-rate of 78 kbit·s[-1] is achievable. This lies well beyond the state-of-the-art of ≈40 kbit·s[-1], with significant headroom for further optimizations. We also highlight the advantages of NP-FET readout based on the larger signal size and sinusoidal signal shape.},
}

@article {pmid38712231,
year = {2024},
author = {Yang, L and Liu, F and Hahm, H and Okuda, T and Li, X and Zhang, Y and Kalyanaraman, V and Heitmeier, MR and Samineni, VK},
title = {Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.24.590975},
pmid = {38712231},
abstract = {Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.},
}

@article {pmid38709890,
year = {2024},
author = {Li, W and Miller, D and Liu, X and Tosi, L and Chkaiban, L and Mei, H and Hung, PH and Parekkadan, B and Sherlock, G and Levy, SF},
title = {Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae332},
pmid = {38709890},
issn = {1362-4962},
support = {R01HG011676/NH/NIH HHS/United States ; },
abstract = {Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.},
}

@article {pmid38709485,
year = {2024},
author = {Wang, S and Chi, WY and Au, G and Huang, CC and Yang, JM and Huang, CH},
title = {Reconstructing Signaling Networks Using Biosensor Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2800},
number = {},
pages = {189-202},
pmid = {38709485},
issn = {1940-6029},
mesh = {*Biosensing Techniques/methods ; *Signal Transduction ; Humans ; ErbB Receptors/metabolism/genetics ; },
abstract = {Understanding how signaling networks are regulated offers valuable insights into how cells and organisms react to internal and external stimuli and is crucial for developing novel strategies to treat diseases. To achieve this, it is necessary to delineate the intricate interactions between the nodes in the network, which can be accomplished by measuring the activities of individual nodes under perturbation conditions. To facilitate this, we have recently developed a biosensor barcoding technique that enables massively multiplexed tracking of numerous signaling activities in live cells using genetically encoded fluorescent biosensors. In this chapter, we detail how we employed this method to reconstruct the EGFR signaling network by systematically monitoring the activities of individual nodes under perturbations.},
}

*Biosensing Techniques/methods
*Signal Transduction
Humans
ErbB Receptors/metabolism/genetics

@article {pmid38705596,
year = {2024},
author = {Schulz, AR and Rademacher, J and Bockhorn, V and Mei, HE},
title = {Harmonized analysis of PBMC by mass cytometry.},
journal = {Methods in cell biology},
volume = {186},
number = {},
pages = {107-130},
doi = {10.1016/bs.mcb.2024.02.015},
pmid = {38705596},
issn = {0091-679X},
mesh = {Humans ; *Leukocytes, Mononuclear/cytology/immunology ; *Flow Cytometry/methods/standards ; Immunophenotyping/methods ; Single-Cell Analysis/methods ; },
abstract = {Mass cytometry permits the high dimensional analysis of cellular systems at single-cell resolution with high throughput in various areas of biomedical research. Here, we provide a state-of-the-art protocol for the analysis of human peripheral blood mononuclear cells (PBMC) by mass cytometry. We focus on the implementation of measures promoting the harmonization of large and complex studies to aid robustness and reproducibility of immune phenotyping data.},
}

Humans
*Leukocytes, Mononuclear/cytology/immunology
*Flow Cytometry/methods/standards
Immunophenotyping/methods
Single-Cell Analysis/methods

@article {pmid38705187,
year = {2024},
author = {Meier, R and Hartop, E and Pylatiuk, C and Srivathsan, A},
title = {Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230120},
doi = {10.1098/rstb.2023.0120},
pmid = {38705187},
issn = {1471-2970},
mesh = {*Insecta/physiology/classification/genetics ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; },
abstract = {Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

*Insecta/physiology/classification/genetics
Animals
*DNA Barcoding, Taxonomic/methods
Biodiversity

@article {pmid38705185,
year = {2024},
author = {Łukasik, P and Kolasa, MR},
title = {With a little help from my friends: the roles of microbial symbionts in insect populations and communities.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230122},
doi = {10.1098/rstb.2023.0122},
pmid = {38705185},
issn = {1471-2970},
mesh = {Animals ; *Insecta/microbiology/physiology ; *Symbiosis ; *Microbiota/physiology ; Biodiversity ; },
abstract = {To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

Animals
*Insecta/microbiology/physiology
*Symbiosis
*Microbiota/physiology
Biodiversity

@article {pmid38705177,
year = {2024},
author = {Li, Y and Devenish, C and Tosa, MI and Luo, M and Bell, DM and Lesmeister, DB and Greenfield, P and Pichler, M and Levi, T and Yu, DW},
title = {Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230123},
doi = {10.1098/rstb.2023.0123},
pmid = {38705177},
issn = {1471-2970},
mesh = {*Arthropods/classification ; *Biodiversity ; Animals ; *DNA, Environmental/analysis ; *Remote Sensing Technology/methods ; Forests ; Animal Distribution ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km[2] temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

*Arthropods/classification
*Biodiversity
Animals
*DNA, Environmental/analysis
*Remote Sensing Technology/methods
Forests
Animal Distribution
DNA Barcoding, Taxonomic/methods

@article {pmid38705075,
year = {2024},
author = {Li, X and Liu, R and Zhang, N and Zhao, J and Zhou, Y and Zhou, Q and Gu, Z and Zhang, D},
title = {Carbon nanotubes integrated photonic barcodes in Herringbone Microfluidics for Multiplex Biomarker Quantification.},
journal = {Biosensors & bioelectronics},
volume = {258},
number = {},
pages = {116350},
doi = {10.1016/j.bios.2024.116350},
pmid = {38705075},
issn = {1873-4235},
abstract = {Early monitoring of cardiovascular disease (CVD) is crucial for its treatment and prognosis. Hence, highly specific and sensitive detection method is urgently needed. In this study, we propose a novel herringbone microfluid chip with aptamer functionalized core-shell photonic crystal (PhC) barcode integration for high throughput multiplex CVD detection. Based on the PhC derived from co-assembled carboxylated single-wall carbon nanotubes and silicon dioxide nanoparticles, we obtain core-shell PhC barcodes by hydrogel replicating and partially etching. These core-shell PhC barcodes not only retain the original structural colors coding element, but also fully expose a large number of carboxyl elements in the ore for the probe immobilization. We further combine the functionalized barcodes with herringbone groove microfluidic chip to elucidate its acceptability in testing clinical sample. It is demonstrated that the special design of microfluidic chip can significantly enhance fluid vortex resistance and contact frequency, improving the sample capture efficiency and detection sensitivity. These features indicate that our core-shell PhC barcodes-integrated herringbone microfluidic system possesses great potential for multiplex biomarker detection in clinical application.},
}

@article {pmid38705192,
year = {2024},
author = {van Klink, R},
title = {Delivering on a promise: futureproofing automated insect monitoring methods.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230105},
doi = {10.1098/rstb.2023.0105},
pmid = {38705192},
issn = {1471-2970},
mesh = {Animals ; *Insecta/physiology ; *Biodiversity ; Entomology/methods/instrumentation/trends ; Automation/methods ; },
abstract = {Due to rapid technological innovations, the automated monitoring of insect assemblages comes within reach. However, this continuous innovation endangers the methodological continuity needed for calculating reliable biodiversity trends in the future. Maintaining methodological continuity over prolonged periods of time is not trivial, since technology improves, reference libraries grow and both the hard- and software used now may no longer be available in the future. Moreover, because data on many species are collected at the same time, there will be no simple way of calibrating the outputs of old and new devices. To ensure that reliable long-term biodiversity trends can be calculated using the collected data, I make four recommendations: (1) Construct devices to last for decades, and have a five-year overlap period when devices are replaced. (2) Construct new devices to resemble the old ones, especially when some kind of attractant (e.g. light) is used. Keep extremely detailed metadata on collection, detection and identification methods, including attractants, to enable this. (3) Store the raw data (sounds, images, DNA extracts, radar/lidar detections) for future reprocessing with updated classification systems. (4) Enable forward and backward compatibility of the processed data, for example by in-silico data 'degradation' to match the older data quality. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

Animals
*Insecta/physiology
*Biodiversity
Entomology/methods/instrumentation/trends
Automation/methods

@article {pmid38705180,
year = {2024},
author = {Li, R and Ratnasingham, S and Zarubiieva, I and Somervuo, P and Taylor, GW},
title = {PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230124},
doi = {10.1098/rstb.2023.0124},
pmid = {38705180},
issn = {1471-2970},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Algorithms ; Classification/methods ; Computer Graphics ; Animals ; },
abstract = {DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX's key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

*DNA Barcoding, Taxonomic/methods
*Algorithms
Classification/methods
Computer Graphics
Animals

@article {pmid38703100,
year = {2024},
author = {Molero-Baltanás, R and Mitchell, A and Gaju-Ricart, M and Robla, J},
title = {Worldwide revision of synanthropic silverfish (Insecta: Zygentoma: Lepismatidae) combining morphological and molecular data.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {3},
pages = {},
doi = {10.1093/jisesa/ieae045},
pmid = {38703100},
issn = {1536-2442},
support = {//the Australian Museum Research Institute/ ; //University of Córdoba/ ; },
mesh = {Animals ; *Phylogeny ; *Insecta/genetics/anatomy & histology/classification ; Female ; Male ; Animal Distribution ; },
abstract = {Synanthropic silverfish are the best-known and most widely distributed insects of the order Zygentoma. However, there is a great gap in the knowledge and confusion about the geographic distribution and the diagnostic characteristics that allow their identification. In this work, we provide an exhaustive and deep analysis of the most common 9 synanthropic silverfish of the world, combining previously published and newly derived morphological and molecular data. Updated descriptions of Ctenolepisma calvum (Ritter, 1910) and Ctenolepisma (Sceletolepisma) villosum (Fabricius, 1775) are included, and morphological remarks, illustrations, and photographs of the remaining synanthropic species are provided to clarify their diagnosis and differentiation among them and from other free-living species. In addition, Ctenolepisma targionii (Grassi and Rovelli, 1889) is synonymized with C. villosum. A molecular phylogeny is presented based on the COI sequences of all the synanthropic species deposited in BOLD and GenBank, with 15 new sequences provided by this study. This has allowed us to detect and correct a series of identification errors based on the lack of morphological knowledge of several species. Moreover, 2 different lineages of Ctenolepisma longicaudatumEscherich, 1905 have also been detected. To help future studies, we also provide a taxonomic interpretation guide for the most important diagnostic characters of the order Zygentoma, as well as an identification key for all the Synanthropic studied species. Finally, an approximation of the global distribution of synanthropic silverfish is discussed. Several new records indicate that the expansion of these species, generally associated with the transport of goods and people, is still far from over.},
}

