@article {pmid42793264,
year = {2026},
author = {Fu, Y and Li, F and Wang, H and Wang, X and Wang, H},
title = {Rapid Generation of High-Affinity Rabbit Anti-Mouse IgG Monoclonal Antibodies by High-Throughput Single-B-Cell Sorting and Recombinant Expression.},
journal = {Current issues in molecular biology},
volume = {48},
number = {9},
pages = {},
pmid = {42793264},
issn = {1467-3045},
support = {YDZJ202402030CXJD//Jilin Province Science and Technology Department/ ; },
abstract = {Rabbit monoclonal antibodies (RabMAbs) are valuable for biomedical research and diagnostic applications because of their high affinity, specificity, and broad epitope recognition; here, we established an integrated phenotype-linked workflow for rapid RabMAb discovery using serum-derived polyclonal mouse IgG as a proof-of-concept model antigen. Three Big-Eared White rabbits were immunized in parallel, and the rabbit exhibiting the highest serum endpoint titer was selected for the complete downstream single-B-cell discovery workflow. Approximately 5 × 10[5] activated B cells were subjected to polydisperse oblate dispersion system (POD)-based screening, yielding 13,266 antigen-positive POD events. Following recovery and 10× Genomics single-cell V(D)J sequencing, 4294 B-cell barcodes yielded valid/interpretable V(D)J data, of which 2099 contained at least one complete, productive, and translatable heavy-chain/light-chain pair, generating 2199 functional VH/VL pairing records. AbFinder™-assisted prioritization generated a computationally recommended pool of 158 candidates, and the five highest-ranked VH/VL pairs within this pool were selected for recombinant expression and validation. All five yielded antigen-reactive RabMAbs with an endpoint ELISA titer of 1:256,000 and BLI-derived apparent KD values ranging from 4.19 × 10[-10] to 9.79 × 10[-9] M. The antibodies showed differential concentration-dependent reactivity toward mouse IgG1, IgG2a, IgG2b, and IgG3 preparations, weak reactivity toward human IgG, and clone-dependent reactivity toward rat IgG. The workflow from spleen collection to functional validation was completed within approximately three weeks. Because only five prioritized candidates from one selected responder rabbit were evaluated, the 5/5 validation outcome should not be interpreted as an overall platform hit rate or definitive validation of the prioritization algorithm. These findings support the feasibility of this workflow for research-grade and diagnostic antibody discovery, while broader evaluation will require larger candidate cohorts, independent biological validation, and additional antigen classes.},
}

@article {pmid42791790,
year = {2026},
author = {Ekimova, I and Fedorov, D and Grishina, D and Schepetov, D},
title = {High Intraspecific mtDNA Polymorphisms and Mitonuclear Discordance: A Case Study of the Cadlina laevis (Linnaeus, 1767) Species Complex.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
pmid = {42791790},
issn = {2076-2615},
support = {# 25-74-10006//Russian Science Foundation/ ; No. #3/2023-gr//Nonprofit Charitable Foundation "Support for Biological Research BIOM"/ ; # FEFF-2026-0009//Sakhalin State University/ ; },
abstract = {The Cadlina laevis (Linnaeus, 1767) species complex in the White Sea exhibits a high mitochondrial DNA polymorphism, with two divergent haplogroups (HA and HB) showing ~2.5% COI divergence, consistent with minimal interspecific mtDNA differences within this group. This study integrates complete mitochondrial genomes of both haplogroups of the White Sea Cadlina laevis, nuclear markers (18S, ITS1, ITS2, 28S, H3), and species-delimitation analyses to test whether mitochondrial lineages correspond to distinct species. Comparative mitogenomics revealed conserved gene order but heterogeneous divergence, with protein-coding genes showing p-distances from 1.0% (COX2) to 5.1% (ATP6) between haplogroups. Phylogenetic reconstructions based on nuclear markers consistently collapsed HA and HB into single, undifferentiated clade, demonstrating mitonuclear discordance. Similar patterns emerged for other mitochondrial lineages: C. laevis and North Pacific C. vavilovi Korshunova & Martynov, 2024, as well as C. koltzovi Korshunova & Martynov, 2024 and Cadlina sp. 3 showed no nuclear differentiation despite substantial COI p-distances. Species-delimitation methods yielded conflicting results, failing to provide consistent support for mitochondrial-defined species. The COI-wide distance distribution placed the HA-HB comparison within the "grey zone" of ambiguous species boundaries. The study demonstrates that mitochondrial data alone are unreliable for species delimitation in this group, suggesting that the current taxonomy may over-split mitochondrial lineages and require genome-wide nuclear evidence for robust taxonomic revision.},
}

@article {pmid42792887,
year = {2026},
author = {Chen, L and Zhong, YZ and Xu, XQ and Wu, YS and Mai, DN and Tong, Y and Lan, W},
title = {Comparative Chloroplast Genome Analysis of Anchusa and the Adulterants of HERBA ANCHUSAE.},
journal = {Genes},
volume = {17},
number = {9},
pages = {},
pmid = {42792887},
issn = {2073-4425},
support = {TSYC202401B132//The High-level Talent Project in the medical and health field under the "Tianshan Talents" Training Program/ ; },
mesh = {*Genome, Chloroplast/genetics ; Phylogeny ; *Plants, Medicinal/genetics/classification ; DNA Barcoding, Taxonomic ; },
abstract = {BACKGROUND: The genus Anchusa L. includes plants used in Uyghur medicine for their anti-inflammatory and analgesic effects. However, in China, the botanical origin of HERBA ANCHUSAE (Niushecao, a Uyghur medicinal herb) is severely confused. Traditional identification methods and standard DNA barcodes do not work well for these close relatives. Chloroplast genomes are known to contain variable regions that can help distinguish species, yet no such study has been done for Anchusa. Therefore, We compared the complete chloroplast genomes of six Anchusa species and the main adulterants of Niushecao.

METHODS: We analyzed genome structure, repeat sequences, codon usage bias, and nucleotide diversity (Pi), as well as conducted comparative and phylogenetic analyses.

RESULTS: All genomes shared a typical ring-shaped quadripartite structure, ranged from 150,178 to 150,844 bp in size, and contained the same set of genes. Despite this overall conservation, we identified several highly variable spots, mostly located in non-coding intergenic spacer regions. Using two complementary approaches-sliding window analysis and mVISTA-based sequence visualization-we identified three overlapping regions (rbcL-psaI, petA-psbJ, and trnC-GCA-petN) as candidate DNA barcodes for species identification. Our phylogenetic tree showed that Anchusa strigosa Banks & Sol. is most closely related to the true medicinal species Anchusa azurea Mill. (Bootstrap support (BS) = 100%), while other look-alikes formed separate branches.

CONCLUSIONS: These findings provide the first chloroplast genomic resources for this genus and offer potential molecular markers for authenticating Anchusa medicinal materials, laying a foundation for future development of molecular authentication methods.},
}

*Genome, Chloroplast/genetics
Phylogeny
*Plants, Medicinal/genetics/classification
DNA Barcoding, Taxonomic

@article {pmid42783285,
year = {2026},
author = {Khan, R and Li, Z and Liao, H and Chen, H and Adam, A and Kanwal, F and Peng, L},
title = {Integrative Taxonomic Study of Chinese Anastatus (Hymenoptera: Eupelmidae) Based on Morphology and COI Barcoding, with Description of Eleven New Species.},
journal = {Insects},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/insects17090918},
pmid = {42783285},
issn = {2075-4450},
support = {32170462//National Natural Science Foundation of China/ ; 2023J01439//Natural Science Foundation of Fujian/ ; },
abstract = {Thirty-two Chinese Anastatus species (Hymenoptera: Chalcidoidea: Eupelmidae) are studied, comprising 20 previously described species and 11 new species. Ten of the new species belong to the subgenus A. (Anastatus): A. (Anastatus) nozdormusp. nov., A. (Anastatus) kryptossp. nov., A. (Anastatus) napoleonissp. nov., A. (Anastatus) yalinisp. nov., A. (Anastatus) battutaisp. nov., A. (Anastatus) beagleisp. nov., A. (Anastatus) neltharionsp. nov., A. (Anastatus) tigrinussp. nov., A. (Anastatus) huijuanaesp. nov., A. (Anastatus) ashrafisp. nov. One belongs to the subgenus A. (Cladanastatus): A. (Cladanastatus) alexstraszasp. nov. One additional species is newly recorded from China: A. (Anastatus) mantoidae Motschulsky rec. nov. A new synonymy is also proposed: A. (Anastatus) flavaeratus Peng & Tang, 2020 syn. nov. under A. (Anastatus) gastropachae Ashmead, 1904. Morphologically similar species were assigned to three informal species groups (formosanus, fulloi, and japonicus groups) based on morphology. Of the already-described species of the Chinese Anastatus, 15 were newly recorded from different provinces of China; this was true for all species except A. colemani, A. bifasciatus, A. polikiarkoudus, A. taibaiensis, and A. zdenekbouceki. Molecular analyses based on the mitochondrial cytochrome c oxidase subunit I (COI) gene were conducted on a total of 34 species (26 species derived from the specimens collected from China and eight species' sequences downloaded from the BOLD and NCBI). Multivariate morphometric analyses (PCA, LDA, MANOVA) were employed to distinguish morphologically similar species. A comprehensive diagnostic key to all Chinese Anastatus species is also provided, accompanied by photographs of diagnostic characters.},
}

@article {pmid42783296,
year = {2026},
author = {Bizhani, N and Ashfaq, M and Hebert, PDN and Prosser, S and Dupouy-Camet, J and Ali, A and Stöllner, T and Boenke, N and Naddaf, SR and Mowlavi, G},
title = {DNA Barcoding of Head Lice from a ~1500-Year-Old Salt-Preserved Mummy from the Chehrabad Salt Mine, Iran.},
journal = {Insects},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/insects17090929},
pmid = {42783296},
issn = {2075-4450},
support = {University of Guelph's "Food From Thought" research program (Project 000054)//Canada First Research Excellence Fund (CFREF)/ ; MSI 42450//Canada Foundation for Innovation/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; },
abstract = {Human lice can be classified into several mitochondrial clades with distinct geographic distributions, reflecting long-term coevolution with ancient hominids and possibly with human populations. Analysis of ancient lice DNA from archaeological human remains can provide insights into the geographic origins of these clades and the timing of their dispersal. This study analyzes the COI barcode region of lice recovered from the ~1500-year-old salt-preserved mummy (Salt Man 2) at the Chehrabad salt mine in Zanjan Province, Iran. The sequences were compared with those of recent lice from Iran and other regions, available in the GenBank database, to determine clade affiliation and possible historical relationships. Our phylogenetic analysis recovered the five recognized mitochondrial clades (A-E). Ancient lice clustered within clade A but displayed novel haplotypes. Recent nits from Gilan and Kurdistan provinces were grouped within clades A and B, the only clades reported in Iran. The most complete ancient sequence (MLICE005-18) showed close similarity to sequences from Iraq, Pakistan, Egypt, and Iran. These findings, along with future research, could help determine when ancient lice lineages were established or introduced into specific regions. They could also clarify whether they represent haplotypes that have since disappeared or a lineage that still exists in understudied human populations.},
}

@article {pmid42789432,
year = {2026},
author = {Nevendra, M and Singh, D},
title = {Protein FT-Transformer: Species Classification via Amino Acid-Encoded DNA Sequences.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2026.3737459},
pmid = {42789432},
issn = {2998-4165},
abstract = {DNA barcoding is widely used for species identification, yet many computational classifiers continue to operate directly on raw nucleotide sequences. For large and heterogeneous barcode repositories, this representation can introduce avoidable computational cost because long nucleotide strings often contain redundant codon-level information and highly uneven class distributions. This study investigates whether a biologically grounded representation can improve supervised barcode classification while reducing the effective input length. Each DNA barcode is translated codon by codon into its corresponding amino acid sequence, preserving protein-level constraints that remain informative for species discrimination. The translated sequence provides a compact and interpretable input for learning, without requiring large-scale pretraining or an additional decompression stage. On this representation, we propose Protein FT-Transformer, an amino-acid-based transformer architecture for species classification. The model employs a dual-stream feature tokenizer to combine residue-level information with broader contextual features, followed by a multi-head self-attention encoder that models dependencies across distant sequence positions. Training further incorporates class-weighted focal loss to address class imbalance, class-wise temperature scaling to improve probability calibration, and lightweight ensemble classification heads to improve prediction stability. The proposed framework is evaluated on six publicly available DNA barcode benchmarks spanning invertebrate, vertebrate, and plant taxa. Protein FT-Transformer outperforms classical machine learning classifiers and nucleotide-based deep learning baselines, achieving an average classification accuracy of 98.20% with improved F1-score and AUC values under modest computational and memory requirements. t-SNE visualizations of the learned embeddings also show more coherent species-level grouping. The results suggest that codon translation coupled with a task-specific transformer provides an effective supervised strategy for DNA barcode-based species identification.},
}

@article {pmid42790996,
year = {2026},
author = {Morrissey, KL and Atkinson, LJ and Botha, TPA and Gibbons, MJ and Baxter, J and Boonzaaier-Davids, MK and Brokensha, R and Clarke, DT and Duma, NM and Britz, K and Filander, Z and Griffiths, C and Hendricks, MGJ and Herbert, DG and Hiller, N and Janion-Scheepers, C and Jones, G and Kara, J and Karenyi, N and Landschoff, J and Leslie, RW and Lipiński, MR and MacKay, F and Mah, C and Manukuza, NM and Matcher, G and Mazeka, B and Mwale, M and Olbers, JM and Parker-Nance, S and Payne, RP and Porter, SN and Samaai, T and Schleyer, MH and Shibe, SS and Simon, CA and Thandar, A and Tshingana-Bali, B and Sink, KJ},
title = {Marine benthic invertebrate biodiversity in South Africa: Advances and gaps in taxonomic and genetic knowledge.},
journal = {Advances in marine biology},
volume = {104},
number = {},
pages = {117-230},
doi = {10.1016/bs.amb.2026.07.001},
pmid = {42790996},
issn = {2162-5875},
mesh = {Animals ; *Biodiversity ; *Invertebrates/classification/genetics ; South Africa ; *Aquatic Organisms/classification/genetics ; },
abstract = {Traditional taxonomy is the foundation of biodiversity science with modern molecular techniques and integrated approaches now essential for advancing our understanding of ocean life. Without improved knowledge of marine biodiversity, it is impossible to address the biodiversity crisis or develop the fundamental science needed to assess, plan and manage marine biodiversity and maintain its many benefits. South Africa harbours exceptional marine biodiversity and has ongoing efforts to systematically list, map, monitor, assess and conserve this national asset. This review consolidates progress in taxonomic knowledge, species lists and molecular barcoding and identifies gaps for benthos-associated invertebrates, a group receiving the least taxonomic attention in the country. Building on previous efforts that revealed major capacity and knowledge gaps, this review updates the state of knowledge, providing a new and accessible baseline and evaluates progress over the past 27 years to guide the next phase of marine invertebrate biodiversity research. Taxonomic advances across 11 major phyla are presented, nine of which have received some level of dedicated revision at phylum, class or family level. Although the taxonomic crisis persists and progress is variable across groups, there has been an appreciable increase in species discovery over the last two decades with more than a thousand invertebrate species added to national lists. Key challenges that hamper efforts and enabling factors supporting progress are identified, with recommendations to consolidate and increase knowledge and capacity, accelerate marine biodiversity discovery and mapping, and address key gaps in our understanding of South Africa's marine invertebrate fauna.},
}

Animals
*Biodiversity
*Invertebrates/classification/genetics
South Africa
*Aquatic Organisms/classification/genetics

@article {pmid42791216,
year = {2026},
author = {Selvakumar, H and Koderi Valappil, S and Piya, D and Mutalik, VK},
title = {Scaling Phage-Bacteria Interaction Contexts: From Pairwise Mechanisms to Community Dynamics.},
journal = {Annual review of virology},
volume = {13},
number = {1},
pages = {223-248},
doi = {10.1146/annurev-virology-100424-123645},
pmid = {42791216},
issn = {2327-0578},
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; Host-Pathogen Interactions ; DNA Barcoding, Taxonomic ; Microbiota ; Genome, Viral ; Host Specificity ; },
abstract = {Bacteriophages (phages), viruses that parasitize bacteria, hold tremendous potential as antimicrobial agents, microbiome modulators, and industrial biocontrol tools; yet clinical and environmental applications remain frustratingly inconsistent. Decades of research on isolated phage-bacteria pairs have revealed fundamental mechanisms governing infection specificity, coevolutionary arms races, and resistance trade-offs. These foundational studies, however, do not help predict outcomes when phages encounter multi-species assemblages characteristic of natural ecosystems. In this review, we integrate recent advances examining how interaction complexity shapes phage efficacy across four scales, gradually from simple phage-bacteria pairs to phage-bacterial communities. At every scale, emergent properties arise from complex interactions. Dissecting these dynamics requires technologies that can track multiple lineages simultaneously. DNA barcoding, which inserts unique genetic identifiers into bacterial and phage genomes, offers a promising solution. While barcoding all members in a synthetic community is unrealistic, we propose that even foundational reference sets of barcoded phage-bacteria pairs would enable systematic investigation of resistance evolution, competitive interactions, and functional outcomes in realistic contexts. Bridging laboratory insights and field performance demands integrating genetic engineering, high-throughput tracking, functional profiling, and predictive modeling into a coordinated research framework.},
}

*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
Host-Pathogen Interactions
DNA Barcoding, Taxonomic
Microbiota
Genome, Viral
Host Specificity

@article {pmid42791355,
year = {2026},
author = {Piscopio, RA and Chialastri, A and Wang, C and Godzik, M and Heom, KA and Wang, W and Li, LJ and Saxena, N and Wilson, MZ and Dey, SS},
title = {Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42791355},
issn = {1546-1696},
support = {R01HD099517//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HG011013//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; 2339849//National Science Foundation (NSF)/ ; },
abstract = {We introduce scSTAMP-seq (single-cell spatial transcriptomic and multiomic profiling), a modular light-encoded barcoding strategy that preserves spatial information while leveraging standard single-cell platforms. scSTAMP-seq labels live and fixed cells with cholesterol-conjugated, photocleavable hashtag oligonucleotides, followed by patterned light exposure that 'stamps' spatial coordinates onto individual cells before single-cell multiome sequencing. Here we apply scSTAMP-seq to human embryoids showing how spatial organization and epigenetic states coregulate cellular programs in heterogeneous biological systems.},
}

@article {pmid42781795,
year = {2026},
author = {Bonsignore, CP and Nugnes, F and Pezzi, M and Bonacci, T and Bernardo, U},
title = {Sex ratio and mating behaviour of Anisandrus dispar (Fabricius) (Coleoptera: Curculionidae: Scolytinae) in hybrid chestnut orchards.},
journal = {Bulletin of entomological research},
volume = {},
number = {},
pages = {1-9},
doi = {10.1017/S0007485326101370},
pmid = {42781795},
issn = {1475-2670},
abstract = {Anisandrus dispar is an economically important ambrosia beetle associated with damage in hybrid chestnut orchards in southern Italy. This study investigated the haplotype diversity, infestation patterns, seasonal emergence, sex ratio, and mating behaviour of A. dispar populations in three hybrid chestnut orchards in Calabria. Branches were sampled monthly (April-June) and during winter. Ten females were used for cytochrome c oxidase subunit I barcoding and haplotype analyses. Gallery traits, emergence patterns, sex ratios, and mating behaviour of overwintering males were assessed under laboratory conditions. Molecular analyses revealed six European haplotypes with none shared among orchards or invasive. A total of 708 adults emerged from rearing cages, 111 adults were recovered by branch dissection, 97 adults emerged from winter-collected branches, and 64 were identified through winter dissections. Adult emergence from reared branches was recorded from May to mid-December, with the highest numbers observed in early June, and showed a pronounced female bias, with male-to-female ratios of 0.23:1 in emergence cages and 0.37:1 in dissected woody tissues. This skewed sex ratio persisted in branches collected during winter, while gallery spacing decreased as branch diameter increased. The number of exit holes, averaging 3.31 per branch, was positively correlated with branch diameter. Overwintering males successfully copulated under laboratory conditions. The high infestation levels and associated tree mortality indicate that A. dispar is well established in these orchards and may require host-specific monitoring and management in chestnut agroecosystems.},
}

@article {pmid42782080,
year = {2026},
author = {Ackiss, AS and Vinson, MR and Ropp, AJ and Gruenthal, KM and Krabbenhoft, TJ and Siegel, JV and Stott, W and Yule, DL and Larson, WA},
title = {A Genomic Tool to Tackle Cryptic Diversity Demonstrates the Potential for Off-Target Use of GT-Seq Panels.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70203},
pmid = {42782080},
issn = {1755-0998},
support = {//U.S. Environmental Protection Agency/ ; },
mesh = {Animals ; *Salmonidae/genetics/classification ; *Genotyping Techniques/methods ; Polymorphism, Single Nucleotide ; *Genomics/methods ; *Genetic Variation ; Sequence Analysis, DNA/methods ; Lakes ; },
abstract = {A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the Coregonus artedi complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the C. artedi complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish (C. clupeaformis) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish (Prosopium spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for Prosopium-specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3066 coregonine larvae and juveniles collected in spring 2019-2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.},
}

Animals
*Salmonidae/genetics/classification
*Genotyping Techniques/methods
Polymorphism, Single Nucleotide
*Genomics/methods
*Genetic Variation
Sequence Analysis, DNA/methods
Lakes

@article {pmid42783282,
year = {2026},
author = {Lashkari, M and Serbina, LŠ},
title = {On the Identity of Pear Psyllids in Iran: A Plea Against the Continued Misuse of Cacopsylla pyricola (Hemiptera: Psylloidea).},
journal = {Insects},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/insects17090915},
pmid = {42783282},
issn = {2075-4450},
support = {03.3359//Graduate University of Advanced Technology/ ; },
abstract = {Pear psyllids are among the most serious pests of cultivated pear. In the past, repeated misidentifications and the uncritical application of species names led to considerable confusion in biodiversity records and pest monitoring of pear psyllids. Although several revisions clarified many of these issues, misidentifications have persisted, particularly in records attributed to Cacopsylla pyricola (Foerster) in Iran, which may result in serious problems in quarantine and pest management. Currently, 34 species of Cacopsylla are known to be associated with Pyrus spp., five of which are confirmed to occur in Iran, while the occurrence of C. pyricola in the country remains likely but unconfirmed. In this study, we demonstrate that the examined Cacopsylla species differ significantly in their COI barcodes, which can be reliably used for species identification. The COI sequences for C. permixta are published here for the first time. Our results suggest that the GenBank and literature records of C. pyricola from Iran likely represent misidentifications of other species that occur throughout the pear-producing regions of Iran. These misidentifications likely resulted from the application of species names without adequate morphological or molecular confirmation. Our findings highlight the need for careful validation of species records and demonstrate that GenBank sequences should be used cautiously unless they are linked to reliably identified voucher specimens.},
}

@article {pmid42762496,
year = {2026},
author = {Lee, M and Kim, H and Oh, J and Kanturski, M and Lee, SK and Lee, S},
title = {Life Cycle and Mass Occurrence of Paracolopha morrisoni (Hemiptera: Aphididae) in South Korea.},
journal = {Archives of insect biochemistry and physiology},
volume = {123},
number = {1},
pages = {e70216},
doi = {10.1002/arch.70216},
pmid = {42762496},
issn = {1520-6327},
mesh = {Animals ; *Aphids/growth & development/physiology/genetics ; Republic of Korea ; Seasons ; Mites/physiology ; *Life Cycle Stages ; Poaceae/parasitology ; DNA Barcoding, Taxonomic ; Nymph/growth & development/physiology ; Larva/growth & development/physiology ; },
abstract = {Paracolopha morrisoni (Baker, 1919) (Aphididae: Eriosomatinae) is a gall-forming aphid that alternates between Zelkova serrata (Thunb.) Makino (Ulmaceae) and bamboo hosts in East Asia. Here, we provide field-based documentation of its seasonal biology and host alternation in South Korea, supported by DNA barcoding. Subterranean colonies on the roots of Pseudosasa japonica (Siebold & Zucc. ex Steud.) Makino ex Nakai (Poaceae), together with observations of migratory alates and larviposition, confirmed this bamboo as a secondary host. Phyllostachys heterocycla (Carrière) Matsum. (Poaceae) was identified as a potential secondary host based on settlement and larviposition by migratory alates, although subterranean colony establishment remains unconfirmed. We also documented the predatory mite Anystis baccarum (Linnaeus, 1758) (Anystidae) in association with P. morrisoni and a conspicuous mass occurrence of returning alates in a recreational environment during late autumn. These observations expand current knowledge of the field biology of P. morrisoni and provide ecological information useful for recognizing its seasonal stages and host associations in South Korea.},
}

