@article {pmid40119005,
year = {2025},
author = {Li, H and Bao, S and Farzad, N and Qin, X and Fung, AA and Zhang, D and Bai, Z and Tao, B and Fan, R},
title = {Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40119005},
issn = {1750-2799},
support = {U54AG076043//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54AG079759//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; UG3CA257393//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; UH3CA257393//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01CA245313//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; RF1MH128876//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54CA274509//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U01CA294514//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54CA268083//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The epigenome of a cell is tightly correlated with gene transcription, which controls cell identity and diverse biological activities. Recent advances in spatial technologies have improved our understanding of tissue heterogeneity by analyzing transcriptomics or epigenomics with spatial information preserved, but have been mainly restricted to one molecular layer at a time. Here we present procedures for two spatially resolved sequencing methods, spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq, that co-profile transcriptome and epigenome genome wide. In both methods, transcriptomic readouts are generated through tissue fixation, permeabilization and in situ reverse transcription. In spatial-ATAC-RNA-seq, Tn5 transposase is used to probe accessible chromatin, and in spatial-CUT&Tag-RNA-seq, the tissue is incubated with primary antibodies that target histone modifications, followed by Protein A-fused Tn5-induced tagmentation. Both methods leverage a microfluidic device that delivers two sets of oligonucleotide barcodes to generate a two-dimensional mosaic of tissue pixels at near single-cell resolution. A spatial-ATAC-RNA-seq or spatial-CUT&Tag-RNA-seq library can be generated in 3-5 d, allowing researchers to simultaneously investigate the transcriptomic landscape and epigenomic landscape of an intact tissue section. This protocol is an extension of our previous spatially resolved epigenome sequencing protocol and provides opportunities in multimodal profiling.},
}

@article {pmid40119004,
year = {2025},
author = {Li, L and Bowling, S and Lin, H and Chen, D and Wang, SW and Camargo, FD},
title = {DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40119004},
issn = {1750-2799},
support = {32470700//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
abstract = {Lineage tracing is a powerful tool to study cell history and cell dynamics during tissue development and homeostasis. An increasingly popular approach for lineage tracing is to generate high-frequent mutations at given genomic loci, which can serve as genetic barcodes to label different cell lineages. However, current lineage tracing mouse models suffer from low barcode diversity and limited single-cell lineage coverage. We recently developed the DARLIN mouse model by incorporating three barcoding arrays within defined genomic loci and combining Cas9 and terminal deoxynucleotidyl transferase (TdT) to improve editing diversity in each barcode array. We estimated that DARLIN generates 10[18] distinct lineage barcodes in theory, and enables the recovery of lineage barcodes in over 70% of cells in single-cell assays. In addition, DARLIN can be induced with doxycycline to generate stable lineage barcodes across different tissues at a defined stage. Here we provide a step-by-step protocol on applying the DARLIN system for in vivo lineage tracing, including barcode induction, estimation of induction efficiency, barcode analysis with bulk and single-cell sequencing, and computational analysis. The execution time of this protocol is ~1 week for experimental data collection and ~1 d for running the computational analysis pipeline. To execute this protocol, one should be familiar with sequencing library generation and Linux operation. DARLIN opens the door to study the lineage relationships and the underlying molecular regulations across various tissues at physiological context.},
}

@article {pmid40117582,
year = {2025},
author = {Catalano, R and Zhao, Y and Pecak, M and Korten, T and Diez, S},
title = {Barcoding Microtubules: Encoding Information onto Macromolecules by Photobleaching.},
journal = {Nano letters},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.nanolett.5c00105},
pmid = {40117582},
issn = {1530-6992},
abstract = {Kinesin-1-powered microtubules have emerged as versatile components in biocomputing and biosensing technologies. However, the inability to identify and track individual microtubules has constrained their applications to ensemble behaviors, limiting their potential for single-entity-based nanotechnologies. To address this challenge, we present a novel method for encoding digital information directly onto individual microtubules using photobleaching patterns. Binary numbers (1 to 15) were encoded within ∼12 μm segments of moving microtubules by photobleaching with a stationary pulsed laser, creating spatial frequency patterns corresponding to distinct bits of information. Fourier analysis enabled the accurate retrieval of the encoded data, demonstrating the feasibility of direct information storage and retrieval on macromolecular structures. This approach offers a transformative solution for recording microtubule trajectories within nanotechnological devices by encoding path information directly onto microtubules at branch points, obviating the need for video-based tracking. We anticipate that this innovation will advance the development of individualized microtubule-based technologies.},
}

@article {pmid40117330,
year = {2025},
author = {Abdel-Glil, MY and Brandt, C and Pletz, MW and Neubauer, H and Sprague, LD},
title = {High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001372},
pmid = {40117330},
issn = {2057-5858},
mesh = {*Nanopore Sequencing/methods ; Reproducibility of Results ; *Genome, Bacterial ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.},
}

*Nanopore Sequencing/methods
Reproducibility of Results
*Genome, Bacterial
*Bacteria/genetics/classification
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid40115270,
year = {2025},
author = {Wu, Q and Xiang, P and Wang, C and Jing, C and Lin, X and Wang, Y and Chen, G and Lin, M and Xing, B},
title = {Diversity of lanternfish (Myctophidae) larvae along the Ninety East Ridge, Indian Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19144},
pmid = {40115270},
issn = {2167-8359},
mesh = {Animals ; Indian Ocean ; *Larva/genetics ; *Phylogeny ; Fishes/genetics/classification ; Biodiversity ; Haplotypes ; Salinity ; },
abstract = {Since the 19th century, the impact of seamounts on the distribution of plankton has been a topic of considerable interest. The influence of seamounts on the biogeographic patterns of marine organisms is complex, with some aspects still under debate. It is generally accepted that seamounts can drive the upwelling of nutrient-rich deep waters. Tidal amplification, flow acceleration, and internal waves can further enhance vertical mixing, leading to increased primary productivity near seamounts. Seamounts may also act as barriers to the migration of marine organisms, affecting gene flow. Research on Pacific seamounts suggests these features might serve as "stepping stones" for the dispersal of marine species across the ocean. However, investigations of seamounts in the eastern Indian Ocean remain limited. Focusing on the Ninety East Ridge region in the eastern Indian Ocean, this study collected zooplankton samples using horizontal (surface) and vertical (0-200 m) plankton nets and measured temperature and salinity profiles with a conductivity, temperature, and depth (CTD) sensor. A total of 544 fish larvae were identified, including 260 lanternfish larvae, representing 38 species across 12 genera, determined through COI DNA barcoding. Phylogenetic trees and haplotype networks were constructed to analyze genetic distances and population structures of lanternfish species. Among the samples, intra-specific genetic distances ranged from 0% to 2.99%, while inter-specific distances ranged from 1.88% to 25.71%. Except for Notolychnus valdiviae (Brauer, 1904), the maximum intra-specific distances were lower than the minimum inter-specific distances for all species. Haplotype analysis of nine species revealed significant variations in haplotype number, structure, and spatial distribution. Specifically, Ceratoscopelus warmingii (Lütken, 1892) and N. valdiviae exhibited a notable north-south divergence pattern, consistent with the temperature and salinity distribution of the region's water masses. This conclusion was supported by analysis of molecular variance analysis, suggesting that larval stages of certain lanternfish species may struggle to cross boundaries between water masses. However, the remaining species showed no significant north-south distribution differences, possibly due to their adaptive capabilities, vertical migration patterns, or the duration of their planktonic larval stages. These findings suggest that seamounts and water mass distribution have varying implications for lanternfish species, potentially influencing gene flow and horizontal distribution patterns, which could contribute to speciation. Global climate change-induced alterations in ocean currents may profoundly impact the genetic diversity of fish species. This study provides new insights into the diversity of lanternfish in the Ninety East Ridge region and offers valuable data for understanding the biogeography of seamounts.},
}

Animals
Indian Ocean
*Larva/genetics
*Phylogeny
Fishes/genetics/classification
Biodiversity
Haplotypes
Salinity

@article {pmid40114347,
year = {2025},
author = {Kefelegn, H and Couvreur, M and Meressa, BH and Wesemael, WML and Teklu, MG and Bert, W},
title = {First Report of the Root-Knot Nematode, Meloidogyne luci Parasitizing Chickpea (Cicer arietinum L.) in Ethiopia.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-25-0096-PDN},
pmid = {40114347},
issn = {0191-2917},
abstract = {Chickpea (Cicer arietinum L.) is a significant legume crop, with Ethiopia being the largest producer in Africa and the fifth globally (FAO 2022). However, various factors, including plant-parasitic nematodes, reduce its yield. Among these, root-knot nematodes (RKN; Meloidogyne spp.) pose a severe threat by causing root galling and stunted growth (Castillo et al. 2008). Despite the impact, research on plant-parasitic nematodes, their diversity and effect on chickpea yield in Ethiopia is limited (Kefelegn et al. 2024). In 2021, a survey was conducted to assess diversity of nematodes associated with chickpea in Ethiopia. Root-knot nematodes collected from galled chickpea roots of the 'Arerti' cultivar in the Minjar district, Ethiopia (8°54'21.1"N, 39°24'46.5"E), were identified as M. luci using multiple approaches. Esterase isozyme patterns of egg-laying females (n=10) were consistent with those described for M. luci by Carneiro et al. (2014) and Gerič Stare et al. (2017). PCR amplification with M. luci-specific primers (Maleita et al. 2021) confirmed its identity . Additionally, various sequences obtained from second-stage juveniles (J2), following the method described in Janssen et al. (2016) and Kefelegn et al. (2024): COX1 (PQ448335), Nad5 (PQ462657), COX2 (PQ619863) of mtDNA, and the D2-D3 region of 28S rDNA (PQ454017), were found identical to the M. luci sequences KU372172, KU372417, KU372211, and KX130766, respectively. Populations of M. luci were established from single egg masses and maintained on tomato plants (cv. 'Marmande'). To evaluate the pathogenicity of M. luci on the 'Arerti' chickpea cultivar, seedlings were inoculated with initial population densities (Pi) of 1000, 4000 and 8000 J2 (pot)-1 (2-liter capacity, n= 8) in a temperature controlled growth chamber in the Flanders Research Institute for Agriculture, Fisheries, and Food (ILVO), Belgium. After eight weeks, all inoculated plants exhibited stunted growth and visible root galling, consistent with typical field symptoms. The nematode reproduction factor (RF = final population (Pf) /initial population (Pi)) was calculated from the whole root and soil samples. Rf values were 31, 11.5 and 9.5 for Pi 1000, 4000 and 8000 J2 (pot)-1, respectively, corresponding to Pf values of 32000, 46000 and 76000 J2 (pot)-1, respectively. This clear pattern of increasing Pf with higher Pi levels, coupled with the declining RF trend, reflects the expected dynamics of a pathogenicity test. Nematodes extracted from the roots were reisolated and identified as M. luci using PCR amplification with M. luci-specific primers and esterase isozyme patterns analysis of egg-laying females (n = 10), confirming the species identity. These results confirmed that the 'Arerti' cultivar is a suitable host for M. luci. Meloidogyne luci has previously been reported in chickpea fields in Türkiye (Şen & Aydinli 2021), in common bean and soybean in Brazil (Bellé et al. 2016), and various horticultural crops in Europe (Gerič Stare et al. 2017). This study marks the first report of M. luci parasitizing chickpea roots in Ethiopia and its first documented occurrence in Africa. Therefore, further investigations are essential to determine the distribution of M. luci and assess its damage potential on legumes and other crops in Ethiopia and across Africa.},
}

@article {pmid40114041,
year = {2025},
author = {Guo, X and Xie, P and Zhang, G and Wang, T and Li, J and Zhang, X and Su, W and Ji, Y},
title = {Complete plastomes serve as desirable molecular makers for precise identification of Asparagus cochinchinensis (Asparagaceae) and nine other congeneric species frequently utilized as its adulterants.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {366},
pmid = {40114041},
issn = {1471-2229},
support = {202305AT350001//Yunnan Revitalization Talent Support Program "Top Team" Project/ ; },
mesh = {*Asparagus Plant/genetics ; *Phylogeny ; *Genome, Plastid ; Drug Contamination/prevention & control ; Plant Roots/genetics ; DNA, Plant/genetics ; DNA, Ribosomal/genetics ; Genetic Markers ; },
abstract = {BACKGROUD: The processed tuberous roots of Asparagus cochinchinensis (Asparagaceae), known as Asparagi Radix, have long been used in East Asia (particularly in China) as traditional medicines and play an indispensable role in the pharmaceutical industry. However, the frequent adulteration of Asparagi Radix with processed tuberous roots obtained from nine other congeneric species could potentially compromise the quality control measures for related pharmaceutical products, while also posing challenges to the conservation and rational exploitation of the nine adulterant congeneric species that are also used as traditional ethnomedicines. Given this issue, this study aims to develop a molecular authentication method for the accurate identification of A. cochinchinensis and the nine congeneric adulterants, employing the genome skimming approach to generate complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) arrays as the candidate molecular markers.

RESULTS: Through comprehensive phylogenetic and genetic distance analyses based on extensive sampling at both inter- and intra-specific levels, the efficacy of the two candidate molecular markers was assessed by investigating whether their inter-specific genetic divergences align with the taxonomically delineated species boundaries.

CONCLUSION: The results indicated that complete plastomes exhibit superior performance for accurately identifying A. cochinchinensis (the botanical source of Asparagi Radix) and the nine congeneric adulterants, thus can serve as the optimal molecular markers for effective authentication of Asparagi Radix. The desirable discriminative power demonstrated by complete plastomes suggests that the PCR-free molecular authentication method developed in this study will not only contribute to the quality control of pharmaceutical products derived from Asparagi Radix but also facilitate the conservation efforts and rational exploitation of the nine Asparagus species commonly used as adulterants.},
}

*Asparagus Plant/genetics
*Phylogeny
*Genome, Plastid
Drug Contamination/prevention & control
Plant Roots/genetics
DNA, Plant/genetics
DNA, Ribosomal/genetics
Genetic Markers

@article {pmid40093169,
year = {2025},
author = {Manian, KV and Ludwig, CH and Zhao, Y and Abell, N and Yang, X and Root, DE and Albert, ML and Comander, J},
title = {A comprehensive map of missense trafficking variants in rhodopsin and their response to pharmacologic correction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40093169},
issn = {2692-8205},
support = {P30 EY014104/EY/NEI NIH HHS/United States ; R01 EY031036/EY/NEI NIH HHS/United States ; },
abstract = {Rhodopsin (RHO) missense variants are a leading cause of autosomal dominant retinitis pigmentosa (adRP), a progressive retinal degeneration with no currently approved therapies. Interpreting the pathogenicity of the growing number of identified RHO variants is a major clinical challenge, and understanding their disease mechanisms is essential for developing effective therapies. Here, we present a high-resolution map of RHO missense variant trafficking using two complementary deep mutational scanning (DMS) approaches based on a surface abundance immunoassay and a membrane proximity assay. We generated a comprehensive dataset encompassing all 6,612 possible single-residue missense variants, revealing a strong correlation between the two methods. Over 700 variants were identified with pathogenic trafficking scores, significantly expanding the number of RHO variants with functional evidence supporting pathogenicity. We demonstrate a high concordance between the trafficking scores and ClinVar pathogenicity classifications, highlighting this approach's utility in resolving variants of uncertain significance (VUS). The data also identified structurally clustered trafficking-deficient variants, predominantly within the N-terminal region and second extracellular loop, in and above the extracellular/intradiscal beta-plug region. Furthermore, we evaluated the efficacy of the non-retinoid pharmacological chaperone YC-001, observing significant rescue of trafficking defects in a majority of mistrafficking variants. This comprehensive functional map of RHO missense variants provides a valuable resource for pathogenicity assessment, genotype-phenotype correlations, and the development of targeted therapeutic strategies for RHO-adRP, paving the way for improved diagnosis and treatment for patients.},
}

@article {pmid40109892,
year = {2025},
author = {Gastineau, R and Mianowicz, K and Dąbek, P and Otis, C and Stoyanova, V and Krawcewicz, A and Abramowski, T},
title = {Genomic investigation of benthic invertebrates from the Clarion-Clipperton fields of polymetallic nodules.},
journal = {ZooKeys},
volume = {1231},
number = {},
pages = {11-44},
pmid = {40109892},
issn = {1313-2989},
abstract = {The abyssal plains of the Clarion-Clipperton Zone (CCZ) are famous for their fields of polymetallic nodules, which are inhabited by benthic invertebrates. Ten specimens from the Interoceanmetal Joint Organisation (IOM) licence area in the CCZ were collected in 2014 and submitted to a short-read genome skimming sequencing. In total, mitochondrial genomes and nuclear ribosomal genes were retrieved for nine different organisms belonging to Ophiuroidea, Holothuroidea, Polychaeta, Bryozoa, Porifera, and Brachiopoda (assigned to these phyla immediately upon retrieval from the seafloor). As many of these samples were partial and physically deteriorated following their seven-year storage in IOM's collections, their morphology-based taxonomic identification could rarely be performed at the lowest possible level (species or genus) prior to preparing the samples for molecular or genomic investigations. Therefore, it was not possible to apply the reverse identification scheme recommended for such investigations. However, several of these specimens represent poorly studied groups for which few molecular references are available as of now. In two cases, the presence of introns in the mitochondrial genome questions the practicability of using the cox1 gene for further routine molecular barcoding of these organisms. These results might be useful in future DNA primers design, molecular barcoding, and phylogeny or population genetic studies when more samples are obtained.},
}

@article {pmid40106513,
year = {2025},
author = {Vielma-Puente, JE and Santos-Ordóñez, E and Cornejo, X and Chóez-Guaranda, I and Pacheco-Coello, R and Villao-Uzho, L and Moreno-Alvarado, C and Mendoza-Samaniego, N and Fonseca, Y},
title = {DNA Barcode, chemical analysis, and antioxidant activity of Psidium guineense from Ecuador.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0319524},
doi = {10.1371/journal.pone.0319524},
pmid = {40106513},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; Ecuador ; *Psidium/chemistry/genetics ; *Antioxidants/chemistry/pharmacology ; Plant Extracts/chemistry/pharmacology ; Flavonoids/analysis ; Plant Leaves/chemistry/genetics ; DNA, Plant/genetics ; Phenols/analysis ; },
abstract = {This study investigates the phytochemical, genetic, and antioxidant properties of Psidium guineense, a species native to the tropical dry forests of Ecuador. Leaves were collected, preserved in recognized herbaria, and subjected to Soxhlet extraction using polar and non-polar solvents. Phytochemical screening revealed the presence of secondary metabolites, while GC-MS analysis detected chemical compounds in the extracts. Antioxidant assays demonstrated high phenolic (54.34 ± 0.49 mg GAE/g) and flavonoid (6.43 ± 0.38 mg QE/g) content, with significant antioxidant activity in DPPH (0.57 ± 0.04 mg TE/g), FRAP (105.52 ± 6.85), and ABTS (1.25 ± 0.01 mg TE/g) assays. DNA barcoding of nine loci, (seven from the chloroplast genome and two nuclear genome) using a CTAB extraction protocol and PCR, provides the first genetic characterization of this species, contributing to genetic diversity assessments and phylogenetic studies. These findings underscore the importance of P. guineense as a source of potent bioactive compounds with significant antioxidant potential, highlighting its applicability in nutritional and pharmaceutical industries. Additionally, the genetic insights gained support efforts to expand DNA barcoding databases for tropical biodiversity conservation.},
}

*DNA Barcoding, Taxonomic
Ecuador
*Psidium/chemistry/genetics
*Antioxidants/chemistry/pharmacology
Plant Extracts/chemistry/pharmacology
Flavonoids/analysis
Plant Leaves/chemistry/genetics
DNA, Plant/genetics
Phenols/analysis

@article {pmid40106335,
year = {2025},
author = {Chen, A and Nchinda, N and Cira, NJ},
title = {Scalable genotyping of microbial colonies.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001378},
pmid = {40106335},
issn = {2057-5858},
mesh = {*RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation & purification ; *Polymerase Chain Reaction/methods ; *Genotyping Techniques/methods ; Genotype ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Gene Library ; DNA Primers/genetics ; },
abstract = {The sequence of the 16S region is taxonomically informative and widely used for genotyping microbes. While it is easy and inexpensive to genotype several isolates by Sanger sequencing the 16S region, this method becomes quite costly if scaled to many isolates. High-throughput sequencing provides one potential avenue for obtaining 16S sequences at scale but presents additional challenges. First, DNA purification workflows for high-throughput sample preparation are labour-intensive and expensive. Second, cost-effective multiplexing and library preparation schemes are difficult to implement for many libraries on a single sequencing run. Therefore, we implemented a scalable protocol for isolate genotyping involving colony polymerase chain reaction (PCR) with simple cell lysis as well as a four-barcode indexing scheme that enables scalable multiplexing and streamlined library preparation by amplifying with four primers simultaneously in a single reaction. We tested this protocol on 93 colonies cultured from environmental samples, and we were able to ascertain the identity of ~90% of microbial isolates.},
}

*RNA, Ribosomal, 16S/genetics
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification/isolation & purification
*Polymerase Chain Reaction/methods
*Genotyping Techniques/methods
Genotype
DNA, Bacterial/genetics
Sequence Analysis, DNA/methods
Gene Library
DNA Primers/genetics