Animals
*Phylogeny
*Insecta/genetics/anatomy & histology/classification
Female
Male
Animal Distribution

@article {pmid38703052,
year = {2024},
author = {Burg, S and Ovaskainen, O and Furneaux, B and Ivanova, N and Abrahamyan, A and Niittynen, P and Somervuo, P and Abrego, N},
title = {Experimental evidence that root-associated fungi improve plant growth at high altitude.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17376},
doi = {10.1111/mec.17376},
pmid = {38703052},
issn = {1365-294X},
support = {101057437//H2020 European Research Council/ ; 101059492//H2020 European Research Council/ ; 856506//H2020 European Research Council/ ; 30865//Research Council of Finland/ ; 336212//Research Council of Finland/ ; 342374//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 346492//Research Council of Finland/ ; },
abstract = {Unravelling how species communities change along environmental gradients requires a dual understanding: the direct responses of the species to their abiotic surroundings and the indirect variation of these responses through biotic interactions. Here, we focus on the interactive relationships between plants and their symbiotic root-associated fungi (RAF) along stressful abiotic gradients. We investigate whether variations in RAF community composition along altitudinal gradients influence plant growth at high altitudes, where both plants and fungi face harsher abiotic conditions. We established a translocation experiment between pairs of Bistorta vivipara populations across altitudinal gradients. To separate the impact of shifting fungal communities from the overall influence of changing abiotic conditions, we used a root barrier to prevent new colonization by RAF following translocation. To characterize the RAF communities, we applied DNA barcoding to the root samples. Through the utilization of joint species distribution modelling, we assessed the relationship between changes in plant functional traits resulting from experimental treatments and the corresponding changes in the RAF communities. Our findings indicate that RAF communities influence plant responses to stressful abiotic conditions. Plants translocated from low to high altitudes grew more when they were able to associate with the resident high-altitude RAF compared to those plants that were not allowed to associate with the resident RAF. We conclude that interactions with RAF impact how plants respond to stressful abiotic conditions. Our results provide experimental support that interactions with RAF improve plant stress tolerance to altitudinal stressors such as colder temperatures and less nutrient availability.},
}

@article {pmid38701091,
year = {2024},
author = {Aggarwal, S and Walker, FC and Weagley, JS and McCune, BT and Wu, X and Schriefer, LA and Makimaa, H and Lawrence, D and Sridhar, P and Baldridge, MT},
title = {Interferons and tuft cell numbers are bottlenecks for persistent murine norovirus infection.},
journal = {PLoS pathogens},
volume = {20},
number = {5},
pages = {e1011961},
doi = {10.1371/journal.ppat.1011961},
pmid = {38701091},
issn = {1553-7374},
abstract = {Noroviruses (NoVs) are a leading cause of viral gastroenteritis. Despite global clinical relevance, our understanding of how host factors, such as antiviral cytokines interferons (IFNs), modulate NoV population dynamics is limited. Murine NoV (MNoV) is a tractable in vivo model for the study of host regulation of NoV. A persistent strain of MNoV, CR6, establishes a reservoir in intestinal tuft cells for chronic viral shedding in stool. However, the influence of host innate immunity and permissive cell numbers on viral population dynamics is an open question. We generated a pool of 20 different barcoded viruses (CR6BC) by inserting 6-nucleotide barcodes at the 3' position of the NS4 gene and used this pool as our viral inoculum for in vivo infections of different mouse lines. We found that over the course of persistent CR6 infection, shed virus was predominantly colon-derived, and viral barcode richness decreased over time irrespective of host immune status, suggesting that persistent infection involves a series of reinfection events. In mice lacking the IFN-λ receptor, intestinal barcode richness was enhanced, correlating with increased viral intestinal replication. IL-4 treatment, which increases tuft cell numbers, also increased barcode richness, indicating the abundance of permissive tuft cells to be a bottleneck during CR6 infection. In mice lacking type I IFN signaling (Ifnar1-/-) or all IFN signaling (Stat1-/-), barcode diversity at extraintestinal sites was dramatically increased, implicating different IFNs as critical bottlenecks at specific tissue sites. Of interest, extraintestinal barcodes were overlapping but distinct from intestinal barcodes, indicating that disseminated virus represents a distinct viral population than that replicating in the intestine. Barcoded viruses are a valuable tool to explore the influence of host factors on viral diversity in the context of establishment and maintenance of infection as well as dissemination and have provided important insights into how NoV infection proceeds in immunocompetent and immunocompromised hosts.},
}

@article {pmid38699348,
year = {2024},
author = {Berleant, JD and Banal, JL and Rao, DK and Bathe, M},
title = {Scalable search of massively pooled nucleic acid samples enabled by a molecular database query language.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.12.24305660},
pmid = {38699348},
abstract = {The surge in nucleic acid analytics requires scalable storage and retrieval systems akin to electronic databases used to organize digital data. Such a system could transform disease diagnosis, ecological preservation, and molecular surveillance of biothreats. Current storage systems use individual containers for nucleic acid samples, requiring single-sample retrieval that falls short compared with digital databases that allow complex and combinatorial data retrieval on aggregated data. Here, we leverage protective microcapsules with combinatorial DNA labeling that enables arbitrary retrieval on pooled biosamples analogous to Structured Query Languages. Ninety-six encapsulated pooled mock SARS-CoV-2 genomic samples barcoded with patient metadata are used to demonstrate queries with simultaneous matches to sample collection date ranges, locations, and patient health statuses, illustrating how such flexible queries can be used to yield immunological or epidemiological insights. The approach applies to any biosample database labeled with orthogonal barcodes, enabling complex post-hoc analysis, for example, to study global biothreat epidemiology.},
}

@article {pmid38699326,
year = {2024},
author = {Zhuang, X and Vo, V and Moshi, MA and Dhede, K and Ghani, N and Akbar, S and Chang, CL and Young, AK and Buttery, E and Bendik, W and Zhang, H and Afzal, S and Moser, D and Cordes, D and Lockett, C and Gerrity, D and Kan, HY and Oh, EC},
title = {Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.18.24306052},
pmid = {38699326},
abstract = {Genome sequencing from wastewater has emerged as an accurate and cost-effective tool for identifying SARS-CoV-2 variants. However, existing methods for analyzing wastewater sequencing data are not designed to detect novel variants that have not been characterized in humans. Here, we present an unsupervised learning approach that clusters co-varying and time-evolving mutation patterns leading to the identification of SARS-CoV-2 variants. To build our model, we sequenced 3,659 wastewater samples collected over a span of more than two years from urban and rural locations in Southern Nevada. We then developed a multivariate independent component analysis (ICA)-based pipeline to transform mutation frequencies into independent sources with co-varying and time-evolving patterns and compared variant predictions to >5,000 SARS-CoV-2 clinical genomes isolated from Nevadans. Using the source patterns as data-driven reference "barcodes", we demonstrated the model's accuracy by successfully detecting the Delta variant in late 2021, Omicron variants in 2022, and emerging recombinant XBB variants in 2023. Our approach revealed the spatial and temporal dynamics of variants in both urban and rural regions; achieved earlier detection of most variants compared to other computational tools; and uncovered unique co-varying mutation patterns not associated with any known variant. The multivariate nature of our pipeline boosts statistical power and can support accurate and early detection of SARS-CoV-2 variants. This feature offers a unique opportunity for novel variant and pathogen detection, even in the absence of clinical testing.},
}

@article {pmid38695131,
year = {2024},
author = {Ramos, SC and Culver, M},
title = {Integration of Indigenous Research Methodologies, Traditional Ecological Knowledge and molecular scatology in an assessment of mesocarnivore presence, diet and habitat use on Yurok Ancestral Lands.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13963},
doi = {10.1111/1755-0998.13963},
pmid = {38695131},
issn = {1755-0998},
support = {2010-3-03//The University of Arizona/Sloan Indigenous Graduate Partnership Program/ ; 1906338//National Science Foundation/ ; },
abstract = {Partnerships between Tribes and researchers in wildlife monitoring and application of Traditional Ecological Knowledge (TEK) have taken a variety of forms, and some scholars have noted a need for culturally sensitive approaches. Guided by Indigenous Research Methodologies, this research is coupled with Yurok TEK, or hlkelonah 'ue-megetohl ('to take care of the earth'), enabling an applied, culturally sensitive approach in partnership with the Yurok Tribe. We present results from a molecular scatology study of wildlife within the ancestral territory of the Yurok Tribe. Scats were collected opportunistically on road transects. All samples (N = 132) were analysed via DNA barcoding and results matched to documented 'Oohl 'we-toh (Yurok language) names to determine the depositor species (N = 8). Though there were four focal mesocarnivore species in our study, only bobcat (Chmuuek; Lynx rufus) and gray fox (Wergers; Urocyon cinereoargenteus) were detected as depositor species. Post hoc analyses were conducted to explore distribution, habitat use and selection in a use-availability context, and food habits of these two species. We found almost complete separation of bobcat and gray fox use of transects, as well as indication of partitioning of vegetation cover types and food. We demonstrate an integrated framework of Western and Indigenous sciences that allows the Indigenous researcher to transcend structured academic disciplinary boundaries. Our approach can be modified for partnerships between Tribes, agencies, academics and students for wildlife monitoring in broader geographic regions in various research applications.},
}