Animals
*Aphids/growth & development/physiology/genetics
Republic of Korea
Seasons
Mites/physiology
*Life Cycle Stages
Poaceae/parasitology
DNA Barcoding, Taxonomic
Nymph/growth & development/physiology
Larva/growth & development/physiology

@article {pmid42764010,
year = {2026},
author = {Shao, F and Hu, J and Traylor, A and Lei, H and Zhang, P and Akarapipad, P and Park, JS and Hsieh, K and Wang, TH},
title = {CRISPR-AMPED: A CRISPR/Cas-based immunoassay with attomolar sensitivity enabled by magnetic proximity extension and detection.},
journal = {Biosensors & bioelectronics},
volume = {315},
number = {},
pages = {119227},
doi = {10.1016/j.bios.2026.119227},
pmid = {42764010},
issn = {1873-4235},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-associated systems have emerged as powerful tools for next-generation molecular diagnostics, particularly for nucleic acid detection. However, ultrasensitive protein detection is equally critical across diverse applications in biology and medicine, especially for diagnosing and prognosing diseases such as cancer, traumatic brain injury (TBI), Alzheimer's disease, and cardiovascular diseases. Despite recent efforts to adapt CRISPR/Cas systems for protein detection, these methods have typically achieved sensitivity in the femtomolar to picomolar range, underscoring the need for enhanced detection capabilities. Here, we developed CRISPR-AMPED, a CRISPR/Cas-based immunoassay enhanced by magnetic proximity extension and detection. This approach combines proximity extension assay (PEA) with magnetic beads to convert protein targets into DNA barcodes while enabling effective washing to reduce background noise. The resulting DNA barcodes are detected through recombinase polymerase amplification (RPA) coupled with CRISPR/Cas12a, eliminating thermocycling and providing simultaneous target and signal amplification. CRISPR-AMPED achieves attomolar-level sensitivity, surpassing ELISA by over three orders of magnitude and outperforming existing immunoassays and CRISPR/Cas-based protein detection systems. As an initial demonstration of clinical utility, we applied CRISPR-AMPED to detect the inflammatory biomarker interleukin-8 (IL-8) in serum samples from patients with TBI and healthy controls. Further integration with a smartphone-based detection device demonstrates its potential for portable testing, while the digital format extends the dynamic range and enhances quantitation precision. Together, these results establish CRISPR-AMPED as a sensitive protein detection approach using IL-8 as an initial model target and provide a framework for future adaptation to additional protein biomarkers.},
}

@article {pmid42765363,
year = {2026},
author = {Farooq, M and Luong, V and Galico, DA},
title = {Composition-tuned lanthanide molecular cluster aggregates for solid-state time-gated logic and security materials.},
journal = {Materials horizons},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6mh01452f},
pmid = {42765363},
issn = {2051-6355},
abstract = {Traditional optical anti-counterfeiting tags and molecular computers are severely hindered by replication vulnerability, complex multi-wavelength and varying temperature inputs, and slow, diffusion-limited solution kinetics. We report an active, solid-state anti-counterfeiting material using hourglass-shaped {Ln9}
lanthanide molecular cluster-aggregates (MCAs) operating under a single excitation wavelength and temperature. By systematically tuning the stoichiometry of bimetallic {Tb9-xEux}
metal cores, we demonstrate a proof-of-concept on how to program internal energy transfer (ET) pathways to dictate digital workflows exclusively within the time domain using MCAs. This deterministic kinetic control enables the design of temporal barcodes and the realization of a versatile suite of logic circuits (YES, NOT, AND, and INHIBIT) driven by non-invasive electronic detection gating. Operating within a rigid crystalline network, these systems, exhibit stability over at least 15 runs. This kinetic programming strategy bridges synthetic coordination chemistry and molecular optoelectronics, establishing compositional design strategies for ET kinetics towards multi-dimensional optical information encryption.},
}

@article {pmid42767804,
year = {2026},
author = {Yu, X and Wang, Z and Zhang, Z and Wang, Y and Lin, Y and Hong, L and Chen, X and He, X and Yang, JR and Zhang, J},
title = {Decoding cell division history and lineage-resolved phenotypic patterns from single-cell barcode and transcriptomic data.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.281734.125},
pmid = {42767804},
issn = {1549-5469},
abstract = {The cell division tree encodes how proliferation and differentiation generate cellular diversity during multicellular development. Advances in single-cell RNA sequencing and CRISPR-based lineage tracing have enabled retrospective reconstruction of these histories at single-cell resolution. Here, we present FateScape, a statistical framework that integrates paired lineage barcodes and transcriptomic profiles to infer cell division topology and characterize depth-resolved phenotypic patterns. FateScape combines barcode consistency with transcriptome-derived state continuity through overlapping state-lineage decomposition and barcode-guided subtree integration. To analyze phenotypic patterns on the inferred tree, we introduce entropy paths, which measure how cells of each state are distributed across depth-defined subtrees, and Moran's I-derived statistics for same-state autocorrelation and cross-state association. In simulations, FateScape shows robust reconstruction performance across varying mutation rates, dropout levels, sample sizes, and barcode target-site numbers. In the Caenorhabditis elegans data analysis, FateScape accurately recovers lineage topology and identifies depth-resolved state patterns, including concentrated intestinal cells and broadly distributed neuronal and glial states. In mouse embryos, FateScape quantifies distinct germ-layer patterns, including early endodermal concentration, broad ectodermal distribution across shallow-to-intermediate depths, and intermediate mesodermal distribution followed by deeper concentration. Together, FateScape provides a framework for reconstructing cell division histories and quantifying state dispersion, concentration, and tree-based association across lineage depth.},
}

@article {pmid42770504,
year = {2026},
author = {Peng, R and Dong, Y and Wang, Y and Hou, K and Zhao, Z and Wang, Y and Liu, P and Hu, L and Zhao, Y},
title = {Systematic evaluation of rDNA ITS2 as a DNA barcode for molecular identification of cyclorrhapha flies in China.},
journal = {Genome},
volume = {69},
number = {},
pages = {1-15},
doi = {10.1139/gen-2026-0070},
pmid = {42770504},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; China ; Phylogeny ; *DNA, Ribosomal Spacer/genetics ; *Diptera/genetics/classification ; *Calliphoridae/genetics/classification ; Sarcophagidae/genetics/classification ; Muscidae/genetics/classification ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Morphological identification of medically important flies is often hindered by incomplete or damaged specimens, cryptic species, and morphological conservatism among closely related species. In this study, common fly species were collected from 15 cities across 10 provinces in China to evaluate rDNA internal transcribed spacer 2 (ITS2) as a potential DNA barcode for molecular identification. A total of 1252 fly specimens were collected, of which 933 were morphologically classified into 19 species, 15 genera, 9 families, and 3 superfamilies; 319 remained unidentified due to the loss of key morphological characters. Seventeen mitochondrial and ribosomal candidates were evaluated using sequences retrieved from GenBank across Cyclorrhapha. ITS2 was selected based on its relatively low intraspecific divergence, higher interspecific divergence, and conserved flanking regions suitable for universal primer design. The designed ITS2 primers successfully amplified and sequenced all 144 tested specimens, including morphologically damaged samples. Integrating morphological and molecular data, 27 fly species were identified. Barcode gap analyses indicated clear interspecific discrimination in the genera of Muscidae, Calliphoridae, and Sarcophagidae. Phylogenetic analyses further supported species-level identification and revealed ITS2 sequence diversity within Musca domestica specimens. These results demonstrate that ITS2 is a promising candidate DNA barcode for Cyclorrhapha flies, particularly for specimens with ambiguous or damaged morphology.},
}

Animals
*DNA Barcoding, Taxonomic/methods
China
Phylogeny
*DNA, Ribosomal Spacer/genetics
*Diptera/genetics/classification
*Calliphoridae/genetics/classification
Sarcophagidae/genetics/classification
Muscidae/genetics/classification
Sequence Analysis, DNA
Species Specificity

@article {pmid42779630,
year = {2026},
author = {Gomez-Cano, F and Jiang, L and Welch, JD and Marand, AP},
title = {Empirical Estimation of Ambient Contamination in Combinatorial Single-Cell Methods Using Multi-Reference Mapping.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.11.750809},
pmid = {42779630},
issn = {2692-8205},
abstract = {Droplet-based microfluidics and combinatorial indexing (scifi-ATAC and scifi-RNA) have made single-cell experiments massively scalable. However, higher-order multiplexing complicates data quality, introduces noise, and affects the potential for biological discovery. Here, we show that ambient chromatin accumulates through the experimental workflow and distorts chromatin profiles, most drastically in low-depth nuclei and in minority populations. Standard cell calling relies heavily on read count thresholds, while existing decontamination methods generally operate on aggregated count matrices rather than the underlying reads. We introduce scifi-demux, for preprocessing scifi-ATAC libraries, and AmbientMapper, a generative model that maps reads competitively against multiple references, learns the ambient profile from empty and low-complexity barcodes, and separates nuclei from background and singlets from doublets by Bayesian Information Criterion. Using interspecies ground truth experiments, published multi-genotype libraries, and simulated read-level synthetic barcodes in which every contaminating read is traceable, we show that calls are robust to parameter variation and stable across designs, achieving a wrong-genome rate of 0.19% on a 26-genome reference panel. Finally, we evaluated the impact of removing contaminants, showcasing how AmbientMapper rescues low-depth nuclei discarded by standard pipelines and restores biological structure obscured by contamination.},
}

@article {pmid42779810,
year = {2026},
author = {Du, P and Kohno, S and Wang, M and Papanicolaou, M and Vaughan-Jackson, A and Daigh, L and Peng, Q and Spees, K and McCormick, A and Diehl, M and Bintu, L and Qiu, X and Satpathy, A and Bassik, M},
title = {In vivo intercellular CRISPR screens using viral proximity barcoding reveal regulators of tumor-immune interactions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.16.752238},
pmid = {42779810},
issn = {2692-8205},
abstract = {Cell-cell interactions shape tumor growth, immune evasion, and therapeutic response, but systematically dissecting their genetic regulators in vivo remains challenging. Existing cell-cell interaction tracing technologies rely largely on protein labels or enzymatic reactions, limiting their information content and scalability. To overcome these limitations, we developed match-seq, an imaging-free, sequencing-based cell proximity tracing system that uses virus-like particles to transmit barcodes between neighboring cells. Barcoded mRNAs are transmitted from sender cells to nearby receiver cells, thereby establishing a spatial linkage that can be computationally reconstructed by barcode sequencing after tissue dissociation. We apply this system to an in vivo syngeneic murine tumor model, where we observe robust labeling of all immune cell lineages, and leverage barcode labeling to reconstruct cell type niches that recapitulate known tumor spatial biology. Furthermore, we couple this system with CRISPR perturbations and single-cell RNA sequencing to perform genetic screens in vivo on tumor-immune interactions at single-cell resolution. We use this method to infer cell-cell spatial relationships and uncover genetic dependencies in cancer cells that change the composition and cell state of their local microenvironments. By calculating a local immune activation signature, we are able to prioritize targets whose deletion enhances anti-tumor immunity through distinct effector cell types: loss of Tgfb1 engages CD8 T cells and macrophages, Traf7 loss elicits a CD4 T cell response, and Nectin3 loss promotes NK cell-mediated immunity, relationships that we validate by in vivo immune cell depletion. Notably, Tgfb1 and Nectin3 deletion had little effect on cancer cell fitness in the pooled screen yet suppressed tumor growth when deleted throughout the tumor, demonstrating the potential of match-seq to reveal functionally important tumor-immune interactions that would otherwise remain hidden. Together, these results establish a general framework for pooled genetic dissection of cell-cell interactions in vivo, extending CRISPR screening from cell-intrinsic phenotypes to the mechanisms by which cells shape and respond to their local microenvironments.},
}

@article {pmid42780503,
year = {2026},
author = {Lee, S and Lee, M and Kim, W},
title = {First South Korean Record of Beetle Suborder Myxophaga Extends Its Documented Range in Continental East Asia.},
journal = {Ecology and evolution},
volume = {16},
number = {9},
pages = {e74411},
doi = {10.1002/ece3.74411},
pmid = {42780503},
issn = {2045-7758},
abstract = {Myxophaga is a minute beetle suborder that is easily overlooked because of its small body size and specialization on wet microhabitats. Here, we report Sphaerius from two riparian localities in South Korea, representing the first record of Myxophaga from the Korean Peninsula. This discovery also represents the northeasternmost known record of Myxophaga from continental East Asia, distinct from previous island records in Japan and Taiwan. Specimens were collected from saturated riparian substrates near the active waterline. Scanning electron microscopy confirmed characters consistent with Sphaerius, and the Korean COI barcode sequences were distinct from all other available Sphaerius sequences, although their position within the genus remained unresolved. Because records of East Asian Sphaerius remain taxonomically undetermined, we identify the Korean material as Sphaerius sp. This record expands the known continental distribution of Myxophaga in East Asia and highlights the value of targeted surveys in riparian microhabitats.},
}

@article {pmid42761484,
year = {2026},
author = {Kajimoto, A and Tanaka, A and Ohira, T and Toyota, K},
title = {Seasonal Dynamics of Sex Ratio, Reproduction, and Parasite-specific Feminization in the Hermit Crab Pagurus filholi at a Fixed Coastal Site in Chiba, Japan.},
journal = {Zoological studies},
volume = {65},
number = {},
pages = {e36},
pmid = {42761484},
issn = {1810-522X},
abstract = {Reproductive output in intertidal crustaceans is reshaped by seasonal changes in host demography and its interaction with parasitic castration, yet parasite-species-resolved time series remain scarce for hermit crabs. We conducted year-round monitoring of the hermit crab Pagurus filholi at a fixed intertidal site in Chiba Prefecture, Japan, with monthly sampling from January to December 2025. Hosts were sexed and female reproductive status (ovigerous vs. non-ovigerous) was recorded, and rhizocephalan infections were diagnosed by externa morphology and subsequently assigned to Peltogasterella gracilis or Peltogaster postica using DNA barcoding. Across 12 sampling occasions, 3,134 crabs were recorded (1,586 males; 1,548 females). Sex ratio varied significantly among months, shifting from female-biased in December (early winter)-May (late spring) to strongly male-biased in June (early summer)-November (late autumn). The proportion of ovigerous females also showed strong seasonality, peaking in mid-winter, declining through spring, reaching zero in August-September, and increasing again toward winter. Both parasites exhibited sharply seasonal prevalence with a pronounced June peak: for Peltogasterella gracilis, 29/166 in June vs. 8/2,968 in other months, and for Peltogaster postica, 19/166 vs. 36/2,968. Male secondary sexual morphology responded in a parasite-specific manner: infected males were more likely to bear a second pleopod, a female-specific egg-brooding structure, than males without externae, driven primarily by Peltogasterella gracilis (26/28) rather than Peltogaster postica (3/35). Together, these results provide a high-resolution baseline linking reproductive phenology and parasite-specific feminization in a single P. filholi population.},
}

@article {pmid42758132,
year = {2026},
author = {Chan-Chable, RJ and Rodríguez-Luna, CR and Espinal-Palomino, R and Arana Guardia, R and Suzán, G and Ávila-Cabadilla, LD and Álvarez-Añorve, MY and Montes de Oca-Aguilar, AC and Ortega-Morales, AI and Ibarra-Cerdeña, CN},
title = {Geographic distribution and environmental associations of Psorophora mexicana (Diptera: Culicidae) in the Yucatan Peninsula, Mexico.},
journal = {Journal of medical entomology},
volume = {63},
number = {5},
pages = {},
doi = {10.1093/jme/tjag143},
pmid = {42758132},
issn = {1938-2928},
mesh = {Animals ; Mexico ; *Animal Distribution ; *Culicidae/physiology/genetics/classification ; Phylogeny ; Electron Transport Complex IV/analysis ; *Ecosystem ; Environment ; DNA Barcoding, Taxonomic ; },
abstract = {Psorophora mexicana (Bellardi) is a rare mosquito species with limited information on its taxonomy, geographic distribution, and ecological preferences. In Mexico, presence records are scarce and largely outdated, particularly in the Yucatan Peninsula. Here, we document the current distribution of Ps. mexicana based on collections conducted between 2017 and 2025 across 14 localities in Campeche, Quintana Roo, and Yucatan states, including the first confirmed record for Quintana Roo. Specimens were identified morphologically and genetically using the mitochondrial region cytochrome c oxidase I DNA barcoding. Generated sequences, representing the first records for Ps. mexicana in NCBI and BOLD Systems, and a phylogeny including 19 species of Psorophora was generated using a Bayesian phylogenetic framework. Environmental variables were explored using principal component analysis, revealing that Ps. mexicana currently occupies a broad spectrum of environmental conditions spanning multiple land-use types and gradients of habitat integrity. These results contrast clearly with previous Mexican records for this species, which have consistently characterized its distribution as restricted to anthropogenically disturbed habitats, predominantly urban environments, particularly in proximity to coastal regions. Our findings expand the known distribution of Ps. mexicana in southeastern Mexico and provide updated ecological and molecular insights into a poorly known species, highlighting its potential for increased human-mosquito contact in suitable environments.},
}

Animals
Mexico
*Animal Distribution
*Culicidae/physiology/genetics/classification
Phylogeny
Electron Transport Complex IV/analysis
*Ecosystem
Environment
DNA Barcoding, Taxonomic

@article {pmid42760298,
year = {2026},
author = {Tian, D and Zheng, X and Yu, Z and Wang, D and Chen, W and Liu, Y and Liu, Z and Xia, B and Jin, X and Yan, H and Wu, Y and Zhao, Y and Zhang, C and Pu, Q and Chen, J and Sato, M and Liu, L},
title = {An integrated multiomic single-vesicle atlas delineates graft exosome heterogeneity in chronic lung allograft dysfunction.},
journal = {Signal transduction and targeted therapy},
volume = {11},
number = {1},
pages = {},
pmid = {42760298},
issn = {2059-3635},
mesh = {Animals ; *Lung Transplantation/adverse effects ; Rats ; *Exosomes/genetics/metabolism/pathology ; Allografts/pathology/metabolism ; *Lung/pathology/metabolism ; Humans ; Multiomics ; Proteomics ; *Graft Rejection/genetics/pathology/metabolism ; Male ; },
abstract = {The underlying mechanisms of exosomes in chronic lung allograft dysfunction (CLAD) remain poorly understood. The primary challenge lies in the substantial functional heterogeneity of exosomes in CLAD. In this study, lung transplantation was initially performed, followed by the generation of a chronic rejection (CR) model in rats to simulate CLAD in humans. Exosomes from lung graft tissues were extracted, purified, and subjected to proximity barcoding assay-based single-vesicle membrane proteomic profiling. Additionally, bulk proteomic and metabolomic profiling of the graft tissues was conducted. Exosomes were categorized into 14 clusters. Compared with the syngeneic group, the CR group had significantly lower levels of clusters 7 (Nphs1[high]), 13 (Aqp1[high]), and 14 (Csf3r[high]), and higher levels of clusters 2 (Lrp2[high] Mrc1[high]) and 4 (Nt5e[high]). The abundance of cluster 12 (Ilk[high]) exosomes was strongly correlated with pleural thickness (r = -0.90, P < 0.001). Cluster 12 exosomes exhibited the greatest number of related differentially expressed proteins and metabolites. The proteins correlated with cluster 12 were enriched in the "complement and coagulation cascades", whereas the metabolites were enriched in the "glycerophospholipid metabolism". Further verification in patients with restrictive allograft syndrome revealed the same decrease in abundance of cluster 12 exosomes as that observed in the rat model. Finally, the core molecular network of cluster 12 that contributes to pleural thickening in CLAD was constructed. In this study, the heterogeneous composition of exosomes in lung grafts was mapped to expand the understanding of their effects and to drive their application in CLAD.},
}

Animals
*Lung Transplantation/adverse effects
Rats
*Exosomes/genetics/metabolism/pathology
Allografts/pathology/metabolism
*Lung/pathology/metabolism
Humans
Multiomics
Proteomics
*Graft Rejection/genetics/pathology/metabolism
Male

@article {pmid42756017,
year = {2026},
author = {Lv, T and Zhang, Y and Guo, L and Hu, X and Ju, J and Tang, N},
title = {Comparative genomics, phylogenomic reconstruction and divergence time analysis of 32 Delphinium species based on complete chloroplast genomes.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1925719},
pmid = {42756017},
issn = {1664-462X},
abstract = {Delphinium, characterized by distinctive spurred flowers, comprises numerous high-altitude endemic species with significant ornamental and medicinal value. However, the intrageneric phylogenetic relationships and evolutionary history of Delphinium have remained poorly resolved, primarily due to the limited variability of traditional DNA markers and complex morphological homoplasy. In this study, complete chloroplast genomes of three Delphinium spp. were sequenced and combined with those of 29 Delphinium spp. publicly available plastomes to conduct a comprehensive phylogenomic analysis and divergence time estimation. The Delphinium plastomes exhibited a highly conserved quadripartite structure, with genome sizes ranging from 153,769 to 157,339 bp. Comparative genomic analyses revealed 2,426 SSRs, and although narrow variable windows (π > 0.02) were detected within or adjacent to five loci (ndhA-ndhH, ycf2, trnG-trnfM-rps14, rrn23, trnI), their overall sequences remained highly conserved at the species level. Given their moderate overall divergence and reduced substitution saturation, these five loci are suitable for higher-level phylogeny, whereas conventional DNA barcodes and SSC-derived regions remain more effective for species-level discrimination. Phylogenomic reconstruction based on whole plastomes robustly supported the monophyly of Delphinium and resolved six well-supported primary clades, outperforming concatenated protein-coding genes in topological resolution. Furthermore, divergence time estimation revealed that the Delphinium crown group originated in the early Eocene (ca. 53.23 Ma; 95% HPD: 51.68-54.77 Ma). An initial major lineage divergence occurred during the Oligocene (ca. 28.53 Ma) driven by global cooling, followed by exPLoSive diversification during the Pliocene and Pleistocene (e.g., rapid radiation of core clades at 3.47 Ma). This recent rapid radiation was likely triggered by the intense uplift of the Qinghai-Tibet Plateau and recurrent Northern Hemisphere glaciations. Collectively, our study provides new insights into the plastome evolution and phylogeny of Delphinium, offering a robust evolutionary framework for understanding its diversification and facilitating future population genetic analyses.},
}

@article {pmid42751001,
year = {2026},
author = {Sabroux, R},
title = {The Sea Spider Genus Hannonia Hoek, 1881 (Pycnogonida): A Review and Two New Species.},
journal = {Zoological studies},
volume = {65},
number = {},
pages = {e31},
pmid = {42751001},
issn = {1810-522X},
abstract = {Hannonia is a particularly rare and poorly studied genus, which includes four species distributed along the shores of Africa and Europe. Here, two new species are described from the southern shores of Madagascar, Hannonia arnaudae sp. nov. and Hannonia laurae sp. nov. sampled during the ATIMO VATAE expedition (Muséum national d'Histoire Naturelle survey, 2010). DNA barcoding data were successfully obtained for the holotype of H. arnaudae sp. nov. Besides, additional material sampled by Bernard Thomassin at Nosy-Vé and Tuléar in July 1972 are reported: these specimens present strong affinities to the newly described H. arnaudae sp. nov., but consistently exhibit slight morphological deviations from the holotype description. In absence of DNA barcoding data for this material, it was not possible to estimate whether these variations were significant, preventing their formal identification to the species level. A checklist and a new identification key for the genus are also provided, together with additional morphological information for Hannonia stocki Munilla, 1993.All Hannonia species except Hannonia typica Hoek, 1881 were sampled in only one locality, making their geographic and bathymetric distribution range unpredictable. The genus is potentially present on the western shores of the African continent, highlighting the need for further investigation in these regions where sea spiders are rarely surveyed. The affinities of Hannonia with the 11 currently accepted pycnogonid families need to be investigated through phylogenetic studies to be properly understood. Morphological comparisons suggest possible affinities between this genus and two other Southern Africa pycnogonid genera of uncertain taxonomic placement, Boehmia, and Queubus, highlighting further the importance of integrating African pycnogonids to future research on sea spider diversity and evolution.},
}