@article {pmid40104553,
year = {2025},
author = {Cazal-Martínez, CC and Reyes-Caballero, YM and Chávez, AR and Pérez-Estigarribia, PE and Kohli, MM and Rojas, A and Arrua, AA and Moura-Mendes, J and Souza-Perera, R and Zúñiga Agilar, JJ and Gluck-Thaler, E and Lopez-Nicora, H and Iehisa, JCM},
title = {Pyricularia pennisetigena and Pyricularia oryzae isolates from Paraguay's wheat-growing regions and the impact on wheat.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100361},
pmid = {40104553},
issn = {2666-5174},
abstract = {The Pyricularia genus includes species causing blast disease in monocots, posing significant challenges for disease management due to their ability to infect multiple hosts. This study aimed to identify the pathogenicity and species identity of Pyricularia isolates from 11 plant species in wheat-growing regions of Paraguay and assess their capacity to infect wheat. Twenty-four monosporic isolates were analyzed based on macroscopic and microscopic and phylogenetic characteristics. Three phylogenetic clades corresponding to P. oryzae, P. grisea, and P. pennisetigena were identified through five barcoding genes. For the first time, wheat blast was reported in San Pedro Department, and blast disease was observed in weeds in Cordillera and Central Departments. In greenhouse trials, P. oryzae isolates from wheat successfully infected both susceptible and resistant wheat cultivars, whereas isolates from non-wheat hosts did not elicit symptoms. Notably, P. pennisetigena isolates derived from Cenchrus echinatus were capable of infecting wheat spikes, producing typical blast symptoms, highlighting the potential for cross-species pathogen transmission. This finding suggests P. pennisetigena may pose an emerging threat to wheat in Paraguay, as its primary host is prevalent near wheat fields. These results highlight the critical importance of integrated disease management strategies, particularly the identification of inoculum sources, to mitigate cross-species pathogen transmission. This approach aligns with the One Health paradigm by addressing interconnected risks to plant health, food security, and environmental sustainability.},
}

@article {pmid40103772,
year = {2025},
author = {Al-Dhafer, HM and Balaji, R and Abdel-Dayem, MS and Rasool, I and Mohamed, A and Palanisamy, S},
title = {Simple DNA extraction for museum beetle specimens to unlock genetic data from historical collections.},
journal = {MethodsX},
volume = {14},
number = {},
pages = {103236},
pmid = {40103772},
issn = {2215-0161},
abstract = {Museum beetle specimens are valuable resources for genetic analyses; however, obtaining DNA from aged specimens remains challenging due to degradation, desiccation, and contamination. In this study, we present a simple, low-cost protocol for extracting DNA from museum beetles, optimized using cetyltrimethylammonium bromide (CTAB). This method effectively addresses common issues such as DNA fragmentation and contamination, enabling the recovery of DNA suitable for downstream applications such as PCR and next-generation sequencing. It provides a reproducible, non-destructive approach to extracting genetic material from fragile beetle specimens, thereby facilitating molecular investigations in fields such as taxonomy and conservation biology. The protocol is summarized as follows:•A method for DNA extraction is optimized for museum beetle specimens preserved for over 45 years.•The protocol is non-destructive and compatible with PCR and next-generation sequencing.•Multiple extractions can be pooled to increase yields, particularly when DNA concentrations are low. This method broadens the possibilities for genetic analysis of historical specimens, offering new insights into long-term ecological and evolutionary processes.},
}

@article {pmid40102722,
year = {2025},
author = {Luo, C and Peters, BA and Zhou, XM},
title = {Large indel detection in region-based phased diploid assemblies from linked-reads.},
journal = {BMC genomics},
volume = {26},
number = {Suppl 2},
pages = {263},
pmid = {40102722},
issn = {1471-2164},
support = {R35 GM146960/NH/NIH HHS/United States ; GET 300538//Complete Genomics/ ; },
mesh = {*INDEL Mutation ; *Diploidy ; Humans ; *Algorithms ; Haplotypes ; Sequence Analysis, DNA/methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Genome, Human ; },
abstract = {BACKGROUND: Linked-reads improve de novo assembly, haplotype phasing, structural variant (SV) detection, and other applications through highly-multiplexed genome partitioning and barcoding. Whole genome assembly and assembly-based variant detection based on linked-reads often require intensive computation costs and are not suitable for large population studies. Here we propose an efficient pipeline, RegionIndel, a region-based diploid assembly approach to characterize large indel SVs. This pipeline only focuses on target regions (50kb by default) to extract barcoded reads as input and then integrates a haplotyping algorithm and local assembly to generate phased diploid contiguous sequences (contigs). Finally, it detects variants in the contigs through a pairwise contig-to-reference comparison.

RESULTS: We applied RegionIndel on two linked-reads libraries of sample HG002, one using 10x and the other stLFR. HG002 is a well-studied sample and the Genome in a Bottle (GiaB) community provides a gold standard SV set for it. RegionIndel outperformed several assembly and alignment-based SV callers in our benchmark experiments. After assembling all indel SVs, RegionIndel achieved an overall F1 score of 74.8% in deletions and 61.8% in insertions for 10x linked-reads, and 64.3% in deletions and 36.7% in insertions for stLFR linked-reads, respectively. Furthermore, it achieved an overall genotyping accuracy of 83.6% and 80.8% for 10x and stLFR linked-reads, respectively.

CONCLUSIONS: RegionIndel can achieve diploid assembly and detect indel SVs in each target region. The phased diploid contigs can further allow us to investigate indel SVs with nearby linked single nucleotide polymorphism (SNPs) and small indels in the same haplotype.},
}

*INDEL Mutation
*Diploidy
Humans
*Algorithms
Haplotypes
Sequence Analysis, DNA/methods
Genomics/methods
High-Throughput Nucleotide Sequencing/methods
Genome, Human

@article {pmid40102719,
year = {2025},
author = {Zhang, S and Ma, A and Xie, X and Lian, Z and Wang, Y},
title = {CacPred: a cascaded convolutional neural network for TF-DNA binding prediction.},
journal = {BMC genomics},
volume = {26},
number = {Suppl 2},
pages = {264},
pmid = {40102719},
issn = {1471-2164},
mesh = {*Neural Networks, Computer ; *Transcription Factors/metabolism/genetics ; *DNA/metabolism ; Chromatin Immunoprecipitation Sequencing/methods ; Binding Sites ; Computational Biology/methods ; Software ; Protein Binding ; Algorithms ; Humans ; },
abstract = {BACKGROUND: Transcription factors (TFs) regulate the genes' expression by binding to DNA sequences. Aligned TFBSs of the same TF are seen as cis-regulatory motifs, and substantial computational efforts have been invested to find motifs. In recent years, convolutional neural networks (CNNs) have succeeded in TF-DNA binding prediction, but existing DL methods' accuracy needs to be improved and convolution function in TF-DNA binding prediction should be further explored.

RESULTS: We develop a cascaded convolutional neural network model named CacPred to predict TF-DNA binding on 790 Chromatin immunoprecipitation-sequencing (ChIP-seq) datasets and seven ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode, and single ligation) datasets. We compare CacPred to six existing DL models across nine standard evaluation metrics. Our results indicate that CacPred outperforms all comparison models for TF-DNA binding prediction, and the average accuracy (ACC), matthews correlation coefficient (MCC), and the area of eight metrics radar (AEMR) are improved by 3.3%, 9.2%, and 6.4% on 790 ChIP-seq datasets. Meanwhile, CacPred improves the average ACC, MCC, and AEMR of 5.5%, 16.8%, and 12.9% on seven ChIP-nexus datasets. To explain the proposed method, motifs are used to show features CacPred learned. In light of the results, CacPred can find some significant motifs from input sequences.

CONCLUSIONS: This paper indicates that CacPred performs better than existing models on ChIP-seq data. Seven ChIP-nexus datasets are also analyzed, and they coincide with results that our proposed method performs the best on ChIP-seq data. CacPred only is equipped with the convolutional algorithm, demonstrating that pooling processing of the existing models leads to losing some sequence information. Some significant motifs are found, showing that CacPred can learn features from input sequences. In this study, we demonstrate that CacPred is an effective and feasible model for predicting TF-DNA binding. CacPred is freely available at https://github.com/zhangsq06/CacPred .},
}

*Neural Networks, Computer
*Transcription Factors/metabolism/genetics
*DNA/metabolism
Chromatin Immunoprecipitation Sequencing/methods
Binding Sites
Computational Biology/methods
Software
Protein Binding
Algorithms
Humans

@article {pmid40102641,
year = {2025},
author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J},
title = {Information storage across a microbial community using universal RNA barcoding.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40102641},
issn = {1546-1696},
support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; },
abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.},
}

@article {pmid40102404,
year = {2025},
author = {Nadal-Ribelles, M and Solé, C and Díez-Villanueva, A and Stephan-Otto Attolini, C and Matas, Y and Steinmetz, L and de Nadal, E and Posas, F},
title = {A single-cell resolved genotype-phenotype map using genome-wide genetic and environmental perturbations.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2645},
pmid = {40102404},
issn = {2041-1723},
mesh = {*Single-Cell Analysis/methods ; *Saccharomyces cerevisiae/genetics ; *Genotype ; *Phenotype ; *Transcriptome/genetics ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Mutation ; Gene Expression Profiling/methods ; },
abstract = {Heterogeneity is inherent to living organisms and it determines cell fate and phenotypic variability. Despite its ubiquity, the underlying molecular mechanisms and the genetic basis linking genotype to-phenotype heterogeneity remain a central challenge. Here we construct a yeast knockout library with a clone and genotype RNA barcoding structure suitable for genome-scale analyses to generate a high-resolution single-cell yeast transcriptome atlas of 3500 mutants under control and stress conditions. We find that transcriptional heterogeneity reflects the coordinated expression of specific gene programs, generating a continuous of cell states that can be responsive to external insults. Cell state plasticity can be genetically modulated with mutants that act as state attractors and disruption of state homeostasis results in decreased adaptive fitness. Leveraging on intra-genetic variability, we establish that regulators of transcriptional heterogeneity are functionally diverse and influenced by the environment. Our multimodal perturbation-based single-cell Genotype-to-Transcriptome Atlas in yeast provides insights into organism-level responses.},
}

*Single-Cell Analysis/methods
*Saccharomyces cerevisiae/genetics
*Genotype
*Phenotype
*Transcriptome/genetics
Gene Expression Regulation, Fungal
Genome, Fungal
Mutation
Gene Expression Profiling/methods

@article {pmid40100602,
year = {2025},
author = {Ayala, LA and Nguyen, PU and Zhou, C and Hisoire, GL and Ahmedani, AH and Chen, X and Daud, A and Valdovinos, A and Varady, ES and Inlay, MA and Scarfone, VM},
title = {Mass Cytometry Immunophenotyping of Graft-Conditioned Cells Following Major Histocompatibility Complex Mismatched Murine Allograft.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2907},
number = {},
pages = {259-286},
pmid = {40100602},
issn = {1940-6029},
mesh = {Animals ; Mice ; *Immunophenotyping/methods ; *Flow Cytometry/methods ; *Graft vs Host Disease/immunology ; Hematopoietic Stem Cell Transplantation/methods/adverse effects ; Transplantation Conditioning/methods ; Major Histocompatibility Complex/immunology ; Transplantation, Homologous ; Allografts/immunology ; T-Lymphocytes/immunology/metabolism ; },
abstract = {Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative therapy for a variety of blood disorders but primarily reserved for blood cancer patients due to the life-threatening risk of acute graft-versus-host disease (aGVHD). Development of aGVHD is driven by alloreactive T cells that recognize the recipient's tissues as foreign and initiate a robust immune response causing severe tissue damage of the skin, liver, and gut. While methods to reduce aGVHD incidence and severity exist including posttransplant cyclophosphamide, relapse rates and transplantation-related mortality remain. We previously published a study using graft conditioning with glucocorticoids as a strategy to modify the immune repertoire in the donor grafts prior to transplantation to reduce aGVHD. Here, we describe a protocol to characterize the T-cell response in recipient mice given transplantation of graft-conditioned allogeneic donor cells via mass cytometry. Mass cytometry is a technology that uses heavy metal tags in place of fluorochromes to allow high-dimensional flow cytometric analysis. In this protocol, we include an antibody panel of 39 different antibodies conjugated to 41 different heavy metal tags that have been validated and titrated for barcoding and immunophenotyping by lineage markers, activation markers, cytokine secretion, and transcription factors. This chapter details the graft conditioning, transplantation, processing, barcoding, staining, and mass cytometric analysis of immune cells following murine allo-HCT.},
}

Animals
Mice
*Immunophenotyping/methods
*Flow Cytometry/methods
*Graft vs Host Disease/immunology
Hematopoietic Stem Cell Transplantation/methods/adverse effects
Transplantation Conditioning/methods
Major Histocompatibility Complex/immunology
Transplantation, Homologous
Allografts/immunology
T-Lymphocytes/immunology/metabolism

@article {pmid40097444,
year = {2025},
author = {Jin, W and Ma, J and Rong, L and Huang, S and Li, T and Jin, G and Zhou, Z},
title = {Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2635},
pmid = {40097444},
issn = {2041-1723},
mesh = {Animals ; Mice ; Humans ; *Chromatin/genetics/metabolism ; *Cell Differentiation/genetics ; *Leukocytes, Mononuclear/metabolism ; *Single-Cell Analysis/methods ; Chromatin Assembly and Disassembly ; High-Throughput Nucleotide Sequencing/methods ; Mouse Embryonic Stem Cells/metabolism ; Chromatin Immunoprecipitation Sequencing/methods ; Epigenomics/methods ; Sequence Analysis, DNA/methods ; Gene Library ; },
abstract = {Single-cell ATAC-seq (scATAC-seq) enables high-resolution mapping of chromatin accessibility but is often limited by throughput, cost, and equipment requirements. Here, we present indexed Tn5 tagmentation-based scATAC-seq (IT-scATAC-seq), a semi-automated, cost-effective, and scalable approach that leverages indexed Tn5 transposomes and a three-round barcoding strategy. This workflow prepares libraries for up to 10,000 cells in a single day, reduces the per-cell cost to approximately $0.01, and maintains high data quality. Comprehensive benchmarking demonstrates that IT-scATAC-seq achieves robust library complexity, high signal specificity, and improved cost-efficiency compared to existing methods. We apply IT-scATAC-seq to mouse embryonic stem cells, capturing chromatin remodelling during early differentiation, and to human peripheral blood mononuclear cells, resolving cell-type-specific regulatory programs. Here, we show that IT-scATAC-seq provides a robust and efficient approach for high-resolution single-cell epigenomic investigations, balancing scalability, data quality, and accessibility.},
}

Animals
Mice
Humans
*Chromatin/genetics/metabolism
*Cell Differentiation/genetics
*Leukocytes, Mononuclear/metabolism
*Single-Cell Analysis/methods
Chromatin Assembly and Disassembly
High-Throughput Nucleotide Sequencing/methods
Mouse Embryonic Stem Cells/metabolism
Chromatin Immunoprecipitation Sequencing/methods
Epigenomics/methods
Sequence Analysis, DNA/methods
Gene Library

@article {pmid40095752,
year = {2025},
author = {Suetsugu, K and Okada, H},
title = {Green, variegated, and albino Cremastra variabilis provide insight into mycoheterotrophic evolution associated with wood-decaying fungi.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70014},
pmid = {40095752},
issn = {1438-8677},
support = {JPMJPR21D6//Precursory Research for Embryonic Science and Technology/ ; },
abstract = {With approximately 31,000 species, orchids begin life as mycoheterotrophs, relying on fungi to meet their carbon demands. Notably, some green orchids retain the ability to acquire carbon through fungal associations (partial mycoheterotrophy) and occasionally produce albino or, more rarely, variegated phenotypes. A linear relationship has been observed between leaf chlorophyll content and dependence on fungal-derived carbon, particularly in orchids associated with ectomycorrhizal (ECM) fungi, but whether such plasticity is similarly robust among orchids associated with non-ECM fungi remains underexplored. Here, we focused on the green, variegated, and albino forms of Cremastra variabilis, which likely lack ECM associations, to investigate (i) whether the degree of mycoheterotrophy, indicated by [13]C enrichment, correlates with chlorophyll content, and (ii) whether nutritional shifts align with changes in plant structure and mycorrhizal communities. Our results show that rhizoctonia fungi were dominant in green individuals with high chlorophyll levels and lacking coralloid rhizomes, whereas albino and most variegated individuals possessing coralloid rhizomes primarily associate with Psathyrellaceae fungi. Chlorophyll content and carbon stable isotope abundances were negatively correlated, indicating a gradient of increasing mycoheterotrophy from green to albino forms in individuals with coralloid rhizomes. In conclusion, C. variabilis maintains a flexible balance between photosynthesis and mycoheterotrophy, likely shaped by its subterranean morphology and fungal associations, with wood-decaying Psathyrellaceae fungi providing greater support for mycoheterotrophic nutrition than rhizoctonia fungi.},
}

@article {pmid40094434,
year = {2025},
author = {Mukherjee, A and Kar, O and Mukherjee, K and Mukherjee, B and Naskar, A and Banerjee, D},
title = {Molecular Identification of Onchocerciasis Vectors (Diptera: Simuliidae) from the Central Himalayan Landscape of India: A DNA Barcode Approach.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/vbz.2024.0123},
pmid = {40094434},
issn = {1557-7759},
abstract = {Background: Black flies (Diptera: Simuliidae) are a notorious group of blood-sucking insects acting as vectors of various diseases in humans and other animals, most notable being Onchocerciasis. Due to its medical and veterinary significance, accurate and quick species identification is of utmost importance in the field of black fly research. DNA barcoding is one such taxonomic tool, aiding in quick and efficient species identification using molecular methods. Despite sporadic reports of ocular and cutaneous Onchocerciasis, especially from North-East India, Indian Simuliidae has been understudied due to lack of expertise on morphological taxonomy and lack of genetic library. Materials and Methods: Blackflies were collected from eight distinct locations in the Central Himalayan region that are part of the West Bengal, India, districts of Kalimpong and Darjeeling. Various traps were used to collect the specimens, and they were kept it in 70% ethyl alcohol. Following the morphological identification of each fly specimen, genomic DNA was extracted from its dissected legs using the QIAmp DNA extraction kit (QIAGEN, Germany). The voucher specimen slide was deposited in the National Zoological collection, ZSI, Kolkata, India. Results: This is the first comprehensive DNA barcoding study of black flies (Feuerborni and Multistriatum species group) using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences along with morphological identification from the Central Himalayan region of West Bengal involving four species: Simulium dentatum, Simulium digitatum, Simulium praelargum, and Simulium senile. DNA barcode approach through ML tree clearly distinguished all the species with supporting PTP, ASAP, and GMYC analysis. Interspecific genetic distances were also calculated where S. dentatum and S. digitatum showed minimum distances in the study area. Conclusion: Coupled with a robust morpho-taxonomic framework, the DNA barcodes generated here will help with accurate species identification, which will lead to better management and control strategies for these harmful vector species at the study site.},
}

@article {pmid40087979,
year = {2025},
author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A},
title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14099},
doi = {10.1111/1755-0998.14099},
pmid = {40087979},
issn = {1755-0998},
support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; },
abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.},
}

@article {pmid40081365,
year = {2025},
author = {Vicario, R and Fragkogianni, S and Pokrovskii, M and Meyer, C and Lopez-Rodrigo, E and Hu, Y and Ogishi, M and Alberdi, A and Baako, A and Ay, O and Plu, I and Sazdovitch, V and Heritier, S and Cohen-Aubart, F and Shor, N and Miyara, M and Nguyen-Khac, F and Viale, A and Idbaih, A and Amoura, Z and Rosenblum, MK and Zhang, H and Karnoub, ER and Sashittal, P and Jakatdar, A and Iacobuzio-Donahue, CA and Abdel-Wahab, O and Tabar, V and Socci, ND and Elemento, O and Diamond, EL and Boisson, B and Casanova, JL and Seilhean, D and Haroche, J and Donadieu, J and Geissmann, F},
title = {Role of clonal inflammatory microglia in histiocytosis-associated neurodegeneration.},
journal = {Neuron},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuron.2025.02.007},
pmid = {40081365},
issn = {1097-4199},
abstract = {Langerhans cell histiocytosis (LCH) and Erdheim-Chester disease (ECD) are clonal myeloid disorders associated with mitogen-activated protein (MAP)-kinase-activating mutations and an increased risk of neurodegeneration. We found microglial mutant clones in LCH and ECD patients, whether or not they presented with clinical symptoms of neurodegeneration, associated with microgliosis, astrocytosis, and neuronal loss, predominantly in the rhombencephalon gray nuclei. Neurological symptoms were associated with PU.1[+] clone size (p = 0.0003) in patients with the longest evolution of the disease, indicating a phase of subclinical incipient neurodegeneration. Genetic barcoding analysis suggests that clones may originate from definitive or yolk sac hematopoiesis, depending on the patients. In a mouse model, disease topography was attributable to a local clonal proliferative advantage, and microglia depletion by a CSF1R-inhibitor limited neuronal loss and improved survival. These studies characterize a neurodegenerative disease associated with clonal proliferation of inflammatory microglia. The long preclinical stage represents a therapeutic window before irreversible neuronal depletion.},
}

@article {pmid40079026,
year = {2025},
author = {Ossowska, EA and Moncada, B and Lücking, R and Sérusiaux, E and Magain, N},
title = {Stictaflakusiorum and S.kukwae-two additional new species from the Neotropics (Peltigerales, Peltigeraceae).},
journal = {MycoKeys},
volume = {114},
number = {},
pages = {259-276},
doi = {10.3897/mycokeys.114.139681},
pmid = {40079026},
issn = {1314-4049},
abstract = {Two additional species of Sticta are described as new to science based on material from Bolivia and Peru and supported by phylogenetic analysis of the fungal ITS barcoding marker. The two new species represent lineages within clade I on the global Sticta phylogeny. Stictaflakusiorum Ossowska, B. Moncada & Lücking is a species in the S.humboldtii morphodeme and is characterized by lobes partly to entirely covered with white hairs, also covering the margins of submarginal and laminal apothecia, and the scabrid basal membrane of cyphellae, which is white to yellow, or partly brown, and when yellow K+ purple. The taxon was discovered at a single locality in Bolivia, but it is closely related to a potentially new Sticta species from Peru, which is here left undescribed. The other new species, S.kukwae Ossowska, Magain & Sérus., belongs to the S.weigelii morphodeme. It has lobes with sinuous margins and dark, palmate to corymbose phyllidia. It was collected at several locations in Peru and a single locality in Bolivia.},
}

@article {pmid40078476,
year = {2025},
author = {Zhang, M and Zhai, X and He, L and Wang, Z and Cao, H and Wang, P and Ren, W and Ma, W},
title = {Morphological description and DNA barcoding research of nine Syringa species.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1544062},
doi = {10.3389/fgene.2025.1544062},
pmid = {40078476},
issn = {1664-8021},
abstract = {INTRODUCTION: Syringa plants are highly valued for their ornamental qualities. However, traditional morphological identification methods are inefficient for discriminating Syringa species. DNA barcoding has emerged as a powerful alternative for species identification, but research on Syringa DNA barcodes is still limited.