@article {pmid38694266,
year = {2024},
author = {Ossowska, EA and Moncada, B and Lücking, R and Flakus, A and Rodriguez-Flakus, P and Olszewska, S and Kukwa, M},
title = {Additional new species and new records of the genus Sticta (lichenised Ascomycota, lobarioid Peltigeraceae) from Bolivia.},
journal = {MycoKeys},
volume = {105},
number = {},
pages = {21-47},
doi = {10.3897/mycokeys.105.120810},
pmid = {38694266},
issn = {1314-4049},
abstract = {Four species of the genus Sticta are described as new from Bolivia, based on morphological examination and phylogenetic analysis of the fungal ITS barcoding marker. Additionally, two species are reported as new to Bolivia (their identification confirmed by molecular data) and one previously reported species is confirmed by molecular data for the first time. Detailed morphological and anatomical descriptions are provided for all new species. Two of the new species, S.isidiolobulata Ossowska, B. Moncada, Lücking & Kukwa and S.madidiensis Ossowska, B. Moncada, Lücking & Kukwa belong to clade I, as defined in previous studies. In contrast, S.montepunkuensis Ossowska, B. Moncada, Lücking & Kukwa and S.macrolobata Ossowska, B. Moncada, Lücking & Kukwa, also described here as new to science, belong to clade III. Stictaisidiolobulata has an irregular to suborbicular thallus of medium size, with isidia developing into spathulate lobules, cyanobacterial photobiont and apothecia with entire to weakly-crenate margins. The large irregular thallus of the cyanobacteria-associated S.macrolobata has broad lobes, apothecia with verrucous to tomentose margins and cyphellae with raised margins, whereas S.madidiensis has a medium-sized, palmate to irregular thallus with a stipe, but without vegetative propagules and apothecia. Stictamontepunkuensis has large and irregular thalli with green algae as photobiont, apothecia with crenate to verrucous margins and urceolate cyphellae with a wide pore and a scabrid basal membrane. Two species, S.beauvoisii Delise and S.riparia Merc.-Díaz are reported as new to Bolivia (the latter also as new to South America) and belong to clade III. Stictatomentosa (Sw.) Ach., species confirmed from Bolivia by molecular data, belongs to clade II. Stictabeauvoisii is characterised by a smooth yellowish-brown upper surface with darker apices and abundant, marginal isidia and a brown lower surface with golden-chocolate brown primary tomentum and sparse, golden-brown rhizines. Stictariparia has a strongly branched thallus, with undulate lobes and abundant, marginal, palmate, grey to dark brown phyllidia and greyish-brown lower surface with the primary tomentum absent towards the margins. Stictatomentosa has palmate, bluish thalli with white cilia and abundant, submarginal apothecia and creamy-white lower surface with a sparse, white primary tomentum.},
}

@article {pmid38693183,
year = {2024},
author = {Moustafa, MAM and Mohamed, WMA and Chatanga, E and Nagib, D and Matsuno, K and Gofton, AW and Barker, SC and Nonaka, N and Nakao, R},
title = {Unraveling the phylogenetics of genetically closely related species, Haemaphysalis japonica and Haemaphysalis megaspinosa, using entire tick mitogenomes and microbiomes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9961},
pmid = {38693183},
issn = {2045-2322},
support = {16H06431//Japan Society for the Promotion of Science/ ; 19H03118//Japan Society for the Promotion of Science/ ; 19F19097//Japan Society for the Promotion of Science/ ; 20K21358//Japan Society for the Promotion of Science/ ; 20KK0151//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Phylogeny ; *Ixodidae/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Genome, Mitochondrial ; Genetic Variation ; },
abstract = {Ticks have a profound impact on public health. Haemaphysalis is one of the most widespread genera in Asia, including Japan. The taxonomy and genetic differentiation of Haemaphysalis spp. is challenging. For instance, previous studies struggled to distinguish Haemaphysalis japonica and Haemaphysalis megaspinosa due to the dearth of nucleotide sequence polymorphisms in widely used barcoding genes. The classification of H. japonica japonica and its related sub-species Haemaphysalis japonica douglasi or Haemaphysalis jezoensis is also confused due to their high morphological similarity and a lack of molecular data that support the current classification. We used mitogenomes and microbiomes of H. japonica and H. megaspinosa to gain deeper insights into the phylogenetic relationships and genetic divergence between two species. Phylogenetic analyses of concatenated nucleotide sequences of protein-coding genes and ribosomal DNA genes distinguished H. japonica and H. megaspinosa as monophyletic clades, with further subdivision within the H. japonica clade. The 16S rRNA and NAD5 genes were valuable markers for distinguishing H. japonica and H. megaspinosa. Population genetic structure analyses indicated that genetic variation within populations accounted for a large proportion of the total variation compared to variation between populations. Microbiome analyses revealed differences in alpha and beta diversity between H. japonica and H. megaspinosa: H. japonica had the higher diversity. Coxiella sp., a likely endosymbiont, was found in both Haemaphysalis species. The abundance profiles of likely endosymbionts, pathogens, and commensals differed between H. japonica and H. megaspinosa: H. megaspinosa was more diverse.},
}

Animals
*Phylogeny
*Ixodidae/microbiology/genetics
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
Genome, Mitochondrial
Genetic Variation

@article {pmid38690989,
year = {2024},
author = {Li, J and Li, M and Wuethrich, A and Guan, R and Zhao, L and Hu, C and Trau, M and Sun, Y},
title = {Molecular Stratification and Treatment Monitoring of Lung Cancer Using a Small Extracellular Vesicle-Activated Nanocavity Architecture.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c00558},
pmid = {38690989},
issn = {1520-6882},
abstract = {Development of molecular diagnostics for lung cancer stratification and monitoring is crucial for the rational planning and timely adjustment of treatments to improve clinical outcomes. In this regard, we propose a nanocavity architecture to sensitively profile the protein signature on small extracellular vesicles (sEVs) to enable accurate, noninvasive staging and treatment monitoring of lung cancer. The nanocavity architecture is formed by molecular recognition through the binding of sEVs with the nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and mirrorlike, asymmetric gold microelectrodes. By imposing an alternating current on the gold microelectrodes, a nanofluidic shear force was stimulated that supported the binding of sEVs and the efficient assembly of the nanoboxes. The binding of sEVs further induced a nanocavity between the nanobox and the gold microelectrode that significantly amplified the electromagnetic field to enable the simultaneous enhancement of Raman signals from four SERS barcodes and generate patient-specific molecular sEV signatures. Importantly, evaluated on a cohort of clinical samples (n = 76) on the nanocavity architecture, the acquired patient-specific sEV molecular signatures achieved accurate identification, stratification, and treatment monitoring of lung cancer patients, highlighting its potential for transition to clinical utility.},
}

@article {pmid38688969,
year = {2024},
author = {Blanc-Benigeri, A and Poirier, V and Narango, D and Elliott, KH and Frei, B},
title = {Diet of moulting Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) at a stopover site during fall migration measured with fecal DNA metabarcoding.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9913},
pmid = {38688969},
issn = {2045-2322},
support = {#522431//Natural Sciences and Engineering Research Council of Canada-Undergraduate Student Research Award (NSERC USRA)/ ; #320544//Graduate Scholarship-Master's (CGS M) award, a Fonds de recherche du Québec-Nature et technologies (FRQNT)/ ; },
mesh = {Animals ; *Animal Migration/physiology ; *Songbirds/physiology ; *Diet ; *Feces/chemistry ; DNA Barcoding, Taxonomic/methods ; Seasons ; },
abstract = {Moult and migration are energetically demanding and require adequate nutrition. In some species, individuals may interrupt their fall migration to moult at discrete stopover locations outside of their breeding grounds (i.e., moult-migration) leading to competing nutritional demands for moult and migration. Here, we use DNA barcoding of fecal samples to compare the diet of moulting and actively migrating (post-moult) Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) during their fall migration stopover at a large urban greenspace in Montreal, Canada. Diet differed according to moult status, species, and seasonality. Swainson's Thrushes had a broad diet with frequent detections of both insects and berry-producing shrubs; while detections in Tennessee Warblers' diets were mainly arthropods. For both species, more actively migrating individuals consumed fleshy-fruiting plants than moulting individuals. A higher proportion of moulting birds consumed arthropods compared to active migrants, due to either arthropod availability or a dietary preference for proteinaceous foods to grow feathers. Both species and moult classes consumed more native plants than non-native plants later in the season. We show the importance of managing urban greenspaces with native plants and diverse food sources that can provide for the different dietary needs of migratory birds.},
}

Animals
*Animal Migration/physiology
*Songbirds/physiology
*Diet
*Feces/chemistry
DNA Barcoding, Taxonomic/methods
Seasons

@article {pmid38684618,
year = {2024},
author = {Wang, X and Zhang, Z and Shi, Y and Man, J and Huang, Y and Zhang, X and Liu, S and He, G and An, K and Amu, L and Chen, W and Liu, Z and Wang, X and Wei, S},
title = {Population identification and genetic diversity analysis of Fritillaria ussuriensis (Fritillaria) based on chloroplast genes atpF and petB.},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {38684618},
issn = {2190-3883},
support = {20221156//study on breeding and cultivation technology of precision medicine Bupleurum bupleurum based on molecular anti-counterfeiting technology/ ; 2020110031009385//research project on molecular anti-counterfeiting technology of 4 precision medicinal materials such as Platycodon grandiflorus/ ; 2022YFC3501505//National Key Research and Development Program of China/ ; },
abstract = {The chloroplast genomes of five Fritillaria ussuriensis materials from different production areas were comparatively analyzed, atpF and petB were screened as specific DNA barcodes, and the population identification and genetic diversity of F. ussuriensis were analyzed based on them. The F. ussuriensis chloroplast genome showed a total length of 151 515-151 548 bp with a typical tetrad structure and encoded 130 genes. atpF and petB were used to amplify 183 samples from 13 populations, and they could identify 6 and 9 haplotypes, respectively. Joint analysis of the two sequences revealed 18 haplotypes, named H1-H18, with the most widely distributed and most abundant being H4. Ten haplotypes were unique for 7 populations that they could be used to distinguish from others. Haplotype diversity and nucleotide diversity were 0.99 and 2.09 × 10[-3], respectively, indicating the genetic diversity was relatively rich. The results of the intermediary adjacency network showed that H5 was the oldest haplotype, and stellate radiation was centered around it, indicating that population expansion occurred in genuine production areas. This study lays a theoretical foundation for the population identification, genetic evolution, and breed selection of F. ussuriensis.},
}

@article {pmid38683343,
year = {2024},
author = {Vences, M and Miralles, A and DeSalle, R},
title = {A Glossary of DNA Barcoding Terms.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {561-572},
pmid = {38683343},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Terminology as Topic ; DNA/genetics ; Humans ; },
abstract = {This chapter provides a reference glossary for the protocols in this volume. We have chosen only the very basic terms in the DNA barcode lexicon to include, and provide clear and concise definitions of these terms. We hope the reader finds this glossary useful.},
}