@article {pmid42754580,
year = {2026},
author = {Qian, J and Milles, LF and Wicky, BIM and Ragotte, RJ and Motmaen, A and Borst, AJ and Skotheim, R and Ols, S and Coventry, B and Li, X and Kibler, RD and Goreshnik, I and Expòsit, M and Loré, K and Stewart, L and Baker, D},
title = {Accelerating protein design by scaling experimental characterization.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42754580},
issn = {2041-1723},
mesh = {*Protein Engineering/methods ; Respiratory Syncytial Viruses/drug effects ; *Proteins/chemistry/genetics ; Reproducibility of Results ; },
abstract = {Recent advances in de novo protein design have greatly outpaced standard protein biochemistry workflows, making experimental validation a bottleneck. Here, we describe workflows to address the scale, speed and reproducibility of common in vitro protein testing methods, enabling at least an order of magnitude increase in throughput while reducing wetlab time. Semi-Automated Protein Production (SAPP) is a rapid, modular, scalable and cost-effective protocol, enabling up to milligram-scale protein production and standardized characterization - including yield, dispersity, and oligomeric state - of hundreds of designs per day, at the cost-equivalent of a few DNA oligos per construct. End-to-end protocol execution takes 48 hours, with ~6 hours spent benchside using standard laboratory equipment. We showcase the platform by rapidly screening redesigned fluorescent proteins, as well as identifying de novo binders that potently neutralize respiratory syncytial virus. We also developed a barcoding and demultiplexing protocol (DMX) to further reduce gene synthesis cost 5-fold by leveraging oligo pools as input DNA for the generation of thousands of sequence-verified arrayed clones. These protocols which combine optimized molecular biology, automated analysis, and optional open-source robotics should be widely adoptable, accelerating protein design.},
}

*Protein Engineering/methods
Respiratory Syncytial Viruses/drug effects
*Proteins/chemistry/genetics
Reproducibility of Results

@article {pmid42755224,
year = {2026},
author = {Onda, Y and Ochi, Y and Araki, T and Kageoka-Takahashi, M and Takeda, S and Yamada, K and Ueda, T and Ohno, K and Tanaka, M and Sakai, D and Hasegawa, M and Tanaka, Y},
title = {PhenoDEL: A Novel Screening Strategy Based on Intracellular Protein Degradation Activity.},
journal = {ACS chemical biology},
volume = {21},
number = {9},
pages = {2157-2168},
doi = {10.1021/acschembio.6c00234},
pmid = {42755224},
issn = {1554-8937},
mesh = {Humans ; *Proteolysis/drug effects ; Proteolysis Targeting Chimera ; *Single-Cell Analysis/methods ; *Small Molecule Libraries/pharmacology/chemistry ; Cell Line, Tumor ; DNA ; Gene Library ; Green Fluorescent Proteins/metabolism ; },
abstract = {Targeted protein degradation (TPD), including proteolysis targeting chimeras (PROTACs) and molecular glue degraders (MGDs), is a promising therapeutic approach. However, systematic discovery of such small molecules remains a major challenge. Here, we present PhenoDEL, a novel phenotypic DNA-encoded library (DEL) screening platform that integrates one-bead one-compound DEL (OBOC-DEL) with the Beacon optofluidic system for single-cell analysis. By coculturing individual OBOC-DEL beads and engineered reporter cells in nanoliter-scale chambers, PhenoDEL enables time-resolved, single-cell phenotypic evaluation and direct linkage between compound identity and intracellular response. As a proof-of-concept, we demonstrate discrimination of active and inactive on-bead compounds using an FKBP12F36V-EGFP degradation reporter in PC-3 cells, followed by DNA barcode decoding.},
}

Humans
*Proteolysis/drug effects
Proteolysis Targeting Chimera
*Single-Cell Analysis/methods
*Small Molecule Libraries/pharmacology/chemistry
Cell Line, Tumor
DNA
Gene Library
Green Fluorescent Proteins/metabolism

@article {pmid42742070,
year = {2026},
author = {Li, R and Pal Singh, M and Yang, X and Fang, Z and Ju, Q and Liao, J and Chen, X},
title = {Scalable synthesis of core-shell MOF single crystals with spatially segregated multicolour luminescence for optical encoding.},
journal = {Dalton transactions (Cambridge, England : 2003)},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6dt01583b},
pmid = {42742070},
issn = {1477-9234},
abstract = {The development of millimetre-scale optically resolvable tags that combine information density with mass-producible uniformity is crucial for advanced anti-counterfeiting and colour barcoding. Despite the excellent luminescence tunability of metal-organic framework (MOF) materials, the scalable fabrication of single-crystal MOFs with spatially defined multicolour emission remains a major challenge. Here, we report a scalable solution-phase epitaxial growth strategy to construct multicolour luminescent heterostructures based on uniform Ce[3+]-MOF (IAM19-1) single crystals. Through sequential and regioselective overgrowth of different emissive lanthanide (e.g., Tb[3+], Eu[3+]) doped MOF shells, we programmatically construct core-shell architectures within individual crystals, where distinct lanthanide-emitting domains (e.g., Tb[3+] for green, Eu[3+] for red) are programmed with separation distances tailored for optical discrimination. This method overcomes the spatial and scalability limitations of traditional postsynthetic modification routes, yielding more than 0.1 g quantities of single-crystal heterostructures with sharp, well-defined luminescent domains. Under UV excitation (254 nm), these heterostructures exhibit bright, domain-specific multicolour photoluminescence, where each colour corresponds to a pre-defined spatial region. Leveraging this unique spatial-optical coupling feature, we successfully construct a high-capacity optical encoding system for anti-counterfeiting. This work establishes a scalable materials platform for fabricating luminescent millimetre-scale tags with complex, embedded optical information, bridging the gap between bottom-up crystal engineering and practical device applications in security.},
}

@article {pmid42748834,
year = {2026},
author = {Strand, IW and Draskau, MK and Axelstad, M and Evrard, B and Elmelund, E and Pedersen, M and Crisopulli, S and Chalmel, F and Svingen, T},
title = {Comparative transcriptomics reveals a core molecular signature of hypothyroid testis development across three TPO inhibitors.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120797},
doi = {10.1016/j.ecoenv.2026.120797},
pmid = {42748834},
issn = {1090-2414},
abstract = {Thyroid hormone (TH) signaling is critical for normal testis development; however, the molecular mechanisms linking developmental hypothyroidism to adverse testis outcomes remain poorly understood. Improved mechanistic insight is needed to support predictive approaches in chemical risk assessment. Here, we build on previous work to define a molecular signature in testes from hypothyroid rats induced by three thyroperoxidase (TPO)-inhibiting chemicals: the pharmaceuticals propylthiouracil (PTU), and methimazole (MMI), and the pesticide amitrole (AMI). Transcriptomic data for MMI and AMI were obtained from a previously published study. For the PTU study, pregnant Sprague-Dawley rat dams were exposed by oral gavage to PTU (1.25 or 2.5 mg/kg bw/day) from gestational day (GD) 7 to pup day (PD) 28. Reproductive toxicity endpoints were assessed, and testes were collected from offspring on GD21, PD16, and PD78 for bulk RNA barcoding and sequencing (BRBseq). Comparative transcriptomic analysis across PTU, MMI, and AMI revealed substantial transcriptional disruption, with effects that were both age- and chemical-dependent. Notably, at PD16, there was an overlap of 278 differentially expressed genes between the three chemicals, a finding that was preserved when applying a previous bioinformatic pipeline. The shared transcriptional changes were associated with biological processes related to cell cycle regulation, developmental growth, and pathways involved in Sertoli cell proliferation, germ cell development, and testis morphogenesis. Collectively, these findings support the existence of a TH-mediated molecular signature that aligns with the classical morphologic phenotype of hypothyroid testis and underscores its potential value for the development of alternative, mechanism-based test methods for regulatory purposes.},
}

@article {pmid42749243,
year = {2026},
author = {Kumar, S and Sharma, V and Roy, D and Hari, I and Balachandran, C and Sharma, YP and Sreelakshmi, PR and Deoshatwar, AR and Chavan, SP and Patil, DR and Sawant, PM and Dhaygude, S and Gaikwad, P and Kesare, V and Shinde, S and Adhav, B and Balasubramanian, R and Bondre, VP},
title = {DNA barcoding of sand flies from Chandipura-affected districts of Gujarat, India.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {145},
number = {},
pages = {106027},
doi = {10.1016/j.meegid.2026.106027},
pmid = {42749243},
issn = {1567-7257},
abstract = {Phlebotomine sand flies are important vectors of various pathogens, including the Chandipura virus (CHPV), a neurotropic rhabdovirus associated with fatal pediatric encephalitis outbreaks in India. Gujarat, a CHPV-endemic region, lacks comprehensive molecular data on sand fly species. Accurate species identification is important for effective vector surveillance and control strategies. 2950 sand flies were collected from 14 districts using aspirators and traps. Morphological identification was performed by using standard taxonomic keys. DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) gene was performed using universal barcoding primers. Sequence alignment, phylogenetic analysis, and genetic divergence calculations were performed through MEGA and BOLD Systems databases. Seven species were identified: Sergentomyia babu, Se. punjabensis, Se. insularis, Se. bailyi, Se. shorttii, Phlebotomus argentipes, and Ph. papatasi. Phylogenetic clustering showed strong bootstrap support (>90%), confirming congruence between morphological and molecular identification. Intraspecific divergence was low (0.5 to 2.0%), while interspecific divergence was comparatively higher (5.4 to 18.9%), indicating a clear "barcode gap" that validated species boundaries. COI DNA barcoding reliably distinguished sand fly species from CHPV-endemic Gujarat. The study highlights the presence of epidemiologically relevant vectors, supports the use of molecular taxonomy in entomological surveillance, and emphasizes the need to expand DNA barcode reference libraries for Indian sand flies.},
}

@article {pmid42749397,
year = {2026},
author = {Jamdade, R and Alsallani, M and Al Shaer, K and Gairola, S and Mahmoud, T and Shabana, HA},
title = {DNA barcoding to delineate species boundaries and assess genetic divergence in halophytes of the United Arab Emirates.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {3},
pages = {100716},
doi = {10.1016/j.jgeb.2026.100716},
pmid = {42749397},
issn = {2090-5920},
abstract = {Halophytes represent a unique group of salt-tolerant plants that are critical to the ecology of arid and semi-arid environments, yet taxonomic resolution of some taxa remains challenging due to morphological plasticity and limited molecular data. This study employed a multilocus DNA barcoding approach using two chloroplast markers, rbcL and matK, and the nuclear ribosomal marker ITS2 to assess species-level resolution among halophytic plants from the United Arab Emirates (UAE). A total of 137 field-collected samples representing 38 species were processed, generating 373 high-quality barcode sequences across the three loci. Because PCR amplification and sequencing success varied among markers, not all samples yielded usable sequences for every locus. Consequently, the final marker-specific datasets comprised 132 sequences for rbcL, 125 for matK, and 116 for ITS2. To improve representation of species sampled by one or two individuals, 36 additional sequences were retrieved from GenBank, resulting in 409 sequences analyzed in total. The rbcL showed the highest amplification and sequencing success but the lowest species-level discrimination. In contrast, matK and ITS2 exhibited higher sequence variability and interspecific divergence, with ITS2 providing the strongest resolution for closely related taxa. Barcode gap and OTU-based ASAP analyses revealed limitations in resolving species within taxonomically complex genera, particularly Cyperus, Zygophyllum, and Tamarix. Supervised machine learning classifiers, especially Support Vector Machines, improved taxonomic assignment compared with traditional distance-based methods and achieved up to 97.7% classification accuracy. However, unresolved cases remained in closely related genera, reflecting biological constraints such as low interspecific divergence, recent divergence, hybridization, polyploidy, and limited barcode gaps. The present study demonstrates that multilocus barcoding combined with machine learning can improve species identification of UAE halophytes, while also highlighting the limitations of standard barcode loci in complex plant groups. The generated reference dataset contributes to the regional DNA barcode library and provides a molecular framework for biodiversity monitoring, conservation, and the sustainable utilization of salt-tolerant plant diversity in arid ecosystems.},
}

@article {pmid42741543,
year = {2026},
author = {Hollingsworth, PM and Fantoni, K and Koureas, D and Arakelyan, M and Aravanopoulos, FA and Bacela-Spychalska, K and Ballesteros-Mejia, L and Beja, P and Bonchev, GN and Bou Dagher Kharrat, M and Bourlat, SJ and Chkhartishvili, T and Čiampor, F and Costa, FO and Csabai, Z and Dankova, G and Ekrem, T and Emerson, B and Ferreira, S and Gadawski, P and Gkagkavouzis, K and Hebert, PDN and Ichim, MC and Jelić, M and Kaitetzidou, E and Kalamujić Stroil, B and Kamenova, S and Keskin, E and Laini, A and Lawniczak, M and Madesis, P and Montagna, M and Mutanen, M and Peters, RS and Price, B and Rewicz, T and Rougerie, R and Rulik, B and Szucsich, N and Vos, R and Goodall-Copestake, WP and Triantafyllidis, A and Grabowski, M},
title = {Species identification, discovery, and biomonitoring: Strategic priorities for DNA barcoding in Europe, set in a global context.},
journal = {Bioscience},
volume = {76},
number = {9},
pages = {776-786},
pmid = {42741543},
issn = {0006-3568},
abstract = {The International Barcode of Life (iBOL) initiative is building a globally accessible DNA-based system for species identification and discovery. This paper outlines the mission and strategic priorities for the iBOL community in Europe (iBOL Europe), set in a global context. The mission of iBOL Europe is to produce, curate, and provide access to a complete DNA barcode reference library of European eukaryotic biodiversity, catalyzing species discovery and enabling comprehensive, harmonized species identification and biomonitoring, and supporting the global iBOL program. Immediate objectives include completing reference libraries for priority taxa, democratizing access to sequencing technologies, and strengthening a distributed community of practice. Key actions identified span five thematic areas: community building, sample collection and taxonomic verification, sequencing infrastructure, data management, and mainstreaming DNA-based approaches to meet societal needs. The strategy emphasizes integration with European research infrastructures to ensure long-term sustainability and resilience for biodiversity genomics in Europe.},
}

@article {pmid42736590,
year = {2026},
author = {Eguchi, A and Iwamoto, Y and Tokuda, H and Narita, H and Martin, AM and Ota, S},
title = {Decoupling Fabrication From Encoding: DNA-Addressable Template Microparticles for Large, User-Defined Optical Barcode Libraries.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77407},
pmid = {42736590},
issn = {2198-3844},
support = {25H01359//Japan Society for the Promotion of Science/ ; 24K23030//Japan Society for the Promotion of Science/ ; 25K17926//Japan Society for the Promotion of Science/ ; 25K24884//Japan Society for the Promotion of Science/ ; JPMJCR19H1//Japan Science and Technology Agency/ ; JPMJCR23B6//Japan Science and Technology Agency/ ; JPMJGX23B1//Japan Science and Technology Agency/ ; JPMJAP2416//Japan Science and Technology Agency/ ; JPMJAP24B5//Japan Science and Technology Agency/ ; JPMJAX2534//Japan Science and Technology Agency/ ; },
abstract = {Optical barcodes for pooled high-throughput screening must support large libraries while remaining decodable in a single imaging step. Existing approaches often trade design control for manufacturability: deterministic barcodes often require per-code redesign of particle fabrication, whereas stochastic combinatorial barcodes are difficult to generate as predefined batches. Here we introduce a chemically programmable barcoding architecture that decouples particle fabrication from barcode assignment. Using a contact-free multilaminar flow lithography platform with all-around three-dimensional sheathing, we continuously fabricate a universal hydrogel scaffold containing five spatially segregated DNA-addressable domains at rates > 10[6] particles/h. Chosen barcode identities are subsequently written on demand onto the same template batch by domain-selective DNA hybridization. Single-domain measurements resolved 64 candidate optical states, indicating an experimentally informed theoretical upper bound of 64[5] ≈ 1.1 × 10[9] barcodes. We further implemented a predefined 59,049-code library by split-pool labeling, achieving an 83.6% recovery of decoded beads at a stringent posterior threshold (≥ 0.95). After 11 days, >7,800 beads were correctly re-identified at ≥ 0.95 accuracy in matched fields of view. This strategy provides a highly scalable, chemically programmable route to build large, user-defined optical barcode libraries with single-image optical readout and longitudinal traceability.},
}

@article {pmid42737991,
year = {2026},
author = {Saengprajak, J and Pakdeenarong, N},
title = {Multilocus DNA Barcoding Resolves Area-Based Genetic Variation in Freshwater Shrimps (Macrobrachium sp. and Caridina sp.) from Saline and Non-Saline Habitats in Northeastern Thailand.},
journal = {Biology},
volume = {15},
number = {17},
pages = {},
pmid = {42737991},
issn = {2079-7737},
abstract = {Freshwater prawns are important components of freshwater ecosystems, yet their diversity and genetic structure in northeastern Thailand remain insufficiently documented, particularly across habitats differing in soil salinity. This study assessed freshwater prawn diversity and phylogenetic relationships in saline and non-saline habitats using an integrative taxonomic approach combining morphological examination with mitochondrial and nuclear DNA barcoding. A total of 225 mature specimens were collected from 15 sampling sites in Maha Sarakham province (saline habitats) and Mukdahan province (non-saline habitats). Representative specimens were examined morphologically and characterized using four barcode loci: cytochrome c oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), 18S ribosomal RNA (18S rRNA), and the internal transcribed spacer (ITS). Morphological assessment identified three taxa, Macrobrachium lanchesteri, Macrobrachium niphanae and Caridina sp. Molecular analyses recovered three principal lineages broadly corresponding to these taxonomic groups, although the resolution varied among loci. COI provided consistent species-level discrimination, while 16S rRNA revealed additional genetic variation within Macrobrachium. The conserved 18S rRNA marker supported separation of the major taxonomic lineages, whereas ITS contributed complementary sequence variation for lineage assessment. The concatenated multilocus dataset provided the most stable phylogenetic reconstruction, with strong support for the principal lineages. Samples from saline and non-saline habitats were not consistently separated, suggesting that salinity was not the primary factor underlying the observed genetic structure. Overall, integrating morphological and multilocus molecular evidence provided a robust framework for assessing freshwater prawn diversity and phylogenetic relationships and establishes a baseline for future taxonomic, phylogeographic, and conservation studies in the Mekong region.},
}

@article {pmid42739503,
year = {2026},
author = {Jiang, S and Ye, S and Wang, Y and Zhu, H and Wu, Y and Li, Z and Hang, J and Li, X and Yin, Y and Lu, Q and Guo, X},
title = {Performance Profiles of Short DNA Barcode Segments for Family Level Detection of Asteraceae Within Asterales.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42739503},
issn = {2223-7747},
support = {32372124//National Natural Science Foundation of China/ ; 82504949//National Natural Science Foundation of China/ ; YLS-2026-ZY01016//Yuelu Mountain Laboratory Project/ ; 2024M750883//China Postdoctoral Science Foundation/ ; 2026M792817//China Postdoctoral Science Foundation/ ; 2025JJ60641//Hunan Provincial Natural Science Foundation of China/ ; 2025JJ40024//Hunan Provincial Natural Science Foundation of China/ ; 2026JJ60385//Hunan Provincial Natural Science Foundation of China/ ; H20250813//National Foreign Experts Program/ ; },
abstract = {Short DNA barcodes may facilitate sequence recovery from degraded material, but their ability to retain target-family identity while excluding related taxa varies among genomic regions. We computationally evaluated 16 nuclear, plastid, and mitochondrial marker regions from 11 Asterales families using 279,956 NCBI locus-record matches and an accession-disjoint discovery/test design. Thirty-one candidate segments of 50-200 bp (mean, 98.55 bp) were screened in discovery data and evaluated for within-Asteraceae sequence recall, differentiation from non-Asteraceae Asterales, in silico primer behavior, phylogenetic placement, and exploratory matching across 808 metadata-defined metagenomic samples. Conserved regions such as matR and rbcL showed high within-Asteraceae identity, whereas ITS1, ITS, and trnH-psbA showed larger differences from related-family backgrounds; ITS2 and ycf1 showed intermediate profiles. Candidate segments were placed within or immediately adjacent to Asteraceae reference branches in segment-specific maximum-likelihood analyses, although support and topology varied among regions. Metadata-defined target-containing groups had higher mean query coverage and identity than background groups; because target presence was not independently verified and no classifier was fitted, these comparisons were descriptive and did not estimate diagnostic accuracy. Definitionally linked sequence statistics were interpreted as structural associations rather than evidence of causal evolutionary mechanisms. These results provide a family-level computational comparison of candidate short segments for Asteraceae detection within Asterales. Species identification, operational marker combinations, threshold robustness, and laboratory performance require validation using taxonomically dense, voucher-linked, and experimentally characterized datasets.},
}

@article {pmid42732702,
year = {2026},
author = {Zhou, Y and Wei, Y and Wang, F and Chen, S and Chen, M and Xu, C and Wei, X and Gu, Z and He, Z},
title = {Photonic crystal barcode microfluidic chip for smart screening of lactogenic Chinese herbs using human mammary organoids.},
journal = {Biomaterials},
volume = {338},
number = {Pt A},
pages = {124626},
doi = {10.1016/j.biomaterials.2026.124626},
pmid = {42732702},
issn = {1878-5905},
abstract = {Postpartum insufficient lactation is challenging to maternal and infant health, yet safe and effective lactation-promoting drugs remain lacking. Here, we present an integrated smart screening platform that combines human mammary organoids with a photonic crystal barcode microfluidic chip for high-throughput identification and mechanistic elucidation of lactation-promoting traditional Chinese medicines (TCMs). Human mammary organoids recapitulate key structural and functional features of native mammary tissue and, critically, acquire the capacity to stably secrete milk proteins including TIMP1, which serves as a quantifiable lactogenic marker. The photonic crystal barcodes, fabricated as monodisperse silica colloidal crystal microspheres with tunable structural colors, are functionalized with capture antibodies and embedded in a herringbone-structured microfluidic chip, enabling in situ, visual, and highly sensitive fluorescence-based detection of secreted proteins. Using this system, we screen 18 TCM compounds and identify curcumin, puerarin, and forsythoside H as the three most effective candidates for enhancing TIMP1 secretion in vitro. Notably, in vivo experiments in a postpartum mouse model demonstrated that all three TCMs markedly induced milk yield and mammary alveolar development. RNA-seq analysis further unveils that forsythia uniquely regulates a series of pathways involving reprogramming of carbohydrate metabolism, amplification of estrogen/prolactin hormone signaling cascades, and induction of mammary epithelial differentiation. This synergistic activation of core lactogenic pathways provides a molecular basis for forsythia's superior lactation-promoting efficacy. These findings demonstrate that the present platform shows potential for efficient screening of lactation-promoting herbs and advancing the modernization of TCMs in lactation management.},
}

@article {pmid42733790,
year = {2027},
author = {Hou, X and Yu, C and Xue, Y and Liu, Y and Kang, DD and Bennett, JL and Bliss-Moreau, E and Ni, M and Liu, Y and Fang, G and Zheng, YY and Wang, S and Tian, M and Zhong, Y and Li, H and Liu, Z and Cao, D and Dong, Y},
title = {Barcoded oligonucleotide system (BOLT) for targeted organ delivery.},
journal = {Bioactive materials},
volume = {68},
number = {},
pages = {231-240},
pmid = {42733790},
issn = {2452-199X},
abstract = {The therapeutic potential of oligonucleotides (oligos) is limited by insufficient delivery to extrahepatic tissues. In vitro assays often fail to accurately predict in vivo behavior, while testing each oligo candidate in animals remains inherently low throughput. Here, we conceive a barcoded oligonucleotide system (BOLT), a platform that enables high-throughput in vivo evaluations of small-molecule ligands and identifies tissue-specific oligo delivery. BOLT integrates rational design of oligo barcodes, modular conjugation chemistry, and next-generation sequencing (NGS)-based quantification, allowing simultaneous evaluation of many chemically diverse ligand-oligo conjugates within a single animal. Notably, this platform is applicable in both mice and nonhuman primates (NHPs). Using BOLT, we discovered ligands with tropism for tissues such as the brain, lung, and muscle. Collectively, these results indicate that the BOLT platform can accelerate the discovery of tissue-targeting ligands for broad oligo therapeutics.},
}