METHODS: This study employed a multi-locus strategy, combining the nuclear ITS2 region with chloroplast genome regions psbA-trnH, trnL-trnF, and trnL to evaluate the effectiveness of Syringa DNA barcodes. The assessment involved genetic distance analysis, BLAST searches in NCBI, sequence character analysis, and phylogenetic tree construction, examining both individual and combined sequences.

RESULTS: The genetic distance analysis showed that the sequence combination of ITS2 + psbA-trnH + trnL-trnF exhibited a variation pattern where most interspecific genetic distances were greater than intraspecific genetic distances. The Wilcoxon signed-rank test results indicated that, except for psbA-trnH, the interspecific differences of the ITS2 + psbA-trnH + trnL-trnF sequence were greater than those of all single and combined sequences. BLAST analysis revealed that the identification rate for nine Syringa species using ITS2 + psbA-trnH + trnL-trnF could reach 98.97%. The trait-based method also demonstrated that ITS2 + psbA-trnH + trnL-trnF could effectively identify the nine Syringa species. Furthermore, the neighbor-joining (NJ) tree based on ITS2 + psbA-trnH + trnL-trnF clustered each of the nine Syringa species into distinct clades.

DISCUSSION: The study ultimately selected the barcode ITS2 + psbA-trnH + trnL-trnF, with an identification rate of 93.6%, as the optimal barcode for identifying nine species of Syringa trees. This combination proved to be highly effective in discriminating Syringa species, highlighting the potential of DNA barcoding as a reliable tool for species identification in Syringa. Future research could focus on expanding the sample size and exploring additional genetic markers to further enhance the accuracy and applicability of DNA barcoding in Syringa species identification.},
}

@article {pmid40078454,
year = {2025},
author = {Sterling, MJ and Price, BW and Lees, DC},
title = {A revision of the hitherto neglected genus Topiris Walker, 1863 (Lepidoptera, Xyloryctidae) with taxonomic notes on the genus Athrypsiastis Meyrick, 1910.},
journal = {ZooKeys},
volume = {1229},
number = {},
pages = {297-368},
doi = {10.3897/zookeys.1229.119155},
pmid = {40078454},
issn = {1313-2989},
abstract = {The genus Topiris Walker, 1863 is revised. This genus, previously neglected or deemed unrecognisable, comprised only Walker's damaged and misrepaired type specimen of Topiriscandidella Walker, 1863. Evidence is provided that this specimen was collected by Alfred Russel Wallace in 1855-56 in Sarawak, Malaysian Borneo. The mitogenome of this specimen was assembled using low coverage whole genome sequencing (genome skimming). The COI-5P portion of this mitogenome (658 bp) differs by 1-3 bp from two haplotypes sequenced from early 1990's Brunei specimens. Another specimen recently discovered at NHMUK with an identical label to that of the type perfectly matches the Brunei specimens in its genitalia. Based on these four specimens, we present a fuller description of the morphology of T.candidella. Topiris includes the following additional species authored by Sterling and Lees: Topirisalbidella sp. nov., T.albogrisella sp. nov., T.cinderella sp. nov., T.digiticosta sp. nov., T.lacteella sp. nov., T.madonna sp. nov., T.meyricki sp. nov., T.ochrotincta sp. nov., T.schneeweissella sp. nov., T.sericella sp. nov., and T.thunbergella sp. nov. The following new combinations are also established: T.salva (Meyrick, 1932), comb. nov. and T.sampitella (Lvovsky, 2014), comb. nov. The type of Athrypsiastissalva Meyrick is confirmed as lost and so a neotype and paraneotype of this species are designated. A published mitogenome of "Linoclostisgonatias" is shown to be correctly identified as T.salva, and references to L.gonatias, identified in some literature as a pest of Theaceae, are likely misidentified. The genus Topiris is divided into three groups, the candidella group, the salva group, and the albidella group, based on characters in the male genitalia. The candidella group and albidella group are supported sub-clades of Topiris. The phylogenetic placement of Topiris and Athrypsiastis within 'core' Xyloryctidae (as subtended by its type species, X.luteotactella) is confirmed by analysis of COI and seven nuclear genes, whereas the genera Eumenodora Meyrick, 1906 and Izatha Walker, 1864 do not fall within this clade. The morphology of Athrypsiastisphaeoleuca Meyrick, 1910 (the type species of Athrypsiastis; Xyloryctidae) is more fully described. The following new species authored by Sterling and Lees are described: Athrypsiastischeesmanae sp. nov., A.edelweissella sp. nov., and A.penumbrella sp. nov. Two taxa are newly combined: Athrypsiastishalmaherella (Lvovsky, 2014), comb. nov. and Paralectarosiflora (Meyrick, 1930), comb. nov.},
}

@article {pmid40077453,
year = {2025},
author = {Wildbacher, M and Andronache, J and Pühringer, K and Dobrovolny, S and Hochegger, R and Cichna-Markl, M},
title = {Authentication of EU-Authorized Edible Insect Species in Food Products by DNA Barcoding and High-Resolution Melting (HRM) Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/foods14050751},
pmid = {40077453},
issn = {2304-8158},
abstract = {The consumption of edible insects is a promising approach to meet the increasing global demand for food. Commercialization of edible insects in the EU is regulated by the Novel Food regulation. To date, the yellow mealworm (Tenebrio molitor larva), the migratory locust (Locusta migratoria), the house cricket (Acheta domesticus), and the buffalo worm (Alphitobius diaperinus larva) have been authorized in the EU for human consumption. We aimed to develop a method based on DNA barcoding and high-resolution melting (HRM) analysis for the identification and differentiation of these four EU-authorized edible insect species in food. A primer pair previously designed for DNA metabarcoding, targeting a ~200 bp sequence of mitochondrial 16S rDNA, allowed discrimination between the four insect species in highly processed food. However, house cricket and migratory locust could not unambiguously be differentiated from tropical house cricket, desert locust, superworm, cowpea weevil, and sago worm, respectively. This problem could be solved by designing primers specific for house cricket and migratory locust. By combining these primers with the insect primers, additional polymerase chain reaction (PCR) products for house cricket and migratory locust were obtained, resulting in more complex melt curves compared to the unauthorized insect species. The optimized PCR-HRM assay is a very cost-efficient screening tool for authentication of EU-authorized edible insect species in food.},
}

@article {pmid40076024,
year = {2025},
author = {Miller, C and Linzey, D and Hallerman, E},
title = {Morphological and Genetic Assessments of Coyote Diet in Qualla Boundary, North Carolina, Show Interaction with Humans.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/ani15050741},
pmid = {40076024},
issn = {2076-2615},
abstract = {Throughout the 20th century, coyotes (Canis latrans) expanded from their historical geographic range west of the Mississippi River to a current range of almost all of North America. Over the course of this expansion, coyotes have demonstrated diverse and variable omnivorous diets that change with the food resources available. This study examined the stomach contents of 25 coyotes in an area where they are relatively new, the Qualla Boundary in North Carolina, to better understand the diets of coyotes in this area. A combination of morphological identification and DNA barcoding was used to characterize the stomach contents of coyotes. Both plant and animal material were identified from anthropogenic and natural sources, the latter including native mammals. This study provides one example of the breadth and flexibility of coyote diets and helps build an understanding of how coyotes can adapt to new conditions.},
}

@article {pmid40075470,
year = {2025},
author = {Miao, K and Zhang, A and Yang, X and Zhang, Y and Lin, A and Wang, L and Zhang, X and Sun, H and Xu, J and Zhang, J and Feng, Y and Shao, F and Guo, S and Weng, Z and Luo, P and Wang, D and Gao, S and Zhao, XY and Xu, X and Deng, CX},
title = {Lymphatic system is the mainstream for breast cancer dissemination and metastasis revealed by single-cell lineage tracing.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {75},
pmid = {40075470},
issn = {1476-4598},
mesh = {*Breast Neoplasms/pathology/genetics/metabolism ; Female ; Humans ; *Tumor Microenvironment ; Animals ; *Single-Cell Analysis/methods ; Mice ; *Cell Lineage/genetics ; Lymphatic System/pathology ; Cell Line, Tumor ; Lymphatic Metastasis/pathology ; Neoplasm Metastasis ; },
abstract = {Cancer metastasis is the primary cause of cancer-related death, yet the forces that drive cancer cells through various steps and different routes to distinct target organs/tissues remain elusive. In this study, we applied a barcoding system based single-cell lineage tracing approach to study the metastasis rate and route of breast cancer cells and their interactions with the tumor microenvironment (TME) during metastasis. The results indicate that only a small fraction of cells, accounting for fewer than 3% of total barcodes, can intravasate from the primary site into the blood circulation, whereas more cells disseminate through the lymphatic system to different organs. Tumor cells derived from the same progenitor cell exhibit different gene expression patterns in different soils, and the cancer cell-TME communication paradigm varies significantly between primary and metastatic tumors. Furthermore, metastable cells require a prewired particular cytokine expression ability which may be specific for lymph metastasis route although the underlying mechanism requires further investigation. In summary, leveraging a single-cell lineage tracing system, we demonstrate that the crosstalk between tumor cells and the TME is the driving force controlling the preferential metastatic fate of cancer cells through the lymphatic system.},
}

*Breast Neoplasms/pathology/genetics/metabolism
Female
Humans
*Tumor Microenvironment
Animals
*Single-Cell Analysis/methods
Mice
*Cell Lineage/genetics
Lymphatic System/pathology
Cell Line, Tumor
Lymphatic Metastasis/pathology
Neoplasm Metastasis

@article {pmid40067649,
year = {2025},
author = {Cho, JM and Kang, M and Park, S and Oh, J and Ku, H and Shin, HY and Koh, JH and Cho, S and Kim, Y and Lee, S and Kim, YC and Han, SS and Joo, KW and Kim, YS and Yang, SH and Moon, KC and Lee, H and Kim, HJ and Kim, DK and , },
title = {Identification of conserved gene expression changes across common glomerular diseases by spatial transcriptomics.},
journal = {Journal of nephrology},
volume = {},
number = {},
pages = {},
pmid = {40067649},
issn = {1724-6059},
support = {RS-2024-00403375//Ministry of Health & Welfare, Republic of Korea/ ; RS-2024-00345867//National Research Foundation of Korea (NRF)/ ; },
abstract = {BACKGROUND: Glomerular diseases encompass a group of kidney diseases that may share common gene expression pathways. Here, we analyzed glomerular-specific gene expression profiles across various glomerular diseases.

METHODS: We performed spatial transcriptomic profiling using formalin-fixed paraffin-embedded kidney biopsy specimens of controls and patients with five types of glomerular diseases using the GeoMx Digital Spatial Profiler. Disease-representative glomerular regions of interest (ROIs) were configured, probed with oligonucleotide barcodes linked with target complimentary sequence. The UV-cleaved barcodes were amplified to generate libraries and subsequently sequenced. Common differentially expressed genes across glomerular diseases were identified and Gene Ontology annotation was performed using the ToppGene suite.

RESULTS: The mean age of patients with glomerular diseases and kidney donors was 49.5 ± 12.2 and 49.5 ± 9.8 years, respectively. A total of 35 differentially expressed genes were consistently downregulated in glomeruli across the disease compared to the control, while none of the differentially expressed genes were consistently upregulated. Twelve of 35 downregulated differentially expressed genes, including the two hub genes JUN and FOS, were annotated with molecular function Gene Ontology terms related to DNA-binding transcription factor activity. The annotated biological process Gene Ontology terms included response to lipid-related (17/35 differentially expressed genes), response to steroid hormone (12/35 differentially expressed genes), or cell cycle regulation (10/35 differentially expressed genes). Xenium and immunofluorescence staining confirmed the reduced expression of JUN, ZFP36, and KLF9 in intraglomerular cells of glomerular diseases.

CONCLUSIONS: Identifying common differentially expressed genes by spatial transcriptomic analysis provides insights into the underlying molecular mechanisms of glomerular diseases and may lead to novel assessment or therapeutic strategies.},
}

@article {pmid40066677,
year = {2025},
author = {Ascenzi, A and Wührl, L and Feng, V and Klug, N and Pylatiuk, C and Cerretti, P and Meier, R},
title = {EntoSieve: Automated Size-Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14097},
doi = {10.1111/1755-0998.14097},
pmid = {40066677},
issn = {1755-0998},
support = {B85F21005360001//Ministero dell'Università e della Ricerca, Programma Operativo Nazionale/ ; },
abstract = {Widespread insect decline necessitates the development and use of standardized protocols for regular monitoring. These methods have to be rapid, efficient and cost-effective to allow for large-scale implementation. Many insect sampling and molecular methods have been developed. These include Malaise trapping, high-throughput DNA barcoding ('megabarcoding') and metabarcoding. The latter allows for assessing the species diversity in whole samples using few steps, but sample heterogeneity in terms of body size remains a challenge since large insects contribute disproportionately more mtDNA than small ones. This can potentially overwhelm the template DNA from small species that then go undetected. Size-sorting can mitigate this problem, but no satisfying automated, rapid and non-destructive solutions are available. We introduce the EntoSieve, a low-cost and DIY motorized instrument that disentangles and sorts abundant insect bulk samples into several body size fractions while minimizing damage to specimens, thus reducing the risk of DNA contamination across size fractions (e.g. legs of large specimens in small body size fraction). EntoSieve utilizes readily available components, 3D-printed parts and customizable meshes, thus enabling parallelization at low cost. We here show the efficiency of the EntoSieve for three samples with more than 10,000 specimens using three sieving protocols and assess the impact on specimen integrity. Efficiency ranged from 92% to 99%, achieved within 18-60 min, and specimen damage was not significant for subsamples. By facilitating rapid pre-processing, the device contributes to producing morphologically valuable vouchers for megabarcoding and is likely to improve compositional diversity accuracy across size classes when using metabarcoding.},
}

@article {pmid40066512,
year = {2025},
author = {Lv, Y and Liu, X and Liang, J and Dong, L and Zhang, Y and Lin, C and Xiang, S and Chen, B and Zhang, Z},
title = {Monochromatic Responsive HOF Heterostructures via VIA-Group-Based Framework Hybridization for Fully-Covert Photonic Barcode.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2420486},
doi = {10.1002/adma.202420486},
pmid = {40066512},
issn = {1521-4095},
support = {22475047//National Natural Science Foundation of China/ ; 22373015//National Natural Science Foundation of China/ ; W2431013//National Natural Science Foundation of China/ ; 22271046//National Natural Science Foundation of China/ ; 22105039//National Natural Science Foundation of China/ ; 22425102//National Science Fund for Distinguished Young Scholars/ ; HFNKL2023WW04//Foundation of National Key Laboratory of Human Factors Engineering/ ; },
abstract = {Luminescent responsive heterostructures with region-domained emission and integrated responsiveness exhibit great potential in information security, but always suffer from the direct exposure of fingerprint information at the initial state, making it easy to decode the hidden confidential information. Herein, the first monochromatic responsive hydrogen-bonded organic framework (HOF) heterostructures are reported based on VIA-group-based framework hybridization toward fully-covert photonic barcodes. Designed HOF blocks with different VIA-group elements are integrated via a configuration-assimilation-based assembly method to generate the intrinsic monochromatic HOF heterostructures. Differentiated electronegativity of VIA-group elements endows each HOF block with distinct bonding stability, which triggers different responsive actions to the same stimuli, finally forming the multicolor emission mode at a responsive state. These monochromatic responsive HOF heterostructures can effectively hide the intrinsic fingerprint information, which further demonstrates the fully-covert photonic coding capability as high-security anti-counterfeiting labels. These findings offer novel insight on the exploitation of smart-responsive hetero-HOF systems for advanced information encryption and anticounterfeiting applications.},
}

@article {pmid40065744,
year = {2025},
author = {Marline, L and Ranaivoson, NAS and Smith, R and Ah-Peng, C and Hedderson, TAJ and Wilding, N and Antonelli, A},
title = {Advancing bryophyte research and conservation, a case study on Madagascar.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcaf035},
pmid = {40065744},
issn = {1095-8290},
abstract = {BACKGROUND: Bryophytes are a group of plant that are ecologically important, diverse and include many undescribed species. Setting like Madagascar is well known for its charismatic species, less conspicuous groups, such as bryophytes, are virtually unknown to the public and the scientific community. Bryophyte diversity is a highly overlooked component of Madagascar's rich biodiversity, underlined by geographical sampling biases, sparse representation, and an evident research and conservation deficit as compared to more charismatic groups. With a significant bryophytes research gap and conservation, Madagascar can serve as model for addressing knowledge gaps and talking the global issue of bryophytes blindness. Here we first summarise historical research and current knowledge on the diversity and distribution of Malagasy bryophytes; address the issue of 'bryophyte blindness'; and propose future directions.

SCOPE: We give reason to think that to advance research and ensure the effective conservation of the bryophytes, it is crucial to build robust foundations for their study and appreciation. Investments on herbarium collections paired with leveraging technology and resources for identification, including an image bank and DNA barcodes, will facilitate taxonomic revisions, evolutionary biology and ecological research. Addressing geographical imbalances and fostering comprehensive research to elevate the scientific and public appreciation of bryophytes are key to advancing the integration of bryophytes into national, regional and global conservation initiatives. Key prospects also include research on ecosystems with high and/or endemic bryophyte diversity, facilitating the integration of bryophytes into conservation programs. Training the new generation of students and professionals on bryophytes is an imperative underlying all these initiatives. This is highly important to foster more equitable research and conservation in countries like Madagascar and help tackle bryophyte blindness in science and society, alongside with an urgently needed financial support for professional training to advance bryophytes research.

CONCLUSIONS: Overall, bryophytes need urgent research and conservation investments. Researchers, organisations, governments, and universities should collaborate to raise scientific and public awareness of their importance. Addressing key questions about bryophyte diversity, threats, and conservation requires a holistic, collaborative, and inclusive approach to bryophyte research.},
}

@article {pmid40063875,
year = {2025},
author = {Suzuki, M and Terada, R},
title = {DNA-based floristic survey of red algae (Rhodophyta) growing in the mesophotic coral ecosystems (MCEs) offshore of Tanegashima Island, northern Ryukyu Archipelago, Japan.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0316067},
doi = {10.1371/journal.pone.0316067},
pmid = {40063875},
issn = {1932-6203},
mesh = {*Rhodophyta/genetics ; Japan ; *Anthozoa/genetics ; *Ecosystem ; Animals ; Biodiversity ; Phylogeny ; DNA Barcoding, Taxonomic ; Islands ; DNA, Algal/genetics ; Coral Reefs ; },
abstract = {A molecular-based floristic survey of marine red algal biodiversity was conducted offshore Tanegashima Island, which is located at the northern end of mesophotic coral ecosystems (MCEs), in the Ryukyu Archipelago, Japan. This study provides the first comprehensive catalog of red algae comprising the sublittoral marine flora of offshore Tanegashima Island, Japan, and represents the first exhaustive molecular-assisted survey of red algal marine flora in Japan. Morphological and molecular analyses using plastid-encoded rbcL and mitochondrion-encoded cox1 genes revealed a total of 129 species, which included nine newly recognized species in Japan. Morphologically, 82 species were assigned to known species. Among the 82 species, 17 included cryptic species, and 25 appeared to have misapplied names. The remaining 47 species could not be identified to the species level, which indicates the necessity of a detailed reference library containing validated DNA barcodes and further taxonomic studies based on morpho-molecular analyses.},
}

*Rhodophyta/genetics
Japan
*Anthozoa/genetics
*Ecosystem
Animals
Biodiversity
Phylogeny
DNA Barcoding, Taxonomic
Islands
DNA, Algal/genetics
Coral Reefs