*DNA Barcoding, Taxonomic/methods
Terminology as Topic
DNA/genetics
Humans

@article {pmid38683342,
year = {2024},
author = {Williams, J and Nash, B and Ghiban, C and Khalfan, M and Hilgert, U and Lauter, S and Yang, CH and Micklos, DA},
title = {Analysis of DNA Barcodes Using DNA Subway.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {551-560},
pmid = {38683342},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; DNA/genetics ; Workflow ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads. During analysis, users can view trace files and sequence quality, pair and align forward and reverse reads, create and trim consensus sequences, perform BLAST searches, select reference data, align multiple sequences, and compute phylogenetic trees. High-quality sequences with the required metadata can also be submitted as barcode sequences to NCBI GenBank.},
}

*DNA Barcoding, Taxonomic/methods
*Software
*Computational Biology/methods
Phylogeny
DNA/genetics
Workflow
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid38683341,
year = {2024},
author = {Shumskaya, M},
title = {DNA Barcoding for an Undergraduate Class.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {537-550},
pmid = {38683341},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Students ; Universities ; DNA/genetics/analysis ; Humans ; Curriculum ; Polymerase Chain Reaction/methods ; },
abstract = {DNA technique is a topic mandatorily covered in a biology and biochemistry undergraduate curriculum. Inquiry-based pedagogy is proven to be the most effective way of learning, and DNA barcoding method allows to merge necessary-to-study experimental techniques such as DNA isolation and purification, PCR, and basic BLAST search into a two- or three-week inquiry-based student project. It also provides a research-based experience to the students, who, when organized in groups, can design their own DNA-barcoding project if they wish. Here, we describe how DNA barcoding can be offered in an undergraduate college or advanced high school settings. This chapter is intended to help college and high school instructors to include DNA barcoding in their classes.},
}

*DNA Barcoding, Taxonomic/methods
*Students
Universities
DNA/genetics/analysis
Humans
Curriculum
Polymerase Chain Reaction/methods

@article {pmid38683340,
year = {2024},
author = {Wright, L and Garbarino, J and Marizzi, C},
title = {Engaging Students and Teachers as Community Scientists in DNA Barcoding Initiatives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {525-535},
pmid = {38683340},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Students ; Humans ; Curriculum ; Faculty ; },
abstract = {Historically, contributions to scientific knowledge have been perceived as something that only professional scientists have the ability to affect. This has led to the belief that scientific pursuits are done not by everyday people but by individuals who have no connection to the communities that their discoveries might impact. DNA barcoding initiatives have the potential to bridge this gap. Community leaders, students, teachers, and other community members can come together with engaged scientists to solve relevant issues that affect them. Over the last 20 years, DNA barcoding has been used successfully in a variety of educational contexts to incorporate original research into school curricula and informal outreach and education programs. DNA barcoding is especially suitable for educational settings because it is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and free and open-access online tools exist that allow participants to contribute high-quality data to international research efforts. DNA barcoding also offers a unique service-learning opportunity, where participants gain both knowledge and confidence in science. This is important because a growing body of evidence suggests that actively conducting research increases student and teacher engagement and retention of students in science. Here, we describe a framework and case studies in different educational settings that can be modeled and adapted to various educational contexts.},
}

*DNA Barcoding, Taxonomic/methods
*Students
Humans
Curriculum
Faculty

@article {pmid38683339,
year = {2024},
author = {Pepenella, S and Hackett, J and Fernandez-Marco, C and Petracca, J and Marizzi, C and Nash, B and Micklos, DA},
title = {A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {517-523},
pmid = {38683339},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA/isolation & purification/genetics ; DNA, Plant/genetics/isolation & purification ; Plants/genetics ; Chromatography/methods ; Lichens/genetics ; },
abstract = {This rapid, equipment-free DNA isolation procedure using chromatography paper is a simple method that can be performed in less than 30 min and requires no wet lab experience. With minimal expense, it offers an affordable alternative for anyone wanting to explore biodiversity. It also provides an excellent option for use in classrooms or other activities that are time limited. The method works best for plants or lichens, producing stable DNA on Whatman® chromatography paper at room temperature, which can be eluted as needed.},
}

*DNA Barcoding, Taxonomic/methods
DNA/isolation & purification/genetics
DNA, Plant/genetics/isolation & purification
Plants/genetics
Chromatography/methods
Lichens/genetics

@article {pmid38683338,
year = {2024},
author = {Wangh, LJ and Rice, JE and Sanchez, JA},
title = {Recent Applications of FastFish-ID.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {503-514},
pmid = {38683338},
issn = {1940-6029},
mesh = {Animals ; *Fishes ; *Sharks ; *DNA Barcoding, Taxonomic/methods ; Animal Fins ; },
abstract = {FastFish-ID via Closed-Tube barcoding is a portable platform for rapid and accurate identification of fish species that was conceived at Brandeis University, commercialized at Thermagenix, Inc., and further improved at Ecologenix, LLC (see Chap. 17 in this volume). This chapter focuses on the use of FastFish-ID for (1) identification of intraspecies variants, (2) quantitative use of FastFish-ID to measure the decay of fresh fish, and (3) use of FastFish-ID for the identification of dried and processed shark fins.},
}

Animals
*Fishes
*Sharks
*DNA Barcoding, Taxonomic/methods
Animal Fins

@article {pmid38683337,
year = {2024},
author = {Gwiazdowski, R},
title = {Principles for Constructing DNA Barcode Reference Libraries.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {491-502},
pmid = {38683337},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Gene Library ; Reference Standards ; DNA/genetics ; Humans ; },
abstract = {All DNA barcode methods rely on reference sequences linked to well-curated voucher specimens. Definitions for and locations of DNA barcode reference libraries are not standardized, and vary throughout the literature. Standardizing, and centralizing reference specimens would provide an unambiguous source, analogous to reference genomes, to reproduce identifications and improve a library. This chapter proposes a working definition of a DNA barcode reference library, consistent with DNA barcode data standards, along with principles and methods to consider when producing or using such a library. These methods allow explicit traceback to sequence-sources which elevate the value of voucher specimens, and create a potential for community curation.},
}

*DNA Barcoding, Taxonomic/methods
*Gene Library
Reference Standards
DNA/genetics
Humans

@article {pmid38683336,
year = {2024},
author = {O'Brien, TD and Blanco-Bercial, L and Questel, JM and Batta-Lona, PG and Bucklin, A},
title = {MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {475-489},
pmid = {38683336},
issn = {1940-6029},
mesh = {Animals ; *Aquatic Organisms/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Ecosystem ; Databases, Genetic ; Databases, Nucleic Acid ; },
abstract = {The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles). DNA sequences currently included are mitochondrial cytochrome oxidase I (COI), 12S, and 16S rRNA, and nuclear 18S and 28S rRNA. The MZGdb provides data and mapping tools for assembling and downloading compilations of reference sequence data that are specific to selected genes, taxonomic groups, and/or ocean regions. An additional feature of the MZGdb is the Atlas which summarizes data coverage and proportional completeness based on statistics of species with available sequences versus species commonly found in each ocean region.This chapter is a collaborative effort of the Scientific Committee for Ocean Research (SCOR) Working Group WG157: MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases (https://metazoogene.org).},
}

Animals
*Aquatic Organisms/genetics/classification
*DNA Barcoding, Taxonomic/methods
*Biodiversity
Ecosystem
Databases, Genetic
Databases, Nucleic Acid

@article {pmid38683335,
year = {2024},
author = {Whitley, BS and Li, Z and Jones, L and de Vere, N},
title = {Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {445-473},
pmid = {38683335},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants/genetics ; *DNA, Plant/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Gene Library ; },
abstract = {Plant DNA barcoding has a multitude of applications ranging from species detection and biomonitoring to investigating ecological networks and checking food quality. The ability to accurately identify species, using DNA barcoding, depends on the quality and comprehensiveness of the reference library that is used. This chapter describes how to create plant reference libraries using the rbcL, matK, and ITS2 DNA barcode regions. It covers the creation of species lists, the collection of specimens from the field and herbarium, DNA extraction, PCR amplification, and DNA sequencing. This methodology gives special attention to using samples from herbaria, as they represent important collections of easily accessible, taxonomically verified plant material.},
}

*DNA Barcoding, Taxonomic/methods
*Plants/genetics
*DNA, Plant/genetics
Polymerase Chain Reaction/methods
Sequence Analysis, DNA/methods
Gene Library

@article {pmid38683334,
year = {2024},
author = {Ratnasingham, S and Wei, C and Chan, D and Agda, J and Agda, J and Ballesteros-Mejia, L and Boutou, HA and El Bastami, ZM and Ma, E and Manjunath, R and Rea, D and Ho, C and Telfer, A and McKeowan, J and Rahulan, M and Steinke, C and Dorsheimer, J and Milton, M and Hebert, PDN},
title = {BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {403-441},
pmid = {38683334},
issn = {1940-6029},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; Software ; DNA/genetics ; },
abstract = {BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, makes it a central resource for biodiversity science. It enables rapid, accurate identification of specimens and also reveals patterns of genetic diversity and evolutionary relationships among taxa.Launched in 2005, BOLD has become an increasingly powerful tool for advancing the understanding of planetary biodiversity. It currently hosts 17 million specimen records and 14 million barcodes that provide coverage for more than a million species from every continent and ocean. The platform has the long-term goal of providing a consistent, accurate system for identifying all species of eukaryotes.BOLD's integrated analytical tools, full data lifecycle support, and secure collaboration framework distinguish it from other biodiversity platforms. BOLD v4 brought enhanced data management and analysis capabilities as well as novel functionality for data dissemination and publication. Its next version will include features to strengthen its utility to the research community, governments, industry, and society-at-large.},
}

*Biodiversity
*DNA Barcoding, Taxonomic/methods
*Computational Biology/methods
Software
DNA/genetics

@article {pmid38683333,
year = {2024},
author = {Damaso, N and Elwick, KE and Robertson, JM},
title = {Guidelines for the Analysis of DNA Barcoding/Metabarcoding Sequencing Data and Interpretation of Publicly Available Databases.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {391-402},
pmid = {38683333},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Databases, Nucleic Acid ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Databases, Genetic ; Software ; },
abstract = {This chapter describes procedures for the use of DNA sequence data to obtain and compare taxonomic identification using the public databases GenBank and Barcode of Life Data System (BOLD). The chapter begins by describing procedures used to prepare quality sequences for uploading into GenBank and BOLD. Next, steps used to query the DNA sequences against the public databases are described using GenBank BLAST and BOLD identification engines. Interpretation guidelines for the taxonomic identification assignments are presented. Finally, a procedure for evaluating the accuracy and reliability of sequences from GenBank and BOLD is provided.},
}