@article {pmid42733832,
year = {2026},
author = {Benyahia, N and Bouguerche, C and Kechemir-Issad, N},
title = {"Not flying solo": phylogenetic identification and life-cycle insights of larval cestodes in the European flying squid Todarodes sagittatus (Cephalopoda: Ommastrephidae).},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {31},
number = {},
pages = {101272},
pmid = {42733832},
issn = {2213-2244},
abstract = {The European flying squid Todarodes sagittatus Lamarck is a widely distributed ommastrephid cephalopod in the Northeast Atlantic and Mediterranean Sea, yet its parasite fauna remains poorly documented in the Mediterranean Sea. In this study, two cestode larvae species infecting T. sagittatus from the Algerian coast (Western Mediterranean) were investigated using an integrative approach combining morphological observations and molecular analyses. A total of 63 squids were examined for parasitic infection. Cestodes in plerocercoid stage were detected in 31 individuals (prevalence of 46%), primarily located within the gastrointestinal tract, including the stomach, intestine, and caecum. Morphological features of the larvae were consistent with members of the order Phyllobothriidea but did not allow identification to the species level. Molecular analysis of the D1-D3 region of the 28S rDNA revealed two distinct larval lineages belonging to the genus Crossobothrium Linton, 1889. One lineage showed 100% sequence identity with the adult cestode Crossobothrium dohrnii (Oerley, 1885), a parasite of hexanchid sharks, confirming the identity of these larvae as plerocercoids of C. dohrnii. The second lineage clustered within the Crossobothrium clade but could not be assigned to a known species and is therefore referred to as Crossobothrium sp. The occurrence of these larvae in T. sagittatus, together with ecological data on squid diet and predator-prey relationships, suggests that this cephalopod acts as an intermediate or paratenic host in the life cycle of hexanchid cestodes. Infection likely occurs through predation on crustaceans acting as first intermediate hosts, while transmission to definitive hosts occurs when infected squids are consumed by sharks. These findings provide the first molecular identification of cestode larvae from T. sagittatus in the Mediterranean and highlight the important role of ommastrephid squids in the trophic transmission of elasmobranch parasites in pelagic ecosystems.},
}

@article {pmid42734661,
year = {2026},
author = {de Oliveira, MDS and Ribeiro da Silva, RC and Rodrigues, BL and Rodrigues, JC and Guimarães E Silva, AS and Pinheiro, VCS},
title = {Application of COI DNA barcode to identify phlebotomine sand flies (Diptera: Psychodidae) from Maranhão in leishmaniasis-endemic areas, Northeast Brazil.},
journal = {Journal of medical entomology},
volume = {63},
number = {5},
pages = {},
doi = {10.1093/jme/tjag145},
pmid = {42734661},
issn = {1938-2928},
support = {//Training and Capacity Building of Human Resources in Biological Taxonomy - CNPq/MCTI/CONFAP-FAPs/ ; //State University of Maranhão/ ; },
mesh = {Animals ; *Psychodidae/genetics/classification ; *DNA Barcoding, Taxonomic ; Brazil ; *Electron Transport Complex IV/genetics/metabolism ; Phylogeny ; Insect Proteins/genetics/metabolism ; Leishmaniasis/transmission ; },
abstract = {This study evaluated the effectiveness of DNA barcoding, based on the mitochondrial COI gene, in delimiting species of the subfamily Phlebotominae from Maranhão, in addition to generating new molecular information and detecting possible cryptic species. Fragments of the COI gene were sequenced and integrated into public GenBank data. The species was delimited by means of species delimitation algorithms based on genetic distance (ABGD and ASAP) and phylogenetic gene trees (PTP), making it possible to identify patterns of cryptic diversity. In total, 54 consensus sequences were obtained, representing 23 species. Among these, Lutzomyia gomezi (Nitzulescu, 1931) and Psathyromyia punctigeniculata (Floch & Abonnenc, 1941) represent the first COI barcode sequences for these species in Brazil. BLAST and BOLD analysis coincided with morphological identification in most cases. The species Lu. sherlocki (Martins, Silva & Falcão, 1971) showed the greatest intraspecific distance and split into 2 clusters/MOTUs, suggesting the presence of distinct COI lineages or cryptic diversity. Unique clusters merging individuals of morphologically recognized species were also observed, such as Evandromyia lenti (Mangabeira, 1938)/Ev. carmelinoi (Ryan, Fraiha, Lainson & Shaw, 1986) and Psychodopygus complexus (Mangabeira, 1941)/Ps. wellcomei Fraiha, Shaw & Lainson, 1971. In view of these results, the need for further investigations using other molecular markers is evident, in order to expand the taxonomic resolution of these groups. Still, DNA barcoding (COI) proved to be efficient in delimiting most species and detecting possible cryptic species, while substantially expanding the molecular reference database for sand flies from Maranhão.},
}

Animals
*Psychodidae/genetics/classification
*DNA Barcoding, Taxonomic
Brazil
*Electron Transport Complex IV/genetics/metabolism
Phylogeny
Insect Proteins/genetics/metabolism
Leishmaniasis/transmission

@article {pmid42735357,
year = {2026},
author = {Weng, X and Di, M and Zhou, B and Zhang, C and Zheng, J and Lu, P},
title = {Species composition of small mammal communities and prevalence of Schistosoma japonicum in the Poyang Lake region, China.},
journal = {Parasite (Paris, France)},
volume = {33},
number = {},
pages = {52},
pmid = {42735357},
issn = {1776-1042},
support = {32160264//National Natural Science Foundation of China/ ; 32460251//National Natural Science Foundation of China/ ; //Natural Science Foundation of Jiangxi Province/ ; },
mesh = {Animals ; China/epidemiology ; *Schistosoma japonicum/genetics/isolation & purification ; Prevalence ; *Schistosomiasis japonica/epidemiology/veterinary/parasitology ; Female ; Lakes ; Male ; Ecosystem ; Seasons ; Murinae/parasitology ; *Rodent Diseases/parasitology/epidemiology ; *Mammals/parasitology/classification ; },
abstract = {Small mammals are an important part of the ecosystem and can serve as the definitive host of Schistosoma japonicum. The Poyang Lake region of Jiangxi Province is one of the most important endemic areas of schistosomiasis japonica in China. However, data on the prevalence of schistosomiasis in local small mammal communities are lacking. Therefore, from 2021 to 2022, we captured 409 small mammals in four townships in this region, with a total capture rate of 6.89% (409/5938). There were significant differences in the capture rate among different habitats (χ[2] = 100.74, p < 0.001) and different sampling sites (χ[2] = 100.74, p < 0.001), but there was no significant difference between sampling seasons (χ[2] = 4.437, p = 0.109). Traditional morphology combined with molecular DNA-barcoding was effective in identifying species, and four species, Apodemus agrarius, Rattus losea, R. norvegicus and Crocidura attenuata were identified. PCR of the Sjr2 gene showed a total prevalence of S. japonicum of 2.85% (8/281) in A. agrarius and 2.83% (3/106) in R. losea. The species, sex, age, sampling sites, seasons, and habitats were not significant factors influencing the prevalence of S. japonicum in small mammals. This study revealed the molecular prevalence of S. japonicum in the wild small mammal community in the Poyang Lake region for the first time. Monitoring schistosomiasis prevalence in A. agrarius and R. losea may contribute to future elimination efforts around Poyang Lake.},
}

Animals
China/epidemiology
*Schistosoma japonicum/genetics/isolation & purification
Prevalence
*Schistosomiasis japonica/epidemiology/veterinary/parasitology
Female
Lakes
Male
Ecosystem
Seasons
Murinae/parasitology
*Rodent Diseases/parasitology/epidemiology
*Mammals/parasitology/classification

@article {pmid42735460,
year = {2026},
author = {Ma, H and Xu, N and Zhen, X and Liu, J and Xun, X and Lai, J},
title = {Plant and fungal eDNA metabarcoding for geographic sourcing of forensic palynological evidence across urban functional zones.},
journal = {Forensic science international},
volume = {389},
number = {},
pages = {113135},
doi = {10.1016/j.forsciint.2026.113135},
pmid = {42735460},
issn = {1872-6283},
abstract = {Plant pollen and spores are promising forensic indicators for geographic sourcing because their DNA is persistent and their community composition is shaped by local vegetation and environmental conditions. However, reference datasets designed specifically for forensic palynological applications remain limited. Here, we evaluated the feasibility of environmental DNA (eDNA) metabarcoding for geographic sourcing of palynological trace evidence across urban functional zones in Xi'an, China. Airborne palynomorphs were collected from nine city-wide sites representing seven functional zones in spring and summer. High-throughput amplicon sequencing was performed using the plant rbcL and matK barcodes and the fungal ITS1 region, followed by diversity analysis, LEfSe biomarker screening, random forest classification and SourceTracker-based source attribution. Plant and fungal palynomorph communities differed significantly among urban functional zones. Plant assemblages showed marked seasonal succession, with wind-pollinated trees dominant in spring and insect-pollinated plants, ferns and vines increasing in summer. Fungal assemblages contained a stable core community together with season-specific taxa. Random forest models achieved site-level accuracies of 84.38% for spring rbcL and nearly 87.5% for summer matK in plant datasets, and > 95% for fungal ITS1 datasets in both seasons. In the forensic validation analysis, SourceTracker assigned 30%-56% of plant-derived and 41%-48% of fungal-derived components in summer dust samples to their true sampling site. These results demonstrate that airborne palynomorph eDNA contains strong spatial and seasonal information. Plants and fungi provide complementary forensic signals: plants are informative seasonal indicators, whereas fungi offer higher spatial resolution. The rbcL barcode showed greater amplification stability in airborne samples, and the integration of metabarcoding with machine-learning classification provides a practical framework for forensic geographic sourcing.},
}

@article {pmid42735995,
year = {2026},
author = {Moshavernia, S and Shahabi, S and Paksa, A},
title = {Global genetic diversity and phylogenetic analysis of Pseudolynchia canariensis based on the COI gene with first molecular detection of Wolbachia (wsp and 16S rRNA) from Iran.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {74},
number = {},
pages = {101549},
doi = {10.1016/j.vprsr.2026.101549},
pmid = {42735995},
issn = {2405-9390},
mesh = {Animals ; *Wolbachia/genetics/isolation & purification ; Iran ; *Genetic Variation ; *Phylogeny ; RNA, Ribosomal, 16S/genetics/analysis ; *Diptera/genetics/microbiology ; Electron Transport Complex IV/genetics ; Bacterial Outer Membrane Proteins/genetics ; },
abstract = {Pseudolynchia canariensis (Diptera: Hippoboscidae) is a hematophagous ectoparasite of pigeons with recognized veterinary and epidemiological importance due to its association with avian hemoparasites and bacterial microorganisms. Despite its wide geographic distribution, molecular data remain limited in several regions, including Iran, and Wolbachia infection has not previously been documented in Iranian populations of this species. The present study aimed to molecularly confirm P. canariensis from southern Iran, evaluate global genetic diversity based on mitochondrial COI sequences, and screen for Wolbachia infection. A total of 100 adult flies were collected from five districts of Shiraz, Iran, and identified using morphological characters and COI barcoding. Phylogenetic relationships were reconstructed using Maximum Likelihood inference, and global diversity indices were calculated from a comparative COI dataset comprising 45 sequences trimmed to a 261 bp overlapping region. Genetic diversity analysis revealed moderate haplotype diversity (Hd = 0.736) and low nucleotide diversity (π = 0.00773) at the global level, with no statistically significant deviation from neutrality. The overall mean evolutionary divergence was low (K2P = 0.01 substitutions per site), indicating limited mitochondrial differentiation among global populations. Wolbachia infection was detected in pooled samples from two districts using both wsp and 16S rRNA markers. Phylogenetic analyses of both markers consistently placed Iranian Wolbachia sequences within supergroup B. These findings represent the first molecular evidence of Wolbachia infection in P. canariensis from Iran and provide baseline genetic data supporting future investigations into host-symbiont interactions and the potential epidemiological role of this ectoparasitic fly.},
}

Animals
*Wolbachia/genetics/isolation & purification
Iran
*Genetic Variation
*Phylogeny
RNA, Ribosomal, 16S/genetics/analysis
*Diptera/genetics/microbiology
Electron Transport Complex IV/genetics
Bacterial Outer Membrane Proteins/genetics

@article {pmid42729719,
year = {2026},
author = {Brown, GE and Nastasi, LF and Davis, C and Sierra, N and Lewis, CJ and Steffensen, MJ and Sweezer, D and Forbes, AA},
title = {From two putative inquilines to one definitive parasitoid: clarifying feeding ecology and species limits in Nearctic Euceroptres Ashmead, 1896 wasps (Hymenoptera: Figitidae).},
journal = {Annals of the Entomological Society of America},
volume = {119},
number = {5},
pages = {386-395},
pmid = {42729719},
issn = {0013-8746},
abstract = {Oak galls are structures of modified plant tissue, induced by an ovipositing female oak gall wasp (Hymenoptera: Cynipidae: Cynipini), that provide food and shelter for her progeny. Myriad other wasp species exploit galls, feeding on either the gall wasp larva (parasitoidism), the gall tissue (inquilinism/kleptoparasitism), or other parasites within the gall (hyperparasitism). Though many oak gall-associated wasps are now described, their feeding ecology often remains poorly documented, particularly in the species-rich communities across North America. Wasps in the genus Euceroptres (Hymenoptera: Figitidae) exemplify this problem, long having been assumed to be inquilines based on limited evidence. We used dissections, microcomputed tomography scanning, and DNA barcoding to discover that Euceroptres do not modify the internal composition of their host gall. We also found a Euceroptres larva feeding on gall-inducer larva within an unaltered gall wasp larval chamber. Thus, Euceroptres are parasitoids, not inquilines. While sequencing larval and adult Euceroptres, we also found that the 2 previously described species in eastern North America, Euceroptres whartoni Buffington and Liljeblad, 2008 and Euceroptres primus Ashmead, 1896, did not separate into distinct clades, suggesting they are a single species. Subsequent morphological comparisons support this finding, allowing the establishment of E. whartoni as a syn. nov. of E. primus.},
}

@article {pmid42729832,
year = {2026},
author = {Yi, J and Su, G and Yang, Q and Song, H and Xu, J and Chen, M and Zhou, J and Yin, H and Gafforov, Y and Hu, D},
title = {Assessing genetic and phenotypic diversity to advance multi-trait selection in Cyclocybe chaxingu.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e194629},
pmid = {42729832},
issn = {2210-6340},
abstract = {Cyclocybe chaxingu is a major cultivated edible mushroom in China; however, the relationship between its genetic diversity and agronomic performance remains insufficiently characterised. In this study, 100 strains were sampled, sequenced at two gene fragments (LSU and TEF1-α) and analysed for strain relationships at these loci. Ten agronomic traits were quantified under standardised cultivation conditions. Significant differences amongst strains were observed for all traits (ANOVA, p < 0.01). Amongst the ten traits, the greatest variation was found in the total number of fruiting bodies (CV 45.6%), followed by average fruiting-body weight (CV 35.0%). Principal component analysis accounted for 83.98% of the variance across three axes: PC1 (57.74%) represented a size and mass gradient (cap thickness, stipe diameter, cap diameter, gill width, average fruiting-body weight versus fruiting-body number), PC2 (15.87%) reflected stipe elongation and PC3 (10.37%) captured the timing of first harvest and earliest yield. Hierarchical clustering identified four phenotypic branches and five operational colour groups, each displaying strong differences across traits. Phylogenetic analysis at the two loci grouped strains into four distinct clusters, which partially overlapped with phenotype-based clusters. Yield was positively correlated with size-related traits and gill width and negatively correlated with fruiting-body number. Time to first harvest and earliest yield were associated with cap thickness and gill width. Stipe diameter, stipe length and gill width are proposed as practical DUS indicator traits for breeding, with size traits serving as complementary selection targets, thereby providing a quantitative breeding framework for C. chaxingu.},
}

@article {pmid42729970,
year = {2026},
author = {Thinnabut, K and Maleewong, W and Pramual, P and Sanpool, O and Tangkawanit, U},
title = {An Integrative Assessment of Tabanus rubidus (Diptera: Tabanidae) in Thailand: Distribution, Population Genetics, and Pathogen Surveillance.},
journal = {Journal of tropical medicine},
volume = {2026},
number = {},
pages = {8877101},
pmid = {42729970},
issn = {1687-9686},
abstract = {Tabanus rubidus (Diptera: Tabanidae) is a significant species of the Tabanidae family, known for its veterinary and medical relevance, and is found across Thailand. This study examines the species distribution, genetic diversity, demographic history, and vector-pathogen transmission of T. rubidus collected from all six different regions in Thailand. Molecular techniques, utilizing the cox1 gene, were used to assess genetic diversity, genetic structure, and demographic history. The 16S ribosomal RNA gene was used to detect Anaplasma and Ehrlichia, while the 18S ribosomal RNA gene was used to identify Trypanosoma and Theileria. Tabanus rubidus was found in 23 out of 26 provinces in Thailand, indicating its widespread presence across the country. Negative binomial regression showed that fly abundance was negatively affected by monthly mean temperature but positively influenced by rainfall and site temperature. There was high haplotype diversity and low nucleotide diversity. The median-joining network network revealed three lineages: Lineage I, which includes Thailand, Malaysia, and Bangladesh; Lineage II, which is found in India and Bangladesh; and Lineage III, which is found in India. Analysis of the demographic history suggested that population expansion started at the end of the Pleistocene. In this study, T. rubidus tested negative for Ehrlichia and Theileria, with Trypanosoma theileri (T. theileri) and Anaplasma marginale being the only detected pathogens. These findings are epidemiologically significant, confirming tabanid-mediated transmission of T. theileri (indicator of trypanosomiasis) and A. marginale (agent of bovine anaplasmosis), both of which pose health risks and economic losses to livestock.},
}

@article {pmid42732319,
year = {2026},
author = {Jiménez Cano, NG and Dettaï, A and Mansoor Al-Nabhani, H and Abu El-Regal, M and Al-Jabri, A and Béarez, P},
title = {Fish mtDNA COI sequences from local fish markets in the Red Sea and Arabian Sea: A reference dataset.},
journal = {ZooKeys},
volume = {1291},
number = {},
pages = {195-204},
pmid = {42732319},
issn = {1313-2989},
abstract = {This data paper describes a dataset of mitochondrial cytochrome c oxidase subunit I (COI) sequences from 51 fish specimens obtained from local fish markets in eight coastal localities in Oman and Saudi Arabia. For each vouchered specimen, basic metadata such as locality, date of purchase, and morphometric data was documented, and a photographic record was made. Tissue samples were collected for DNA analysis. The COI gene was amplified and sequenced using standard DNA protocols. The resulting COI sequences were curated and deposited in the Barcode of Life Data System (BOLD). The dataset enhances the genetic representation of marine fishes from the Red Sea and Arabian Sea and adds three novel fish COI records in BOLD, Plectropomus marisrubri, Scarus zufar, and Scorpaenopsis lactomaculata, as well as numerous fish taxa which are currently poorly documented. These sequences represent a reference resource for specimen identification and verification, and can be used to underpin taxonomic revisions, comparative phylogenetic and phylogeographic studies, assessments of regional biodiversity and sea food authentication. In making these data freely available, this contribution promotes reproducibility, data reuse, and collaboration among researchers working on marine ecology, conservation, and fisheries management, as well as monitoring and consumer protection.},
}

@article {pmid42729572,
year = {2026},
author = {Leontyev, DV and Schnittler, M and Shchepin, ON},
title = {Short-read genome skimming enables molecular barcoding of old myxomycete collections.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e201932},
pmid = {42729572},
issn = {2210-6340},
abstract = {This study evaluates the effectiveness of Illumina-based genome skimming for barcoding myxomycete herbarium collections ranging from 29 to 91 years in age. We successfully retrieved partial sequences of the standard marker gene (nucSSU) in all cases, as well as additional markers (mtSSU, EF1a, and COI) for certain collections. Altogether, 28 genes were recognized in the studied material. In a 33-year-old specimen of Lindbladia tubulina, the assembly reached an N50 of 4.19 kb, enabling the recovery of extended functional loci. The input genomic DNA quantity emerges as the primary determinant of sequencing success. Samples with high DNA yields provide representative amounts of contigs coming confirmedly (matching sequences in the NCBI nucleotide database) or potentially (no-hit fraction) from myxomycetes, regardless of specimen age. In addition to target DNA, we revealed distinct signals of both anthropogenic contamination (human DNA and skin microflora) and natural substrate inhabitants, including oribatid mites and bacteria from dead wood, soil, and grass litter. Thus, even in old collections, metagenomic data still carry information regarding the substrate upon which the myxomycete developed. The results demonstrate that short-read genome skimming may help to integrate historical type material of myxomycetes into contemporary phylogenetic research. This method overcomes the length-dependent limitations of traditional Sanger sequencing, thus providing a roadmap for the future of museomics in myxomycetology.},
}

@article {pmid42729667,
year = {2026},
author = {Ascenzi, A and Marini, L and Geppert, C and Feng, V and Rosso, E and Meier, R and Cerretti, P},
title = {Beyond conventional pollinators: advancing diversity assessments of neglected insect taxa.},
journal = {Annals of the Entomological Society of America},
volume = {119},
number = {5},
pages = {372-385},
pmid = {42729667},
issn = {0013-8746},
abstract = {Ideally, biodiversity surveys would sample insect assemblages randomly and without taxonomic bias, yet most protocols still prioritize conspicuous, charismatic, or economically important taxa (eg pollinators). Consequently, Diptera, one of the most species-rich and ecologically important insect orders, remain largely overlooked, with only a few families like Syrphidae routinely included in biodiversity assessments. To address this imbalance, here we tested a protocol designed to better capture the diversity of non-charismatic dipteran groups by comparing hand-netting and pan traps and by overcoming taxonomic impediments with cost-efficient DNA "megabarcoding" using non-destructive DNA extraction and third-generation sequencing. We applied it to brachyceran fly (Diptera: Brachycera) assemblages across four Mediterranean coastal habitats, key for coastal protection and tourism yet poorly documented. We clustered 13,877 cytochrome c oxidase subunit I barcodes into 823 molecular operational taxonomic units (MOTUs) at a 2% distance threshold, more than 10% of all Diptera species recorded for Italy. MOTUs were assigned to 48 families by morphological inspection of a single representative specimen. We then assigned ecological guilds at the family level, enabling joint assessment of taxonomic and functional diversity. Pan traps collected twice as many specimens and reached higher sample coverage than transect counts, while total MOTU richness was similar. However, assemblages differed in composition, indicating that the two methods are complementary, and still shared 27% to 40% of ecological-guild representation across habitats. Our integrative discovery framework reveals outstanding Diptera diversity and provides a scalable framework combining multiple sampling techniques with high-throughput molecular workflows, applicable to other neglected insect taxa and ecosystems.},
}

@article {pmid42724731,
year = {2026},
author = {Maupetit-Méhouas, S and Maurelia, F and Hosseinnia, P and Allègre, N and Renaud, Y and Cruzel, J and Chazaud, C and Guillot, C},
title = {Single-cell mapping of homocysteine-induced perturbations in avian embryogenesis using LMO and BD rhapsody transcriptomics.},
journal = {iScience},
volume = {29},
number = {9},
pages = {117392},
pmid = {42724731},
issn = {2589-0042},
abstract = {Single-cell RNA sequencing enables the study of cellular heterogeneity and the effects of environmental perturbations across complex tissues. However, subtle biological responses can be obscured by experimental noise, sample-specific processing, and computational integration. Here, we combined lipid-modified oligonucleotide cell tagging with the BD Rhapsody platform to multiplex early embryonic chick cells exposed to different homocysteine conditions. This species-agnostic approach enabled robust sample barcoding, simultaneous processing of treatment conditions, and recovery of high-quality single-cell transcriptomes from heterogeneous embryonic tail tissues. By comparing non-integrated and integrated analyses, we found that integration preserved broad cell identities but could mask cluster-specific transcriptional signatures in sensitive populations. Using the non-integrated multiplexed dataset, we identified homocysteine-associated transcriptional changes in neuromesodermal progenitor-derived populations and linked them to posterior mesodermal and axis elongation defects. This workflow provides an adaptable strategy for detecting subtle treatment effects in non-traditional developmental models.},
}