@article {pmid40063774,
year = {2025},
author = {Trollip, C and Carnegie, A},
title = {First record of Graphium species associated with Euwallaceae perbrevis in Australia.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-02-25-0319-PDN},
pmid = {40063774},
issn = {0191-2917},
abstract = {In the wake of the detection of polyphagous shot hole borer (Euwallaceae fornicatus) in Perth, Western Australia, in 2021 (Cook and Broughton 2023), and ongoing surveillance for Fusarium dieback associated with ambrosia beetles in New South Wales (NSW) (Callaghan et al. (2024), there is a growing need to characterize fungal associates of already-established Euwallaceae species in Australia. Historically, plant health diagnostics targeting fungi vectored by tea shot hole borer, Euwallaceae perbrevis, in Australia has focused on Fusarium species, with only Fusarium obliquiseptatum and F. metavorans reported to date (Aoki et al. 2019; Callaghan et al. 2024). No other fungal associates have been reported from this vector in Australia despite the presence of key symbionts found in association with Euwallaceae beetles globally (Lynch et al. 2016, Na et al. 2018). In 2024, three cases of beetle infestation associated with dieback and tree mortality reported to forest biosecurity staff of NSW provided an opportunity for more detailed diagnostic investigations. The first was from Acer paxii at the Royal Botanic Garden of Sydney in April, the second from a stand of Cupaniopsis anacardioides at Lennox Head, northern NSW, in August, and the third from Ficus obliqua at the Royal Botanic Garden of Sydney in November. Isolations were performed from stained wood tissue, beetle galleries, and directly from beetle specimens, similar to described protocols (Lynch et al. 2016). Fusarium obliquiseptatum was confirmed in all cases (data not shown), however, Graphium spp. were readily observed in beetle galleries and in low abundance co-occuring with F. obliquiseptatum on isolation plates. Graphium isolates were recovered by picking conidial spore drops from synnemata and hyphal tipping to produce axenic cultures. Molecular identification was achieved by PCR and sequencing the internal transcribed spacer (ITS) and the translation elongation factor 1α barcoding regions using primers ITS1-ITS4 and EF2F-EF2R, respectively (Marincowitz et al. 2015). Three Graphium taxa were identified, viz. Graphium euwallaceae (DAR 86890) isolated from A. paxii in Sydney, the currently undescribed Graphium sp. II (DAR 86892) isolated from C. anacardioides in Lennox Head, and a putatively novel Graphium taxon, Graphium cf. basitruncatum (DAR 86894), isolated from F. obliqua in Sydney. These detections represent the first records of Graphium species associated with E. perbrevis in Australia. Graphium euwallaceae is a well-established fungal symbiont of E. fornicatus and E. perbrevis globally, previously reported in the United States, Vietnam and most recently in Perth, Western Australia (Lynch et al. 2016, Wright and Kehoe pers. comm.). In contrast, Graphium sp. II has only been previously recorded from a Durio sp. in Thailand (Na et al. 2018). The taxon identified as Graphium cf. basitruncatum is most closely related to G. basitruncatum, originally found in forest soils in the Solomon Islands and Japan (Okada et al. 2000). Graphium species are often regarded as saprobes or nutritional symbionts of ambrosia beetles, however their role in the lifecycle of Euwallaceae beetles and demonstrated pathogenic potential is arguably underappreciated in biosecurity (EPPO 2020, Lynch et al. 2016, Na et al. 2018). Future research in this regard might provide better assessment of the risks posed by fungal symbionts that goes beyond predetermined views of pathogenicity.},
}

@article {pmid40061916,
year = {2025},
author = {Arabeyyat, Z and Sweiss, M and Alajlouni, A and Al-Ajlouni, N and Mahmoud, M and Shartooh, S and Alsoqi, F and Kteifan, M},
title = {Identification and phylogenetic analysis of marine sponges in the Jordanian Gulf of Aqaba using DNA barcoding.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42771},
pmid = {40061916},
issn = {2405-8440},
abstract = {Sponges (Porifera) are the largest biomass component of coral reefs benthic fauna among marine organisms and are very morphologically diverse. In the present work, we aimed to identify marine sponges in the Jordanian Gulf of Aqaba using the partial 18S rRNA and the 28S rRNA genes as DNA barcoding markers. A total of nine morphologically different marine sponge samples from 6.6m to approximately 22m depth were collected. Sponge fragments were frozen at -80 °C prior to DNA extraction. The sponge's DNA was extracted using a commercial kit and subjected directly to PCR amplification for the 18S rRNA and 28S rRNA genes. The DNA sequences were analyzed using the Basic Local Alignment Search Tool (BLAST) to determine the sponge's identity, and phylogenetic trees were constructed to clarify the relationship among the samples. The results obtained revealed the presence of the following genera: Axinella, Negombata, Siphonochalina, Diacarnus, and an unidentified genus within the order Haplosclerida. Identification of sponge species was difficult due to the scarcity of diagnostic morphological characters. To our knowledge, this is the first study in the Jordanian Gulf of Aqaba that focuses on the morphological and molecular taxonomy of marine sponges using DNA barcoding markers.},
}

@article {pmid40060715,
year = {2025},
author = {Moura, CJ and Wirtz, P and Nhanquê, FT and Barbosa, C and Serrão, E},
title = {Hotspot of Exotic Benthic Marine Invertebrates Discovered in the Tropical East Atlantic: DNA Barcoding Insights From the Bijagós Archipelago, Guinea-Bissau.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e70964},
pmid = {40060715},
issn = {2045-7758},
abstract = {This study aimed to explore and document putative exotic marine benthic invertebrate species in the Bijagós Archipelago, Guinea-Bissau, to enhance understanding of marine biodiversity and address the extent of marine species introductions. The research was conducted in the Bijagós Archipelago, a UNESCO Biosphere Reserve located in Guinea-Bissau. The study involved the region's first scuba-diving survey of marine biodiversity. DNA barcoding was employed to assist in the identification of benthic invertebrate species. Molecular phylogenetic analyses were conducted with the available DNA barcodes to ensure accurate taxonomic assignments, detect cryptic species, and investigate the phylogeography of the taxa. The survey resulted in the discovery of 28 new species records for the Bijagós Archipelago, including octocorals, scleractinians, hydroids, bryozoans, barnacles, and ascidians. Among these, six species were documented for the first time in the East Atlantic: Stragulum bicolor, Nemalecium lighti, Diphasia sp., Amathia alternata, A. distans, and Symplegma rubra. Molecular analyses revealed pervasive cryptic diversity within species previously listed as exotic, suggesting that some, such as the hydroids Plumularia setacea, Obelia geniculata, and Dynamena disticha, are not exotic due to their restricted biogeographic distributions. Many other species reported as introduced present only a few genetic lineages capable of long-distance dispersal due to human activities. The study highlights considerable gaps in the knowledge of West African marine biodiversity and suggests a substantial underestimation of the anthropogenic trade in exotic marine species between the Tropical East Atlantic and the Americas, and between the Indo-Pacific, Mediterranean, and West Africa. Detailed taxonomic and genomic analyses are necessary for understanding marine exotic species' biogeography and adaptive traits. Our findings challenge current classifications of exotic species and underscore the need for improved monitoring and management to prevent the spread of non-native marine species.},
}

@article {pmid40060547,
year = {2025},
author = {Feldman, D and Sims, JN and Li, X and Johnson, R and Gerben, S and Kim, DE and Richardson, C and Koepnick, B and Eisenach, H and Hicks, DR and Yang, EC and Wicky, BIM and Milles, LF and Bera, AK and Kang, A and Brackenbrough, E and Joyce, E and Sankaran, B and Lubner, JM and Goreshnik, I and Vafeados, D and Allen, A and Stewart, L and MacCoss, MJ and Baker, D},
title = {Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.24.639402},
pmid = {40060547},
issn = {2692-8205},
abstract = {Library screening and selection methods can determine the binding activities of individual members of large protein libraries given a physical link between protein and nucleotide sequence, which enables identification of functional molecules by DNA sequencing. However, the solution properties of individual protein molecules cannot be probed using such approaches because they are completely altered by DNA attachment. Mass spectrometry enables parallel evaluation of protein properties amenable to physical fractionation such as solubility and oligomeric state, but current approaches are limited to libraries of 1,000 or fewer proteins. Here, we improved mass spectrometry barcoding by co-synthesizing proteins with barcodes optimized to be highly multiplexable and minimally perturbative, scaling to libraries of >5,000 proteins. We use these barcodes together with mass spectrometry to assay the solution behavior of libraries of de novo -designed monomeric scaffolds, oligomers, binding proteins and nanocages, rapidly identifying design failure modes and successes.},
}

@article {pmid40060545,
year = {2025},
author = {Jang, J and Ko, KP and Zhang, J and Jun, S and Park, JI},
title = {Deciphering Precursor Cell Dynamics in Esophageal Preneoplasia via Genetic Barcoding and Single-Cell Transcriptomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.26.637920},
pmid = {40060545},
issn = {2692-8205},
abstract = {Cancer cells exhibit high heterogeneity and lineage plasticity, complicating studies of tumorigenesis and development of therapies. Recently, preneoplastic cells, although histologically normal, have been shown to possess high plasticity and early genetic alterations, yet their origins and lineage trajectories remain unclear. Herein, we introduce a lineage-tracing tool integrating genetic barcoding with single-cell RNA sequencing to map preneoplastic esophageal cell lineages. We identified preneoplastic precursor cells (PNPCs) as a distinct progenitor-like population with unique transcriptional profiles and high plasticity, contributing to proliferative and basal cell populations. To enhance lineage mapping, we developed the eXamined Ridge (XR) score, accurately identifying high-plasticity cells. Nfib and Qk emerged as conserved PNPC markers, peaking in early preneoplasia and declining after malignant transformation. These findings reveal PNPCs as key players in early tumorigenesis and highlight their potential as biomarkers for early cancer detection and therapeutic intervention, offering new strategies for preventing esophageal cancer progression.},
}

@article {pmid40058416,
year = {2025},
author = {Johnthini, MA and Dahms, HU and Schizas, NV and James, RA and Ouddane, B and Huang, YL},
title = {Isolation of Pseudonocardia strains associated with the shallow water hydrothermal vent crab Xenograpsus testudinatus from a metal-rich environment: biochemical characterization and enzymatic characterization, molecular identification, antibacterial, antibiofilm and antioxidant activity.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107457},
doi = {10.1016/j.micpath.2025.107457},
pmid = {40058416},
issn = {1096-1208},
abstract = {A shallow hydrothermal vent at Kueishantao Island, Taiwan provides a challenging environment and has been less explored for its microbial communities, especially the actinomycetes and their antibacterial and antioxidant activity. Nine actinomycete strains were isolated from the endemic hydrothermal vent crab Xenograpsus testudinatus and were identified as belonging to the otherwise rare actinomycete genus Pseudonocardia sp. Physiochemical results showed that the optimum growth conditions of these nine isolates were at pH 7, 35 °C, and 0.5-2% NaCl. Biochemical characterization showed differences between the strains. These isolates were further characterized at genetic barcoding (16s rRNA sequencing) and phenotypic levels and identified at the species/ strain level as Pseudonocardia alni SCSW01, Pseudonocardia yuanmonensis SCSW02, Pseudonocardia sp. strains SCSW03, SCSW04, SCSW05, SCSW06, BCSW29, ECSW09, and ECSW018. The morphology of the strains was analyzed using an environmental scanning electron microscope (ESEM). The nine isolates showed potential antibacterial activity against gram-positive and gram-negative pathogenic strains. The confocal laser scanning microscopy (CLSM) images show live and dead cells and biofilm/ antibiofilm activity of the actinomycete supernatant and crude extracts against pathogenic bacterial strains. The crude extracts of SCSW02, SCSW06, BCSW29, ECSW09, and ECSW018 showed antibiofilm activity against P. aeruginosa, E. coli, and S. aureus. The antioxidant activity such as DPPH and H2O2 scavenging assay results showed that the nine actinomycetes crude extracts hold more substantial radical scavenging properties than supernatants. Our results marked the first report of Pseudonocardia genera from the vent crab Xenograpsus testudinatus of the HV region at Kueishantao island, Taiwan.},
}

@article {pmid40057837,
year = {2025},
author = {Zajta, E and Peskó, G and Knapp, GD and Vad, E and Bödör, C and Sinkó, J},
title = {[Opportunities offered by molecular diagnostics in the management of invasive fungal infections of oncohematological patients].},
journal = {Orvosi hetilap},
volume = {166},
number = {10},
pages = {363-376},
doi = {10.1556/650.2025.33241},
pmid = {40057837},
issn = {1788-6120},
mesh = {Humans ; *Invasive Fungal Infections/diagnosis ; Hematologic Neoplasms/complications/diagnosis ; Hungary ; Polymerase Chain Reaction/methods ; Molecular Diagnostic Techniques/methods ; Antifungal Agents/therapeutic use ; },
}

Humans
*Invasive Fungal Infections/diagnosis
Hematologic Neoplasms/complications/diagnosis
Hungary
Polymerase Chain Reaction/methods
Molecular Diagnostic Techniques/methods
Antifungal Agents/therapeutic use

@article {pmid40056601,
year = {2025},
author = {Wu, SR and Sharpe, J and Tolliver, J and Groth, AJ and Chen, R and Guerra García, ME and Valentine, V and Williams, NT and Jacob, S and Reitman, ZJ},
title = {Combining the RCAS/tv-a retrovirus and CRISPR/Cas9 gene editing systems to generate primary mouse models of diffuse midline glioma.},
journal = {Neoplasia (New York, N.Y.)},
volume = {62},
number = {},
pages = {101139},
doi = {10.1016/j.neo.2025.101139},
pmid = {40056601},
issn = {1476-5586},
abstract = {Diffuse midline gliomas (DMGs) are lethal brain tumors that arise in children and young adults, resulting in a median survival of less than two years. Genetically engineered mouse models (GEMMs) are critical to studying tumorigenesis and tumor-immune interactions, which may inform new treatment approaches. However, current midline glioma GEMM approaches are limited in their ability to multiplex perturbations and/or target specific cell lineages in the brain for genetic manipulation. Here, we combined the RCAS/tv-a avian retrovirus system and CRISPR/Cas9 genetic engineering to drive midline glioma formation in mice. CRISPR/Cas9-based disruption of Trp53, a tumor suppressor that is frequently disrupted in midline gliomas, along with the oncogene PDGF-B resulted in high grade tumor formation with moderate latency (median time to tumor formation of 12 weeks). We confirmed CRISPR-mediated Trp53 disruption using next-generation sequencing (NGS) and immunohistochemistry (IHC). Next, we disrupted multiple midline glioma tumor suppressor genes (Trp53, Pten, Atm, Cdkn2a) in individual mouse brains. These mini-pooled in vivo experiments generated primary midline gliomas with decreased tumor latency (median time to tumor formation of 3.6 weeks, P < 0.0001, log-rank test compared to single-plex gRNA). Quantification of gRNA barcodes and CRISPR editing events revealed that all tumors contained cells with various disruptions of all target genes and suggested a multiclonal origin for the tumors as well as stronger selection for Trp53 disruption compared to disruption of the other genes. This mouse modeling approach will streamline midline glioma research and enable complex experiments to understand tumor evolution and therapeutics.},
}

@article {pmid40052334,
year = {2025},
author = {Lu, Y and Dong, Y and Zhang, M and Mao, L},
title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14095},
doi = {10.1111/1755-0998.14095},
pmid = {40052334},
issn = {1755-0998},
support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; },
abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.},
}

@article {pmid40052073,
year = {2025},
author = {Schnittler, M and Leontyev, D and Yatsiuk, I and Ronikier, A},
title = {Species descriptions in myxomycetes - can we settle on rules for good taxonomic practice?.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e141199},
pmid = {40052073},
issn = {2210-6340},
abstract = {Myxomycetes are a unique branch of life, recognisable by sporophores showing a fungus-like dispersal biology. These structures bear nearly all diagnostic characters for species identification and develop by rapid transformation of plasmodia. During this short period of time, external factors can significantly influence the formation of morphological characters. Therefore, the description of a new species must be carried out with utmost care. Over the last 50 years, approximately 10-15 new species of myxomycetes have been described per year and only some of the latest publications underpin this with molecular data. In this paper, we discuss a set of recommendations for the description of myxomycete species new to science, striving for the following goals: (i) to minimise the number of erroneous descriptions of the species, whose names later have to be put into synonymy; (ii) to make all respective data easily accessible for the scientific community; and (iii) to comply with existing rules of nomenclature. We recommend (1) whenever possible not to describe a new taxon from a single specimen; however, an exception could be made only if supported by molecular data and by unique morphological characters which are unlikely to fall in the range of infraspecific variation of related species; (2) preparing detailed descriptions, including data on developmental stages, microhabitats, ecology, phenology and associated species; (3) providing at least two independent diagnostic characters that tell the new species apart from all others; (4) obtaining a molecular barcode and, whenever possible, providing proof for reproductive isolation of the new species from related taxa; and (5) depositing type specimens in public herbaria. To comply with nomenclatural rules, (6) the new name must be registered in a recognised repository, (7) all published names should be checked for usability before proposing a new name and (8) a unique name should be chosen, preferably highlighting a distinct character of the new species.},
}

@article {pmid40051454,
year = {2025},
author = {Zavala, E and Britzke, R and Siccha-Ramírez, Z and Ramirez, JL},
title = {DNA barcoding of marine rocky reef fishes from northern Peru suggests a parapatric speciation in the Tropical Eastern Pacific.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e70125},
pmid = {40051454},
issn = {2045-7758},
abstract = {Northern Peru marks the end of an extensive coastal marine region: The Panama province, which is characterized by predominantly tropical and equatorial features and is home to the only rocky reefs known in Peruvian territory. This unique ecosystem could explain the presence of a diverse range of fish species. However, due to the difficulty of sampling and accessing reef areas, our knowledge of this biodiversity is incomplete. To address this issue, we used DNA barcoding for the study of the fish biodiversity and revealed patterns that may have influenced their evolution throughout the Tropical Eastern Pacific (TEP). A fragment of Cytochrome oxidase subunit I (COI) of 177 samples of rocky reef fishes was sequenced. Intra and interspecific K2P distances were calculated and three species delimitation methods (GMYC, PTP, and bPTP) were used to obtain MOTUs. Both analyses support the conformation of additional MOTUs in samples of Mugil cephalus, Ophichthus zophochir, Malacoctenus tetranemus, Ariopsis seemanni and Halichoeres dispilus, species with a divergence above 2%. By comparing these sequences with public data, our analysis revealed the existence of COI lineages and suggested potential ecological parapatric speciation in the TEP. More studies using other markers and different approaches are required to confirm the existence of species complexes that could be related to the presence of cryptic species.},
}

@article {pmid40048560,
year = {2025},
author = {Bi, W and Cao, X and Li, J and Gao, Y and Song, Y and He, B},
title = {Ultrasensitive Detection of Extracellular Vesicles Based on Metal-Organic Framework DNA Biobarcodes Triggered G-Quadruplex Coupled with Rolling Circle Amplification Assay.},
journal = {ACS sensors},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssensors.4c03384},
pmid = {40048560},
issn = {2379-3694},
abstract = {Extracellular vesicles (EVs), as liquid biopsy markers for accurate tumor diagnosis, are considered to hold great promise. However, effectively isolating and sensitively detecting EVs with convenience still face challenges. Herein, we propose a highly sensitive and specific platform for EV detection by integrating a metal-organic framework (MOF)-based DNA biobarcodes strategy with a rolling circle amplification (RCA)/G-quadruplex system. In this study, first, Zr-MOFs act as signal converters by comodification with DNA barcodes and antibodies, converting and amplifying the abundance of EVs into DNA barcodes. Second, the released DNA can trigger RCA, followed by G-quadruplex formation to further amplify the signal. Consequently, this approach significantly enhances the sensitivity for EV biomarker detection, achieving a low limit of detection of 100 EVs mL[-1]. Furthermore, the strategy offers high sensitivity, specificity, accuracy, and simplicity, highlighting its potential for clinical applications in noninvasive EV detection.},
}

@article {pmid40047956,
year = {2025},
author = {Meghana, BN and Reshma, SV},
title = {DNA barcoding of geographical indication tagged Byadagi chilli and its cultivars using ITS2, matK and rbcL coding sequences.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {286},
pmid = {40047956},
issn = {1573-4978},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Capsicum/genetics/classification ; DNA, Plant/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Byadagi chilli, a Geographical Indication (GI)-tagged chilli variety known for its special aroma and bright red colour, was accorded the GI tag in February 2011 with the GI number 129. The two traditional varieties of Byadagi chilli, namely: Dabbi and Kaddi, are the GI-tagged varieties. In this study, GI-tagged Byadagi Dabbi, Byadagi Kaddi and other cultivars of Byadagi chilli, such as Byadagi Lali (BL), Byadagi HPH 2043 (B2), Byadagi BSS 355 (B3) and another popular GI-tagged chilli variety, Guntur Sannam, were analysed to assess their inter-relationships. Due to the high market value and demand, it is important to identify and differentiate the original variety of Byadagi chilli and its associated cultivars from the other chilli cultivars, which are sold under the name of Byadagi chilli. In this study, molecular assessment by DNA barcoding was performed to establish the identity of authentic Byadagi chilli varieties.

METHODS AND RESULTS: Five samples of Byadagi chilli and another GI-tagged chilli variety, Guntur Sannam, were analysed using three DNA barcodes: ITS2, matK and rbcL. The PCR products were sequenced, nucleotide BLAST was performed and ITS2 showed 97.7% identity, matK 99.1%, and rbcL 99.19% with Capsicum annuum at the genus and species levels. Phylogenetic analysis of the DNA sequences of all the six chilli samples was performed using ClustalW multiple sequence alignment in MEGA11. The genetic distance between the six samples was calculated using the maximum likelihood approach.