*DNA Barcoding, Taxonomic/methods
*Databases, Nucleic Acid
Computational Biology/methods
Sequence Analysis, DNA/methods
Databases, Genetic
Software

@article {pmid38683332,
year = {2024},
author = {Phillips, JD and Griswold, CK and Young, RG and Hubert, N and Hanner, RH},
title = {A Measure of the DNA Barcode Gap for Applied and Basic Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {375-390},
pmid = {38683332},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Coleoptera/genetics/classification ; DNA/genetics/analysis ; Species Specificity ; },
abstract = {DNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a "DNA barcode gap"-the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives. Furthermore, both theory and empirical work indicate a gap may not occur for related pairs of biological species. Here, we present a novel evaluation approach in the form of an easily calculated set of nonparametric metrics to quantify the extent of proportional overlap in inter- and intraspecific distributions of pairwise differences among target species and their conspecifics. The metrics are based on a simple count of the number of overlapping records for a species falling within the bounds of maximum intraspecific distance and minimum interspecific distance. Our approach takes advantage of the asymmetric directionality inherent in pairwise genetic distance distributions, which has not been previously done in the DNA barcoding literature. We apply the metrics to the predatory diving beetle genus Agabus as a case study because this group poses significant identification challenges due to its morphological uniformity despite both relative sampling ease and well-established taxonomy. Results herein show that target species and their nearest neighbor species were found to be tightly clustered and therefore difficult to distinguish. Such findings demonstrate that DNA barcoding can fail to fully resolve species in certain cases. Moving forward, we suggest the implementation of the proposed metrics be integrated into a common framework to be reported in any study that uses DNA barcoding for identification. In so doing, the importance of the DNA barcode gap and its components for the success of DNA-based identification using DNA barcodes can be better appreciated.},
}

*DNA Barcoding, Taxonomic/methods
Animals
Coleoptera/genetics/classification
DNA/genetics/analysis
Species Specificity

@article {pmid38683331,
year = {2024},
author = {Mahmoud, MAB},
title = {Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {359-373},
pmid = {38683331},
issn = {1940-6029},
mesh = {*Algorithms ; *Neural Networks, Computer ; DNA/genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; Humans ; Deep Learning ; },
abstract = {This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-fixed dimensions, which correspond to the length of the sequences. Through computational procedures such as one-hot encoding, numerical encoding plays an important role in DNA sequence evaluation (OHE). However, the OHE method has some disadvantages: (1) It does not add any details that could result in an additional predictive variable, and (2) if the variable has many classes, OHE significantly expands the feature space. To address these shortcomings, this chapter proposes a computationally efficient framework for classifying DNA sequences of living organisms in the image domain. A multilayer perceptron trained by a pseudoinverse learning autoencoder (PILAE) algorithm is used in the proposed strategy. The learning control parameters and the number of hidden layers do not have to be specified during the PILAE training process. As a result, the PILAE classifier outperforms other deep neural network (DNN) strategies such as the VGG-16 and Xception models.},
}

*Algorithms
*Neural Networks, Computer
DNA/genetics
Computational Biology/methods
DNA Barcoding, Taxonomic/methods
Sequence Analysis, DNA/methods
Humans
Deep Learning

@article {pmid38683330,
year = {2024},
author = {Bergmann, T},
title = {CAOS-R: Character-Based Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {347-357},
pmid = {38683330},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; },
abstract = {CAOS-Barcoding is a culmination of traditional taxonomy and modern DNA barcoding. CAOS identifies taxa by diagnostic characters as is done in traditional taxonomy and produces an identification matrix for taxon discrimination similar to DNA barcoding distance matrices. Here, I describe how to set up the CAOS-Barcoder and CAOS-Classifier software, which input data is needed, and how to interpret the output data. With the CAOS-Barcoder, single marker or concatenated data can be processed into diagnostic barcodes for taxon discrimination. The CAOS-Classifier can use the diagnostic barcodes for specimen identification.},
}

*DNA Barcoding, Taxonomic/methods
*Software

@article {pmid38683329,
year = {2024},
author = {Ramanan, V and Sarkar, IN},
title = {Characteristic Attribute Organization System (CAOS): Identifying Classification Rules Based on Phylogenetically Organized Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {335-345},
pmid = {38683329},
issn = {1940-6029},
mesh = {*Phylogeny ; *Software ; Computational Biology/methods ; Algorithms ; Sequence Alignment/methods ; },
abstract = {Classification is a technique that labels subjects based on the characteristics of the data. It often includes using prior learned information from preexisting data drawn from the same distribution or data type to make informed decisions per each given subject. The method presented here, the Characteristic Attribute Organization System (CAOS), uses a character-based approach to molecular sequence classification. Using a set of aligned sequences (either nucleotide or amino acid) and a maximum parsimony tree, CAOS will generate classification rules for the sequences based on tree structure and provide more interpretable results than other classification or sequence analysis protocols. The code is accessible at https://github.com/JuliaHealth/CAOS.jl/ .},
}

*Phylogeny
*Software
Computational Biology/methods
Algorithms
Sequence Alignment/methods

@article {pmid38683328,
year = {2024},
author = {Puillandre, N and Miralles, A and Brouillet, S and Fedosov, A and Fischell, F and Patmanidis, S and Vences, M},
title = {Species Delimitation and Exploration of Species Partitions with ASAP and LIMES.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {313-334},
pmid = {38683328},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Biodiversity ; Phylogeny ; Species Specificity ; Animals ; Genetic Speciation ; },
abstract = {DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES).},
}

*DNA Barcoding, Taxonomic/methods
*Software
*Computational Biology/methods
Biodiversity
Phylogeny
Species Specificity
Animals
Genetic Speciation

@article {pmid38683327,
year = {2024},
author = {Fedosov, A and Puillandre, N and Fischell, F and Patmanidis, S and Miralles, A and Vences, M},
title = {DNA Barcode-Based Species Diagnosis with MolD.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {297-311},
pmid = {38683327},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; Biodiversity ; },
abstract = {Rapid biodiversity loss sets new requirements for taxonomic research, prompting updating some long-established practices to maximize timely documentation of species before they have gone extinct. One of the crucial procedures associated with the description of new taxa in Linnean taxonomy is assigning them a diagnosis, which is an account of the specific features of the taxon, differentiating it from already described species. Traditionally, diagnostic characters have been morphological, but especially in the case of morphologically cryptic species, molecular diagnoses become increasingly important. In this chapter, we provide detailed protocols for molecular taxon diagnosis with the bioinformatic tool MolD which is available as open-source Python code, command-line driven binary, GUI-driven executable for Windows and Mac, and Galaxy implementation. MolD identifies diagnostic combinations of nucleotides (DNCs) in addition to single (pure) diagnostic sites, enabling users to base DNA diagnoses on a minimal number of diagnostic sites necessary for reliable differentiation of taxa.},
}

*DNA Barcoding, Taxonomic/methods
*Software
*Computational Biology/methods
Phylogeny
Biodiversity

@article {pmid38683326,
year = {2024},
author = {Vences, M and Patmanidis, S and Fedosov, A and Miralles, A and Puillandre, N},
title = {iTaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {281-296},
pmid = {38683326},
issn = {1940-6029},
mesh = {*Software ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA/genetics ; },
abstract = {The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output.},
}

*Software
*DNA Barcoding, Taxonomic/methods
Computational Biology/methods
DNA/genetics

@article {pmid38683325,
year = {2024},
author = {Sanchez, JA and Rice, JE and Wangh, LJ},
title = {Recent Advances in Closed-Tube Barcoding for FastFish-ID.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {267-278},
pmid = {38683325},
issn = {1940-6029},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; Seafood ; Polymerase Chain Reaction/methods ; DNA, Mitochondrial/genetics ; Fisheries ; },
abstract = {FastFish-ID for rapid and accurate identification of fish species was conceived at Brandeis University based on pioneering work on Closed-Tube Barcoding (Rice et al., Mitochondrial DNA Part A 27(2):1358-1363, 2016; Sirianni et al., Genome 59:1049-1061, 2016). FastFish-ID was subsequently validated and commercialized at Thermagenix, Inc. using a portable device and high-precision PCR (Naaum et al., Food Res Int 141:110035, 2021). The motivation for these efforts was the pressing need for a technology that could be widely used throughout the seafood supply chain to combat IUU Fishing (Helyar et al., PLOS ONE 9, 2014) and overfishing (FAO, State of the World Fisheries and Aquaculture 2018. http://www.fao.org/documents/card/en/c/I9540EN/ , 2018), along with seafood fraud and mislabeling (Watson et al., Fish Fish 17:585-595, 2015). These destructive practices are wasting fish stocks, frustrating attempts to achieve seafood sustainability, endangering oceanic ecosystems, and causing consumers billions of dollars each year (Porterfield et al., Oceana: February, 2022). During the past three Covid19 pandemic years, EcologeniX, LLC has taken over further development and optimization of FastFish-ID. The present chapter provides an overview of the improvements introduced throughout the FastFish-ID process.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/genetics/classification
Seafood
Polymerase Chain Reaction/methods
DNA, Mitochondrial/genetics
Fisheries

@article {pmid38683323,
year = {2024},
author = {Liu, R and Wang, Y and Yao, X and Liu, C},
title = {Generating 2D Barcode for DNA Barcode Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {239-246},
pmid = {38683323},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; DNA/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {DNA barcode sequence is a short DNA sequence representing a sample from a particular species. The commonly used DNA barcodes are at least 200 bps long. This large number of characters cannot be encoded in two-dimensional codes for sample recognition and tracking. In the present study, we described a method that can be used to compress the DNA sequences and then generate the corresponding QR code. With the large numbers of software and hardware, the QR code can be used efficiently for printing, labeling, and scanning.},
}

*DNA Barcoding, Taxonomic/methods
*Software
DNA/genetics
Sequence Analysis, DNA/methods