@article {pmid42724751,
year = {2026},
author = {Liu, H and Liao, S and Chen, C and Huo, W and Safaei, Z and Rocchi, A and Huang, Y and Sariyer, IK and Collins, ME and Lawrence, JM and Dampier, W and Nonnemacher, MR and Wigdahl, B and Burdo, TH and Gordon, J and Lewis, M and Lee, CA and Khalili, K},
title = {In vivo genome editing of central nervous system SIV reservoirs in ART-suppressed rhesus macaques.},
journal = {Molecular therapy. Nucleic acids},
volume = {37},
number = {3},
pages = {103063},
pmid = {42724751},
issn = {2162-2531},
abstract = {Latent human immunodeficiency virus type 1 (HIV-1) reservoirs in the central nervous system (CNS) may sustain viral persistence and neuroinflammation contributing to HIV-associated neurocognitive disorders (HAND) despite suppressive ART. AAV9-delivered CRISPR has successfully edited SIV proviral DNA in peripheral tissues with acceptable safety profiles, but the extent of in vivo genome editing in the brain remains unclear. Using SIV-infected rhesus macaques, we mapped intact proviral DNA across CNS regions and tested systemic AAV9-CRISPR-Cas9 targeting conserved sites within Ψ packaging signal and Gag region. Ten adult rhesus macaques were infected with genetically barcoded SIVmac239, suppressed with ART, then randomized to receive intravenous AAV9-SaCas9 with dual gRNAs (Ψ + Gag) or a Cas9-only control. At necropsy after viral rebound, SIV genomes were detected in multiple brain regions as well as lymphoid tissues, confirming the CNS as a persistent reservoir during ART. Barcode analysis revealed region-specific patterns consistent with compartmentalized CNS persistence. In CRISPR-treated animals, proviral editing was measurable across anatomically distinct CNS sites. These findings demonstrate that intact and potentially replication-competent virus persists in the primate brain under ART and that systemic AAV9-CRISPR can reach and edit proviral DNA in this sanctuary, supporting genome editing as a strategy toward durable remission of CNS reservoirs.},
}

@article {pmid42724778,
year = {2026},
author = {Chaibi, CA and Kniesz, K and Zettler, ML},
title = {Why genetic validation is crucial for identifying larval stages of Arctica islandica (Venerida, Arcticidae).},
journal = {ZooKeys},
volume = {1291},
number = {},
pages = {55-73},
pmid = {42724778},
issn = {1313-2989},
abstract = {The ocean quahog Arctica islandica is a long-lived marine bivalve widely distributed in the western Baltic Sea and commonly used as a model organism in ecological and climatic research. Despite its importance, aspects of its early development remain poorly understood. This study attempts to provide a morphological description of A. islandica larvae. Plankton samples were collected in Kiel Bay (Baltic Sea) in June 2024, September 2024, and April 2025, using a WP2 net (mesh size 100 µm). Larvae were identified by sequencing the mitochondrial cytochrome oxidase subunit I (COI) gene and subsequently documented using light and scanning electron microscopy (SEM). A benthic juvenile was additionally examined for comparison. Larvae of A. islandica were detected exclusively in June and September, yielding a total of 17 COI sequences. Genetically confirmed veliger larvae were detected in September (shell length 143-185 µm), whereas larger larvae interpreted as pediveligers were detected in a separate sampling event in June (shell length 217-505 µm). Larval anatomical structures and the apparent absence of certain organs are discussed. This study provides the first genetically confirmed description of the veliger and pediveliger stages of A. islandica and demonstrates that morphology alone is insufficient for reliable identification of A. islandica larvae and emphasizes the necessity of genetic validation.},
}

@article {pmid42725142,
year = {2026},
author = {Rehman, SU},
title = {Comparative phylogenetic analysis of breast cancer susceptibility genes reveals evolutionary conservation supporting diagnostic barcode design.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {9},
pages = {5721-5732},
pmid = {42725142},
issn = {2049-0801},
abstract = {BACKGROUND: Breast cancer susceptibility genes play essential roles in DNA repair, cell-cycle regulation, and tumor suppression. The development of gene-specific DNA barcodes for diagnostic and therapeutic applications requires a clear understanding of the evolutionary conservation and specificity of these genes across related species.

METHODS: Nucleotide sequences of nine major breast cancer-associated genes (BRCA1, BRCA2, PALB2, ATM, TP53, CHEK2, CDH1, STK11, and BRIP1) were retrieved and analyzed. Orthologous sequences from primate species were identified with BLAST. Multiple sequence alignment was performed, followed by construction of phylogenetic trees using standard distance-based and maximum-likelihood approaches. Trees were visualized and compared to assess evolutionary relationships and gene-level specificity.

RESULTS: All analyzed genes demonstrated clear phylogenetic clustering, with Homo sapiens sequences grouping closely with primate orthologs, particularly Pan troglodytes and Gorilla. Highly conserved genes such as BRCA1, BRCA2, and TP53 showed tight clustering with short branch lengths, whereas moderate variability was observed in genes such as CHEK2 and BRIP1. No cross-gene clustering or unexpected lineage mixing was detected, supporting accurate gene annotation and specificity.

CONCLUSION: The phylogenetic analyses confirm strong evolutionary conservation of key breast cancer susceptibility genes across primates. These findings support the reliability of gene-derived DNA barcode regions for diagnostic and therapeutic assay development and highlight the importance of evolutionary validation in barcode-based molecular diagnostics.},
}

@article {pmid42725663,
year = {2026},
author = {Furneaux, B and Roslin, T and Hardwick, B and Kerdraon, D and Autto, H and Banelyte, G and deWaard, JR and deWaard, SL and Farrell, A and Kalttopää, O and Kristensen, E and Rogers, HMK and Sones, JE and Zakharov, EV and Ovaskainen, O},
title = {Is There a Fly in My Soup? To What Extent Do Metabarcoding and Individual Barcoding Tell the Same Story?.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70195},
doi = {10.1111/1755-0998.70195},
pmid = {42725663},
issn = {1755-0998},
support = {336212//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 101059492//HORIZON-CL6-2021-BIODIV-01/ ; 856506/ERC_/European Research Council/International ; 225-20-002//Naturvårdsverket/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; MSI 42450//Canadian Foundation for Innovation/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; *Metagenomics/methods ; *Insecta/classification/genetics ; },
abstract = {Metabarcoding has become the method of choice for characterizing complex arthropod communities. The extent to which metabarcoded bulk samples will recover the same community composition as individual sequencing of all individuals in the sample remains poorly quantified. Biases such as unequal extraction of DNA from different taxa, primer mismatches and non-random PCR may cause the selective drop-out of species from metabarcoding data. At the same time, DNA metabarcoding may reveal arthropod taxa present not as individuals, but as DNA residues on the surface or in the gut of insects. To quantify the consistency in sample contents established by different means, we metabarcoded 45 bulk insect samples, then extracted all arthropods and sequenced them individually. Metabarcoding targeted 418 bp at the 3' end of the Folmer barcoding region, while individual barcodes captured the entire 658 bp Folmer region. The metabarcoding workflow, including PCR amplification, sequencing and bioinformatics, was performed in three replicates from three separate lysate aliquots per sample. For the main analyses, sequences were assigned to Barcode Index Numbers (BINs) as identical taxonomic categories across data types, thereby allowing the detection of even rare but biologically true taxa. Since such reference-based validation will be unavailable to any researcher dealing with metabarcoding data alone, we validated our key findings through an alternative workflow, i.e., de novo clustering of sequences. We found that metabarcoding is replicable, as different replicates of the same sample recover similar species richness and composition. Individual barcoding and metabarcoding provide similar impressions of relative differences in community structure: species-rich vs. species-poor samples rank similarly among data types (Spearman's ⍴ = 0.88-0.99) as do differences in relative dissimilarity between sample pairs (Spearman's ⍴ = 0.55-0.90). Dissimilarity between data types varies with BIN richness in the sample, but this relationship reflects nestedness rather than turnover: metabarcoding recovers the same set of core species as individual barcoding but adds hundreds of species on top. Any BIN recovered as an individual occurred with high probability in the metabarcoding data, and any BIN found in high read abundances by metabarcoding was likely found as an individual (p > 0.8). In terms of abundances, the number of individual insects per BIN was well predicted by the number of metabarcoding reads (R[2] > 0.68 for a model including taxonomy as a random effect). Our analysis suggests that metabarcoding data will be informative of the sample contents in terms of arthropod species richness, composition and taxon-specific abundances. Taxa recovered in low copy numbers in metabarcoding sequence data will likely represent DNA left as residues from past biotic interactions. Barring sequencing errors, both types of data yield biologically relevant insights into the taxa present in the source community.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Sequence Analysis, DNA
*Metagenomics/methods
*Insecta/classification/genetics

@article {pmid42728677,
year = {2026},
author = {Bones, FLV and Russi, CH and Lopes, FAC and Carvalho-Silva, M and Convey, P and Rosa, LH and Câmara, PEAS},
title = {Non-Fungi Diversity Present in Soil and Snow Impacted by Anthropogenic Activity in King George Island, Maritime Antarctica Using Metabarcoding Approach.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {5},
pages = {e70122},
doi = {10.1111/jeu.70122},
pmid = {42728677},
issn = {1550-7408},
support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Antarctic Regions ; *DNA Barcoding, Taxonomic/methods ; *Snow/microbiology ; *Biodiversity ; *Soil/parasitology/chemistry ; Anthropogenic Effects ; Sequence Analysis, DNA ; DNA, Environmental/genetics ; },
abstract = {The Antarctic Peninsula shows a fast-rising temperature trend, increasing the risk of colonization by non-native species, such as the invasive Poa annua. The "cryptic diversity" of largely unknown microscopic propagules in soil and snow poses a significant threat, as traditional morphological surveys are inadequate. Therefore, DNA metabarcoding of environmental DNA was applied to achieve a broader and more accurate assessment. We investigated non-fungi eDNA diversity in soil (three sites) and freshly deposited snow (five sites) from Martel Inlet, King George Island, with sites categorized by proximity to human activity. DNA was extracted, and the internal transcribed spacer 2 (ITS2) was used as the DNA barcode. Sequencing was performed using an Illumina MiSeq V3. Sequences were classified into 72 ASVs, representing four kingdoms and 10 phyla, with 18% not previously recorded in Antarctica. Soils hosted richer communities (mean of 30 ASVs per sample) than snow (mean of 16.2 ASVs per sample); however, there was no statistically significant difference in abundance nor diversity between the sample types. The data did not reveal differences between the sampled areas or suggest anthropogenic influence on any of the sampled communities. This work underscores the value of eDNA metabarcoding in assessing cryptic biodiversity.},
}

Antarctic Regions
*DNA Barcoding, Taxonomic/methods
*Snow/microbiology
*Biodiversity
*Soil/parasitology/chemistry
Anthropogenic Effects
Sequence Analysis, DNA
DNA, Environmental/genetics

@article {pmid42710096,
year = {2026},
author = {Kaszyca-Taszakowska, N and Kanturski, M},
title = {Deeper view on Patchiella reaumuri (Kaltenbach, 1843) (Hemiptera: Aphididae: Pemphiginae): General morphology and sensilla diversity.},
journal = {Micron (Oxford, England : 1993)},
volume = {208},
number = {},
pages = {104115},
doi = {10.1016/j.micron.2026.104115},
pmid = {42710096},
issn = {1878-4291},
abstract = {Scanning electron microscopy (SEM) methods were used for the first time to elucidate the external morphology of Patchiella reaumuri reaumuri (Kaltenbach, 1843) (Hemiptera: Aphididae: Pemphiginae). We examined and compared the external morphology of stem mothers and alate viviparous females from the parthenogenetic generation. Analysis identified diverse sensilla types, including coleoconic, campaniform, placoid, and trichoid sensilla, occurring on the antennae, mouthparts, and legs. Beyond the sensilla previously documented in the literature, we identified for the first time in aphids chaetic-type sensilla on the legs of alate viviparous females. In addition, species identity was confirmed by DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene, and the obtained sequence was deposited in GenBank under accession number PP535559.},
}

@article {pmid42710746,
year = {2026},
author = {Kazemian, S and Pedroza, S and Santana-Pereira, ALR and Neasham, PJ and North, JF and Huber, L and Criado, MF and Kyriakis, CS},
title = {An enhanced multisegment RT-PCR method for influenza A virus sequencing: Improved performance and reduced preparation time over traditional methods.},
journal = {Journal of virological methods},
volume = {347},
number = {},
pages = {115453},
doi = {10.1016/j.jviromet.2026.115453},
pmid = {42710746},
issn = {1879-0984},
abstract = {Influenza A viruses (IAVs) remain a major global health threat, affecting both human and animal populations. Whole-genome sequencing is essential for monitoring viral evolution, zoonotic transmission, and emerging variants. However, conventional RT-PCR methods often result in incomplete gene coverage, amplification biases, and reduced sequencing accuracy, particularly in clinical samples. We developed a robust In-house method for IAV full-genome sequencing using the Oxford Nanopore Technologies (ONT) long-read sequencing platform. This method integrates an in-house multisegment Reverse Transcription PCR (RT-PCR) method with a streamlined 2-pool primer design targeting all eight IAV gene segments. RNA extracted from clinical and stock virus samples was reverse-transcribed and amplified using Superscript IV-based chemistry, followed by magnetic bead purification to ensure high-quality amplicons. Sequencing libraries were prepared with the Native Barcoding Kit 24 (SQK-NBD114.24) and sequenced on R10.4.1 flow cells on the MinION MK1C device. Data analysis using the Iterative Refinement Meta-Assembler (IRMA) confirmed improved read depth, uniform coverage, and complete genome recovery. Compared to conventional methods, our In-House Multisegment 2-Pool (IH-MS2P) RT-PCR method generated higher numbers of matched read counts, minimized chimeric artifacts, and delivered superior genome coverage across human, swine, and avian isolates. This optimized RT-PCR method provides a high-performance, time-efficient, and portable solution for influenza genomics, demonstrating robust applicability even with clinical samples of low RNA yield.},
}

@article {pmid42711039,
year = {2026},
author = {Boateng, EF and Nasiru, MM and Dankwa, R and Bassey, AP and Owusu-Kwarteng, J and Bordoh, PK and Alnadari, F},
title = {Nexus of innovative packaging, food quality and sustainability.},
journal = {Advances in food and nutrition research},
volume = {122},
number = {},
pages = {325-378},
doi = {10.1016/bs.afnr.2026.03.005},
pmid = {42711039},
issn = {1043-4526},
mesh = {*Food Packaging/methods ; *Food Quality ; Food Loss and Waste ; Humans ; Food Preservation ; },
abstract = {Packaging research is one of the primary fields of study in the food ecosystem that go beyond conventional containment and protection. Innovative packaging recognizes the importance of food shelf-life stability, minimizes environmental effect, promotes health, and supports the circular economy. Highlighting the innovations in food packaging is crucial to ensuring that consumers enjoy healthful food. Consequently, insights into the incorporation of agents like antioxidants, antimicrobial, oxygen/moisture absorbers directly into the packaging material to achieve desired functionalities are underpinned. Food waste is also decreased by using sensors like biosensors and time-temperature indicators to track food parameters like freshness or temperature exposure and to give retailers and customers visible data in real time. Modern food packaging systems consider the use of barcodes, radio frequency identification tags, fast response codes, artificial intelligence, and internet of things devices to enhance food product monitoring and ensure food safety and quality throughout the supply chain. While packaging innovations are promising, challenges include higher production costs for sophisticated food packages development and comprehensive risk assessment of food contact chemicals. Hence, the need for better recycling infrastructure, and ensuring that sustainable materials can provide the same level of synergistic impact of barrier protection and functionalities of consumer quality food demands. Future developments in edible packaging, coatings based on nanotechnology, and food contact material packaging systems mechanisms call for the development of packaging that is readily recyclable, compostable, or reusable to harness sustainability issues.},
}

*Food Packaging/methods
*Food Quality
Food Loss and Waste
Humans
Food Preservation

@article {pmid42715084,
year = {2026},
author = {Liu, Z and Padmanabhan, K and He, J and Hector, K and Semsch, B and Sun, J and Knoflach, V and Giatrellis, S and Lorentz, J and Dallakyan, K and Göritz, C and Andersson, ER and Marklund, U},
title = {Resolving cell lineages and gene functions in the developing mouse gastrointestinal tract using in utero transduction.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {37},
pages = {e2614077123},
doi = {10.1073/pnas.2614077123},
pmid = {42715084},
issn = {1091-6490},
support = {101045026//EC | European Research Council (ERC)/ ; 101171156//EC | European Research Council (ERC)/ ; 2020.0109//Knut och Alice Wallenbergs Stiftelse (kawforskning)/ ; 2020-01129; 2022-01570//Vetenskapsrådet (VR)/ ; 2024-03113; 2021-03537; 2017-01054//Vetenskapsrådet (VR)/ ; FO2025-0169; FO2023-0130//Hjärnfonden (Brain Foundation)/ ; FO2025-0271//Hjärnfonden (Brain Foundation)/ ; },
mesh = {Animals ; *Cell Lineage/genetics ; Mice ; Enteric Nervous System/cytology/embryology/metabolism ; *Gastrointestinal Tract/embryology/cytology/metabolism/innervation ; Female ; Neural Crest/cytology/metabolism/embryology ; Gene Expression Regulation, Developmental ; Cell Differentiation ; },
abstract = {How diverse cell lineages emerge and are genetically regulated during organogenesis are central questions in understanding the developmental origins of disease. However, the mouse gut, including its intrinsic enteric nervous system (ENS) derived from migratory neural crest, has remained difficult to experimentally target. Here, we introduce an in utero lentiviral nano-injection strategy that enables early and efficient access to progenitor cells of all major cell types within the developing gut as well as gut-innervating ganglia. Leveraging this approach in combination with DNA barcoding and single-cell transcriptomics, we resolve clonal relationships in all gut lineages, including epithelial, neural, immune, and mesenchymal cell types. Clonal coupling between distinct subsets of fibroblasts and either pericytes, mesothelial cells, or interstitial cells of Cajal, suggested a developmental logic whereby the mesenchymal compartment arises from a set of fate-biased progenitors. Yet, mesenchymal regionalization along the anterior-posterior axis establishes early, whereas the ENS displays broad clonal dispersion across gut regions and acquires subsequent regional identities. We further adapted the platform for temporally controlled cell-type specific gene manipulation and, as a proof-of-principle, show that induced expression of the proneural factor Ascl1 biases ENS progenitor cells toward neuronal differentiation. Together, this work provides insights into refined spatiotemporal lineage relationships within a multigerm-layer organ and establishes a broadly applicable in vivo framework for probing gene function during gastrointestinal and neural crest development.},
}

Animals
*Cell Lineage/genetics
Mice
Enteric Nervous System/cytology/embryology/metabolism
*Gastrointestinal Tract/embryology/cytology/metabolism/innervation
Female
Neural Crest/cytology/metabolism/embryology
Gene Expression Regulation, Developmental
Cell Differentiation

@article {pmid42719027,
year = {2026},
author = {Gauche, M and Fontanié, N and Grangaud, E and Wilding, N and Rougerie, R and Lapègue, M and Ah-Peng, C},
title = {Contribution to the DNA barcode reference library for Réunion Pteridophyta.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e199400},
pmid = {42719027},
issn = {1314-2828},
abstract = {BACKGROUND: Expanding DNA barcode reference libraries is essential to support ecological surveys, conservation assessments and future metabarcoding applications. Réunion Island (Mascarene's Archipelago) hosts a rich diversity of pteridophytes despite its small surface area. Although the chloroplastic rbcL sequences are available for several fern taxa in public databases, additional regions with high variability such as trnH-psbA are still under-represented for the Réunion pteridoflora. This dataset has been produced in the framework of the FRBOL (FRench Barcode Of Life) network.

NEW INFORMATION: The current curated DNA barcode dataset contains 84 pteridophyte species from Réunion Island, representing approximately 25% of the pteridophyte species present on the Island. All specimens were morphologically identified by a specialist and are preserved as vouchers in the public herbarium of the University of Réunion (REU). A total of 163 sequences of rbcLa (86) and trnH-psbA (77) were generated and deposited in the Barcode of Life Data System (BOLD) with complete associated metadata and photos. While numerous rbcLa sequences were already available on GenBank, our dataset provides newlygenerated sequences linked to curated vouchers on BOLD and substantially increases the representation of trnH-psbA for the Island's pteridophytes. Additionally, this work documents the first record of Pteris ensiformis Burm.f., an exotic species for Réunion. Morphological examination allowed the identification of this newly-recorded species, which was corroborated by molecular analyses.},
}

@article {pmid42724269,
year = {2026},
author = {Andres-Lopez, Y and El Khouri-Gonzalez, C and Hernando-Herraez, I},
title = {scDynaBar: A Step-By-Step Experimental and Computational Guide for Time-Resolved CRISPR Barcoding at Single-Cell Resolution.},
journal = {Bio-protocol},
volume = {16},
number = {17},
pages = {e5793},
pmid = {42724269},
issn = {2331-8325},
abstract = {CRISPR-Cas9 barcoding technologies enable cells to record molecular events as permanent genetic changes that can be read out retrospectively. This protocol describes the implementation of a CRISPR-based recording system that gradually accumulates mutations over extended periods and is compatible with standard single-cell RNA sequencing (scRNA-seq) workflows. By temporally regulating CRISPR activity, the system generates mutational barcodes that can be captured together with individual cell transcriptomes. These barcodes are subsequently decoded using computational reconstruction approaches to infer temporal information, enabling the joint analysis of cellular states and time-resolved molecular histories. This approach provides a single-cell-compatible framework for studying dynamic biological processes in heterogeneous mouse embryonic stem cell (mESC)-derived systems, with potential extension to other biological systems. Key features • Extended temporal recording: Self-targeting guide RNAs drive progressive and cumulative barcode divergence over time. • Simultaneous barcode and transcriptome detection: Joint recovery of genetic barcodes and whole transcriptomes from the same single cell using standard scRNA-seq workflows. • In inducible scDynaBar designs: Cas9 barcode editing can be coupled to specific biological stimuli or cell-state transitions, e.g., transition of mESCs into the 2C-like state.},
}

@article {pmid42724727,
year = {2026},
author = {Al-Khlifeh, E and Hassanat, A and Al-Abdallat, Y and Maghaireh, M and Al-Rahahleh, M},
title = {Internal transcribed spacer (ITS) barcoding reveals species differentiation and evolutionary lineages of Trypanorhyncha (Cestoda) in teleosts imported to Jordan from the Mediterranean and Red Seas.},
journal = {Helminthologia},
volume = {63},
number = {2},
pages = {134-151},
pmid = {42724727},
issn = {0440-6605},
abstract = {Fish-borne trypanorhynch cestodes are socio-economically important marine parasites with veterinary and public health relevance, yet integrated molecular data from the eastern Mediterranean-Red Sea trans-boundary trading corridors remain scarce. This study utilized internal transcribed spacer (ITS) rDNA barcoding to characterize trypanorhynch larvae infecting commercial teleosts imported to Jordan from Egyptian marine fisheries. Larvae were isolated from 36 examined fish spanning five species: Solea aegyptiaca Chabanaud, 1927, Thunnus spp. South, 1845, and Xiphias gladius Linnaeus, 1758 from the Mediterranean Sea, alongside Plectropomus areolatus (Rüppell, 1830) and Epinephelus tauvina (Forsskål, 1775) from the Red Sea. The core ribosomal ITS cassette was PCR-amplified and sequenced, yielding 20 high-quality operational sequences that were evaluated alongside 101 global GenBank reference entries. Evolutionary and structural dynamics were resolved using distance-based Neighbor-Joining phylogeny, alignment-free 4-mer composition analysis, hierarchical Ward's clustering, and SHAP-based machine-learning classification. Seventeen plerocercoid isolates demonstrated clear genetic homology (>96.3% identity) to global Callitetrarhynchus gracilis references across both marine basins. Six isolates recovered from X. gladius displayed host-driven sub-clustering in the hierarchical dendrogram, positioning close to reference Molicola sequences while verified as C. gracilis via identity metrics. This result highlighting structural population patterns dictated by apex predatory hosts. Crucially, three highly divergent isolates (PV917196-PV917198) derived exclusively from S. aegyptiaca yielded a maximum BLASTN identity of only (~81.5%) to any public sequence, resolving as an independent basal group near the order Lecanicephalidea. Alignment-free machine-learning frameworks achieved perfect binary discrimination (1.000) accuracy) for these three isolates, unmasking systematic oligonucleotide shifts including significant enrichments in TGTG (1.87×) and CTGT (2.72×) motifs, confirming their status as a putative novel species. These findings demonstrate that combining ITS barcoding with alignment-free compositional profiling reliably unmasks host-driven population structures and flags cryptic lines within the Eucestoda, while providing new host and geographical distribution records for the region.},
}