CONCLUSIONS: This study distinctly demonstrates that the chloroplast DNA barcodes matK and rbcL, along with the nuclear DNA barcode, ITS2, can be used for accurate identification of Byadagi chilli cultivars. This study offers significant molecular identification and establishes a robust barcoding foundation for Byadagi chilli. The phylogenetic trees generated from the barcode sequences clearly indicated the relationships among the selected cultivars.},
}

*DNA Barcoding, Taxonomic/methods
*Phylogeny
*Capsicum/genetics/classification
DNA, Plant/genetics
Ribulose-Bisphosphate Carboxylase/genetics
Sequence Analysis, DNA/methods

@article {pmid40046838,
year = {2025},
author = {Yang, G and Wang, W and Tong, Y and Zhou, Z},
title = {Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera).},
journal = {ZooKeys},
volume = {1229},
number = {},
pages = {25-42},
pmid = {40046838},
issn = {1313-2989},
abstract = {DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5' end of the mitochondrial cytochrome c oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Units (MOTUs), namely the distance-based Barcode Index Number (BIN) System, Generalized Mixed Yule Coalescent (GMYC), a Java program that uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Assemble Species by Automatic Partitioning (ASAP), and Bayesian implementation of the Poisson Tree Processes model (bPTP). All species, except Hierodulachinensis Werner, 1929, were recovered as monophyletic on the neighbor-joining (NJ) tree. For the final dataset, 379 COI-5P barcode sequences were assigned to 68 BINs. Fifty-five out of 68 BINs obtained were new to BOLD. The low level of BIN overlap with other nations highlights the importance of constructing a regional DNA barcode reference library. The algorithms ASAP, jMOTU, bPTP, and GMYC clustered barcode sequences into 32, 58, 68, and 60 MOTUs, respectively. All species delimitation algorithms (except ASAP analysis) split Anaxarchasinensis Beier, 1933, Anaxarchazhengi Ren & Wang, 1994, H.chinensis, Spilomantisoccipitalis (Westwood, 1889), Titanodulaformosana Giglio-Tos, 1912 into more than one MOTUs. All algorithms merged Hierodula sp. BCM-2019 and H.chinensis into the same MOTU, as for Tenoderaaridifolia Stoll, 1813 and Tenoderasinensis Saussure, 1871. More accurate identification results need to be supplemented by detailed morphological classification.},
}

@article {pmid40045661,
year = {2025},
author = {Chiyo, PI and King'ori, E},
title = {Genetic identification of Stephanofilaria sp. isolated from ulcerative dermal lesions in black rhinoceros.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e42},
doi = {10.1017/S0022149X25000112},
pmid = {40045661},
issn = {1475-2697},
mesh = {Animals ; *Perissodactyla/parasitology ; *Phylogeny ; *Genetic Variation ; Electron Transport Complex IV/genetics ; DNA, Ribosomal Spacer/genetics ; Filarioidea/genetics/classification/isolation & purification ; DNA Barcoding, Taxonomic ; Sequence Analysis, DNA ; DNA, Helminth/genetics ; Skin Ulcer/parasitology/veterinary ; },
abstract = {Stephanofilaria is a genus of nematodes that cause ulcerative dermal lesions in large mammals. However, there is a dearth of knowledge on the molecular genetics of Stephanofilaria species infecting critically endangered rhinoceros. This study employed genetic barcoding genes to identify Stephanofilaria species and to determine its genetic diversity and evolution. Phylogenetic analyses on partial genes of the second internal transcribed spacer Ribosomal DNA (ITS-2) and cytochrome c oxidase subunit 1 (Cox-1), revealed a 77% and 93% bootstrap support at the Cox-1 and ITS-2 loci respectively to a clade containing previously identified Stephanofilaria species. Morphological examination also confirmed features diagnostic of Stephanofilaria dinniki previously known to infect rhinoceros. Gene diversity of Cox-1 was 0.931 ± 0.030 and 0.579 ± 0.104 for the ITS-2, whereas nucleotide diversity was 0.008 ± 0.002 and 0.00197 ± 0.0016 for the Cox-1 and ITS-2 genes respectively. Neutrality tests (Fu and Li's D* and Fu and Li's F*) were significantly negative (p<0.05) at all loci, whereas Tajima D and Fu's FS were each statistically significant (p<0.05) at the Cox-1 and ITS-2 loci respectively. The high gene diversity, low nucleotide diversity and negative neutrality tests are consistent with positive selection at the Cox-1 gene. Stephanofilaria infection among rhinoceros is currently restricted to highland sanctuaries compared to a widespread distribution in both lowlands and highlands in the 1960s suggesting an adaptation to vectors thriving in cooler highland temperatures. This is the first genetic identification of S. dinniki, in rhinoceros and will aid in diagnosis, treatment, studies, and rhinoceros conservation.},
}

Animals
*Perissodactyla/parasitology
*Phylogeny
*Genetic Variation
Electron Transport Complex IV/genetics
DNA, Ribosomal Spacer/genetics
Filarioidea/genetics/classification/isolation & purification
DNA Barcoding, Taxonomic
Sequence Analysis, DNA
DNA, Helminth/genetics
Skin Ulcer/parasitology/veterinary

@article {pmid40045410,
year = {2025},
author = {Franco Martins, J and Dina Troco, A and Marques, C and Chipepa, V and Seixas, G and Pinto, J and Garcia, L and Pedro Jorge, C and Manuel, E and Alves, G},
title = {Asian tiger mosquito in the oil-producing city of Soyo: the first report of Aedes (Stegomyia) albopictus (Skuse, 1894) in Angola.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {90},
pmid = {40045410},
issn = {1756-3305},
mesh = {Animals ; Angola ; *Aedes/genetics/classification/physiology ; *Mosquito Vectors/genetics/classification/physiology ; *Phylogeny ; Larva/genetics ; Electron Transport Complex IV/genetics ; Humans ; DNA Barcoding, Taxonomic ; Introduced Species ; Cities ; Female ; },
abstract = {BACKGROUND: The Asian tiger mosquito, Aedes albopictus (Skuse, 1894), is a highly invasive species that has successfully colonized many tropical and temperate regions worldwide. Its rapid global spread is strongly associated with human activities and has created favorable conditions for the emergence of human arboviruses in new geographic areas.

METHODS: Mosquito larvae were collected by community health workers from different breeding sites and reared to adults in a field insectary. Adult mosquitoes were morphologically identified to species level. Species identification was confirmed by cytochrome oxidase subunit I DNA barcoding.

RESULTS: We report the first detection of Aedes albopictus in Angola during an Anopheles stephensi survey conducted in Soyo, Zaire Province. Phylogenetic analysis indicated that the Angolan Ae. albopictus population clusters with sequences from Central African countries, suggesting an introduction from within the continent.

CONCLUSIONS: The presence of Ae. albopictus in Angola highlights the need for enhanced vector surveillance and control measures to prevent the emergence of arboviral diseases. This finding emphasizes the relevance of collaboration between local health authorities, communities, and international organizations in monitoring the spread of invasive mosquito species.},
}

Animals
Angola
*Aedes/genetics/classification/physiology
*Mosquito Vectors/genetics/classification/physiology
*Phylogeny
Larva/genetics
Electron Transport Complex IV/genetics
Humans
DNA Barcoding, Taxonomic
Introduced Species
Cities
Female

@article {pmid40043011,
year = {2025},
author = {Tineo, D and Bustamante, DE and Calderon, MS and Oliva, M},
title = {Comparative analyses of chloroplast genomes of Theobroma cacao from northern Peru.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0316148},
doi = {10.1371/journal.pone.0316148},
pmid = {40043011},
issn = {1932-6203},
mesh = {*Cacao/genetics ; Peru ; *Genome, Chloroplast ; *Phylogeny ; Evolution, Molecular ; DNA Barcoding, Taxonomic/methods ; Genotype ; },
abstract = {Theobroma cacao is the most economically important species within the genus Theobroma. Despite its importance, the intraspecific relationships of this species has not been fully elucidated due to insufficient molecular information. To facilitate a better understanding of the intraspecific evolutionary relationships of T. cacao, Sequencing technology has been to decode the plastid genomes, with the objective of identify potential DNA barcode genetic markers, explore intraspecific relationships, and infer divergence times. The plastid genome of the seven cocoa genotypes analyzed in this study, exhibited a typical angiosperm genomic structure. However, the structure of each plastid genome reflects notable changes in each genotype; for example, the infA gene was present in all the analyzed samples, unlike in previously published cocoa plastid genomes, while the complete ycf1 gene sequence has potential for use as DNA Barcoding in T. cacao. The estimated age of the node connecting T. cacao and T. grandiflorum, which was 10.11 Ma, supports this indication. It can be inferred that T. cacao diverged at approximately 7.55 Ma, and it is highly likely that T. cacao populations diversified during the Pliocene or Miocene. Therefore, it is crucial to perform mitochondrial and nuclear-based analyses on a broader spectrum of cocoa samples to validate these evolutionary mechanisms, including genetic estimates and divergence. This approach enables a deeper understanding of the evolutionary relationships among cocoa.},
}

*Cacao/genetics
Peru
*Genome, Chloroplast
*Phylogeny
Evolution, Molecular
DNA Barcoding, Taxonomic/methods
Genotype

@article {pmid40041862,
year = {2025},
author = {Amavet, P and Fernández, GP and Solís Neffa, V},
title = {Editorial: Challenges and prospects for conservation genetics at XXI century.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1554590},
pmid = {40041862},
issn = {1664-8021},
}

@article {pmid40041568,
year = {2025},
author = {Liu, Y and Chen, K and Wang, L and Yu, X and Xu, C and Suo, Z and Zhou, S and Shi, S and Dong, W},
title = {Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae).},
journal = {Plant diversity},
volume = {47},
number = {1},
pages = {115-126},
pmid = {40041568},
issn = {2468-2659},
abstract = {DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification.},
}

@article {pmid40038725,
year = {2025},
author = {Deng, LH and Li, MZ and Huang, XJ and Zhao, XY},
title = {Single-cell lineage tracing techniques in hematology: unraveling the cellular narrative.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {270},
pmid = {40038725},
issn = {1479-5876},
support = {No.82070184, 82350105, 82270228//National Natural Science Foundation of China/ ; No. 2023ZD0501200//National Major Science and Technology Projects of China/ ; No. 2023XACX0004//5511 Science and Technology Innovation Talent Project of Jiangxi Province/ ; JWZQ20240101001//Beijing Outstanding Young Scientists Project/ ; Z240019//Natural Science Foundation of Beijing Municipality/ ; },
abstract = {Lineage tracing is a valuable technique that has greatly facilitated the exploration of cell origins and behavior. With the continuous development of single-cell sequencing technology, lineage tracing technology based on the single-cell level has become an important method to study biological development. Single-cell Lineage tracing technology plays an important role in the hematological system. It can help to answer many important questions, such as the heterogeneity of hematopoietic stem cell function and structure, and the heterogeneity of malignant tumor cells in the hematological system. Many studies have been conducted to explore the field of hematology by applying this technology. This review focuses on the superiority of the emerging single-cell lineage tracing technologies of Integration barcodes, CRISPR barcoding, and base editors, and summarizes their applications in the hematology system. These studies have suggested the vast potential in unraveling complex cellular behaviors and lineage dynamics in both normal and pathological contexts.},
}

@article {pmid40037839,
year = {2025},
author = {Chakravarty, S and Logsdon, G and Lonardi, S},
title = {RAmbler resolves complex repeats in human Chromosomes 8, 19, and X.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279308.124},
pmid = {40037839},
issn = {1549-5469},
abstract = {Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from PacBio HiFi reads. RAmbler (i) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (ii) finds single-copy k-mers from the HiFi reads, (i.e., k-mers that are expected to occur only once in the genome), (iii) uses the relative location of single-copy k-mers to barcode each HiFi read, (iv) clusters HiFi reads based on their shared bar-codes, (v) generates contigs by assembling the reads in each cluster, and (vi) generates a consensus assembly from the overlap graph of the assembled contigs. Here we show that RAmbler can reconstruct human centromeres and other complex repeats to a quality comparable to the manually-curated telomere-to-telomere human genome assembly. Across over 250 synthetic datasets, RAmbler outperforms hifiasm, LJA, HiCANU, and Verkko across various parameters such as repeat lengths, number of repeats, heterozygosity rates and depth of sequencing.},
}

@article {pmid40037039,
year = {2025},
author = {Osman, E and Saxena, S and Qian, S and L'Heureux-Hache, J and Li, P and Manek, J and Gu, J and Hoare, T and Li, Y and Soleymani, L},
title = {Electrochemical detection of Legionella pneumophila using DNAzymes and under continuous flow in cooling tower water.},
journal = {Biosensors & bioelectronics},
volume = {278},
number = {},
pages = {117283},
doi = {10.1016/j.bios.2025.117283},
pmid = {40037039},
issn = {1873-4235},
abstract = {Rapid detection of Legionella pneumophila in cooling tower water is crucial to mitigate the fatal consequences of Legionnaires disease. This study presents a microfluidic system that employs RNA-cleaving DNAzymes (RCDs) for continuous real time monitoring of this pathogen directly in a single sample of cooling tower water without the need for lengthy bacterial culture. The RCDs, coupled to microgel magnetic beads, are programmed to release an electroactive DNA barcode in the presence of L. pneumophila, which is detected by a downstream electrochemical sensor in real time. Our system identifies key parameters such as peak current, slope of signal increase, and lag time that correlate with L. pneumophila concentration, achieving a limit of detection of 1.4 × 10[3] CFU/mL in buffer and 1.9 × 10[3] CFU/mL in cooling tower water, meeting regulatory requirements. This system was further used to identify different serotypes of L. pneumophila amongst other waterborne bacterial species including non pneumophila species of Legionella, creating a highly specific tool for identifying this high-risk pathogen.},
}

@article {pmid40036401,
year = {2025},
author = {Srisuka, W and Aupalee, K and Takaoka, H and Otsuka, Y and Saeung, A},
title = {Taxonomy and molecular phylogeny of a new species of black fly (Diptera: Simuliidae) in the Simulium striatum species-group from central Thailand.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf016},
pmid = {40036401},
issn = {1938-2928},
support = {//National Research Council of Thailand/ ; N42A660464//Chiang Mai University/ ; },
abstract = {Generally, the DNA barcode relying on a short fragment of the cytochrome c oxidase I (COI) gene is a powerful tool for facilitating species discovery and taxonomic resolution in Diptera, including black flies. However, the COI barcode lacks sufficient resolution to identify several species or infer phylogenetic relationships of black flies in the Simulium striatum species-group, whereas the fast-evolving nuclear big zinc finger (BZF) gene has been suggested as a key marker for identifying the species. In this study, a new species of black fly in the S. striatum species-group from Kamphaeng Phet province, central Thailand, was discovered and characterized through an integrated method combining morphological analysis and molecular data based on the BZF gene. The new species, Simulium (Simulium) concitatum sp. nov., was morphologically described for all life stages, excluding the egg. It shares many morphological similarities with other species of the S. striatum species-group, particularly S. thilorsuense Takaoka, Srisuka & Saeung, 2022 described from Tak province, western Thailand. Sequence analysis and phylogeny inferred from the BZF gene further confirmed that S. concitatum sp. nov. is a distinct species of the S. striatum species-group and revealed its close genetic relationship to S. wangkwaiense Takaoka, Srisuka & Saeung, 2020. The morphological differences between the new species and all known species of the S. striatum species-group documented in Thailand and other countries are provided to assist in species identification. Furthermore, this study underscores the BZF gene as an effective genetic marker to differentiate the species.},
}

@article {pmid40035969,
year = {2025},
author = {Feng, Y and Liu, G and Li, H and Cheng, L},
title = {The landscape of cell lineage tracing.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40035969},
issn = {1869-1889},
abstract = {Cell fate changes play a crucial role in the processes of natural development, disease progression, and the efficacy of therapeutic interventions. The definition of the various types of cell fate changes, including cell expansion, differentiation, transdifferentiation, dedifferentiation, reprogramming, and state transitions, represents a complex and evolving field of research known as cell lineage tracing. This review will systematically introduce the research history and progress in this field, which can be broadly divided into two parts: prospective tracing and retrospective tracing. The initial section encompasses an array of methodologies pertaining to isotope labeling, transient fluorescent tracers, non-fluorescent transient tracers, non-fluorescent genetic markers, fluorescent protein, genetic marker delivery, genetic recombination, exogenous DNA barcodes, CRISPR-Cas9 mediated DNA barcodes, and base editor-mediated DNA barcodes. The second part of the review covers genetic mosaicism, genomic DNA alteration, TCR/BCR, DNA methylation, and mitochondrial DNA mutation. In the final section, we will address the principal challenges and prospective avenues of enquiry in the field of cell lineage tracing, with a particular focus on the sequencing techniques and mathematical models pertinent to single-cell genetic lineage tracing, and the value of pursuing a more comprehensive investigation at both the spatial and temporal levels in the study of cell lineage tracing.},
}

@article {pmid40034080,
year = {2025},
author = {Fan, S and Li, X and Liu, H and Ye, M and He, Y and Fu, W and Chen, F and Zhao, Y},
title = {Molecule Differentiation Encoding Microscopy to Dissect Dense Biomolecules in Cellular Nanoenvironments Below Spatial Resolution.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202425136},
doi = {10.1002/anie.202425136},
pmid = {40034080},
issn = {1521-3773},
abstract = {Cellular biomolecules may exhibit dense distribution and organization at the nanoscale to govern vital biological processes. However, it remains a common challenge to digitize the spatially dense biomolecules under spatial resolution of microscopies. Here, we report a proof-of-principle method, molecule differentiation encoding microscopy by orthogonal tandem repeat DNA identifiers, to resolve the copy numbers of dense biomolecules in cellular nanoenvironments. The method encodes each copy of same biomolecules into different types of DNA barcodes based on stochastic multiplexed reactions. It can transform the overlap of the same spectrum into the overlap of different spectra. Furthermore, an algorithm is developed to automatically quantitate overlapping spots and individual spots. Using this method, we dissected RNAs in the cytoplasm, DNA epigenetic modifications in the cell nucleus, and glycans and glycoRNAs on the cell surface, respectively. We found that all these biomolecules presented dense distribution with diverse degrees in crowded cellular nanoenvironments. Especially, averaged 17% copies of U1 glycoRNA of single cells are gathered in various nanoenvironments on cell surface. Our strategy provides a powerful tool for digitally quantitative visualization of dense biomolecules below spatial resolution of microscopies, and could provide insights into underlying functions and mechanisms of the dense distribution information.},
}

@article {pmid40031227,
year = {2025},
author = {Tinarrage, R and Ponciano, JR and Linhares, CDG and Traina, AJM and Poco, J},
title = {ZigzagNetVis: Suggesting temporal resolutions for graph visualization using zigzag persistence.},
journal = {IEEE transactions on visualization and computer graphics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TVCG.2025.3528197},
pmid = {40031227},
issn = {1941-0506},
abstract = {Temporal graphs are commonly used to represent complex systems and track the evolution of their constituents over time. Visualizing these graphs is crucial as it allows one to quickly identify anomalies, trends, patterns, and other properties that facilitate better decision-making. In this context, selecting an appropriate temporal resolution is essential for constructing and visually analyzing the layout. The choice of resolution is particularly important, especially when dealing with temporally sparse graphs. In such cases, changing the temporal resolution by grouping events (i.e., edges) from consecutive timestamps - a technique known as timeslicing - can aid in the analysis and reveal patterns that might not be discernible otherwise. However, selecting an appropriate temporal resolution is a challenging task. In this paper, we propose ZigzagNetVis, a methodology that suggests temporal resolutions potentially relevant for analyzing a given graph, i.e., resolutions that lead to substantial topological changes in the graph structure. ZigzagNetVis achieves this by leveraging zigzag persistent homology, a well-established technique from Topological Data Analysis (TDA). To improve visual graph analysis, ZigzagNetVis incorporates the colored barcode, a novel timeline-based visualization inspired by persistence barcodes commonly used in TDA. We also contribute with a web-based system prototype that implements suggestion methodology and visualization tools. Finally, we demonstrate the usefulness and effectiveness of ZigzagNetVis through a usage scenario, a user study with 27 participants, and a detailed quantitative evaluation.},
}

@article {pmid40030848,
year = {2025},
author = {Pham, P and Bui, QT and Nguyen, NT and Kozma, R and Yu, PS and Vo, B},
title = {Topological Data Analysis in Graph Neural Networks: Surveys and Perspectives.},
journal = {IEEE transactions on neural networks and learning systems},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TNNLS.2024.3520147},
pmid = {40030848},
issn = {2162-2388},
abstract = {For many years, topological data analysis (TDA) and deep learning (DL) have been considered separate data analysis and representation learning approaches, which have nothing in common. The root cause of this challenge comes from the difficulties in building, extracting, and integrating TDA constructs, such as barcodes or persistent diagrams, within deep neural network architectures. Therefore, the powers of these two approaches are still on their islands and have not yet combined to form more powerful tools for dealing with multiple complex data analysis tasks. Fortunately, we have witnessed several remarkable attempts to integrate DL-based architectures with topological learning paradigms in recent years. These topology-driven DL techniques have notably improved data-driven analysis and mining problems, especially within graph datasets. Recently, graph neural networks (GNNs) have emerged as a popular deep neural architecture, demonstrating significant performance in various graph-based analysis and learning problems. Explicitly, within the manifold paradigm, the graph is naturally considered as a topological object (e.g., the topological properties of the given graph can be represented by the edge weights). Therefore, integrating TDA and GNN is considered an excellent combination. Many well-known studies have recently presented the effectiveness of TDA-assisted GNN-based architectures in dealing with complex graph-based data representation analysis and learning problems. Motivated by the successes of recent research, we present systematic literature about this nascent and promising research direction in this article, which includes general taxonomy, preliminaries, and recently proposed state-of-the-art topology-driven GNN models and perspectives.},
}

@article {pmid40028202,
year = {2025},
author = {Silva-Morales, I and Carrera-Parra, LF},
title = {Redescription of Aspidosiphon (Paraspidosiphon) steenstrupii Diesing, 1859 (Sipuncula: Aspidosiphonidae) and the reinstatement of three species.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19003},
pmid = {40028202},
issn = {2167-8359},
mesh = {Animals ; *Phylogeny ; Male ; Female ; Trematoda/genetics/classification/anatomy & histology ; Species Specificity ; },
abstract = {Sipuncula, specifically the family Aspidosiphonidae, faces taxonomic challenges due to brief original descriptions and the poor condition or loss of the type material. Detailed standardized redescriptions are essential to understanding the diversification in this group. Herein, a comprehensive redescription of Aspidosiphon (Paraspidosiphon) steenstrupii based on an extensive material collection from the tropical Western Atlantic is provided. Based on morphological data and the analysis of COI sequences, we delimited A. (P.) steenstrupii morphologically, restricting its distribution to the tropical Western Atlantic. Also, the redescriptions and proposals for reinstatement of A. (P.) exostomum, A. (P.) ochrus, and A. (P.) speculator, previously considered junior synonyms of A. (P.) steenstrupii, are included. Furthermore, a comprehensive discussion on diagnostic morphological features to recognize aspidosiphonid species and a detailed revision of synonyms of A. (P.) steenstrupii are included. Notable differences in morphology and genetic data suggest the need for revising the taxonomic status of several synonyms within the family, highlighting underestimated diversity in sipunculans.},
}