@article {pmid38683322,
year = {2024},
author = {Srivathsan, A and Meier, R},
title = {Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {223-238},
pmid = {38683322},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods/economics ; *Nanopore Sequencing/methods ; Cost-Benefit Analysis ; High-Throughput Nucleotide Sequencing/methods/economics ; Software ; Gene Library ; Sequence Analysis, DNA/methods/economics ; Workflow ; DNA/genetics ; },
abstract = {DNA barcodes are useful in biodiversity research, but sequencing barcodes with dye termination methods ("Sanger sequencing") has been so time-consuming and expensive that DNA barcodes are not as widely used as they should be. Fortunately, MinION sequencers from Oxford Nanopore Technologies have recently emerged as a cost-effective and efficient alternative for barcoding. MinION barcodes are now suitable for large-scale species discovery and enable specimen identification when the target species are represented in barcode databases. With a MinION, it is possible to obtain 10,000 barcodes from a single flow cell at a cost of less than 0.10 USD per specimen. Additionally, a Flongle flow cell can be used for small projects requiring up to 300 barcodes (0.50 USD per specimen). We here describe a cost-effective laboratory workflow for obtaining tagged amplicons, preparing ONT libraries, sequencing amplicon pools, and analyzing the MinION reads with the software ONTbarcoder. This workflow has been shown to yield highly accurate barcodes that are 99.99% identical to Sanger barcodes. Overall, we propose that the use of MinION for DNA barcoding is an attractive option for all researchers in need of a cost-effective and efficient solution for large-scale species discovery and specimen identification.},
}

*DNA Barcoding, Taxonomic/methods/economics
*Nanopore Sequencing/methods
Cost-Benefit Analysis
High-Throughput Nucleotide Sequencing/methods/economics
Software
Gene Library
Sequence Analysis, DNA/methods/economics
Workflow
DNA/genetics

@article {pmid38683321,
year = {2024},
author = {Ivanov, V and Lee, KM and Mutanen, M},
title = {ddRAD Sequencing and DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {213-221},
pmid = {38683321},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; DNA/genetics ; Gene Library ; Humans ; },
abstract = {Double-digest restriction site-associated DNA sequencing is a library preparation protocol that enables capturing variable sites across the genome including single-nucleotide polymorphisms (SNPs). These SNPs can be utilized to gain evolutionary insights into patterns observed in DNA barcodes, to infer population structure and phylogenies, to detect gene flow and introgression, and to perform species delimitation analyses. The protocol includes chemically shearing genomic DNA with restriction enzymes, unique tagging, size selection, and amplification of the resulting DNA fragments. Here we provide a detailed description of each step of the protocol, as well as information on essential equipment and common issues encountered during laboratory work.},
}

*DNA Barcoding, Taxonomic/methods
*Polymorphism, Single Nucleotide
*Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
DNA/genetics
Gene Library
Humans

@article {pmid38683320,
year = {2024},
author = {Seth, S and Bhattacharya, A},
title = {DNA Barcodes Using a Dual Nanopore Device.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {197-211},
pmid = {38683320},
issn = {1940-6029},
mesh = {*Nanopores ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; DNA/chemistry/genetics ; },
abstract = {We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.},
}

*Nanopores
*DNA Barcoding, Taxonomic/methods
*Algorithms
DNA/chemistry/genetics

@article {pmid38683319,
year = {2024},
author = {Sethi, S and Wijesinghe, KM and Dhakal, S},
title = {Single-Molecule FRET-Based Multiplexed Detection.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {183-195},
pmid = {38683319},
issn = {1940-6029},
mesh = {*Fluorescence Resonance Energy Transfer/methods ; *Single Molecule Imaging/methods ; *Fluorescent Dyes/chemistry ; Biosensing Techniques/methods ; Humans ; },
abstract = {Single-molecule multiplexed detection is a high-promise toolkit for the expanding field of biosensing and molecular diagnostics. Among many single-molecule techniques available today for biomarker sensing including fluorescence, force, electrochemical, spectroscopic, barcoding, and other techniques, fluorescence-based approaches are arguably the most widely used methods due to their high sensitivity, selectivity, and readily available fluorophore-labeling schemes for a wide variety of biomolecules. However, multiplexed imaging using fluorescence techniques has proven to be challenging due to the sophisticated labeling schemes often requiring multiple FRET (fluorescence resonance energy transfer) pairs and/or excitation sources, which lead to overlapping signals and complicate data analysis. Here, we describe a single-molecule FRET method that enables multiplexed analysis while still using only one FRET pair, and thus the described approach is a significant step forward from conventional FRET methods.},
}

*Fluorescence Resonance Energy Transfer/methods
*Single Molecule Imaging/methods
*Fluorescent Dyes/chemistry
Biosensing Techniques/methods
Humans

@article {pmid38683317,
year = {2024},
author = {Elwick, KE and Damaso, N and Robertson, JM},
title = {DNA Barcoding and Metabarcoding Protocols for Species Identification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {155-169},
pmid = {38683317},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Animals ; *Plants/genetics ; Insecta/genetics/classification ; Fungi/genetics/classification ; Sequence Analysis, DNA/methods ; Gene Library ; DNA/genetics ; },
abstract = {The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.},
}

*DNA Barcoding, Taxonomic/methods
*High-Throughput Nucleotide Sequencing/methods
Animals
*Plants/genetics
Insecta/genetics/classification
Fungi/genetics/classification
Sequence Analysis, DNA/methods
Gene Library
DNA/genetics

@article {pmid38683316,
year = {2024},
author = {David, A and Deepa Arul Priya, J and Gautam, A},
title = {DNA Sequencing Technologies and DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {139-154},
pmid = {38683316},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Biodiversity ; DNA/genetics ; Animals ; },
abstract = {DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger's method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.},
}

*DNA Barcoding, Taxonomic/methods
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Biodiversity
DNA/genetics
Animals

@article {pmid38683315,
year = {2024},
author = {Hyman, O and Cass, A and Enke, R and Storm, A and Nash, B},
title = {Cost-Effective DNA Extraction for DNA Barcoding Diverse Biological Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {129-137},
pmid = {38683315},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA/genetics/isolation & purification ; *Cost-Benefit Analysis ; Polymerase Chain Reaction/methods ; Plants/genetics ; },
abstract = {DNA barcoding employs standard molecular techniques (e.g., DNA extraction, PCR, and Sanger sequencing) to taxonomically identify biological samples. While DNA barcoding is a useful experimental workflow for in-class active learning exercises, extracting DNA from diverse sample types in a time and cost-effective manner can be challenging in a classroom setting. Here, we provide two time and cost-effective methods that have been used by novice students to successfully extract DNA from a variety of animal, fungal, algal, and plant tissues for DNA barcoding.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*DNA/genetics/isolation & purification
*Cost-Benefit Analysis
Polymerase Chain Reaction/methods
Plants/genetics

@article {pmid38683314,
year = {2024},
author = {Hackett, J and Pepenella, S and Marco, CF and Bodt, L and Grajales, LR and Petracca, J and Burke, J and Mayle, A and Nash, B and Micklos, DA},
title = {Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {119-127},
pmid = {38683314},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; *Polymerase Chain Reaction/methods ; Invertebrates/genetics/classification ; DNA/genetics/isolation & purification ; },
abstract = {Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Electron Transport Complex IV/genetics
*Polymerase Chain Reaction/methods
Invertebrates/genetics/classification
DNA/genetics/isolation & purification

@article {pmid38683313,
year = {2024},
author = {Brower, AVZ and DeSalle, R},
title = {DNA Barcodes in Taxonomic Descriptions.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {105-115},
pmid = {38683313},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Software ; DNA/genetics ; Animals ; Phylogeny ; },
abstract = {This chapter discusses methods for incorporating DNA barcode information into formal taxonomic descriptions. We first review what a formal description entails and then discuss previous attempts to incorporate barcode information into taxonomic descriptions. Several computer programs are listed that extract diagnostics from DNA barcode data. Finally, we examine a test case (Astraptes taxonomy).},
}

*DNA Barcoding, Taxonomic/methods
Software
DNA/genetics
Animals
Phylogeny

@article {pmid38683312,
year = {2024},
author = {Miralles, A and Puillandre, N and Vences, M},
title = {DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {77-104},
pmid = {38683312},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Classification/methods ; Phylogeny ; Animals ; Species Specificity ; },
abstract = {Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.},
}

*DNA Barcoding, Taxonomic/methods
Classification/methods
Phylogeny
Animals
Species Specificity

@article {pmid38683311,
year = {2024},
author = {Hubert, N and Phillips, JD and Hanner, RH},
title = {Delimiting Species with Single-Locus DNA Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {53-76},
pmid = {38683311},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Algorithms ; Software ; Biodiversity ; Sequence Analysis, DNA/methods ; Haplotypes/genetics ; },
abstract = {DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.},
}

*DNA Barcoding, Taxonomic/methods
*Phylogeny
*Algorithms
Software
Biodiversity
Sequence Analysis, DNA/methods
Haplotypes/genetics

@article {pmid38683310,
year = {2024},
author = {Ahrens, D},
title = {Species Diagnosis and DNA Taxonomy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {33-52},
pmid = {38683310},
issn = {1940-6029},
mesh = {*DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Classification/methods ; Phylogeny ; Species Specificity ; },
abstract = {The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.},
}

*DNA/genetics
DNA Barcoding, Taxonomic/methods
Classification/methods
Phylogeny
Species Specificity

@article {pmid38683309,
year = {2024},
author = {Schindel, DE and Page, RMP},
title = {Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {7-32},
pmid = {38683309},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Entrepreneurship ; Humans ; Inventions ; },
abstract = {This chapter on the history of the DNA barcoding enterprise attempts to set the stage for the more scholarly contributions in this volume by addressing the following questions. How did the DNA barcoding enterprise begin? What were its goals, how did it develop, and to what degree are its goals being realized? We have taken a keen interest in the barcoding movement and its relationship to taxonomy, collections, and biodiversity informatics more broadly considered. This chapter integrates our two different perspectives on barcoding. DES was the Executive Secretary of the Consortium for the Barcode of Life from 2004 to 2017, with the mission to support the success of DNA barcoding without being directly involved in generating barcode data. RDMP viewed barcoding as an important entry into the landscape of biodiversity data, with many potential linkages to other components of that landscape. We also saw it as a critical step toward the era of international genomic research that was sure to follow. Like the Mercury Program that paved the way for lunar landings by the Apollo Program, we saw DNA barcoding as the proving grounds for the interdisciplinary and international cooperation that would be needed for success of whole-genome research.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
Entrepreneurship
Humans
Inventions