@article {pmid42709875,
year = {2026},
author = {Favuzza, P and Dans, MG and Su, W and Thompson, JK and Hodder, AN and Ngo, A and Penington, JS and Marapana, DS and Dziekan, JM and Papenfuss, AT and de Lera Ruiz, M and Coyle, R and Lee, MCS and McCauley, JA and Lowes, K and Olsen, DB and Sleebs, BE and Cowman, AF},
title = {Dual plasmepsin IX and X inhibitors are refractory to development of resistance.},
journal = {PLoS pathogens},
volume = {22},
number = {9},
pages = {e1014068},
doi = {10.1371/journal.ppat.1014068},
pmid = {42709875},
issn = {1553-7374},
abstract = {Artemisinin-based combination therapies (ACTs) remain the cornerstone of malaria treatment, but emerging resistance threatens their efficacy. The potential for the development of drug resistance against plasmepsin X (PMX)-selective inhibitors and dual plasmepsin IX/X (PMIX/X) inhibitors was investigated in Plasmodium falciparum. A series of PMX-selective (WM4, WM76, WM92) and PMIX/X dual inhibitors (WM382, WM09, WM42) were characterised for potency against parasite growth and enzyme inhibition. In vitro selection experiments showed that all compounds had a high barrier to resistance, although parasites with reduced sensitivity to PMX‑selective inhibitors could still be selected. Resistance mechanisms involved pmx gene amplification and point mutations (D245N, S315P, S359P, I363L) that alter inhibitor binding. Recombinant expression and Michaelis-Menten kinetics demonstrated that these mutations impair drug binding whilst preserving PMX catalytic function. Reverse genetics confirmed that introducing these mutations into the pmx gene resulted in decreased potency of the inhibitors. In this study, resistance to the PMIX/X dual inhibitors evaluated here could not be selected, despite prolonged selection pressure. Antimalarial Resistome Barcoding (AReBar) assays confirmed the absence of pre-existing resistance to either inhibitor class. Critically, PMIX/X dual inhibitors maintained efficacy against parasites with decreased sensitivity to PMX-selective compounds. These findings demonstrate that dual PMIX/X inhibitors present a substantially higher barrier to resistance than PMX-selective inhibitors, informing antimalarial drug development strategies and highlighting dual-target inhibition as a promising approach to mitigate resistance risks.},
}

@article {pmid42709290,
year = {2026},
author = {Gotyal, BS and Shivakumara, KT and Joshi, S and Shreyashwini, HD and Divya, C and Suganya, B and Kavya Yadav, GA and Nagaraja, T},
title = {Unravelling genetic diversity, population connectivity, and evolutionary relationships of Indian mealybugs through mtCO1-based phylogenetic and haplotype analyses.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42709290},
issn = {1573-4978},
mesh = {Animals ; Haplotypes/genetics ; Phylogeny ; India ; *Genetic Variation/genetics ; *Electron Transport Complex IV/genetics ; *Hemiptera/genetics/classification ; Phylogeography ; DNA Barcoding, Taxonomic/methods ; Evolution, Molecular ; Genetics, Population ; DNA, Mitochondrial/genetics ; },
abstract = {BACKGROUND: Mealybugs (Hemiptera: Pseudococcidae) are economically important invasive pests that cause substantial losses in agricultural and horticultural crops worldwide. However, information on their diversity, genetic variation, and population structure in India remains limited. This study investigated the diversity, phylogenetic relationships, and population genetic structure of economically important mealybugs across different agroclimatic regions of India using mitochondrial cytochrome c oxidase subunit I (mtCOI) sequences.

METHODS: A total of 134 mealybug specimens were analysed using an integrative taxonomic approach combining morphological identification and mtCOI-based DNA barcoding. Phylogenetic relationships, haplotype composition, population differentiation, and demographic patterns were assessed using phylogenetic reconstruction, haplotype networks, analysis of molecular variance, neutrality tests, and mismatch distribution analyses.

RESULTS: Fourteen mealybug species belonging to eight genera were identified, with phylogenetic analyses resolving distinct species-specific clades and supporting the utility of mtCOI for species identification. Phenacoccus solenopsis and Planococcus minor exhibited multiple haplotypes and pronounced geographic population structuring. Haplotype networks revealed both widely distributed and geographically restricted haplotypes, indicating historical dispersal, geographic isolation, and localized diversification. Demographic analyses suggested contrasting population histories among geographic regions, including evidence of recent expansion in some populations.

CONCLUSION: The study provides a comprehensive molecular assessment of mealybug diversity and population structure in India. The findings reveal substantial geographic differentiation and complex evolutionary patterns among economically important mealybugs and provide a molecular basis for accurate species identification, invasion monitoring, biosecurity surveillance, and region-specific integrated pest management. These results improve understanding of mealybug dispersal and diversification and support effective management of invasive pest populations in India.},
}

Animals
Haplotypes/genetics
Phylogeny
India
*Genetic Variation/genetics
*Electron Transport Complex IV/genetics
*Hemiptera/genetics/classification
Phylogeography
DNA Barcoding, Taxonomic/methods
Evolution, Molecular
Genetics, Population
DNA, Mitochondrial/genetics

@article {pmid42698851,
year = {2026},
author = {Jukonis, B and Havelka, J and Skujienė, G},
title = {DNA Extraction Optimisation for Minute Land Snails of Vertigo Müller, 1773 (Gastropoda: Vertiginidae): A Comparative Evaluation of Six Methods, Including a Non-Destructive Shell-Preserving Protocol.},
journal = {Ecology and evolution},
volume = {16},
number = {9},
pages = {e74295},
pmid = {42698851},
issn = {2045-7758},
abstract = {No systematic comparison of DNA extraction strategies exists for minute Vertiginidae (shell height < 3 mm), a group posing a dual analytical challenge: extremely low tissue input and co-purified PCR-inhibitory mucus. For legally protected species, an additional requirement to preserve the shell voucher further constrains available protocols. Using Vertigo antivertigo as the model species, we compared six approaches applied to specimens preserved in 96% ethanol (n = 10 per method): two HotSHOT alkaline-lysis protocols (destructive and non-destructive shell-preserving variants), a modified CTAB protocol supplemented with PVP-40 and DTT, and three commercial silica-column kits (GeneJET Genomic, DNeasy Blood & Tissue, QIAamp DNA Micro). DNA yields were quantified by QuantiFluor fluorometry, and PCR performance was subsequently assessed across four loci (COI barcode, COI mini-barcode, ITS1, ITS2). DNeasy Blood & Tissue produced the highest fluorometric concentrations; QIAamp DNA Micro and CTAB + PVP-40 gave intermediate values. The shell-preserving HotSHOT variant yielded lower concentrations but improved A260/230 ratios. BSA and trehalose supplementation increased PCR success in inhibition-prone HotSHOT extracts from 70% to 100%. ITS1 Sanger sequencing of three Vertigo species listed in Annex II of the EU Habitats Directive, all extracted with the shell-preserving protocol, confirmed species-level identification (99.8%-100% BLASTn identity; mean Phred Q > 51). The shell-preserving non-destructive HotSHOT protocol yields sequenceable DNA from protected Vertiginidae while retaining the morphological voucher, making it the preferred option for conservation-genetic monitoring. The practical decision framework documented here-integrating voucher preservation, amplification robustness and per-sample cost-has broad applicability to other minute terrestrial gastropods processed in large-scale biodiversity surveys.},
}

@article {pmid42700117,
year = {2026},
author = {Reeves, LE and Renfro, KL},
title = {Aedes (Ochlerotatus) amateuri Ortega and Zavortink (Diptera: Culicidae) in the Madrean Sky Islands of Arizona, USA: a new country record.},
journal = {Journal of medical entomology},
volume = {63},
number = {5},
pages = {},
doi = {10.1093/jme/tjag126},
pmid = {42700117},
issn = {1938-2928},
support = {//United States Department of Agriculture/ ; },
mesh = {Animals ; Arizona ; *Aedes/anatomy & histology/genetics/classification/physiology ; DNA Barcoding, Taxonomic ; *Ochlerotatus/anatomy & histology/genetics/classification/physiology ; *Animal Distribution ; Female ; Electron Transport Complex IV/analysis ; Phylogeny ; },
abstract = {The mosquito community of the Madrean Sky Islands of southeastern Arizona is diverse and distinct with several species that are endemic or at their northern distributional limits. We collected mosquitoes across many of southeastern Arizona's Sky Island mountain ranges. Here, we present new collection records supported by morphological and molecular evidence that indicate the presence of Aedes (Ochlerotatus) amateuri in at least two Sky Islands ranges, the Santa Rita Mountains and the Dragoon Mountains. Aedes amateuri was described in 2019, previously known only from the type locality in Nuevo Leon and Tamaulipas, Mexico. These records represent the first detection of Ae. amateuri in the USA, and the northernmost collections of this species. The results of DNA barcoding and comparison of Arizona Ae. amateuri cytochrome c oxidase subunit I sequences to those available in publicly accessible databases suggest that Ae. amateuri is present in an additional location in Mexico, south to Honduras. Detailed collection records, ecological information, and a discussion of the morphological and molecular identification of Ae. amateuri are presented.},
}

Animals
Arizona
*Aedes/anatomy & histology/genetics/classification/physiology
DNA Barcoding, Taxonomic
*Ochlerotatus/anatomy & histology/genetics/classification/physiology
*Animal Distribution
Female
Electron Transport Complex IV/analysis
Phylogeny

@article {pmid42702222,
year = {2026},
author = {Sanggari, A and Attah, AO and Rauff-Adedotun, AA and Ridhwan, AM and Bakar, AA and Termizi, FHM},
title = {First Genetic Characterization of Blastocystis sp. Isolated from Captive Wildlife Animals in a Zoological Garden in Perak, Malaysia.},
journal = {Molecular and biochemical parasitology},
volume = {},
number = {},
pages = {111781},
doi = {10.1016/j.molbiopara.2026.111781},
pmid = {42702222},
issn = {1872-9428},
abstract = {Blastocystis, a common eukaryotic symbiont, has gained interest as a potential pathogen affecting animals and humans worldwide. However, there is limited data on Blastocystis prevalence in wildlife animals, especially in Malaysia. To fill this gap, our study aimed to discover the genetic diversity of Blastocystis in captive animals from Taiping Zoo in Perak, Malaysia. We cultured 182 faecal samples from various animal groups using modified Jones medium, incubated at 37°C for warm-blooded animals and 25°C for cold-blooded animals with an incubation period within 48 to 72hours. DNA barcoding was then performed for subtype identification of samples found positive by in-vitro cultivation. Our findings showed an overall Blastocystis sp. prevalence of 19.2% (35/182) with Rodents had the highest prevalence of (50.0% - 3/6) while Artiodactyla had the least (7.7% - 4/52) whereas no Blastocystis was detected in Perissodactyla and Proboscidea. Our study identified various Blastocystis subtypes in different animals including ST1 in wallabies, ST2 in Bornean orangutans, ST3 in African lions, ST4 in ostriches, ST5 in chimpanzees, ST7 in African grey birds, green peafowl, red-billed tree ducks, whooper swans, and small-clawed otters, and ST8 in green peafowls whereas ST37 was found in African spurred tortoise. ST7 was the dominant subtype, while ST1-5, ST8 and ST37 were less common. There were seven Blastocystis subtypes identified as potentially zoonotic (ST1-ST5, ST7 & ST8), highlighting the possible role of captive wild animals as natural reservoirs for human infection.},
}

@article {pmid42702596,
year = {2026},
author = {Shibata, C and Miyata, K and Akao, M and Kumegawa, K and Maruyama, Y and Yang, L and Nagamoto, M and Nozawa, RS and Hirota, T and Iwami, S and Iwanami, S and Maruyama, R},
title = {Plasticity of extrachromosomal DNA segregation during drug adaptation.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42702596},
issn = {2041-1723},
support = {JP24K02312//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP25H01036//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP26K18692//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24K18385//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23KJ2162//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP25K22584//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K18247//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K27446//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24ama221606//Japan Agency for Medical Research and Development (AMED)/ ; JP26ama221228//Japan Agency for Medical Research and Development (AMED)/ ; },
mesh = {*Extrachromosomal DNA/genetics ; Humans ; *Drug Resistance, Neoplasm/genetics ; Single-Cell Analysis/methods ; Cell Line, Tumor ; Mitosis/genetics/drug effects ; *Chromosome Segregation/drug effects ; DNA Copy Number Variations ; },
abstract = {Uneven segregation during mitosis is a striking feature of extrachromosomal DNA (ecDNA). Because ecDNA lacks a centromere, it is thought to segregate stochastically, generating intratumoral heterogeneity in genomic copy number. Drug treatment can readily change ecDNA copy number, enabling cells to acquire drug resistance, yet whether these changes reflect static selection of pre-existing clones or active reconfiguration under stress remains unresolved. To address this, we develop a high-throughput framework combining single-cell DNA sequencing with cellular barcoding for clonal tracking. Single-cell cloning reveals that not all clones exhibit identical segregation modes even under drug-free conditions. Under treatment, resistant populations do not simply arise from pre-existing clones with favorable ecDNA states; instead, some clones actively reconfigure their segregation behavior to generate resistant cells. Thus, although ecDNA generally segregates stochastically, it can undergo nonrandom, actively regulated segregation under drug stress, raising the possibility of therapeutically targeting ecDNA segregation mechanisms to counteract adaptive resistance.},
}

*Extrachromosomal DNA/genetics
Humans
*Drug Resistance, Neoplasm/genetics
Single-Cell Analysis/methods
Cell Line, Tumor
Mitosis/genetics/drug effects
*Chromosome Segregation/drug effects
DNA Copy Number Variations

@article {pmid42703030,
year = {2026},
author = {de Lorenzo, V},
title = {Environmental Release of Genetically Intervened Microorganisms: Towards a New Narrative.},
journal = {Microbial biotechnology},
volume = {19},
number = {9},
pages = {e70441},
pmid = {42703030},
issn = {1751-7915},
support = {CL6-2021-UE 101060625//HORIZON EUROPE Excellent Science/ ; },
mesh = {*Microorganisms, Genetically-Modified/genetics ; Genetic Engineering/legislation & jurisprudence ; *Containment of Biohazards ; Biotechnology/legislation & jurisprudence ; },
abstract = {The deliberate release of genetically engineered microorganisms for environmental applications has remained largely blocked since the early days of recombinant DNA technology, when limited ecological knowledge, lack of success stories and public apprehension shaped a culture of caution and restrictive regulation. Despite profound advances in microbial ecology, synthetic biology and genetic design, current frameworks still rely on outdated assumptions and legacy regulations that equate engineered microbes with inherent danger and demand unrealistic forms of absolute containment. This review examines how laboratory-trained microorganisms exist on a continuum with naturally evolved life, and that their risks are neither categorically different nor greater. Rather than pursuing unachievable containment, governance should shift towards traceability, stewardship and long-term monitoring through genomic barcodes, digital twins and transparent oversight. The vision moves from domination and control to care and partnership recognizing engineered microbes as live amendments capable of restoring degraded ecosystems. Achieving this transformation requires new terminology, phased field-trial frameworks, improved scaling methods, and the integration of epistemological perspectives that emphasize reciprocity and coexistence with nature. Reframing biotechnology in this way could finally unlock the capacity of engineered microorganisms to contribute responsibly and effectively to planetary repair in an era of escalating environmental crises.},
}

*Microorganisms, Genetically-Modified/genetics
Genetic Engineering/legislation & jurisprudence
*Containment of Biohazards
Biotechnology/legislation & jurisprudence

@article {pmid42706506,
year = {2026},
author = {Romano, I and Pasolli, E and Walser, JC and Ventorino, V and Reinhard, S and Magaraci, G and Pepe, O and Bodenhausen, N},
title = {A hybrid and cost-efficient barcoding strategy for full-length 16S rRNA gene nanopore sequencing of environmental samples.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42706506},
issn = {1471-2164},
mesh = {*RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic/methods/economics ; *Nanopore Sequencing/methods/economics ; *Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; Nanopores ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Accurate species-level identification of bacteria in complex environmental samples is essential for applications in biotechnology, ecological monitoring, and clinical diagnostics. Short-read platforms such as Illumina frequently truncate the 16S rRNA gene, limiting taxonomic resolution. In this work, we applied Oxford Nanopore Technology (ONT) long-read sequencing to full-length 16S rRNA amplicon in samples from natural soil amended with lignocellulosic biomass and a simplified microbial community derived from cultures grown on selective and differential carboxymethyl cellulose (CMC)-based substrates, with the aim to evaluate the difference in performance between a real, complex community and a less complex system. To reduce consumable costs, we substituted the standard ONT Barcoding kits with an in-house hybrid barcoding workflow. Specifically, PacBio PCR-based barcoding protocol was used for sample indexing, followed by library preparation using the ONT Ligation Sequencing Kit. This simplified approach retained compatibility with MinION and Flongle flow cells and supported accurate downstream demultiplexing while lowering barcode costs substantially. Additionally, a new bioinformatic workflow tailored to ONT data was implemented.

RESULTS: Overall, the hybrid protocol significantly reduced per-sample barcoding costs while preserving high sequencing quality and throughput. The sequencing run yielded over 5 Gb of quality-filtered data (Q-score ≥ 10). Furthermore, the new bioinformatic workflow allowed taxonomic assignment at the species level for 49.38% of annotated taxa, compared to just 4.59% using Illumina NovaSeq sequencing of the V3-V4 region. ONT also recovered 2.3 times more genera and 1.3 times more families. Although 16S rRNA gene sequencing often cannot distinguish between closely related species, particularly within taxonomically complex groups, in this work, full-length reads substantially improved both taxonomic resolution and database matching.

CONCLUSIONS: These results show that full-length 16S rRNA sequencing with ONT, paired with a low-cost barcoding strategy, enhanced taxonomic resolution compared to short-read workflows. This approach also offers a scalable and cost-effective option for high-resolution microbiome profiling in research and applied settings.},
}

*RNA, Ribosomal, 16S/genetics
*DNA Barcoding, Taxonomic/methods/economics
*Nanopore Sequencing/methods/economics
*Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing
Nanopores
Sequence Analysis, DNA

@article {pmid42708715,
year = {2026},
author = {Zhu, J and Song, C and He, Y and Guan, H and Li, T and Zhang, T and Liao, C and Zhou, J and Huang, L},
title = {Machine Learning-Assisted Nanoplasmonic Barcode Array-Coupled Microfluidic Platforms for Exosome Profiling and Organotropic Metastasis Analysis.},
journal = {Analytical chemistry},
volume = {98},
number = {35},
pages = {25836-25847},
doi = {10.1021/acs.analchem.6c03129},
pmid = {42708715},
issn = {1520-6882},
support = {20200824162253000//Shenzhen Science and Technology Innovation Program/ ; GXWD202012311658//Shenzhen Science and Technology Innovation Program/ ; RCBS20210706092409020//Shenzhen Science and Technology Innovation Program/ ; 2023A1515010647//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 22004135//National Natural Science Foundation of China (NSFC)/ ; A2303049//Shenzhen Medical Research Fund/ ; },
mesh = {*Exosomes/metabolism/chemistry ; *Machine Learning ; Humans ; Surface Plasmon Resonance ; *Microfluidic Analytical Techniques/instrumentation ; Gold/chemistry ; Neoplasm Metastasis ; Tumor Microenvironment ; Coculture Techniques ; },
abstract = {Elucidating the mechanisms of organotropic metastasis requires the in situ profiling of exosomes within the tumor microenvironment. However, conventional assays are normally based on the isolation of exosomes from biological fluids, which disrupts their native spatial context. Moreover, these assays frequently exhibit limited analytical sensitivity, and the types of exosome phenotypes detected simultaneously are inherently restricted by fluorescent spectral overlap. To address the issue, we present an integrated microfluidic platform coupling a biomimetic tumor-stroma coculture system with a nanoplasmonic antibody barcode array, enabling the in situ profiling of exosomes within the cellular microenvironment on-chip. By utilizing gold nanoislands (GNIs) as substrates, the device leverages localized surface plasmon resonance (LSPR) to achieve fluorescence enhancement and improved sensitivity. By employing spatial barcoding, this system overcomes the constraints imposed by spectral overlap and circumvents the limitations associated with the number of conventional multicolor fluorescence detection channels. This platform possesses the capability of conducting multiplexed qualitative analyses of exosome biomarkers. Downstream machine learning decoded these high-dimensional profiles, resolving distinct exosomal subpopulations on the basis of their unique phenotypic profiles. Overall, this platform establishes a robust, universal strategy for investigating exosome-mediated intercellular communication and metastatic niche formation.},
}

*Exosomes/metabolism/chemistry
*Machine Learning
Humans
Surface Plasmon Resonance
*Microfluidic Analytical Techniques/instrumentation
Gold/chemistry
Neoplasm Metastasis
Tumor Microenvironment
Coculture Techniques

@article {pmid42697995,
year = {2026},
author = {Michielsen, L and Prjibelski, AD and Foord, C and Spiegelman, Y and Kim, T and Hu, W and Jarroux, J and Hsu, J and Pfeil, R and Zhang, X and Gan, L and Tomescu, AI and Hajirasouliha, I and Tilgner, HU},
title = {Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.},
journal = {Nature methods},
volume = {23},
number = {9},
pages = {1869-1881},
pmid = {42697995},
issn = {1548-7105},
support = {MIRA R35 GM152101-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; MIRA R35 GM138152//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Brain Initiative grant 1RF1MH121267-01//U.S. Department of Health & Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health)/ ; U01 DA053625-01//U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; 2T32DA039080//U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; GRFP # 2139291//National Science Foundation (NSF)/ ; },
mesh = {Animals ; Protein Isoforms/genetics/metabolism ; Mice ; *Single-Cell Analysis/methods ; *Brain/metabolism/cytology ; Software ; Neurons/metabolism ; Single-Cell Gene Expression Analysis ; },
abstract = {Spatial long-read technologies are increasingly common but usually lack single-cell resolution. This leaves unanswered whether spatially variable isoforms reflect variability within one cell type or differences in region-specific cell-type composition. Here, we developed Spl-ISO-Seq2 (500-nm resolution) and accompanying software, Spl-IsoQuant-2 and Spl-IsoFind, enabling long-read sequencing of >450 million barcodes versus 80,000 previously. Applying this to the adult mouse brain, we compared differential isoform abundance between known regions and spatial isoform patterns independent of predefined regions. Both identified overlapping hits, for example, Rps24 in oligodendrocytes. For known Snap25 spatial isoform variation, we show that it occurs in excitatory neurons. The region-agnostic approach also uncovered patterns missed by region-based comparisons, for example, for Ighm. Notably, many spatial isoform signals are not driven by cell-type composition alone. Finally, our software is applicable to many spatial and single-cell protocols, demonstrating reproducibility between platforms (for example, Visium HD/Stereo-seq). Overall, our experimental/analytical methods enable a submicron-resolution-isoform view and open avenues for spatial isoform disease research.},
}

Animals
Protein Isoforms/genetics/metabolism
Mice
*Single-Cell Analysis/methods
*Brain/metabolism/cytology
Software
Neurons/metabolism
Single-Cell Gene Expression Analysis