Animals
*Phylogeny
Male
Female
Trematoda/genetics/classification/anatomy & histology
Species Specificity

@article {pmid40027782,
year = {2025},
author = {Fukushima, T and Kristiansen, TA and Wong, LP and Keyes, S and Tanaka, Y and Mazzola, M and Zhao, T and He, L and Yagi, M and Hochedlinger, K and Yamazaki, S and Sadreyev, RI and Scadden, DT},
title = {Hematopoietic stem cells undergo bidirectional fate transitions in vivo.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.23.639689},
pmid = {40027782},
issn = {2692-8205},
abstract = {Transitions between subsets of differentiating hematopoietic cells are widely regarded as unidirectional in vivo. Here, we introduce clonal phylogenetic tracer (CP-tracer) that sequentially introduces genetic barcodes, enabling high-resolution analysis of ~100,000 subclones derived from ~500 individual hematopoietic stem cells (HSC). This revealed previously uncharacterized HSC functional subsets and identified bidirectional fate transitions between myeloid-biased and lineage-balanced HSC. Contrary to the prevailing view that the more self-renewing My-HSCs unidirectionally transition to balanced-HSCs, phylogenetic tracing revealed durable lineage bidirectionality with the transition favoring My-HSC accumulation over time1,2. Further, balanced-HSCs mature through distinct intermediates My-HSCs and lymphoid-biased-HSCs with lymphoid competence here shown by CRISPR/Cas9 screening to be dependent on the homeobox gene, Hhex. Hhex enables Ly-HSC differentiation, but its expression declines with age. These findings establish HSC plasticity and Hhex as a determinant of myeloid-lymphoid balance with each changing over time to favor the age-related myeloid bias of the elderly.},
}

@article {pmid40027328,
year = {2025},
author = {Guo, P and Li, C and Liu, J and Wu, T and Chai, B},
title = {Contribution of environmental and biological factors to bacterial community structure and stability in a subalpine lake.},
journal = {Marine life science & technology},
volume = {7},
number = {1},
pages = {176-186},
pmid = {40027328},
issn = {2662-1746},
abstract = {UNLABELLED: Bacterial community play an essential role in regulating water quality and the global biogeochemical cycle in aquatic ecosystems. However, how trophic interactions (i.e., biotic factors) regulate the diversity and composition of bacterial community in lake ecosystems remains unknown. Here, we employed DNA meta-barcoding of water samples to explore the impact of bacterivorous protozoans on the bacterial community. The results showed significant seasonal variations in the diversity and composition of both bacterial and protist communities. The composition of bacterivorous protozoans was identified as the primary predictor for the bacterial community alpha diversity in spring and summer, and for beta diversity in spring and autumn, indicating that biotic interactions play a greater role in driving the diversity of bacterial community across different seasons. Biological factors were more important than environmental factors for explaining the variations in the relative abundance of several bacterial genera (i.e., Pseudoxanthomonas, hgcI_clade, and Pseudorhodobacter). Network analyses showed that bacterial networks differed among seasons, and the autumn network exhibited the highest stability. Our findings indicated that the bacterial community stability was significantly affected by environmental factors, specifically SO4 [2-]and PO4 [3-], rather than bacterivorous protozoans. Overall, our findings provide new perspectives on the role of trophic interactions in maintaining the structure of bacterial community in different seasons, and enhance our understanding of the bacterial community assembly in lake ecosystems.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00256-8.},
}

@article {pmid40027105,
year = {2025},
author = {Flores-Zambrano, K and Tapia, W and Castillejo, P},
title = {Microalgae strains isolated from piggery wastewater in Ecuador: Effective nitrogen compound removal and growth potential in extremophile conditions.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {45},
number = {},
pages = {e00883},
pmid = {40027105},
issn = {2215-017X},
abstract = {Effluents generated by anthropogenic activities are a significant source of pollution and eutrophication in natural water bodies. In Ecuador, the increase in pig production has exacerbated this issue due to the untreated discharge of pig effluents. This study focused on the characterization of native microalgae present in pig effluents and the evaluation of their capacity to remove nitrogenous compounds under various conditions, with the aim of identifying efficient strains for phycoremediation. Four microalgal strains were isolated and molecularly identified as Radiococcus polycoccus, Chlorolobion braunii, Micractinium sp., and Desmodesmus multivariabilis. The cultures were exposed to initial concentrations of 100 mg L[-1] N-NH4 and 49.97 mg L[-1] N-NO3 for 12 days to assess their cellular growth and nutrient removal rates. Growth kinetics were analyzed under conditions of 2000 mg L[-1] N-NH4 and extreme pH levels of 3 and 10. Chlorolobion braunii demonstrated the highest productivity, achieving a removal of 67.73 % of N-NH4 and 30.59 % of N-NO3, and reached the highest cellular density under extreme ammonium conditions, being the only strain capable of growing at acidic pH. Conversely, Micractinium sp. exhibited the highest growth under alkaline conditions. These results highlight the promising potential of native microalgae from pig effluents for wastewater remediation and their adaptation to environmental conditions.},
}

@article {pmid40026382,
year = {2025},
author = {Crabo, LG and Keegan, K},
title = {Revision of the North American genus Supralathosea Barnes & Benjamin (Lepidoptera, Noctuidae, Oncocnemidinae) with description of two genera and three species.},
journal = {ZooKeys},
volume = {1228},
number = {},
pages = {197-223},
pmid = {40026382},
issn = {1313-2989},
abstract = {The noctuid genus Supralathosea Barnes & Benjamin (Noctuidae, Oncocnemidinae) is revised to include three species for the United States of America, Supralathoseababoquivariensis Barnes & Benjamin from southeast Arizona, Supralathoseayavapai sp. nov. from central Arizona, and Supralathoseasolastella sp. nov. from Texas. Two genera are described for species formerly included in Supralathosea. Infralathosea gen. nov. includes Infralathoseapronuba comb. nov. from Arizona and New Mexico and Infralathoseaunicornis sp. nov. from west Texas. Eulathosea gen. nov. contains only Eulathoseaobtusa Smith, comb. nov. from Arizona. A key to genera and species is presented and adults and genitalia of all taxa are illustrated. Infralathosea and Eulathosea are assigned to Oncocnemidinae based on molecular evidence.},
}

@article {pmid40023120,
year = {2025},
author = {Liu, D and Wang, X and Xu, L and Al-Delfi, ZNS and Mekonnen, ZA and Gao, S and Grubor-Bauk, B and Zhao, CX},
title = {Screening lipid nanoparticles using DNA barcoding and qPCR.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {251},
number = {},
pages = {114598},
doi = {10.1016/j.colsurfb.2025.114598},
pmid = {40023120},
issn = {1873-4367},
abstract = {Quantifying the biodistribution of lipid nanoparticles (LNPs) is critical for optimizing mRNA delivery systems, yet current approaches have inherent limitations. This study introduces a cost-effective method utilizing double-stranded DNA (dsDNA) barcodes and quantitative polymerase chain reaction (qPCR) for rapid analysis of a small library of mRNA-LNPs biodistribution and functional delivery in vivo. Three unique 100-bp dsDNA barcodes were designed to represent for three FDA-approved LNP formulations. Concurrently, these three formulations carrying luciferase mRNA were mixed with DNA-barcoding LNPs as a pool. Following intravenous administration of the pooled LNPs in mice, qPCR analysis revealed the highest abundance of DNA barcodes and accumulation of luciferase mRNA in spleen, with positive correlation between barcodes presence and mRNA localization across organs, validating DNA barcodes as reliable indicators of mRNA-LNPs biodistribution in vivo. Bioluminescence imaging further confirmed successful delivery and protein translation of luciferase mRNA facilitated by the LNPs in vivo. Integrating DNA barcodes for biodistribution analysis and luciferase mRNA for assessing functional delivery enabled comprehensive evaluation of LNP performance. This robust methodology provides valuable insights into the localization patterns and mRNA delivery capabilities of different LNP formulations, paving the way for the development of more effective and targeted mRNA-based therapeutics.},
}

@article {pmid40028488,
year = {2023},
author = {Dhar, R and Devi, A},
title = {Exosomes Barcoding: A smart approach for cancer liquid biopsy.},
journal = {The journal of liquid biopsy},
volume = {2},
number = {},
pages = {100129},
pmid = {40028488},
issn = {2950-1954},
abstract = {Cancer is an unsolved health crisis worldwide. Extracellular vesicles (EVs) address this problem in a new way. In cancer, early detection is highly challenging, exosomes (a subpopulation of EVs, originating from endosomes) overcomes this limitation. In cancer, tumor-derived exosomes (TEXs) play a role as signaling molecules in cancer development and progression. TEXs provide detailed investigation for specific cancer biomarkers research. Exosomes heterogeneity (variation in exosomes size, exosomes origin, and inner molecular diversity) has led to complications in understanding and studying cancer liquid biopsies. Single exosome profiling and exosomes barcoding has helped in supporting and overcoming this limitation and has played a significant role in precision oncology. Exosomes barcoding is a promising interdisciplinary approach for screening cancers more specifically.},
}

@article {pmid40019731,
year = {2025},
author = {Sinha, T and Shashank, PR},
title = {A Molecular Phylogeny of the Subfamily Plusiinae (Lepidoptera: Noctuidae) in India Inferred from Mitochondrial and Nuclear Ribosomal DNA Sequences.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40019731},
issn = {1559-0305},
support = {DST-SERB (SB/YS/LS-126/2014)//DST-SERB (SB/YS/LS-126/2014)/ ; },
abstract = {The subfamily Plusiinae, an economically important moth pest group, belongs to the species-rich family Noctuidae (Lepidoptera). Despite their enormous economic importance, the evolutionary history of this subfamily has not been completely resolved. In India, they are represented by a species complex, but the taxonomic delineation among these organisms is unclear. This study represents an insight into the comprehensive phylogenetic relationship among species supported by molecular approach based on mitochondrial (Cytochrome Oxidase I) and nuclear gene markers (Ribosomal Protein S5), emphasizing tribal-level classification. A total of 125 plusiinae taxa were analysed from eight biogeographical zones of India. The results revealed that Plusiinae tribes were monophyletic and considered sister groups that shared many derived characteristics. The ML/MP cladogram based on the barcoding gene successfully separates all species but not all tribes. The nuclear gene marker RPS5, separated all the species according to their tribes. The combined analysis of both genes showed tribe resolution into distinct clades. This is the first comprehensive study on phylogenetic studies of 25 species of plusiinae from India that clarifies deep divergence and gives information about species position and arrangement within taxa.},
}

@article {pmid40018971,
year = {2025},
author = {Kartzinel, TR and Hoff, HK and Divoll, TJ and Littleford-Colquhoun, BL and Anderson, H and Burak, MK and Kuzmina, ML and Musili, PM and Rogers, H and Troncoso, AJ and Kartzinel, RY},
title = {Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17712},
doi = {10.1111/mec.17712},
pmid = {40018971},
issn = {1365-294X},
support = {1930820//Division of Environmental Biology/ ; 2026294//Division of Environmental Biology/ ; 2046797//Division of Environmental Biology/ ; 2033823//Office of Integrative Activities/ ; P22AC00332//National Park Service/ ; P23AC00378//National Park Service/ ; },
abstract = {Genetic technologies such as DNA barcoding make it easier and less expensive to monitor biodiversity and its associated ecosystem services, particularly in biodiversity hotspots where traditional assessments are challenging. Successful use of these data-driven technologies, however, requires access to appropriate reference data. We reviewed the >373,584 reference plant DNA barcodes in public repositories and found that they cumulatively cover a remarkable quarter of the ~435,000 extant land plant species (Embryophyta). Nevertheless, coverage gaps in tropical biodiversity hotspots reflect well-documented biases in biodiversity science - most reference specimens originated in the Global North. Currently, at least 17% of plant families lack any reference barcode data whatsoever, affecting tropical and temperate regions alike. Investigators often emphasise the importance of marker choice and the need to ensure protocols are technically capable of detecting and identifying a broad range of taxa. Yet persistent geographic and taxonomic gaps in the reference datasets show that these protocols rely upon risk undermining all downstream applications of the strategy, ranging from basic biodiversity monitoring to policy-relevant objectives - such as the forensic authentication of materials in illegal trade. Future networks of investigators could work strategically to improve data coverage, which will be essential in global efforts to conserve biodiversity while advancing more fair and equitable access to benefits arising from genetic resources.},
}

@article {pmid40017781,
year = {2025},
author = {Aknine, N and Pelletier, R and Klymchenko, AS},
title = {Lipid-Directed Covalent Labeling of Plasma Membranes for Long-Term Imaging, Barcoding and Manipulation of Cells.},
journal = {JACS Au},
volume = {5},
number = {2},
pages = {922-936},
pmid = {40017781},
issn = {2691-3704},
abstract = {Fluorescent probes for cell plasma membranes (PM) generally exploit a noncovalent labeling mechanism, which constitutes a fundamental limitation in multiple bioimaging applications. Here, we report a concept of lipid-directed covalent labeling of PM, which exploits transient binding to the lipid membrane surface generating a high local dye concentration, thus favoring covalent ligation to random proximal membrane proteins. This concept yielded fluorescent probes for PM called MemGraft, which are built of a dye (cyanine Cy3 or Cy5) bearing a low-affinity membrane anchor and a reactive group: an activated ester or a maleimide. In contrast to specially designed control dyes and commercial Cy3-based labels of amino or thiol groups, MemGraft probes stain efficiently PM, revealing the crucial role of the membrane anchor combined with optimal reactivity of the activated ester or the maleimide. MemGraft probes overcome existing limitations of noncovalent probes, which makes them compatible with cell fixation, permeabilization, trypsinization, and the presence of serum. The latter allows long-term cell tracking and video imaging of cell PM dynamics without the signs of phototoxicity. The covalent strategy also enables staining and long-term tracking of cocultured cells labeled in different colors without exchange of probes. Moreover, the combination of MemGraft-Cy3 and MemGraft-Cy5 probes at different ratios enabled long-term cell barcoding in at least 5 color codes, important for tracking and visualizing multiple populations of cells. Ultimately, we found that the MemGraft strategy enables efficient biotinylation of the cell surface, opening the path to cell surface engineering and cell manipulation.},
}

@article {pmid40015720,
year = {2025},
author = {Gallina, M and Testagrossa, M and Provenzani, A},
title = {Unit dose drug dispensing systems in hospitals: a systematic review of medication error reduction and cost-effectiveness.},
journal = {European journal of hospital pharmacy : science and practice},
volume = {},
number = {},
pages = {},
doi = {10.1136/ejhpharm-2024-004444},
pmid = {40015720},
issn = {2047-9956},
abstract = {BACKGROUND: Medical errors pose significant risks to patient safety and public health. Automated unit dose drug dispensing systems (UDDSs) have emerged as valuable tools to reduce medication errors while optimising economic and logistical resources.

OBJECTIVES: This systematic review aims to evaluate studies specifically focused on the impact of automated UDDSs in reducing medication errors and streamlining processes.

METHODS: A literature search was performed on PubMed, Scopus, and Web of Science, focusing on peer-reviewed articles published between 2019 and 2024. The search, concluded on 24 September 2024, included studies conducted in inpatient hospital settings that assessed automated UDDS effects on medication errors, therapy management and inventory control. Outcomes examined included effects on patient safety, cost-effectiveness and inventory management. Results were synthesised qualitatively.

RESULTS: From 3346 references, four studies met the inclusion criteria: a cost-effectiveness analysis, an uncontrolled before-and-after study, and two observational studies. UDDS improved medication processes, reducing drug-related problems, medication handling and dispensing time by 50% per patient per day. Integrated with barcode scanning, UDDS lowered medication administration errors (MAEs) from 19.5% to 15.8% and harmful MAEs from 3.0% to 0.3%. Overall, medication errors dropped by 45-70%, enhancing safety and reducing manual handling risks. UDDS demonstrated cost-effectiveness by significantly reducing MAEs. The study estimated a reduction in MAEs, with a cost-effectiveness ratio of €17.69 per avoided MAE. For potentially harmful MAEs, the cost-effectiveness ratio was estimated at €30.23 per avoided error. These findings suggest substantial long-term savings potential, though the exact magnitude may vary depending on hospital size and implementation specifics CONCLUSIONS: Automated UDDSs improve patient safety by significantly reducing medication errors and delivering cost savings through better inventory management. Challenges such as high initial costs and workflow adjustments can be mitigated through gradual implementation and staff training. Further integration with other healthcare technologies, such as barcoding, real-time tracking, artificial intelligence (AI)-driven error prevention tools and fully automated restocking systems could enhance UDDS benefits and further support hospital processes.},
}

@article {pmid40015300,
year = {2025},
author = {Prakash, PS and Joshi, FM and Vogelsberg, E and Cremers, GAO and Gür, FN and Sato, Y and de Greef, TFA and Ader, M and Kurth, T and Nunes Gonçalves, DP and Schmidt, TL},
title = {DNA Origami Barcodes for Immunostaining.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.4c19153},
pmid = {40015300},
issn = {1944-8252},
abstract = {In histology, immunostaining of biological samples is a gold standard for studying cellular processes, such as the expression of cell surface markers or the cellular uptake of proteins and drug molecules. Immuno-gold labeling is a commonly used technique to achieve nanometer spatial resolution, but simultaneous visualization of multiple antigens in parallel is an unresolved challenge. Herein, we demonstrate a DNA nanotechnology-based approach to label antigens in transmission electron microscopy images of tissue sections with high contrast patterns. For this, we attached gold nanoparticles to designated binding positions on DNA origami structures that act as visual "barcodes." These barcodes are then hybridized to complementary strands of DNA-modified antibodies that are bound to their respective antigens on ultrathin tissue resin sections. As a proof of concept, we demonstrate several types of barcodes and two different antibody labeling techniques that will expand the multiplexing abilities of immunostaining in a highly modular way.},
}

@article {pmid40013788,
year = {2025},
author = {Pfordt, A and Douanla-Meli, C and Schäfer, BC and Schrader, G and Tannen, E and Chandarana, MJ and von Tiedemann, A},
title = {Phylogenetic analysis of plant-pathogenic and non-pathogenic Trichoderma isolates on maize from plants, soil, and commercial bio-products.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0193124},
doi = {10.1128/aem.01931-24},
pmid = {40013788},
issn = {1098-5336},
abstract = {Fungi of the genus Trichoderma are primarily associated with the mycobiome of dead wood but can also be occasionally found in soil and plant rhizospheres. Several Trichoderma spp. are used in crop health management to promote growth and control plant diseases. Although widely considered beneficial to plants, some members have been reported to be pathogenic to maize, causing a disease called Trichoderma ear rot. Since 2018, Trichoderma afroharzianum has caused significant infections of maize cobs in Germany, France, and Italy. This study aimed to investigate the pathogenicity and phylogenetic relationships among different Trichoderma strains from diverse sources and geographical origins. While previous studies primarily identified T. afroharzianum as the main species causing Trichoderma ear rot, this study found that isolates of T. asperellum, T. atroviride, and T. guizhouense may also exhibit pathogenicity on maize cobs. Additionally, Trichoderma strains from commercial biocontrol products displayed unexpected pathogenicity inducing up to 92% disease severity on maize cobs. Most T. afroharzianum strains induced high levels of disease severity, although some isolates of the same species did not cause any disease, indicating a large heterogeneity in pathogenicity within the species. Notably, phylogeny reconstruction based on the tef1-α and rpb2 genes did not result in any discernible clustering between pathogenic and non-pathogenic isolates. A further novel finding is the isolation of pathogenic Trichoderma isolates from agricultural soil, demonstrating that soil can serve as a reservoir for pathogenic species. This study highlights the need for biosecurity assessment and monitoring of Trichoderma strains for agricultural use, considering their beneficial and pathogenic potential.IMPORTANCEIn this study, we explored the ability of different Trichoderma species to infect maize plants. Trichoderma is a group of fungi known for its beneficial role in agriculture, often used as a biological pesticide to control fungal plant diseases. However, some species within this genus can also act as pathogens, causing infections in crops like maize. We found that one species, T. afroharzianum, is particularly aggressive, capable of infecting maize without the plant being wounded first. This makes it a potentially serious threat to crop health. In contrast, other species, such as T. atroviride and T. asperellum, only caused infections when maize plants were injured before. Our research suggests that pathogenic Trichoderma species not only effectively infect plants but can also survive well in soil, making their control difficult. These findings highlight the need for better understanding of how these fungi operate in order to manage the risks they pose to important crops like maize, while still taking advantage of their beneficial uses in agriculture.},
}

@article {pmid40012563,
year = {2025},
author = {Kim, Y and Park, J and Hwang, UW and Park, JK},
title = {Taxonomic review of Korean Siphonaria species (Mollusca, Gastropoda, Siphonariidae).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e139388},
pmid = {40012563},
issn = {1314-2828},
abstract = {BACKGROUND: Many molluscan species exhibit a high degree of shell morphological plasticity in their shape (including sculptures), size and colour patterns, which can vary significantly depending on environmental conditions. These shell morphological variations make it challenging to differentiate species, based on morphology alone, often resulting in various taxonomic errors, such as misidentifications, overlooking cryptic species diversity or a plethora of nominal species. The genus Siphonaria constitutes a significant component of the macrobenthic invertebrate fauna in intertidal habitats across temperate to tropical regions. Given the limited attention to shell variation in previous taxonomic studies on the Korean Siphonaria species, the extensive range of ecophenotypic shell variations documented in this group raises questions about the taxonomic validity of previously reported Siphonaria species in Korea.