@article {pmid38681421,
year = {2024},
author = {Halue, G and Chieochanthanakij, R and Kittipanyaworakun, T and Passorn, P and Kaewboonsert, D and Tharavichitkul, T and Banjongjit, A and Kanjanabuch, T and Eiam-Ong, S},
title = {Peritonitis Caused by Various Species of Diaporthe in Peritoneal Dialysis Patients: A Plant Pathogen to Human Infection.},
journal = {Cureus},
volume = {16},
number = {3},
pages = {e57016},
pmid = {38681421},
issn = {2168-8184},
abstract = {Peritonitis caused by dematiaceous molds is uncommon but poses a significant threat to patients undergoing peritoneal dialysis (PD), leading to high mortality and morbidity. This report highlights three cases of peritonitis caused by three distinct species of Diaporthe (D. amygdali, D. eucalyptorum, and D. phaseolorum), initially unidentified through conventional culture methods. The nucleotide sequences of internal transcribed spacer regions (ITS), 18S nuclear ribosomal small subunit (SSU), and 28S nuclear ribosomal large subunit (LSU) of the ribosomal DNA gene correctly identified the isolates. Despite early catheter removal and administration of appropriate antifungal medications, all patients experienced fatal outcomes. DNA barcoding emerges as a valuable tool for accurately diagnosing species within the genus of pathogenic microbes, aiding in identifying the root causes of infections. It emphasizes the importance of strict adherence to aseptic techniques during PD exchanges to prevent peritonitis caused by plant-borne pathogens.},
}

@article {pmid38680524,
year = {2024},
author = {Kermek, D and Pischiutta, N and Hlebec, D and Sivec, I and Kučinić, M},
title = {Utilising public sequence databases to investigate genetic diversity of stoneflies in Medvednica Nature Park.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e121398},
pmid = {38680524},
issn = {1314-2828},
abstract = {In Medvednica Nature Park, near Croatia's capital Zagreb, urbanisation significantly impacts the fauna. Comprehensive field research has never been conducted in this area, despite the presence of diverse microhabitats and the discovery of several rare species previously unknown in the Croatian fauna. This study provides the Park with first insight into the genetic and morphological diversity of stoneflies, one of the most endangered groups of organisms. Phylogenetic reconstructions and species delineation methods revealed intraspecific haplotype variation in most species (e.g. Brachypteraseticornis, Isoperlagrammatica and Leuctrabraueri), except for Leuctraprima. Additionally, our study has identified isolated populations that merit further in-depth investigation concerning morphology, genetics and ecology.},
}

@article {pmid38678568,
year = {2024},
author = {Gallaccio, G and Wang, M and Schlickeiser, S and Kunkel, D and Böttcher, C and Fernández-Zapata, C},
title = {Protocol to characterize immune cell subpopulations in cerebrospinal fluid of patients with neuroinflammatory diseases using mass cytometry.},
journal = {STAR protocols},
volume = {5},
number = {2},
pages = {103038},
doi = {10.1016/j.xpro.2024.103038},
pmid = {38678568},
issn = {2666-1667},
abstract = {Phenotypic and compositional changes of immune cells in cerebrospinal fluid (CSF) can be used as biomarkers to help diagnose and track disease activity for neuroinflammatory and neurodegenerative diseases. Here, we present a workflow to perform high-dimensional immune profiling at single-cell resolution using cytometry by time-of-flight (CyTOF) on cells isolated from the CSF of patients with neuroinflammation. We describe steps for sample collection and preparation, barcoding to allow for multiplexing, and downstream data analysis using R. For complete details on the use and execution of this protocol, please refer to Fernández-Zapata et al.[1].},
}

@article {pmid38676334,
year = {2024},
author = {Rong, Q and Deng, Y and Chen, F and Yin, Z and Hu, L and Su, X and Zhou, D},
title = {Polymerase-Based Signal Delay for Temporally Regulating DNA Involved Reactions, Programming Dynamic Molecular Systems, and Biomimetic Sensing.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2400142},
doi = {10.1002/smll.202400142},
pmid = {38676334},
issn = {1613-6829},
support = {32141003//National Natural Science Foundation of China/ ; },
abstract = {Complex temporal molecular signals play a pivotal role in the intricate biological pathways of living organisms, and cells exhibit the ability to transmit and receive information by intricately managing the temporal dynamics of their signaling molecules. Although biomimetic molecular networks are successfully engineered outside of cells, the capacity to precisely manipulate temporal behaviors remains limited. In this study, the catalysis activity of isothermal DNA polymerase (DNAP) through combined use of molecular dynamics simulation analysis and fluorescence assays is first characterized. DNAP-driven delay in signal strand release ranged from 10[0] to 10[2] min, which is achieved through new strategies including the introduction of primer overhangs, utilization of inhibitory reagents, and alteration of DNA template lengths. The results provide a deeper insight into the underlying mechanisms of temporal control DNAP-mediated primer extension and DNA strand displacement reactions. Then, the regulated DNAP catalysis reactions are applied in temporal modulation of downstream DNA-involved reactions, the establishment of dynamic molecular signals, and the generation of barcodes for multiplexed detection of target genes. The utility of DNAP-based signal delay as a dynamic DNA nanotechnology extends beyond theoretical concepts and achieves practical applications in the fields of cell-free synthetic biology and bionic sensing.},
}

@article {pmid38674379,
year = {2024},
author = {Zhang, S and Han, S and Bi, D and Yang, J and Ge, W and Ye, Y and Gao, J and Dai, C and Kan, X},
title = {Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective.},
journal = {Genes},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/genes15040444},
pmid = {38674379},
issn = {2073-4425},
support = {BK20211078//the Basic Research Program of Natural Science Foundation of Jiangsu Province of China/ ; NEL&MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention & Control, Ministry of Agriculture and Rural Affairs/ ; },
mesh = {*Phylogeny ; *Sedum/genetics ; Genome, Plastid ; Evolution, Molecular ; Genetic Variation ; Codon Usage ; Genome, Plant ; Base Composition/genetics ; },
abstract = {Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus.},
}

*Phylogeny
*Sedum/genetics
Genome, Plastid
Evolution, Molecular
Genetic Variation
Codon Usage
Genome, Plant
Base Composition/genetics

@article {pmid38674377,
year = {2024},
author = {Kan, J and Zhang, S and Wu, Z and Bi, D},
title = {Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics.},
journal = {Genes},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/genes15040441},
pmid = {38674377},
issn = {2073-4425},
support = {BK20211078//the Basic Research Program (Natural Science Foundation) of Jiangsu Province (Grant no. BK20211078)/ ; RCYX20200714114538196//the Science Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20220818103212025//the Shenzhen Fundamental Research Program/ ; 2021QN02N792//the Guangdong Pearl River Talent Program/ ; },
mesh = {*Phylogeny ; *Plastids/genetics ; Codon Usage ; Genome, Plastid/genetics ; Evolution, Molecular ; },
abstract = {The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of Sempervivum remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among Sempervivum until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from Sempervivum, revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into Sempervivum evolution and offers potential molecular markers for DNA barcoding.},
}

*Phylogeny
*Plastids/genetics
Codon Usage
Genome, Plastid/genetics
Evolution, Molecular

@article {pmid38672767,
year = {2024},
author = {Vankova, L and Vanek, D},
title = {Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/life14040497},
pmid = {38672767},
issn = {2075-1729},
support = {VJ01010026//Ministry of Interior Czech Republic/ ; },
abstract = {This study aimed to provide an overview of the methodological approach used for the species determination of big cats. The molecular system described herein employs mitochondrial DNA control region (CR-mtDNA)-length polymorphism in combination with highly sensitive and precise capillary electrophoresis. We demonstrated that the described CR-mtDNA barcoding system can be utilized for species determination where the presence of biological material from big cats is expected or used as a confirmatory test alongside Sanger or massive parallel sequencing (MPS). We have also addressed the fact that species barcoding, when based on the analysis of mtDNA targets, can be biased by nuclear inserts of the mitochondrial genome (NUMTs). The CR-mtDNA barcoding system is suitable even for problematic and challenging samples, such as hair. CR-mtDNA-length polymorphisms can also distinguish hybrids from pure breeds.},
}

@article {pmid38671234,
year = {2024},
author = {Rios-Willars, E and Chirinos-Arias, MC},
title = {Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm.},
journal = {Planta},
volume = {259},
number = {6},
pages = {134},
pmid = {38671234},
issn = {1432-2048},
mesh = {*Microsatellite Repeats/genetics ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; *Magnoliopsida/genetics ; DNA, Plant/genetics ; },
abstract = {Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.},
}

*Microsatellite Repeats/genetics
*DNA Barcoding, Taxonomic/methods
*Algorithms
*Magnoliopsida/genetics
DNA, Plant/genetics

@article {pmid38670414,
year = {2024},
author = {Lattos, A and Makri, V and Papadopoulos, DK and Gourzioti, E and Pagonis, C and Georgoulis, I and Karagiannis, D and Theodorou, JA and Michaelidis, B and Giantsis, IA and Feidantsis, K},
title = {Molecular characterization of Lernathropus kroyeri from intensive aquaculture and pathophysiology of infested sea bass.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {109576},
doi = {10.1016/j.fsi.2024.109576},
pmid = {38670414},
issn = {1095-9947},
abstract = {The copepod Lernathropus kroyeri constitutes one of the major parasites for the Mediterranean aquaculture, infesting the sea bass Dicentrarchus labrax causing thus disruptions of growth performance and occasionally mortalities. Despite the large spread and the high frequency of this parasite in mariculture farms of Eastern Mediterranean, L. kroyeri genetic profile from aquaculture as well as the pathophysiological response of D. labrax have not been studied so far. Keeping this in mind, in the present study we investigated the L. kroyeri infestation on D. labrax from two farms in Greece, examining both healthy and heavy parasitized individuals. Assays included histopathology, phylogenetic reconstruction of the parasite and physiological response of the fish by the means of antioxidant, inflammatory metabolic and stress related gene expression analysis at both mRNA and protein levels. Genetic analysis indicated that L. kroyeri composes a monophyletic group, highly phylogenetically distant from other congeneric groups. Heavy infested D. labrax witnessed a significantly increased immune response that further led to oxidative stress and metabolic alterations. Overall, our results demonstrate the, seasonally independent, high infestation of this parasitic copepods, which continue to affect Mediterranean intensive aquaculture systems.},
}