@article {pmid42698735,
year = {2026},
author = {Bienias, J and Trębicki, Ł and Karlik, G and Grabowski, M},
title = {First Taxonomically Curated DNA Barcode Reference Library for Polish Myriapods Fills an Important Knowledge Gap for Soil Invertebrates in Central Europe, Part I: Millipedes (Myriapoda: Diplopoda).},
journal = {Ecology and evolution},
volume = {16},
number = {9},
pages = {e74268},
pmid = {42698735},
issn = {2045-7758},
abstract = {DNA barcoding is a highly effective tool for species identification, complementing taxonomic and phylogenetic studies while also playing a key role in biomonitoring and uncovering cryptic diversity. Techniques such as DNA barcoding, metabarcoding and environmental DNA (eDNA) analysis are widely applied in biodiversity conservation, tracking invasive species and studying trophic interactions. To carry out this type of research effectively, a robust DNA barcode library is essential, built upon high-quality genetic sequences and accurate taxonomic identification. Here, we present the results of a large-scale DNA barcoding study of Polish diplopod species (Myriapoda: Diplopoda), providing an up-to-date checklist of species recorded in Poland and a reference DNA barcode library. We deliver data on 981 individuals identified to species level, of which 468 have COI sequence data. 58 out of 93 species recorded for Poland were successfully barcoded, representing 62% of the national fauna. Additionally, we explore future research directions, potential cryptic diversity and shifts in the national fauna, including newly recorded species for Poland-Melogona broelemanni (Verhoeff, 1897). Our findings highlight the significance of ongoing monitoring and molecular methods in tracking biodiversity changes.},
}

@article {pmid42694576,
year = {2026},
author = {Li, PP and Bai, M and Chang, LX},
title = {Notes on the subfamily Pleganophorinae, with the description of a new species of the genus Trochoideus Westwood, 1833 (Coleoptera, Endomychidae) from China.},
journal = {ZooKeys},
volume = {1290},
number = {},
pages = {293-317},
pmid = {42694576},
issn = {1313-2989},
abstract = {The subfamily Pleganophorinae (Coleoptera, Endomychidae), an unusual group distinguished by its distinctive antennal morphology, is reported for the first time in mainland China with the description of Trochoideus sinensis sp. nov. from Guangdong and Jiangxi and the first records of T. desjardinsi Guérin-Méneville, 1838 and T. tonkineus Strohecker, 1980 from Hainan. Additionally, the male of Dadocerus nitidus Arrow, 1920 is discovered for the first time, and the sex assignment in the original description is corrected. Morphological diagnoses are augmented by comparative analyses of antennal dimorphism and mitochondrial cytochrome c oxidase I (COI) gene barcoding data. A key to the Chinese species of Trochoideus is provided.},
}

@article {pmid42688432,
year = {2026},
author = {Collet, M and Proisy, C and Talaga, S and Guidez, A and Vlandis, I and Keovongsack, A and Carinci, R and Gaborit, P and Davy, D and Duchemin, JB},
title = {A mangrove-based dataset to study the ecology of Neotropical mosquitoes (Diptera, Culicidae) in French Guiana.},
journal = {ZooKeys},
volume = {1290},
number = {},
pages = {227-239},
pmid = {42688432},
issn = {1313-2989},
abstract = {Understanding how mosquitoes are distributed across natural and anthropogenic environments is crucial but remains challenging in tropical regions. Here, we present a sampling-event dataset designed to document Neotropical mosquitoes (Diptera, Culicidae) assemblages associated with mangrove habitats in French Guiana. A total of 334 collection events were carried out across a variety of coastal and estuarine mangrove habitats that differed in species composition, structure, age, and proximity to urban settlements. The dataset comprises 21,765 mosquito specimens belonging to 14 genera and 62 species. The most abundant taxa were unidentified Culex belonging to the subgenus Melanoconion (8,580; 39.4%), Coquillettidia venezuelensis (4,471; 20.5%), Deinocerites magnus (3,354; 15.4%), and Culex portesi (1,496; 6.9%), together representing 82.2% of all collected specimens. The dataset includes voucher specimens, associated DNA barcodes, and incorporates male genitalia dissections for selected taxa to support species identifications. This sampling-event dataset provides standardised data on mosquito occurrence and abundance in mangrove ecosystems.},
}

@article {pmid42688724,
year = {2026},
author = {Alvear, S and Young, CJ and Vasquez-Valverde, LF and Marek, PE},
title = {Identification of Spiropoeus fischeri Brandt, 1833 from captive bred millipedes in Zoos (Diplopoda, Spirostreptida, Spirostreptidae).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e196645},
pmid = {42688724},
issn = {1314-2828},
abstract = {BACKGROUND: Large millipedes of the family Spirostreptidae are often kept in zoos and other educational living collections in the United States where they are commonly known as giant African millipedes. Although accurate species determinations are needed for permitting, live animal care protocols and outreach, many of these millipedes originate from poorly-documented sources (e.g. the exotic species trade). This leaves species determination unclear and hampers understanding and communicating the species natural history and other biological information.

NEW INFORMATION: We found that Spiropoeus fischeri Brandt, 1833 is the identity of a large millipede commonly exhibited alive by zoos in the U.S. Although this large (14 cm-long), easy-to-raise millipede has been kept for decades in living exhibits, its identity was unknown until now. We provide a detailed explanation of the diagnostic morphology to identify S. fischeri, and supply cytochrome oxidase subunit I (COI) DNA barcode sequences of individuals. With accurate knowledge of its identity, zoos and educational collections can now share with the public a species name and rich biological information about S. fischeri, including its life history and home range in sub-Saharan Africa.},
}

@article {pmid42692021,
year = {2026},
author = {Zhu, YJ and Wang, YQ and Xu, HT},
title = {Spatially resolved synaptic connectome mapping with FISH-decodable CASS barcodes.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101579},
doi = {10.1016/j.crmeth.2026.101579},
pmid = {42692021},
issn = {2667-2375},
abstract = {Mapping neuronal connectivity is essential for understanding the structure and function of neural circuits. While high-throughput, cost-effective methods using barcoded rabies viruses provide valuable cellular-level insights, they are limited by the spatial resolution of barcode sequencing. To provide a fluorescent in situ hybridization (FISH)-compatible alternative for spatial barcode readout, we developed the CASS (combination of artificial short sequences) barcode, an error-robust and in situ-hybridization-detectable tool. By combining CASS barcoding with rabies virus monosynaptic tracing, we enable in situ connectome mapping through FISH-based barcode decoding. Using this approach, we identified 1,532 synaptic pairs connected to neurons in the primary visual cortex with spatial precision across three mice, demonstrating its efficiency and scalability. This method provides a FISH-based approach for identifying neuronal connectivity with spatial context and may facilitate future integration of connectivity mapping with molecular profiling, thereby advancing our understanding of neural circuits.},
}

@article {pmid42694350,
year = {2026},
author = {He, Y and Wu, M and Wang, A and Gao, C},
title = {Comparative chloroplast genomics of six Bupleurum (Apiaceae) accessions: candidate barcodes, phylogeny based on available plastomes, and candidate RNA-editing sites.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1916637},
pmid = {42694350},
issn = {1664-462X},
abstract = {INTRODUCTION: Bupleurum L. (Apiaceae), a taxonomically intricate genus of about 190 species and a source of Radix Bupleuri (Chai Hu), is difficult to discriminate because of convergent morphology, infraspecific variation, and limited genomic sampling. This study aimed to characterize plastome variation, identify and validate candidate molecular markers, reconstruct plastid phylogenetic relationships, and assess candidate plastid RNA-editing sites in Bupleurum.

METHODS: We assembled six plastomes from subgenus Bupleurum, screened 51 Bupleurum plastomes for diagnostic loci, reconstructed whole-plastome and partitioned protein-coding-sequence phylogenies, and predicted plastid C-to-U RNA-editing candidates across the six newly assembled plastomes using a PREP-Cp-compatible workflow. Candidate barcode performance was evaluated against the reference plastome phylogenies, and codon-based models were used to test for positive selection.

RESULTS: The plastomes were 154,496-155,778 bp with the canonical quadripartite structure and GC contents of 37.67-37.73%. Gene content was stable (131-132 genes; 86-87 protein-coding genes); B. falcatum subsp. cernuum lacked ycf15 but contained an additional inverted-repeat-associated ycf1 annotation. A/U-ending synonymous codons were favoured. Finite pairwise Ka/Ks estimates were below 1 for most genes, and site-specific codon models detected no positive selection. Each plastome contained 55-61 pure microsatellites, dominated by A/T mononucleotide motifs. MarkerSeek ranked 265 features and identified atpF-atpH, petA-psbJ, rpl32-trnL-UAG, and ycf1 as leading candidate barcodes. ycf1 recovered 38 of 41 nodes strongly supported by both reference trees, whereas a partitioned four-locus analysis recovered 40 of 41 and distinguished all 51 accession sequences. However, only one of seven multi-accession operational binomial groups was monophyletic, and only one showed a positive local barcode gap. The whole-plastome phylogeny recovered Bupleurum as monophyletic relative to Chamaesium. The two sampled Penninervia accessions occupied early-diverging positions without forming an exclusive clade. B. falcatum subsp. cernuum was sister to B. ranunculoides, with B. ranunculoides subsp. telonense sister to that pair. A partitioned 74-CDS analysis recovered the same key relationships and 45 of 50 internal bipartitions. Across the six newly assembled plastomes, 57-63 nonsynonymous C-to-U candidates were predicted per accession (367 total) in 21-22 genes; 269 affected the second codon position and 98 the first.

DISCUSSION: Bupleurum plastomes are structurally conservative but retain localised divergence useful for marker development. Concordant whole-plastome and CDS genealogies support genus monophyly, whereas sparse Penninervia sampling and maternal plastid inheritance preclude rejecting traditional subgeneric classification. The predicted RNA-editing sites represent candidates for future experimental validation rather than an established Bupleurum editome. These genomic resources support authentication, conservation, and evolutionary research in Bupleurum.},
}

@article {pmid42685017,
year = {2026},
author = {Hernandez-Europa, Y and Dickson, G and Ahmed, MZ and Schutze, MK and Tarlinton, B and Williams, B and Hauxwell, C},
title = {An invasive variant of the pasture mealybug Heliococcus summervillei (Hemiptera: Pseudococcidae) and its obligate endosymbiont Tremblaya phenacola (Enterobacterales: Enterobacteriaceae).},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag266},
pmid = {42685017},
issn = {1938-291X},
support = {//Meat & Livestock Australia (MLA), the Australian Government/ ; //Queensland University of Technology (QUT)/ ; },
abstract = {The pasture mealybug Heliococcus summervillei Brookes (Hemiptera: Pseudococcidae) is the cause of extensive pasture dieback in Australia and is an emerging biosecurity threat to pasture and crop grasses in the Americas. In this study, we present a morphological and molecular comparison of contemporary Australian specimens of H. summervillei and the primary bacterial endosymbiont Candidatus Tremblaya phenacola Gruwell (Enterobacterales: Enterobacteriaceae) with reference to historical and published specimens. Molecular analyses were conducted using three host nuclear markers (18S, 28S-D2, dynamin) and the universal bacterial marker (16S V3-V4 region). Our results identify a new, highly invasive variant of H. summervillei associated with the ongoing dieback outbreak in Australia. This work uses 16S barcoding to support host-based morphological and molecular approaches to differentiate this new variant from the type specimens.},
}

@article {pmid42687263,
year = {2026},
author = {Xu, K and Huan, X and Xiao, Y},
title = {m6A-ARTR-DBiT for Spatial Mapping of m6A Epitranscriptome.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.6c00603},
pmid = {42687263},
issn = {1554-8937},
support = {2023CXQD049//Central South University/ ; 25DX2800100//Science and Technology Commission of Shanghai Municipality/ ; },
abstract = {N 6-methyladenosine (m6A) is a widespread RNA modification that regulates RNA metabolism and gene expression, yet most sequencing methods rely on isolated RNA and therefore lose its spatial context. This In Focus article surveys methodological advances in transcriptome-wide m6A detection and highlights m6A-ARTR-DBiT, a spatial m6A profiling assay that leverages reverse-transcription-based detection and deterministic barcoding in tissue to map transcriptome-wide m6A distribution while preserving native tissue context. This platform enables researchers to investigate how m6A patterns vary across distinct tissue regions, developmental structures, and local gene regulatory networks, bridging the gap between spatially patterned epitranscriptomic deposition and gene regulation.},
}

@article {pmid42680524,
year = {2026},
author = {Bandyopadhyay, S and Bickart, LB and Abudayeh, G and Majumdar, S and Farraday, M and Sutton, BP and Chan, J},
title = {19F Activity-Based Barcoding Enables Simultaneous Measurement of pH and Analyte Reactivity.},
journal = {ACS sensors},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssensors.6c02375},
pmid = {42680524},
issn = {2379-3694},
support = {0100085//Division of Biological Infrastructure/ ; //Arnold and Mabel Beckman Foundation/ ; 15-4521//Roy J. Carver Charitable Trust/ ; //University of Illinois at Urbana-Champaign/ ; },
abstract = {Activity-based sensing (ABS) probes are designed to report on analyte activity, but their readouts are often influenced by local pH. Because both probe response and analyte reactivity can vary across physiological pH ranges, signal changes can reflect altered chemistry rather than differences in analyte abundance. Here, we present a 19F magnetic resonance imaging (MRI) platform that converts analyte activation into a pH-dependent chemical shift barcode, enabling simultaneous assignment of both properties within a single measurement. Using nuclear magnetic resonance spectroscopy and MRI, we achieve accurate pH mapping across a broad physiological range and show that F-pHOx, an H2O2-responsive probe, enables quantitative inference of hydrogen peroxide activity across varying pH conditions. We further demonstrate its performance in an ex vivo mouse stomach model, which is a complex environment exhibiting substantial pH heterogeneity. Importantly, the modular fluorophenol reporter is compatible with diverse ABS triggers. This strategy reveals how environmental conditions can influence apparent chemical activity, which is often overlooked.},
}

@article {pmid42681282,
year = {2026},
author = {Berruto, F and Bortolot, M and Lumini, E and Bianciotto, V},
title = {From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3045},
number = {},
pages = {185-208},
pmid = {42681282},
issn = {1940-6029},
mesh = {*Mycorrhizae/genetics/classification/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Soil Microbiology ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {In recent years, DNA sequencing technologies have advanced considerably with the rise of Next-Generation Sequencing (NGS) platforms, which have transformed microbial ecology research. These approaches enable the characterization of entire communities by using DNA traces to identify organisms taxonomically from a single sample. Arbuscular mycorrhizal fungi (AMF) are no exception and represent one of the most extensively studied groups of soil fungi. This chapter presents protocols for high-throughput, sequence-based analysis of AMF communities, covering the complete workflow from DNA extraction in plant or soil samples to the bioinformatic processing of sequencing data. It particularly focuses on rRNA gene metabarcoding, the most common strategy to provide estimates of AMF diversity and community composition through the amplification of DNA with taxon-specific primers followed by sequencing of barcode regions. Alternative strategies are described to accommodate different research objectives, including the selection of molecular markers.},
}

*Mycorrhizae/genetics/classification/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
Soil Microbiology
DNA Barcoding, Taxonomic/methods
DNA, Fungal/genetics
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid42681835,
year = {2026},
author = {Mann, AK and James, L and Patel, HD and Delcheva, I and MacGregor, M and Fraser-Miller, SJ and Gascooke, JR and Sharma, P and Neto, C and Gibson, CT and Chalker, JM},
title = {Direct Photopatterning on Polysulfide Polymers for Engineered Surfaces and Anti-Counterfeiting Technology.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.6c08290},
pmid = {42681835},
issn = {1944-8252},
abstract = {Laser modification of polymer surfaces is critical in many contexts, including self-cleaning materials, microelectronics, and biomedical research. Despite their utility, accessing these modified polymers requires expensive or complex materials and multistep fabrication, masking, and washing processes. Here, we present a simple and direct laser writing method for creating diverse, stable, and highly complex patterns on a polysulfide polymer made by inverse vulcanization. The key innovation is the spatial engineering and patterning of the polymer surface by precise control of the laser irradiation time. The polymer's vitrimer-like S-S bond network preserves complex surface patterns with high fidelity and long-term stability. Motifs such as lines, dots, channels, grids, teardrops, checkerboards, and fish scales were reliably and repeatedly created, highlighting the material's robust and versatile patterning capabilities. Hierarchical patterns could also be achieved by combining nanoscale hot-press templating with laser modification. This patterning versatility allows modulation of hydrophobicity, templated self-assembly of gold particles, and precise micrometer-scale optical structures, including diffraction elements and dynamic optical barcodes, with potential for anti-counterfeiting applications.},
}

@article {pmid42682616,
year = {2026},
author = {He, Y and Gao, C},
title = {Comprehensive plastome variation and RNA editing in Mentha: insights into phylogenetic relationships and candidate DNA barcodes.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1889271},
pmid = {42682616},
issn = {1664-462X},
abstract = {INTRODUCTION: Mentha is an economically and medicinally important genus in Lamiaceae, but its taxonomy and species delimitation remain challenging because of frequent hybridization, polyploidy, and marked morphological plasticity.

METHODS: In this study, we comparatively analyzed 12 plastomes representing major Mentha species, hybrid taxa, and unresolved accessions, including four newly assembled genomes, to characterize plastome structure, repeat composition, sequence divergence, phylogenetic relationships, and plastid RNA editing. The M. arvensis plastome and RNA-seq datasets originated from independent Swiss and Indian accessions, respectively.

RESULTS: The plastomes were highly conserved in overall organization, ranging from 151,824 to 152,154 bp and displaying the typical quadripartite structure. Gene content and order were largely stable across taxa, with only minor variation likely associated with annotation differences at IR/SC boundary regions. Codon usage analysis revealed a clear bias toward A/U-ending synonymous codons, and most shared protein-coding genes showed low Ka/Ks ratios, indicating predominant purifying selection. Repeat analyses showed that simple sequence repeats were mainly composed of A/T-rich mononucleotide motifs, whereas long repeats were concentrated in the 30-40 bp size class. Comparative analyses identified six hypervariable regions, namely ccsA-ndhD, ycf1, ndhD, rpl32-trnL-UAG, rbcL-accD, and petA-psbJ, which represent promising candidate plastid markers for species discrimination. Phylogenetic analysis based on complete plastomes provided strong support for relationships among the sampled taxa and recovered a close affinity among M. aquatica, M. arvensis, and M. canadensis. In addition, RNA-seq analysis of M. arvensis identified 17 candidate plastid RNA editing sites, most of which were C-to-U conversions and nonsynonymous events.

DISCUSSION: Together, these results expand plastid genomic resources for Mentha and provide a useful framework for phylogenetic inference, species identification, and future germplasm utilization.},
}

@article {pmid42666491,
year = {2026},
author = {Xiao, S and Cao, M and Yin, Q and Liu, P and Xie, B and Ouyang, L and Wang, J and Tu, P},
title = {Correlation analysis of secondary metabolites, metal elements, and anti-BSA denaturation activity in different parts of Rhododendron tomentosum from China.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1900896},
pmid = {42666491},
issn = {1664-462X},
abstract = {BACKGROUND: Rhododendron tomentosum (also known as Ledum palustre L.) is a traditional medicinal plant, yet the accumulation patterns of secondary metabolites and the distribution of metal elements across its different parts (roots, old branches, young branches, branches and leaves, leaves, flowers, and fruits) remain largely unclear.

METHODS: UPLC-MS, HPLC, ICP-MS, and chemometric tools were employed to analyze the secondary metabolites (predominantly flavonoids) and the contents of Al, Fe, Cu, Mg, K, Ca, Mn, and Zn in different parts of Chinese R. tomentosum. The anti-inflammatory activity was evaluated by the inhibition rate against bovine serum albumin (BSA) denaturation.

RESULTS: Three coumarin compounds-the glycosides aesculin and fraxin, and their aglycone fraxetin-were present in all parts. Aesculin and fraxin were abundant in young branches, old branches, and roots. Hyperoside, guaijaverin, isoquercitrin, and avicularin were mainly distributed in leaves and young branches. Quercitrin was abundant in flowers, followed by fruits, with the highest levels observed in samples rich in reproductive organs. The contents of Al and Fe were relatively high in roots, whereas the levels of Mg, K, Ca, and Mn were relatively low in roots and old branches. Correlation analysis revealed that Al and Fe showed significant positive correlations with coumarins (aesculin and fraxin), while Al exhibited significant negative correlations with flavonoid glycosides (hyperoside, guaijaverin, isoquercitrin, avicularin, and quercitrin). Mg, K, Ca, and Mn were significantly negatively correlated with coumarins but significantly positively correlated with flavonoid glycosides. Cu was present at relatively low levels and showed significant negative correlations with aesculin and fraxin. Significant positive correlations were also observed between Al and Fe, Al and Zn, and Fe and Zn, as well as among Mn, Mg, K, and Ca. K was positively correlated with Cu, and Mn was positively correlated with Zn. Conversely, Mg was negatively correlated with Al, and K was negatively correlated with both Al and Fe. Inhibition rates of roots, old branches, and young branches were lower than those of branches and leaves, leaves, fruits, and flowers. Flowers and fruits exhibited high inhibition rates. The inhibition rate was negatively correlated with aesculin and fraxin, and positively correlated with hyperoside, guaijaverin, isoquercitrin, avicularin, and quercitrin.