NEW INFORMATION: The present study provides a comprehensive taxonomic review of Korean Siphonaria species using a combination of shell morphology, radula structure and phylogenetic analysis of the mtDNA cox1 sequences. This integrative analysis confirmed the validity of S.acmaeoides, S.japonica and S.sirius in Korea, highlighting differences in shell and siphonal groove morphology amongst these species. Detailed descriptions of shell and radula characteristics, along with mtDNA cox1 sequences as DNA barcodes, are also provided, which are very useful for the accurate identification of Siphonaria species. Unlike these three Siphonaria species, the taxonomic validity of the four other species (S.coreensis, S.javanica, S.laciniosa and S.rucuana) previously reported from Korean waters is questionable, given their documented geographic distribution ranges and the potential misidentification of shell variants in Korean malacofaunal studies.},
}

@article {pmid40012562,
year = {2025},
author = {Bergman, LA and Montenegro, J and Seid, CA and Bachtel, TS and Mann, F and Thuesen, EV and Lindsay, DJ and Drazen, JC},
title = {Checklist of ichthyoplankton of NORI-D polymetallic nodule exploration claim (eastern Clarion-Clipperton Zone) during winter 2021.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e137744},
pmid = {40012562},
issn = {1314-2828},
abstract = {BACKGROUND: There been increasing interest in polymetallic nodule mining within the Clarion-Clipperton Zone (CCZ). Polymetallic nodule mining within NORI-D will release a sediment plume within the water column and a previous mining collector test within the Nauru Ocean Resources Inc. (NORI-D) contract area released surface pollution from mining tailings. The mid-water plume, as well as accidental surface pollution, indicate that polymetallic nodule mining could impact surface plankton. Although the ichthyoplankton within the eastern tropical Pacific have been well-studied, recent data from within polymetallic nodule mining licence areas is lacking. Environmental Expedition C5e conducted an environmental baseline assessment of both pelagic and benthic fauna within the NORI-D region of the CCZ, which included the opportunistic collection of ichthyoplankton.

NEW INFORMATION: Ichthyoplankton were collected within NORI-D from November-December 2021 using two plankton nets and a Remotely Operated Vehicle (ROV). Here, we present a checklist of ichthyoplankton within the NORI-D licence area during this winter campaign. Eighteen samples were collected and identified through morphology, with a limited number identified through genetic sequencing. Specimens were from five orders, including Argentiniformes, Stomiiformes, Myctophiformes, Beloniformes and Scombriformes. This checklist will aid contractors and scientists conducting work within the CCZ to examine how wastewater discharge from polymetallic nodule mining could impact fish reproduction and ichthyoplankton survival.},
}

@article {pmid40011951,
year = {2025},
author = {Liu, LQ and Fu, WQ and Ma, YY and Liu, ZY and Ge, CF and Yang, YR and Qing, X and Zeng, QL},
title = {Draft genome of pin nematode Paratylenchus projectus recovered from rhizosphere of blueberry.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {77},
pmid = {40011951},
issn = {1756-3305},
support = {2023BCF01022//Key Research & Development Project of Ningxia Autonomous Region, China/ ; },
mesh = {Animals ; *Blueberry Plants/parasitology ; *Phylogeny ; *Rhizosphere ; *Plant Roots/parasitology ; Plant Diseases/parasitology ; Genome, Helminth ; Tylenchoidea/genetics/classification ; },
abstract = {BACKGROUND: The pin nematode, belonging to the genus Paratylenchus, parasitizes higher plants, often causing reduced or inhibited root tip development.

METHODS: Pin nematodes were isolated from the roots and rhizosphere of blueberry plants and subsequently identified as representatives of Paratylenchus projectus based on morphological characteristics and molecular barcoding. The P. projectus draft genome was sequenced using the Illumina platform.

RESULTS: Phylogenetic analysis based on 18S, 28S and ITS rRNA placed this species in highly supported clades alongside other P. projectus specimens. The draft genome of P. projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae. The assembled genome, though fragmented, had a total length of 191.36 Mb and an estimated genome size of 64.9 Mb. Protein-coding genes were predicted using four different databases, with particular focus on carbohydrate-active enzymes from the GH5 and GH18 families. The recovered GH5 genes were distributed among three distinct clades: one forming a basal group relative to other nematodes, one as a sister clade to the fungivorous nematode Aphelenchus avenae and one nested within a fungal clade. The GH18 chitinase genes were grouped into two clades: one closely related to sedentary plant-parasitic nematodes of the genera Heterodera and Globodera and the other closely related to the fungivorous nematode Ditylenchus.

CONCLUSIONS: The draft genome of Paratylenchus projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae to our knowledge.},
}

Animals
*Blueberry Plants/parasitology
*Phylogeny
*Rhizosphere
*Plant Roots/parasitology
Plant Diseases/parasitology
Genome, Helminth
Tylenchoidea/genetics/classification

@article {pmid40011622,
year = {2025},
author = {Eroğlu, M and Çelik, I and Düşükcan, M and Ünal, EM and Çoban, MZ and Gündüz, F and Keskin, E},
title = {Author Correction: DNA barcoding of invasive Gambusia holbrooki Girard, 1859 and Atherina boyeri Risso, 1810 inhabiting Upper Euphrates River Basin, Türkiye.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6886},
doi = {10.1038/s41598-025-91131-8},
pmid = {40011622},
issn = {2045-2322},
}

@article {pmid40010350,
year = {2025},
author = {Singh, I and Fernandez-Perez, D and Sanchez, PS and Rodriguez-Fraticelli, AE},
title = {Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemic driver mutations.},
journal = {Cell stem cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.stem.2025.01.012},
pmid = {40010350},
issn = {1875-9777},
abstract = {Cancer cells display wide phenotypic variation even across patients with the same mutations. Differences in the cell of origin provide a potential explanation, but traditional assays lack the resolution to distinguish clonally heterogeneous subsets of stem and progenitor cells. To address this challenge, we developed simultaneous tracking of recombinase activation and clonal kinetics (STRACK), a method to trace clonal dynamics and gene expression before and after the acquisition of cancer mutations. Using mouse models, we studied two leukemic mutations, Dnmt3a-R878H and Npm1c, and found that their effect was highly variable across different stem cell states. Specifically, a subset of differentiation-primed stem cells, which normally becomes outcompeted with time, expands with both mutations. Intriguingly, Npm1c mutations reversed the intrinsic bias of the clone of origin, with differentiation-primed stem cells giving rise to more primitive malignant states. Thus, we highlight the relevance of single-cell lineage tracing to unravel early events in cancer evolution and posit that different cellular histories carry distinct cancer phenotypic potential.},
}

@article {pmid40009639,
year = {2025},
author = {Huang, R and Ting, AY},
title = {Directed evolution of a sequence-specific covalent protein tag for RNA labeling.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {9},
pages = {e2422085122},
doi = {10.1073/pnas.2422085122},
pmid = {40009639},
issn = {1091-6490},
support = {2330686//National Science Foundation (NSF)/ ; N/A//Chan Zuckerberg Biohub - San Francisco/ ; N/A//Stanford University (SU)/ ; },
mesh = {*RNA/metabolism/genetics/chemistry ; *Directed Molecular Evolution/methods ; Circovirus/genetics/metabolism ; Animals ; Humans ; Viral Proteins/metabolism/genetics/chemistry ; RNA-Binding Proteins/metabolism/genetics/chemistry ; },
abstract = {Efficient methods for conjugating proteins to RNA are needed for RNA delivery, imaging, editing, interactome mapping, and barcoding applications. Noncovalent coupling strategies using viral RNA binding proteins such as MS2/MCP have been widely applied but are limited by tag size, sensitivity, and dissociation over time. We took inspiration from a sequence-specific, covalent protein-DNA conjugation method based on the Rep nickase of a porcine circovirus called "HUH tag". Though wild-type HUH protein has no detectable activity toward an RNA probe, we engineered an RNA-reactive variant, called "rHUH", through 7 generations of yeast display-based directed evolution. Our 13.4 kD rHUH has 12 mutations relative to HUH and forms a covalent tyrosine-phosphate ester linkage with a 10-nucleotide RNA recognition sequence ("rRS") within minutes. We engineered the sensitivity down to 1 nM of target RNA, shifted the metal ion requirement from Mn[2+] toward Mg[2+], and demonstrated efficient labeling in mammalian cell lysate. This work paves the way toward a potentially powerful methodology for sequence-specific covalent protein-RNA conjugation in biological systems.},
}

*RNA/metabolism/genetics/chemistry
*Directed Molecular Evolution/methods
Circovirus/genetics/metabolism
Animals
Humans
Viral Proteins/metabolism/genetics/chemistry
RNA-Binding Proteins/metabolism/genetics/chemistry

@article {pmid40009600,
year = {2025},
author = {Tursky, ML and Artuz, CM and Rapadas, M and Wittert, GA and Molloy, TJ and Ma, DD},
title = {Error-corrected ultradeep next-generation sequencing for detection of clonal haematopoiesis and haematological neoplasms - sensitivity, specificity and accuracy.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0318300},
doi = {10.1371/journal.pone.0318300},
pmid = {40009600},
issn = {1932-6203},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Clonal Hematopoiesis/genetics ; *Hematologic Neoplasms/genetics/diagnosis ; *Sensitivity and Specificity ; Reproducibility of Results ; Gene Frequency ; },
abstract = {Clonal haematopoiesis of indeterminate potential (CHIP) is an aging-associated phenomenon that has recently been correlated with a broad spectrum of human diseases, including haematological malignancy, cytopenia, coronary heart disease, stroke, and overall mortality. CHIP is defined as a somatic variant in blood cells with an allele frequency (VAF) ≥ 0.02, however recent reports show smaller clones are associated with poorer clinical outcome. Error-corrected ultradeep next-generation sequencing (NGS) assays detecting variants < 0.02 VAF also have clinical value for monitoring measurable residual disease (MRD) for myeloid neoplasms. However, limited data are available on optimal parameters, limits of detection, and accuracy of ultra-sensitive detection. We investigated parameters to improve accuracy of Illumina sequencing-by-synthesis method, including read depth, input DNA quantity, and molecular barcoding-based data filtering, while adhering to clinical accreditation criteria. Validation data were generated from reference standards and reference samples from a clinically accredited pathology laboratory. Analytical range measurements included linearity and bias, and precision included repeatability, reproducibility and detection rate. The lower limit of detection was ≥ 0.004 (0.4%) at depth > 3,000 × . Trueness measured using reference standards demonstrated a sensitivity, specificity, positive and negative predictive values, and accuracy of 100%, including FLT3-ITD, and 100% concordance was achieved with reference samples for reported variants and absence of variants. Sequencing blood samples from 383 community-dwelling adults (mean depth 3758×) revealed 2,190 somatic variants/sample, > 99.9% were < 0.02 VAF. Our data including cost-benefit analysis enables pathology and research laboratories to make informed decisions for detection of CHIP (VAF ≥ 0.02), sub-CHIP (VAF 0.01-0.02) and MRD (VAF ≥ 0.004).},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Clonal Hematopoiesis/genetics
*Hematologic Neoplasms/genetics/diagnosis
*Sensitivity and Specificity
Reproducibility of Results
Gene Frequency

@article {pmid40006878,
year = {2025},
author = {Peng, Y and Chen, Y and Ding, H and Liu, X and Cao, F and Xu, L},
title = {From Phenotypes to Genotypes: Enhancing the Identification of Cymbidium Species with DNA Barcoding.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/plants14040619},
pmid = {40006878},
issn = {2223-7747},
support = {No. 2019JJ50232//Hunan Provincial Science and Technology Department/ ; },
abstract = {The genus Cymbidium, with its intricate floral elements, pronounced endemicity, and patchy distribution, evolves a rich diversity of morphological forms and a wide variety of species while causing an indistinctness in the classification of its species. To elucidate the phylogenetic relationships among Cymbidium species and enhance their taxonomic classification by DNA barcoding, this study conducted amplification and sequence results of nuclear (ITS) and chloroplast genes (matK, rbcL, trnL-F, psbA-trnH) with phenotypic genetic diversity analysis, genetic distance analysis, and phylogenetic analysis from 48 samples of Cymbidium species. The comparison of genetic distance variations showed that psbA-trnH, ITS + psbA-trnH, and ITS + matK + psbA-trnH exhibit minimal overlap and significant genetic variation within Cymbidium species. The phylogenetic analysis indicated that the combination, ITS + matK + psbA-trnH, has the highest identification rate. Notably, both the phylogenetic analysis and the genetic diversity analysis of phenotypic traits consistently indicated a clear divergence between epiphytic and terrestrial orchids, with epiphytic orchids forming a distinct clade. This provides reference evidence for studying the ecological adaptations and evolutionary differences between epiphytic and terrestrial orchids, as well as a scientific basis for the classification and identification, germplasm conservation, resource utilization, and phylogenetic evolution of orchids.},
}

@article {pmid40005642,
year = {2025},
author = {Chittavichai, T and Sathitnaitham, S and Utthiya, S and Prompichai, W and Prommarit, K and Vuttipongchaikij, S and Wonnapinij, P},
title = {Limitations of 18S rDNA Sequence in Species-Level Classification of Dictyostelids.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020275},
pmid = {40005642},
issn = {2076-2607},
support = {//Kasetsart University through the Graduate School Fellowship Program/ ; FF(KU)13.64//Kasetsart University Research and Development Institute (KURDI)/ ; N42A650286//The National Research Council of Thailand (NRCT) and Kasetsart University Research and Development Institute (KURDI)/ ; },
abstract = {Dictyostelid species classification has traditionally relied on morphology, a time-intensive method requiring expert knowledge. This study evaluated the potential and limitations of using the 18S rDNA sequence for species-level classification. 18S rDNA sequences of 16 samples from the Dicty stock center, including 14 samples found in Thailand, were analyzed. Signature sequence analyses confirmed genus-level identification with high accuracy. These sequences were analyzed alongside 309 database entries retrieved from the GenBank database. The analyses confirmed genus-level identification accuracy but highlighted challenges in distinguishing species due to overlapping intraspecific and interspecific variations, negative barcoding gaps, and incorrectly grouped samples to putative taxa by species delimitation analyses. Species delimitation methods, including maximum likelihood (ML) phylogenetic analysis, achieved limited success, with ML showing the highest accuracy but not exceeding 50%. However, species with high barcoding gaps, such as Raperostelium and Rostrostelium, demonstrated potential for accurate classification. These findings support using 18S rDNA for genus-level identification and suggest its possible application for certain species. Expanded sampling is needed to improve species-level classification and to identify more robust DNA markers for dictyostelid diversity studies.},
}

@article {pmid40003852,
year = {2025},
author = {Jiang, ZH and Kitching, IJ and Xu, XD and Xu, ZB and Yan, M and Yu, WB and Liu, CQ and Hu, SJ},
title = {A Review of the Genus Ambulyx Westwood, 1847 (Lepidoptera: Sphingidae) from China Based on Morphological and Phylogenetic Analyses, with the Description of a New Species.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/insects16020223},
pmid = {40003852},
issn = {2075-4450},
support = {202305AF150037//Academician (Expert) Working Station (202305AF150037), Yunnan Provincial De-partment of Science, Technology/ ; Grant No. 2019FY101800//National Science & Technology Fundamental Resources Investigation Program of Chi-na/ ; Grant Nos. 32100352，32100355//National Natural Science Foundation of China/ ; },
abstract = {The taxonomy of genus Ambulyx Westwood, 1847 from China is reviewed based on analysis of wing morphology, male and female genitalia and phylogenetic relationships derived from DNA barcodes. A new species, Ambulyx wukong sp. nov. is described from NW Yunnan, China. A male of the rare species, A. zhejiangensis from Yintiaoling Nature Reserve, Chongqing, China is examined and its male genitalia illustrated for the first time. Two taxa are newly recorded from China, A. tattina tattina from Xishuangbanna, Yunnan, and A. semiplacida montana from Pingbian, Yunnan. Distribution maps, biological notes, and ecological records are also given.},
}

@article {pmid40003849,
year = {2025},
author = {Gwiazdowska, A and Rutkowski, R and Sielezniew, M},
title = {Conservation Genetics of the Endangered Danube Clouded Yellow Butterfly Colias myrmidone (Esper, 1780) in the Last Central European Stronghold: Diversity, Wolbachia Infection and Balkan Connections.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/insects16020220},
pmid = {40003849},
issn = {2075-4450},
support = {EZ.271.3.7.2021//General Directorate of the Polish State Forests/ ; },
abstract = {The Danube Clouded Yellow (Colias myrmidone) has experienced one of the most dramatic declines among European butterflies. To estimate genetic diversity in the last population in Poland that has survived in the Knyszyn Forest (KF), we analyzed mitochondrial (COI) and nuclear (EF-1α) polymorphisms in individuals sampled in 2014 and 2022. The results were compared with genetic data obtained in 2014 from a recently extirpated nearby population (Czerwony Bór, CB). Because mtDNA polymorphisms in insects can be modulated by endosymbionts, the samples were screened for Wolbachia. The polymorphism of EF-1α indicated that diversity was gradually decreasing. The KF experienced rapid demographic processes, manifested by a significant change in allele frequency. The small differentiation in nuclear markers between the KF and CB in 2014 suggests that the regional population used to be genetically uniform. Four COI haplotypes that were identified in this study probably belong to two different haplogroups. Wolbachia was detected only in individuals with one specific haplotype, and the prevalence was female-biased, suggesting the induction of two reproductive manipulations. The most common COI haplotype found in Poland was the same as that reported from other parts of Europe, not only for C. myrmidone but also C. caucasica. These results allow us to question the distinctiveness of each taxa.},
}

@article {pmid40003799,
year = {2025},
author = {Ricupero, M and Porcu, E and Russo, A and Zappalà, L and Siscaro, G},
title = {New Records of Phenacoccus solenopsis Natural Enemies in Europe and Taxonomic Additions on Anagyrus matritensis.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/insects16020169},
pmid = {40003799},
issn = {2075-4450},
support = {CN00000022//the European Union Next-Generation EU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; E73C22000240006//Agroecology-inspired Strategies and Tools to Enhance Resilience and ecosystem services in to-mato crop" (ASTER), PRIMA SECTION 2 2021 - MULTI-TOPIC/ ; 101136611//the European Union's Horizon Europe research and innovation programme (NextGenBioPest project)/ ; },
abstract = {The cotton mealybug Phenacoccus solenopsis (Hemiptera: Pseudococcidae) is a polyphagous invasive species native to America and considered one of the major cotton pests in Asia. It is currently threatening horticultural and ornamental protected crops in Mediterranean countries. Due to ecological and environmental concerns, the conventional chemical control of P. solenopsis in new areas of introduction is being replaced by exploring the potential of indigenous natural enemies as a sustainable biological control tool. After P. solenopsis introduction in Sicily (Italy), field surveys were conducted on native natural enemies attacking the mealybug to select promising biocontrol agents for field applications. For the first time, Aenasius arizonensis (Hymenoptera: Encyrtidae) was reported in Europe, and the native Anagyrus matritensis (Hymenoptera: Encyrtidae) was recorded in association with P. solenopsis. The two parasitoid species were identified by morphological features and molecularly using a portion of the mitochondrial cytochrome oxidase subunit I (mtCOI) gene. Because of missing information, additional morphological features were provided for the morphological identification of A. matritensis. In addition, the generalist predators Cryptolaemus montrouzieri, Hippodamia variegata and Parexochomus nigripennis (Coleoptera: Coccinellidae) were also recorded attacking the invasive mealybug.},
}

@article {pmid40003760,
year = {2025},
author = {Qian, P and Fan, J and Zhang, X and Zeng, M and Han, X and Li, Y and Luo, X},
title = {Morphogenetic Identification of a New Record Condica capensis (Lepidoptera: Noctuidae) in Yunnan, China.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/insects16020130},
pmid = {40003760},
issn = {2075-4450},
support = {202301BD070001-185//Joint Agricultural Project of Yunnan Province/ ; },
abstract = {Condica capensis (Lepidoptera: Noctuidae), a newly identified pest in Yunnan Province, China, poses a threat to safflower crops. Discovered in Nanhua County in November 2023, the pest damages safflower at multiple life stages, especially during its larval stage, when it feeds on leaves, tender stems, and flower filaments, sometimes causing the entire plant to die. Morphological and molecular analyses, including mitochondrial cytochrome C oxidase I (COI) gene sequencing, confirmed its identity as C. capensis, a new species record for Yunnan. The study also documented the pest's life cycle, reproductive behavior, and natural enemies, highlighting the potential for biological control using parasitic wasps such as Cotesia sp. This research emphasizes the need for accurate pest identification and monitoring to develop effective, sustainable pest management strategies. As safflower cultivation grows in Yunnan, managing C. capensis is critical to safeguarding local agriculture and preventing broader agricultural threats.},
}

@article {pmid40002052,
year = {2025},
author = {Jiang, Y and Wei, S and Ge, H and Zhang, Y and Wang, H and Wen, X and Guo, C and Wang, S and Chen, Z and Li, P},
title = {Advances in the Identification Methods of Food-Medicine Homologous Herbal Materials.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/foods14040608},
pmid = {40002052},
issn = {2304-8158},
support = {(No. 61975053, No. 62271191)//National Natural Science Foundation of China/ ; No. 222300420040//Natural Science Foundation of Henan Province/ ; (No. 22HASTIT017, No. 23HASTIT024)//Program for Science and Technology Innovation Talents in Universities of Henan Province/ ; No. CSKFJJ-2024-26//Open Project of Institute for Complexity Science, Henan University of Technology/ ; No. 201300210100//Major public welfare projects of Henan Province/ ; No. 2021ZKCJ04//Innovative Funds Plan of Henan University of Technology/ ; },
abstract = {As a key component of both traditional medicine and modern healthcare, Food-Medicine Homologous Herbal Materials have attracted considerable attention in recent years. However, issues related to the quality and authenticity of medicinal materials on the market often arise, not only compromising their efficacy but also presenting potential risks to consumer health. Therefore, the establishment of accurate and efficient identification methods is crucial for ensuring the safety and quality of Food-Medicine Homologous Herbal Materials. This paper provides a systematic review of the research progress on the identification methods for Food-Medicine Homologous Herbal Materials, starting with traditional methods such as morphological and microscopic identification, and focusing on the applications of modern techniques, including biomimetic recognition, chromatography, mass spectrometry, chromatography-mass spectrometry coupling, hyperspectral imaging, near-infrared spectroscopy, terahertz spectroscopy, and DNA barcoding. Moreover, it provides a comprehensive analysis of the fundamental principles, advantages, and limitations of these methods. Finally, the paper outlines the current challenges faced by identification methods and suggests future directions for improvement, aiming to offer a comprehensive technical perspective on identifying Food-Medicine Homologous Herbal Materials and foster further development in this field.},
}