@article {pmid38670101,
year = {2024},
author = {Holze, H and Talarmain, L and Fennell, KA and Lam, EY and Dawson, MA and Vassiliadis, D},
title = {Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {100763},
doi = {10.1016/j.crmeth.2024.100763},
pmid = {38670101},
issn = {2667-2375},
abstract = {Cellular barcoding is a lineage-tracing methodology that couples heritable synthetic barcodes to high-throughput sequencing, enabling the accurate tracing of cell lineages across a range of biological contexts. Recent studies have extended these methods by incorporating lineage information into single-cell or spatial transcriptomics readouts. Leveraging the rich biological information within these datasets requires dedicated computational tools for dataset pre-processing and analysis. Here, we present BARtab, a portable and scalable Nextflow pipeline, and bartools, an open-source R package, designed to provide an integrated end-to-end cellular barcoding analysis toolkit. BARtab and bartools contain methods to simplify the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments. We showcase the utility of our integrated BARtab and bartools workflow via the analysis of exemplar bulk, single-cell, and spatial transcriptomics experiments containing cellular barcoding information.},
}

@article {pmid38667952,
year = {2024},
author = {Guerra-Mateo, D and Cano-Lira, JF and Fernández-Bravo, A and Gené, J},
title = {Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {4},
pages = {},
pmid = {38667952},
issn = {2309-608X},
support = {PID2021-128068NB-100//Ministeri de Ciència Innovació i Universitats/ ; },
abstract = {The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.},
}

@article {pmid38667369,
year = {2024},
author = {Aguado-Aranda, P and Ricarte, A and Nedeljković, Z and Hauser, M and Kelso, S and Sainz-Escudero, L and Skevington, JH and Marcos-García, MÁ},
title = {Unveiling the Mainland vs. Insular Variability of the Eumerus barbarus Species Group (Diptera: Syrphidae) in the Western Mediterranean Basin.},
journal = {Insects},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/insects15040239},
pmid = {38667369},
issn = {2075-4450},
support = {PRE2019-087508//Ministerio de Ciencia, Innovación y Universidades (Spain)/ ; PGC2018-095851-A-C65//Ministerio de Ciencia, Innovación y Universidades (Spain)/ ; IME 2022//Institut Menorquí d'Estudis (Spain)/ ; },
abstract = {Comprising nearly 300 described species, Eumerus Meigen, 1822, is one of the most speciose syrphid genera worldwide, and its taxonomic diversity is remarkable in the Mediterranean basin. The Eumerus barbarus (Coquebert, 1804) group consists of four species in the western Mediterranean. Although the phenotypic variability of this species group has been commented on in previous studies, it has never been contrasted with molecular data. In the present work, the morphological variation found in 300+ specimens of this species group from the western Mediterranean is explored and tested against the COI mitochondrial DNA (mtDNA). The highest phenotypic disparity was found in E. barbarus and Eumerus sulcitibius Rondani 1868. The integrative approach has not revealed cryptic diversity within the species E. barbarus but in E. sulcitibius. As a result, a new species close to E. sulcitibius was discovered, Eumerus sardus Aguado-Aranda, Ricarte & Hauser sp. n., from Sardinia, Italy. The new insular species is here described, illustrated, and discussed. A total of twenty-three haplotypes of COI mtDNA were identified amongst the analyzed Mediterranean specimens of E. barbarus, whereas two and five haplotypes were distinguished in the Iberian specimens of E. sulcitibius and Eumerus gibbosus van Steenis, Hauser & van Zuijen, 2017, respectively. Moreover, the first known barcodes of E. gibbosus and Eumerus schmideggeri van Steenis, Hauser & van Zuijen, 2017 were obtained, and the distribution ranges of all species are mapped. An updated dichotomous key to the males of the E. barbarus group from the western Mediterranean is provided.},
}

@article {pmid38667358,
year = {2024},
author = {Wang, L and Wu, H and He, W and Lai, G and Li, J and Liu, S and Zhou, Q},
title = {Diversity of Parasitoid Wasps and Comparison of Sampling Strategies in Rice Fields Using Metabarcoding.},
journal = {Insects},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/insects15040228},
pmid = {38667358},
issn = {2075-4450},
support = {2023KJ113//the Agricultural Science and Technology Innovative and Promotion Program of Guangdong Province/ ; },
abstract = {A comprehensive and precise evaluation of Arthropoda diversity in agricultural landscapes can enhance biological pest control strategies. We used Malaise traps and sweep nets to collect insects from three double-cropping paddy fields. DNA was extracted from the ethanol preservative of the Malaise traps and from tissue samples of selected parasitoid wasps. This was followed by amplification using DNA barcoding primers to prepare high-throughput sequencing libraries. We annotated a total of 4956 operational taxonomic units (OTUs), encompassing 174 genera and 32 families of parasitoid wasps. The ethanol filter method efficiently captured a wide range of information. However, the method has low resolution and may result in a reduced estimate of species abundance. Additional insect species were also identified in the parasitoid samples. This suggests that high throughput sequencing from adult parasitoid wasps can also detect host species, enabling a better understanding of host species and providing insights into food webs.},
}

@article {pmid38666586,
year = {2024},
author = {Wang, J and Zhang, T and Gao, Z and Wei, M and Jia, Y and Tong, X and Hu, F and Zhao, YS},
title = {Two-Dimensional Lanthanide Metal-Organic Framework Heterostructures for Noninvasively Photoresponsive High-Security Photonic Barcodes.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.4c02440},
pmid = {38666586},
issn = {1944-8252},
abstract = {Stimuli-responsive micro/nanoscale photonic barcodes show great capacity for encryption and anticounterfeiting technologies due to multiple authentications, yet their application is commonly restricted by invasive stimuli. Herein, we report noninvasive light-stimulated high-security photonic barcodes based on spatially assembled photoresponsive two-dimensional (2D) 1,3,5-benzenetribenzoate (BTB)@Ln-MOF host-guest heterostructures. The photoluminescence (PL) spectra information on BTB@Ln-MOF heterostructures could be precisely controlled by the different wavelengths of ultraviolet (UV) light trigger. By using the PL properties and 2D heterostructures as cryptographic primitives, spatially resolved smart photonic barcodes based on both spectral and graphical coding are realized in BTB@Ln-MOF host-guest materials. These results will pave an avenue for the development of smart stimuli-responsive photonic barcodes for anticounterfeiting applications.},
}

@article {pmid38665980,
year = {2023},
author = {Li, GS and Leal-Dutra, CA and Cuesta-Maté, A and Conlon, BH and Peereboom, N and Beemelmanns, C and Aanen, DK and Rosendahl, S and de Beer, ZW and Poulsen, M},
title = {Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution.},
journal = {Persoonia},
volume = {51},
number = {},
pages = {257-279},
doi = {10.3767/persoonia.2023.51.07},
pmid = {38665980},
issn = {0031-5850},
abstract = {The genus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based on barcoding genes suggest that the genus comprises several species, but their status is largely unresolved. Here we obtained basidiospores and photographs from 166 fungarium specimens from around the world and generated a phylogeny based on rDNA internal transcribed spacer ITS1,5.8S and ITS2 (ITS), and a phylogenomic analysis of 3 839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that the genus includes at least 16 unambiguous species. Based on 10 type specimens (holotype, paratype, and syntype), four recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic analysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus and designated neotypes, epitypes, or lectotypes for five previously described species, P. aegyptiacus, P. africana, P. beringamensis, P. calyptratus, and P. perraldieri. Lastly, based on phylogenies and morphology of type material, we synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described five new species that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis. Citation: Li GS, Leal-Dutra CA, Cuesta-Maté A, et al. 2023. Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution. Persoonia 51: 257-279. doi: 10.3767/persoonia.2023.51.07.},
}

@article {pmid38665977,
year = {2023},
author = {Crous, PW and Costa, MM and Kandemir, H and Vermaas, M and Vu, D and Zhao, L and Arumugam, E and Flakus, A and Jurjević, Ž and Kaliyaperumal, M and Mahadevakumar, S and Murugadoss, R and Shivas, RG and Tan, YP and Wingfield, MJ and Abell, SE and Marney, TS and Danteswari, C and Darmostuk, V and Denchev, CM and Denchev, TT and Etayo, J and Gené, J and Gunaseelan, S and Hubka, V and Illescas, T and Jansen, GM and Kezo, K and Kumar, S and Larsson, E and Mufeeda, KT and Piątek, M and Rodriguez-Flakus, P and Sarma, PVSRN and Stryjak-Bogacka, M and Torres-Garcia, D and Vauras, J and Acal, DA and Akulov, A and Alhudaib, K and Asif, M and Balashov, S and Baral, HO and Baturo-Cieśniewska, A and Begerow, D and Beja-Pereira, A and Bianchinotti, MV and Bilański, P and Chandranayaka, S and Chellappan, N and Cowan, DA and Custódio, FA and Czachura, P and Delgado, G and De Silva, NI and Dijksterhuis, J and Dueñas, M and Eisvand, P and Fachada, V and Fournier, J and Fritsche, Y and Fuljer, F and Ganga, KGG and Guerra, MP and Hansen, K and Hywel-Jones, N and Ismail, AM and Jacobs, CR and Jankowiak, R and Karich, A and Kemler, M and Kisło, K and Klofac, W and Krisai-Greilhuber, I and Latha, KPD and Lebeuf, R and Lopes, ME and Lumyong, S and Maciá-Vicente, JG and Maggs-Kölling, G and Magistà, D and Manimohan, P and Martín, MP and Mazur, E and Mehrabi-Koushki, M and Miller, AN and Mombert, A and Ossowska, EA and Patejuk, K and Pereira, OL and Piskorski, S and Plaza, M and Podile, AR and Polhorský, A and Pusz, W and Raza, M and Ruszkiewicz-Michalska, M and Saba, M and Sánchez, RM and Singh, R and Śliwa, L and Smith, ME and Stefenon, VM and Strasiftáková, D and Suwannarach, N and Szczepańska, K and Telleria, MT and Tennakoon, DS and Thines, M and Thorn, RG and Urbaniak, J and van der Vegte, M and Vasan, V and Vila-Viçosa, C and Voglmayr, H and Wrzosek, M and Zappelini, J and Groenewald, JZ},
title = {Fungal Planet description sheets: 1550-1613.},
journal = {Persoonia},
volume = {51},
number = {},
pages = {280-417},
doi = {10.3767/persoonia.2023.51.08},
pmid = {38665977},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.},
}