@article {pmid39997428,
year = {2025},
author = {Motta, BDS and Almeida-Silva, F and Teixeira, MM and Bernardes-Engemann, AR and Almeida-Paes, R and de Macedo, PM and Zancopé-Oliveira, RM},
title = {Paracoccidioides Species Circulating in the Endemic Area of Rio de Janeiro, Brazil: Updates into Their Genetic Diversity.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {2},
pages = {},
doi = {10.3390/jof11020134},
pmid = {39997428},
issn = {2309-608X},
support = {001//CAPES/ ; E-26/211.430/2021//FAPERJ/ ; 308315/2021-9//CNPq/ ; E-26/200.381/2023//FAPERJ/ ; },
abstract = {Paracoccidiodomycosis (PCM) is the most important systemic mycosis in Brazil, and is usually associated with rural work. PCM is caused by inhalation of infective propagules of thermodimorphic fungi from the genus Paracoccidioides. In the past, it was believed that Paracoccidioides brasiliensis was the single species responsible for PCM cases. However, recent advances in molecular methods allowed the description of several new species, using phylogenetic concordance as the gold standard. Aside from P. brasiliensis sensu stricto, Paracoccidioides americana is also endemic in Rio de Janeiro state, Brazil. This study aimed to evaluate intraspecific genetic variability of Paracoccidioides isolates from patients diagnosed with PCM at a reference center for endemic mycoses in Rio de Janeiro state, from 2015 to 2021. Among the sixteen retrieved isolates, three (18.75%) were identified as P. americana and thirteen (81.25%) as P. brasiliensis sensu stricto. No intraspecific genetic variation was observed by the M-13 primer in P. americana isolates from this geographic region. However, P. brasiliensis sensu stricto isolates were clustered into two distinct molecular profiles, despite being grouped in a single clade in the phylogenetic tree after partial sequencing of arf and gp43 genes. The results suggest a single P. americana lineage and two P. brasiliensis populations causing PCM in Rio de Janeiro, Brazil.},
}

@article {pmid39997392,
year = {2025},
author = {Zuleta, MC and Gómez, OM and Misas, E and Torres, S and Rúa-Giraldo, ÁL and McEwen, JG and Garcia, AM and Borges, CL and Hernández, O and López, AM},
title = {Species Identification and Orthologous Allergen Prediction and Expression in the Genus Aspergillus.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {2},
pages = {},
doi = {10.3390/jof11020098},
pmid = {39997392},
issn = {2309-608X},
support = {221384467683//Ministerio de Ciencia, Tecnología e Innovación/ ; },
abstract = {The genus Aspergillus comprises a diverse group of fungi that can cause a range of health issues, including systemic infections and allergic reactions. In this regard, A. fumigatus has been recognized as the most prevalent allergen-producing species. This genus taxonomic classification has been subject to frequent updates, which has generated considerable difficulties for its classification when traditional identification methodologies are employed. To demonstrate the feasibility of this approach, we sequenced the whole genomes of 81 Aspergillus isolates and evaluated a WGS-based pipeline for precise species identification. This pipeline employed two methodologies: (i) BLASTn web using four barcode genes and (ii) species tree inference by OrthoFinder. Furthermore, we conducted a prediction of allergenic capacity based on a homology analysis across all the isolated species and confirmed by RT-qPCR the expression of three orthologous allergens (Asp f 1, Asp f 3 and Asp f 22) in fifteen different Aspergillus species. The species-level identification rate with the barcoding and the species tree were calculated at 64.2% and 100%, respectively. The results demonstrated that A. fumigatus, A. flavus and A. niger were the most prevalent species. The species A. hortae, A. uvarum, A. spinulosporus, A. sydowii, A. westerdijkiae, A. amoenus and A. rhizopodus identified in this study represent the inaugural report of their presence in our region. The results of the homology analysis indicated the presence of orthologous allergens in a wide range of non-fumigatus species. This study presents a novel approach based on WGS that enables the classification of new species within the genus Aspergillus and reports the genomic sequences of a great diversity of species isolated in our geographic area that had never been reported before. Additionally, this approach enables the prediction of allergens in species other than A. fumigatus and demonstrates their genetic expression, thereby contributing to the understanding of the allergenic potential of different species within this fungal genus.},
}

@article {pmid39997216,
year = {2025},
author = {Chovanec, P and Yin, Y},
title = {Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.},
journal = {Nucleic acids research},
volume = {53},
number = {4},
pages = {},
doi = {10.1093/nar/gkaf101},
pmid = {39997216},
issn = {1362-4962},
support = {R35GM142511/GF/NIH HHS/United States ; DFS-43-20/DRCRF/Damon Runyon Cancer Research Foundation/United States ; 5R35GM142511/GM/NIGMS NIH HHS/United States ; },
mesh = {*Chromatin/genetics/metabolism/chemistry ; *Single-Cell Analysis/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; RNA/genetics/metabolism ; Sequence Analysis, RNA/methods ; Nucleic Acid Amplification Techniques/methods ; },
abstract = {Single-cell combinatorial indexing (sci) methods have addressed major limitations of throughput and cost for many single-cell modalities. With the incorporation of linear amplification and three-level barcoding in our suite of methods called sci-L3, we further addressed the limitations of uniformity in single-cell genome amplification. Here, we build on the generalizability of sci-L3 by extending it to template strand sequencing (sci-L3-Strand-seq), genome conformation capture (sci-L3-Hi-C), and the joint profiling of RNA and chromatin accessibility (sci-L3-RNA/ATAC). We demonstrate the ease of adapting sci-L3 to these new modalities by only requiring a single-step modification of the original protocol. As a proof of principle, we show our ability to detect sister chromatid exchanges, genome compartmentalization, and cell state-specific features in thousands of single cells. We anticipate sci-L3 to be compatible with additional modalities, including DNA methylation (sci-MET) and chromatin-associated factors (CUT&Tag), and ultimately enable a multi-omics readout of them.},
}

*Chromatin/genetics/metabolism/chemistry
*Single-Cell Analysis/methods
Humans
*High-Throughput Nucleotide Sequencing/methods
RNA/genetics/metabolism
Sequence Analysis, RNA/methods
Nucleic Acid Amplification Techniques/methods

@article {pmid39997191,
year = {2025},
author = {Turner, AD and Maskrey, BH and Stone, D and Mudge, EM and Robertson, A},
title = {First Confirmed Occurrence of Ciguatera Poisoning in the UK from Imported Pinjalo Snapper (Pinjalo pinjalo).},
journal = {Marine drugs},
volume = {23},
number = {2},
pages = {},
doi = {10.3390/md23020067},
pmid = {39997191},
issn = {1660-3397},
support = {Atlantic Area Program project Alertox-Net (EAPA-317-2016//Interreg Atlantic Area/ ; },
mesh = {*Ciguatera Poisoning ; Animals ; Humans ; *Ciguatoxins/toxicity ; Mice ; United Kingdom ; Perciformes ; Male ; Seafood ; Food Contamination/analysis ; Female ; Adult ; },
abstract = {Three people in England consumed fish steaks labeled as Red Snapper (Lutjanus bohar) originating from the Indian Ocean. Within 12 h, all three experienced sickness including nausea, vomiting, diarrhea, as well as myalgia and paresthesia. Three steaks from a single package of fish obtained from a grocery store were consumed, leaving one uneaten, which was submitted for analysis. Cytotoxicity testing via the mouse neuroblastoma assay confirmed the presence of sodium channel specific activity consistent with a ciguatoxin standard, and the levels detected were above established guidance limits for safe consumption. Chemical detection using liquid chromatography coupled with high-resolution mass spectrometry of both intact toxins and periodate oxidation products was used to confirm the presence of chromatographic peaks consistent with tri- and di-hydroxylated Pacific ciguatoxin 3C congeners. Taking the shared medical symptoms of patients, the recent dietary history, and the known potential for ciguatera poisoning to occur in snapper species, the subsequent evidence for CTX-like activity and CTXs in the same fish sample provides very strong evidence that the fish steaks consumed were similarly contaminated with CTXs. Furthermore, given the levels reported, such toxicity would be expected to cause intoxication in humans. Fish species identification based on DNA barcoding confirmed that the fish products were mislabeled, with the tissues instead being the Pinjalo snapper, Pinjalo pinjalo. This is the first confirmed ciguatera poisoning incident in both the UK and from the Pinjalo snapper and highlights the need for monitoring of these emerging toxins in reef fish imports to prevent future human intoxication.},
}

*Ciguatera Poisoning
Animals
Humans
*Ciguatoxins/toxicity
Mice
United Kingdom
Perciformes
Male
Seafood
Food Contamination/analysis
Female
Adult

@article {pmid39996828,
year = {2025},
author = {Zhu, H and Yue, C and Li, H},
title = {Mitochondrial Genome Characteristics and Comparative Genomic Analysis of Spartina alterniflora.},
journal = {Current issues in molecular biology},
volume = {47},
number = {2},
pages = {},
doi = {10.3390/cimb47020107},
pmid = {39996828},
issn = {1467-3045},
support = {2024C02002//"Leading Goose"R&D Program of Zhejiang/ ; 2022SY06//Zhejiang Forestry Science and Technology Project/ ; },
abstract = {The mitochondrial genome of Spartina alterniflora, an invasive species with significant ecological and economic impacts, was analyzed to provide a theoretical basis for understanding its phylogenetic relationships and molecular biology. Mitochondrial genome sequences of S. alterniflora and 23 related species from NCBI were utilized for bioinformatics and comparative genomic analyses. A sliding window analysis identified three genes (rps2, atp9, and nad6) as potential DNA barcodes for species identification. Intracellular gene transfer (IGT) events between mitochondrial and chloroplast genome were detected, highlighting the dynamic nature of genomic evolution. A selective pressure analysis revealed that most protein-coding genes (PCGs) underwent purifying selection (Ka/Ks < 1), while the nad2 and ccmB genes showed signs of positive selection pressure (Ka/Ks > 1), indicating their role in adaptation. A phylogenetic analysis demonstrated a close relationship between S. alterniflora and Eleusine indica, supported by a collinearity analysis, which suggests environmental convergence. This study provides novel insights into the structural and evolutionary characteristics of the S. alterniflora mitochondrial genome, offering valuable genomic resources for future research on invasive species management and evolutionary biology.},
}

@article {pmid39995615,
year = {2025},
author = {Changbunjong, T and Weluwanarak, T and Laojun, S and Chaiphongpachara, T},
title = {Species classification of Tabanus (Diptera: Tabanidae) in Western Thailand: Integrating DNA barcoding and modern morphometrics.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {7},
number = {},
pages = {100243},
pmid = {39995615},
issn = {2667-114X},
abstract = {The species of Tabanus, commonly known as horse flies, are remarkable ectoparasites capable of transmitting various pathogens to animals and humans. Given their role in disease transmission, accurate identification of horse fly species is critical but traditionally relies on morphological characteristics, requiring significant expertise and posing a high potential for error, especially with damaged specimens. To address the limitations of traditional morphological identification, this study highlights the importance of alternative techniques, including DNA barcoding and geometric morphometrics (GM). To enhance the reliability of species identification, DNA barcoding was employed to analyze 30 cytochrome c oxidase subunit 1 (cox1) gene sequences from 15 horse fly species, which were then compared with sequences in the GenBank and BOLD databases. Most cox1 sequences aligned with existing data, with similarity percentages ranging from 96% to 100%. However, discrepancies were noted, including Tabanus helvinus, misidentified as Tabanus aurilineatus, and Tabanus minimus, whose sequences matched those of both Tabanus minimus and Tabanus mesogaeus. Besides DNA barcoding, GM analyses were conducted to enhance species classification accuracy. Our GM analyses employed the landmark-based method for the entire wing and the outline-based method for the first submarginal cell. While shape-based GM analyses demonstrated high reliability, with adjusted total accuracy scores of 97% and 96%, size-based GM analyses yielded significantly lower accuracy, with scores of only 27% and 23%, respectively. These findings provide a foundation for refining horse fly species classification by integrating DNA barcoding and GM approaches, offering valuable advances in species identification and developing targeted control measures.},
}

@article {pmid39994544,
year = {2025},
author = {Wu, Y and Sun, Z and Liu, Z and Qiu, T and Li, X and Leng, L and Chen, S},
title = {Assembly and analysis of stephania japonica mitochondrial genome provides new insights into its identification and energy metabolism.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {185},
pmid = {39994544},
issn = {1471-2164},
support = {030040016/030//This work is supported by the talented person scientific research start funds subsidization project of Chengdu University of Traditional Chinese Medicine/ ; },
abstract = {Stephania japonica, a popular indoor ornamental and medicinal plant widely found in southern China, contains many natural compounds with potential medicinal value. S. japonica is also favored by researchers for its ability to produce catharanthine. Energy metabolism functions in plant development, and the composition of mitochondrial genome is regarded as the foundation for understanding energy metabolism and getting insights into plant environmental adaptation. In present investigation, the whole mitochondrial genome of S. japonica was assembled from both second- and third-generation sequencing data. The mitochondrial genome size of S. japonica is 555,117 bp. It is depicted as a complex polycyclic structure. In addition, we conducted an in-depth study of the cytochrome c oxidase (cox) gene, of which expression levels in different tissues of S. japonica were measured by real-time quantification PCR. Two phylogenetic trees were established in the light of sequences concerning 19 conserved mitochondrial protein-coding genes and cox gene, respectively. Both phylogenetic trees show that S. japonica is more closely related to Aconitum kusnezoffii. The result showed that the cox genes were the most highly expressed in the roots. A high-quality mitochondrial genome exhibits potential application value for the progress of molecular markers, identification of species as super DNA barcoding, and resolve mitochondrial energy metabolism mechanisms in response to the environment using genomic information. With the recognition of the medicinal value of Stephania plants, the genomic information of S. japonica has been thoroughly studied and the comprehensive analysis of its mitochondrial genome in this investigation can offer valuable insights for the breeding of new plant varieties.},
}

@article {pmid39991452,
year = {2025},
author = {Ziganira, M and Downs, CT},
title = {Significant Progress in the Study of African Freshwater Snails Over the Past 260 Years.},
journal = {Ecology and evolution},
volume = {15},
number = {2},
pages = {e71031},
pmid = {39991452},
issn = {2045-7758},
abstract = {Globally, freshwater ecosystems are threatened. Research progress concerning African freshwater snails was reviewed using a systematic review process. Since 1757, the number of publications produced has increased, particularly in the last decade. In the first 50 years (1757-1800), 0.1% of publications on freshwater snails in Africa were conducted, followed by 0% (1801-1850), 3.3% (1851-1900), 3.5% (1901-1950) and 48.7% (1951-2000). The last 23 years (2001-2024) exhibited a large increase (44.3%) in publications of the total conducted. Studies on freshwater snails varied in number across the 10 major African water basins, with the majority of studies in the Nile (21.7%), followed by the Congo Basin (17.6%) and Niger (12.4%). The Orange Basin and Lake Tanganyika also received a high number of studies (10.9%) and (7.2%), respectively. Most freshwater snail study objectives related to conservation and taxonomy (70%), followed by disease vector (20.5%), with genetics/genomic/DNA barcoding/eDNA receiving significant focus as well (5.2%). Studies focusing on geology and palaeontology (2.5%), followed by climate change (1.5%) and machine learning (0.4%). The modern phase in the study of African freshwater snails came around the early 20th century with the discovery of Bulinus truncatus and Biomphalaria alexandrina as intermediate hosts for the parasites causing human schistosomiasis. African freshwater malacology has since then benefited from African and overseas malacologists based at universities and medical laboratories across Africa and overseas. In addition to taxonomic studies, there was a steady rise in contributions relating to ecology, disease vectors, palaeontology and genetics. These contributed knowledge on local endemism and speciation, invasive species, species origins and distribution across African water basins, as well as the spread of infectious diseases and impacts of climate change. In the last decade, there have been shifts in methods with the application of DNA barcoding, genomics, environmental DNA and, most recently, machine learning approaches.},
}

@article {pmid39990951,
year = {2025},
author = {Wang, KC and Young, TL and Chen, J and Tsai, SN and Xu, Y and Varley, AJ and Solek, NC and Gong, F and Lu, RXZ and Hubbard, BP and Li, B},
title = {A Reverse Transcription Nucleic-Acid-Based Barcoding System for In Vivo Measurement of Lipid Nanoparticle mRNA Delivery.},
journal = {ACS bio & med chem Au},
volume = {5},
number = {1},
pages = {35-41},
pmid = {39990951},
issn = {2694-2437},
abstract = {Lipid nanoparticles (LNPs) are the most extensively validated clinical delivery vehicles for mRNA therapeutics, exemplified by their widespread use in the mRNA COVID-19 vaccines. The pace of lipid nanoparticle (LNP) development for mRNA therapeutics is restricted by the limitations of existing methods for large-scale LNP screening. To address this challenge, we developed Quantitative Analysis of Reverse Transcribed Barcodes (QuART), a novel nucleic-acid-based system for measuring LNP functional delivery in vivo. QuART uses a bacterial retron reverse transcription system to couple functional mRNA delivery into the cytoplasm with a cDNA barcode readout. Our results demonstrate that QuART can be used to identify functional mRNA delivery both in vitro in cell culture and in vivo in mice. Multiplexing of QuART could enable high-throughput screening of LNP formulations, facilitating the rapid discovery of promising LNP candidates for mRNA therapeutics.},
}

@article {pmid39990434,
year = {2025},
author = {Kinsler, G and Fagan, C and Li, H and Kaster, J and Dunne, M and Vander Velde, RJ and Boe, RH and Shaffer, S and Herlyn, M and Raj, A and Heyman, Y},
title = {SpaceBar enables clone tracing in spatial transcriptomic data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.10.637514},
pmid = {39990434},
issn = {2692-8205},
abstract = {We report a cellular barcoding strategy, SpaceBar, that enables simultaneous clone tracing and spatial transcriptomics profiling. Our approach uses a library of 96 synthetic barcode sequences that can be robustly detected by imaging based spatial transcriptomics (seqFISH), delivered such that each cell is labeled with a combination of barcodes. We used these barcodes to label melanoma cells in a tumor xenograft model and profiled both clone identity and spatial gene expression in situ . We developed a gene scoring metric that quantifies how strongly gene expression is driven by intrinsic cellular cues or extrinsic environmental signals. Our framework distinguishes between clonal dynamics and environmentally-driven transcriptional regulation in complex tissue contexts.},
}

@article {pmid39990189,
year = {2025},
author = {Faltlhauser, AC and Cabrera, N and Hernández, MC and Sánchez Restrepo, AF and Hill, M and Sosa, AJ},
title = {Lysathiaflavipes and Lysathiacilliersae Cabrera sp. nov. (Coleoptera, Chrysomelidae): genetic and morphological unravelling of biocontrol agents for two invasive aquatic plants.},
journal = {ZooKeys},
volume = {1228},
number = {},
pages = {11-52},
pmid = {39990189},
issn = {1313-2989},
abstract = {In the search for specific natural enemies to control two invasive aquatic plants (IAP) from South America, Ludwigiagrandiflorasubsp.hexapetala (Onagraceae) and Myriophyllumaquaticum (Haloragaceae), taxonomic challenges associated with two Lysathia Bechyné, 1959 (Chrysomelidae; Alticini) species had to be resolved. Lysathiaflavipes (Boheman, 1859) exhibits significant morphological variation, causes heavy damage to both IAPs, and may represent more than one species due to the phylogenetic gap between hosts. Additionally, an undescribed Lysathia species (previously published as Lysathia sp.), sourced from Brazil, has been successfully used as a control agent for M.aquaticum in South Africa since 1994. An integrative taxonomic approach combining genetic and morphological analyses was employed. A lectotype and paralectotypes for Graptoderaflavipes Boheman, 1859 are here designated. Phylogenetic studies revealed that L.flavipes had greater genetic and morphological variation than originally described, and no evidence suggested that L.flavipes represented a species complex associated with its host plants. As a result, the species description was expanded. On the other hand, genetic and morphological differences such as body size, colouration, and genital structures further supported the description of Lysathiacilliersae Cabrera, sp. nov. and its differentiation from other closely related species, including L.flavipes and L.ludoviciana (Fall, 1910). Specimens of L.cilliersae sp. nov. collected in Misiones, Argentina, matched those from South Africa. Genetic sequences correlated with morphological vouchers, images, and illustrations of morphology and genitalia, as well as new distribution records, are provided. This research contributes to the taxonomic knowledge of the Lysathia genus and supports accurate species identification in applied entomological contexts, such as biological control programmes.},
}

@article {pmid39985775,
year = {2025},
author = {Xiong, EH and Zhang, X and Robbins, N and Myers, CL and Cowen, LE},
title = {Protocol to identify genes important for Candida albicans fitness in diverse environmental conditions using pooled bar-seq screening approach.},
journal = {STAR protocols},
volume = {6},
number = {1},
pages = {103645},
doi = {10.1016/j.xpro.2025.103645},
pmid = {39985775},
issn = {2666-1667},
abstract = {Identifying genes important for fitness in Candida albicans advances our understanding of this important pathogen of humans. Here, we present a functional genomics approach for assessing fitness through the quantification of strain-specific barcodes. We describe steps for library preparation, propagation of strains, genomic DNA extraction, amplification of barcodes, and sequencing. We then detail the computational analysis of data to determine effect size and statistical significance. For complete details on the use and execution of this protocol, please refer to Xiong et al.[1].},
}