CONCLUSION: This study provides new insights into the intrinsic relationships among "DNA molecular identification - different parts - chemical composition - function" in Chinese R. tomentosum, facilitating its artificial cultivation, selective breeding, and comprehensive utilization. Specifically, the findings suggest that: (1) R. tomentosum may serve as a candidate woody species for studying the co-accumulation of coumarins with Al/Fe under acidic soil conditions, although this hypothesis requires experimental validation; (2) Al and Fe are highly co-accumulated and may synergistically influence secondary metabolite accumulation in different parts together with Mg and K, also warranting further testing; (3) Hyperoside, avicularin, guaijaverin, isoquercitrin, and quercitrin may be the major potential anti-BSA denaturation components based on correlation and in vitro activity assays; and (4) Combining DNA barcoding (ITS sequences) and flavonoid profiling may help distinguish broad-leaved and fine-leaved types of Chinese Ledum species, pending further verification.},
}

@article {pmid42669352,
year = {2026},
author = {Bolivar-Buitrago, LE and Carrero-Sarmiento, D and Hoyos-Lopez, R},
title = {COI DNA barcoding of phlebotomine sand flies from the Pamplonita River basin, Norte de Santander, Colombia.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108298},
doi = {10.1016/j.actatropica.2026.108298},
pmid = {42669352},
issn = {1873-6254},
abstract = {Leishmaniasis remains a major neglected tropical disease in the Americas, where transmission involves diverse parasites, reservoirs, and phlebotomine sand fly vectors. Accurate sand fly identification is essential for surveillance, but morphology-based diagnosis may be difficult in closely related taxa and isomorphic females. This study evaluated COI DNA barcoding for identifying sand flies from the Pamplonita River basin, Colombia. Adult sand flies were collected in three ecological settings using Centers for Disease Control and Prevention (CDC) light traps, Shannon traps, and active searching. Specimens were morphologically examined and processed for DNA extraction, cytochrome c oxidase subunit I (COI) amplification, and bidirectional sequencing. Sequences were edited, aligned, screened for stop codons and indels, and analyzed using diversity estimates, Kimura two-parameter (K2P) distances, neighbor-joining (NJ), and PhyML maximum-likelihood (ML) clustering under the General Time Reversible model with invariant sites and gamma-distributed rates (GTR+I+G) with 1,000 bootstrap replicates. Sixty-two study sequences representing seven species were analyzed with three external sequences. The curated alignment contained 65 sequences of 660 bp, with no gaps or ambiguous bases. The study dataset included 24 haplotypes and 185 polymorphic sites. Mean interspecific K2P distances ranged from 3.55% between Pintomyia (Pi.) longiflocosa and Pi. torvida to 19.82% between Psathyromyia (Pa.) shannoni and Pi. evansi. Neighbor-joining and maximum-likelihood analyses recovered species-level clusters consistent with morphological assignments. COI barcoding supported the molecular discrimination of medically relevant sand flies from northeastern Colombia and provides a regional baseline for vector surveillance in an area of epidemiological interest.},
}

@article {pmid42670258,
year = {2026},
author = {Ng, CF and Krishnamurthy, D and Dextre, A and Chorlay, A and Ott, M and Fletcher, DA},
title = {LUCas: Light-Uncaged Cas13a using photocleavable interfering guide RNAs.},
journal = {Nucleic acids research},
volume = {54},
number = {16},
pages = {},
pmid = {42670258},
issn = {1362-4962},
support = {//Schmidt Science Fellowship/ ; //Rhodes Trust/ ; //Burroughs Wellcome Career Award/ ; //European Molecular Biology Organization/ ; DBI-1548297//National Science Foundation/ ; //Wagner Foundation/ ; 4R33AI140465-04//National Institute of Allergy and Infectious Diseases/ ; //James B. Pendleton Charitable Trust/ ; //Gordon and Betty Moore Foundation/ ; },
mesh = {*RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *CRISPR-Cas Systems/genetics ; Kinetics ; *CRISPR-Associated Proteins/genetics/metabolism ; Humans ; Ultraviolet Rays ; Photolysis ; Light ; },
abstract = {CRISPR diagnostics enable sensitive detection of infectious diseases, with the RNA endonuclease Cas13a providing specific, amplification-free RNA detection through collateral trans-cleavage of fluorescent reporters. However, background cleavage from unbound enzyme, contaminating nucleases, and unsynchronized initiation of reactions limits assay sensitivity and interpretability. A strategy to precisely control the onset of Cas13a catalytic activity, essentially a molecular "starting gun," would address these challenges. Here, we introduce Light-Uncaged Cas13a (LUCas), a light-controllable system that directly blocks Cas13a trans-cleavage activity using a photocleavable interfering guide RNA, even in the presence of target RNA. Brief UV illumination releases this suppression, restoring full activity. Quantitative kinetic analysis reveals an ~100-fold suppression of trans-cleavage activity prior to photo-uncaging, including suppression of target-independent background activity. Using measured kinetic parameters, we predict and experimentally validate the limit of detection of the LUCas system for direct detection. We further demonstrate a multiplexed detection strategy termed "temporal barcoding," enabling quantitative detection of viral co-infections in a single bulk reaction. Finally, LUCas is shown to be compatible with one-pot isothermal amplification for enhanced sensitivity and direct detection of target RNA spiked into blood plasma. Together, these results establish LUCas as a general framework for mechanistically informed, light-based control of Cas13a activity.},
}

*RNA, Guide, CRISPR-Cas Systems/genetics/metabolism
*CRISPR-Cas Systems/genetics
Kinetics
*CRISPR-Associated Proteins/genetics/metabolism
Humans
Ultraviolet Rays
Photolysis
Light

@article {pmid42677405,
year = {2026},
author = {Zhang, WY and Pei, WK},
title = {[Cellular barcoding and next-generation lineage tracing: concepts and applications].},
journal = {Sheng li xue bao : [Acta physiologica Sinica]},
volume = {78},
number = {4},
pages = {731-740},
doi = {10.13294/j.aps.2026.0063},
pmid = {42677405},
issn = {0371-0874},
mesh = {*Cell Lineage/genetics ; Humans ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; CRISPR-Cas Systems ; Animals ; Single-Cell Analysis ; },
abstract = {Lineage tracing is a fundamental technique for dissecting cell fate decisions and development process. With recent advances in high-throughput sequencing and single-cell sequencing technologies, cellular barcoding-based lineage tracing strategies have transitioned from low-throughput labeling methods to high-resolution, multidimensional lineage reconstruction. In this review, we systematically summarize four major barcoding paradigms: viral integration-based random integration barcodes, transposon-based random integration barcodes, recombinase-mediated DNA rearrangement (e.g., Cre-loxP), and CRISPR-Cas9-based mutation recording systems. We describe their principles, representative studies, technical advantages, and limitations. Furthermore, we discuss the core bottlenecks in terms of editing precision, integration of spatiotemporal information, and non-invasive lineage tracing, with a focus on cutting-edge advancements such as prime editing, sequential recording systems, strategies for integrating spatial transcriptomics, and epigenetic tracing. Overall, single-cell lineage tracing is evolving from clonal labeling toward the multi-dimensional integration of lineage, state, and space. In the future, the deep integration of precise gene-editing tools with high-resolution spatial omics technologies is expected to enable dynamic and systematic analysis of cellular fate trajectories, thereby providing critical technical support for research in developmental biology and regenerative medicine.},
}

*Cell Lineage/genetics
Humans
*DNA Barcoding, Taxonomic
High-Throughput Nucleotide Sequencing
CRISPR-Cas Systems
Animals
Single-Cell Analysis

@article {pmid42663958,
year = {2026},
author = {Liu, Y and Luo, C and Ji, R and Li, Y and Nie, Y and Zhou, Z and Hu, R and Chen, K},
title = {Preparation and Detection of Designed DNA Carriers for Nanopore Sensing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3072},
number = {},
pages = {161-170},
pmid = {42663958},
issn = {1940-6029},
mesh = {*Nanopores ; *DNA/chemistry/genetics ; *Biosensing Techniques/methods ; Humans ; DNA Nanostructures ; },
abstract = {Single-molecule detection is a powerful strategy for early disease diagnosis, allowing the specific identification of nucleic acids and proteins. While nanopore technology enables fluorescent label-free, high-resolution analysis of individual biomolecules, its lack of intrinsic molecular selectivity limits performance in complex biological samples. The DNA carrier strategy addresses this limitation by introducing target recognition capability, incorporating molecular barcodes, and enhancing signal clarity in complex backgrounds. When combined with low-noise, high-resolution glass nanopores, these carriers enable specific and multiplexed biomarker detection for early-stage cancer and other diseases. This chapter presents a detailed and standardized protocol for preparing and detecting assembled DNA carriers using nanopores, providing an accessible workflow for broader adoption in single-molecule sensing and molecular diagnostics.},
}

*Nanopores
*DNA/chemistry/genetics
*Biosensing Techniques/methods
Humans
DNA Nanostructures

@article {pmid42664675,
year = {2026},
author = {Bañón, R and Almón, B and de Carlos, A and Acosta-Morillas, V and Baldó, F},
title = {Pigmentation anomalies in marine fishes: novel records from Spanish coastal waters and a global synthesis of wild flatfish ambicolouration.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 2},
pages = {120300},
doi = {10.1016/j.marpolbul.2026.120300},
pmid = {42664675},
issn = {1879-3363},
abstract = {This study documents unusual pigmentation patterns in marine fishes from Spanish coastal waters and provides a global synthesis of published records of ambicolouration in wild flatfishes. A mixed pigmentation anomaly was recorded in Diplodus sargus (Sparidae), severe hypopigmentation compatible with oculocutaneous albinism was documented in Halobatrachus didactylus (Batrachoididae), and near-complete ambicolouration was observed in Solea senegalensis (Soleidae). Three additional unusual pigmentation patterns involving Labrus bergylta (Labridae) and D. sargus were documented photographically during underwater observations and are regarded as putative pigmentation anomalies because natural colour variation and physiological colour change cannot be excluded. The specimens were obtained opportunistically through fishery bycatch, scientific surveys and underwater observations conducted in Galicia and Andalusia between 2025 and 2026. DNA barcoding confirmed the species identity of the three collected specimens. The discovery of an ambicoloured Solea senegalensis prompted a review of this condition in wild flatfishes worldwide. The literature review identified 100 studies reporting ambicolouration in 79 wild flatfish species from 10 of the 19 recognized families. Pleuronectidae and Paralichthyidae contained the largest numbers and proportions of species with published records, although these patterns may be influenced by uneven research and reporting effort. Pigmentation anomalies, although uncommon in nature, have been associated with genetic, developmental or environmental processes, but their environmental significance cannot be determined from opportunistic records alone. Standardized long-term monitoring accompanied by population and environmental data would be required to assess their potential value in ecosystem assessment.},
}

@article {pmid42661790,
year = {2026},
author = {Jiang, J and Qin, Y and Yu, Z and Chen, J and Wang, J and Yang, S and Liu, Y and Liu, T},
title = {Multi-dimensional identification and quality evaluation of Paris polyphylla cultivated populations using morphological, molecular, cytological and metabolic traits.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1878411},
pmid = {42661790},
issn = {1664-462X},
abstract = {INTRODUCTION: Paris polyphylla is an endangered medicinal herb valued for its steroidal saponins, yet the phenotypic stability, genetic diversity, and quality differentiation of cultivated populations remain insufficiently understood.

METHODS: In this study, 28 representative populations from Yunnan Province were evaluated under common-garden conditions using morphological, molecular, cytogenetic, genomic and phytochemical analyses.

RESULTS: The populations showed generally synchronized phenological development but differed significantly in several agronomic traits. DNA barcoding based on ITS and trnL-trnF sequences achieved high amplification and sequencing success. Among the representative sequences examined, ITS exhibited greater haplotype richness and sequence variation than trnL-trnF. However, because each population was represented by only one consensus sequence, within-population variation and a conventional DNA barcode gap could not be evaluated. Flow cytometry and chromosome counting confirmed that all populations were diploid, although substantial variation in genome size and karyotype characteristics was observed. HPLC analysis further revealed marked differences in steroidal saponin composition and content among populations.Correlation analyses linked saponin variation to multiple agronomic traits, karyotypic features, and genome size. Exploratory partial least squares path modeling showed that temperature was positively associated with plant growth, whereas plant growth was negatively associated with the composite saponin profile. The model explained a limited proportion of the variation in the endogenous constructs, and the identified paths were interpreted as statistical associations rather than causal effects.

DISCUSSION: Overall, this study clarifies the genetic and ecological drivers of saponin variation in cultivated P. polyphylla, providing an integrated framework for germplasm identification, quality evaluation, and sustainable utilization of cultivated resources.},
}

@article {pmid42659830,
year = {2026},
author = {Kim, H and Kang, TM and Park, SH and Park, SH and Bae, YJ},
title = {COI barcode reference dataset for forensic identification of Silphidae (Coleoptera) in Korea.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {86},
number = {},
pages = {102915},
doi = {10.1016/j.legalmed.2026.102915},
pmid = {42659830},
issn = {1873-4162},
abstract = {In forensic entomology, coleopteran evidence can provide important supplementary information when mPMI estimation based primarily on Diptera is limited; however, molecular reference data for Korean Silphidae remain scarce. This study aimed to establish a COI sequence-based reference dataset for forensically important Korean Silphidae and to support DNA barcoding-based species identification. Adult silphids were collected during pig decomposition experiments and identified morphologically. COI sequencing was performed for 38 adult specimens representing seven Silphidae species. Intra- and interspecific genetic distances were calculated using the p-distance model, and sequence similarity to NCBI reference sequences was evaluated. Phylogenetic concordance was further assessed using a neighbor-joining tree. COI sequences were successfully obtained from all 38 specimens. Intraspecific distances were low (0.00-0.57%), whereas interspecific distances were ≥ 10%, indicating sufficient divergence for species-level discrimination. Most species showed high similarity (99-100%) to NCBI reference sequences; however, Thanatophilus rugosus exhibited comparatively lower similarity (97.75-97.95%). Nicrophorus concolor also showed reduced similarity to a U.S. reference sequence (93.41%). In the neighbor-joining tree, specimens formed species-specific clusters consistent with morphological identifications. Overall, this study provides COI reference sequences for seven Korean Silphidae species, expanding the limited national DNA barcode resources and facilitating molecular identification of morphologically challenging samples such as immature stages.},
}

@article {pmid42659645,
year = {2026},
author = {Wulffson, CK and Babin, MM and Andersen Pinotti, MT},
title = {Improving patient safety with triple-scan technology for insulin pen administration.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajhp/zxag247},
pmid = {42659645},
issn = {1535-2900},
abstract = {PURPOSE: High-alert medications such as insulin pose serious risks to patients when used in error. In response to vulnerabilities identified in existing insulin administration workflows, we implemented a comprehensive approach to mitigate the risk of errors in the hospital setting.

SUMMARY: A new electronic health record capability, referred to as the "triple-scan system," was introduced to enhance insulin pen administration safety. This system requires nurses to scan the patient's wristband barcode, the insulin pen manufacturer's barcode, and the pharmacy's linking label barcode applied to the pen before it is retrieved from an automated dispensing machine. Other measures were also implemented to prevent errors, including a 2-nurse verification process and visual aids. A performance dashboard was used to track insulin pen administration. After the triple-scan system was integrated into workflows, the performance dashboard showed increasing numbers of barcodes scanned over a period of 4 months, whereas the number of unscanned barcodes remained low. Postimplementation surveys of 174 nurses indicated high satisfaction with the new system, with 67% (n = 116) reporting improved patient safety and 71% (n = 124) finding it user friendly.

CONCLUSION: The triple-scan system ensures the use of a single insulin pen for each patient, which may enhance patient safety by helping to prevent exposure to blood-borne pathogens. Engaging nurses as essential stakeholders and providing ongoing support and training were critical to the success of this intervention. Continuous monitoring and improvements are necessary to ensure the long-term sustainability of the triple-scan system.},
}

@article {pmid42652530,
year = {2026},
author = {Liang, Z and Ren, K and Sun, B and Xie, T},
title = {Global DNA Barcoding of Sigara (Hemiptera: Corixidae) Reveals Cryptic Species Formation and Climatic-Niche Divergence.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
pmid = {42652530},
issn = {2075-4450},
support = {2022-LHYJ-02-0102//The Yangtze River Joint Research Phase II Program/ ; },
abstract = {The genus Sigara Fabricius, 1775 (Hemiptera: Corixidae) is an important freshwater bioindicator, but its conservative morphology complicates traditional species identification. This study combines DNA barcoding, traditional taxonomy, and climatic factors within an integrative framework to provide new insights into species delimitation. We analyzed cytochrome c oxidase subunit I (COI) sequences from 501 Sigara specimens collected from 15 countries, including 95 newly generated COI barcodes. Our integrated approach included phylogenetic analyses, genetic distance assessments, and ecological niche modeling. The results revealed remarkable diversity, with sequences clustering into 46 Barcode Index Numbers (BINs). COI genetic distances showed a pronounced bimodal pattern, with most intraspecific divergences below 1% and interspecific divergences mainly ranging from 8-16%, while the few intermediate divergences (4-8%) suggested potential cryptic diversity or recent species divergence. Most morphologically defined species corresponded to distinct molecular lineages, supporting traditional taxonomy, whereas some morphospecies exhibited genetic discordance potentially associated with species divergence. Integrative analyses revealed that climatic factors, particularly isothermality and seasonal temperature and precipitation, are major drivers of Sigara MOTU distributions, highlighting the important role of climate in shaping their geographic patterns. These findings indicate that although COI barcodes are not sufficient to define the species boundaries of Sigara alone, they provide a key entry point for the accurate division of species, which in turn promotes the development of molecular tools for freshwater ecological monitoring and conservation.},
}

@article {pmid42653170,
year = {2026},
author = {Rodionov, AV and Machs, EM and Romanova, EL and Dyomin, AG and Shulzhenko, IN and Gnutikov, AA and Nosov, NN and Shneyer, VS and Kalugin, YG},
title = {Nuclear Ribosomal ITS1-5.8S rDNA-ITS2 Region as a Phylogenetic Marker for Selenicereus grandiflorus and Related Species (Cactaceae: Cactoideae: Phyllocacteae).},
journal = {International journal of molecular sciences},
volume = {27},
number = {16},
pages = {},
pmid = {42653170},
issn = {1422-0067},
support = {state assignment topic number: 124020100075-2//The Ministry of Education and Science of the Russian Federation/ ; },
mesh = {*Phylogeny ; *Cactaceae/genetics/classification ; *DNA, Ribosomal Spacer/genetics ; *RNA, Ribosomal, 5.8S/genetics ; *DNA, Ribosomal/genetics ; Base Sequence ; Sequence Analysis, DNA ; Genetic Markers ; },
abstract = {The nuclear ITS1-5.8S rDNA-ITS2 region is among the most widely used markers for phylogenetic studies in plants. We sequenced the ITS1-5.8S rDNA-ITS2 region in several species of Selenicereus, two species of Deamia and Epiphyllum chrysocardium. The newly generated sequences were found to be more closely related to ITS and 5.8S rDNA sequences from representatives of other cactus tribes than to the Selenicereus ITS sequences previously deposited in GenBank by research group O. Plume. Importantly, all these sequences retained three conserved motifs of the 5.8S rRNA gene that are commonly used to distinguish functional copies from pseudogenes. Then we analyzed available genome assemblies representing 12 species of Cactaceae. In contrast to the ribotypes identified in this study, the previously reported 5.8S rDNA variants in the assembled genomes of Selenicereus and Carnegiea were represented by a single copy flanked by highly degraded 18S and 28S rDNA sequences. Phylogenetic analyses based on the newly generated ITS sequences and Genbank data supported the monophyly of the subtribes Hylocereinae, Rhipsalideae, and Trichocereinae, as well as the tribes Rhipsalideae, Notocacteae, and Cylindropuntieae. These results demonstrate that the functional ITS1-5.8S rDNA-ITS2 region represents an informative marker for phylogenetic studies within the Cactaceae.},
}

*Phylogeny
*Cactaceae/genetics/classification
*DNA, Ribosomal Spacer/genetics
*RNA, Ribosomal, 5.8S/genetics
*DNA, Ribosomal/genetics
Base Sequence
Sequence Analysis, DNA
Genetic Markers

@article {pmid42653357,
year = {2026},
author = {Rodionov, AV and Kalugin, YG and Romanova, EL and Zhurbenko, PM and Punina, EO and Dyomin, AG and Shulzhenko, IN and Gnutikov, AA and Nosov, NN},
title = {Intragenomic and Interspecific Polymorphism of 35S rDNA Internal Transcribed Spacer 1 (ITS1) in Selenicereus and Related Species (Cactaceae: Cactoideae: Phyllocacteae).},
journal = {International journal of molecular sciences},
volume = {27},
number = {16},
pages = {},
pmid = {42653357},
issn = {1422-0067},
support = {124020100136-0//The Ministry of Education and Science of the Russian Federation/ ; },
mesh = {*Cactaceae/genetics/classification ; *Polymorphism, Genetic ; *DNA, Ribosomal Spacer/genetics ; Phylogeny ; },
abstract = {Locus-specific Illumina NGS was used to analyze the polymorphism of the partial 18S rDNA, spacer ITS1, and partial 5.8S rDNA sequences across 25 cactus species (53 accessions) of the subtribes Hylocereinae and Echinocereinae. To ensure data reliability, only ribotypes (zero-radius operational taxonomic units, ZOTUs) with a minimum read depth of 10 reads within each genome-read pool were retained. A single ribotype was identified in 18 analyzed genomes. In 23 accessions, two or three ribotypes were detected, typically consisting of a major ribotype (98-99%) and one or two minor ribotypes. In the remaining samples, two distinct ribotypes were present in approximately equal proportions, suggesting that these individuals are recent hybrids. Ribotype patterns clearly distinguish the genus Deamia from Selenicereus, Hylocereus, and Epiphyllum. Putative pseudogenes with deletions in the 18S and 5.8S rDNA, as well as deletions and insertions in the ITS1 spacers, were detected. Their abundance was generally low (usually <1%), except in two Deamia species (5-15%). In ITS1 of some minor ribotypes, deletions eliminated cleavage sites B1, B2, and A3, which are important for pre-rRNA processing. Consequently, the products of these putative pseudogenes could not participate in ribosome formation. In addition, pseudogenic copies exhibited a strong transition bias and A/T enrichment in the ITS1 region.},
}

*Cactaceae/genetics/classification
*Polymorphism, Genetic
*DNA, Ribosomal Spacer/genetics
Phylogeny

@article {pmid42657007,
year = {2026},
author = {De la Sota, A and Hidalgo, M and Estivals, G and Faustino-Fuster, D and Meza-Vargas, V and Caminade, P and Bêche, L and Britzke R, R and Steinke, D and Hubert, N},
title = {Delimiting Andean catfish species of the families Astroblepidae and Loricariidae (Ostariophysi, Siluriformes) in the Peruvian Andes using DNA barcodes.},
journal = {ZooKeys},
volume = {1290},
number = {},
pages = {59-84},
pmid = {42657007},
issn = {1313-2989},
abstract = {The Amazon Basin, the largest on Earth, hosts an exceptionally rich fish fauna shaped by its ancient evolutionary history, vast environmental heterogeneity, and steep altitudinal gradient. Despite this diversity, major taxonomic gaps persist, including the Linnean shortfall-the large number of undescribed species-and the Wallacean shortfall, reflecting limited knowledge of species distributions. During the past two decades, DNA barcoding using the mitochondrial COI gene has helped uncover substantial cryptic diversity in Amazonian fishes, particularly along the Andean slope, where Siluriformes exhibit striking levels of undocumented diversity. In this study, we investigated catfish communities from the families Astroblepidae and Loricariidae in the headwaters of the Madre de Dios and Huallaga rivers in Peru, spanning elevations from 500 to 2,500 m. Using DNA barcoding and multiple species-delimitation methods, we identified 27 MOTUs, most of which could not be assigned to recognized species. Our aim was to examine diversity patterns, species co-occurrence, and phylogenetic community structure along the Andean slope. This framework allows us to evaluate how ecological processes-such as competition, niche partitioning, and ecological specialization-shape community assembly. Combined with evidence of close phylogenetic relationships among MOTUs, our results highlight the likely importance of in situ diversification in driving species turnover and structuring catfish biodiversity across Andean elevational gradients.},
}

@article {pmid42642597,
year = {2026},
author = {Veerappa, A and Guda, C},
title = {A Framework for Analyzing the Epigenetic and Transcriptomic Landscape of Cancers Using Single-Cell Multiomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3005},
number = {},
pages = {241-281},
pmid = {42642597},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; Humans ; Multiomics/methods ; *Neoplasms/genetics ; *Epigenesis, Genetic ; *Transcriptome ; Single-Cell Gene Expression Analysis ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; *Epigenomics/methods ; Chromatin/genetics/metabolism ; Computational Biology/methods ; },
abstract = {Single-cell approaches to study gene regulation using multi-modal data (sc-Multiome), such as genomes, transcriptomes, and chromatin accessibility of tumor cells, offer great insights into the development trajectory. By enabling high-resolution barcoding, single-cell isolation facilitates the detection of subpopulations, uncovers molecular mechanisms, and characterizes cell types to reveal cellular heterogeneity within complex tissues. The pipeline for analyzing multiome data includes four main steps: processing Single-Cell Multiome ATAC + Gene Expression sequencing data, gene expression analysis using Seurat, chromatin accessibility analysis and the joint embedding of the expression and accessibility data using SnapATAC2. Here, we outline a comprehensive protocol for joint embedding of chromatin accessibility and transcriptomic data using best practices developed in our laboratories, along with detailed parameter tuning at each step to fully leveraging this pipeline. This approach enhances our understanding of the intricate tumor microenvironment and aids in determining cellular landscape. This chapter focuses on the integration of single-cell multi-omics methodologies, emphasizing their utility in cancer research.},
}

*Single-Cell Analysis/methods
Humans
Multiomics/methods
*Neoplasms/genetics
*Epigenesis, Genetic
*Transcriptome
Single-Cell Gene Expression Analysis
Gene Expression Profiling/methods
Gene Expression Regulation, Neoplastic
*Epigenomics/methods
Chromatin/genetics/metabolism
Computational Biology/methods

@article {pmid42642982,
year = {2026},
author = {Li, P and Xiao, R and Li, F and Bu, X and Cao, F and Wang, J and Guo, Z},
title = {Siglec Ligand Profiling on Extracellular Vesicles Reveals a Cancer-Related Signature with Immunosuppressive Function in Pancreatic Cancer.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e75407},
doi = {10.1002/smll.75407},
pmid = {42642982},
issn = {1613-6829},
support = {NSFC 32301194//National Natural Science Foundation of China/ ; ZR2022QC165//Natural Science Foundation of Shandong Province/ ; ZR2023QH008//Natural Science Foundation of Shandong Province/ ; ZR2026LMB034//Natural Science Foundation of Shandong Province/ ; ZR2023QC090//Natural Science Foundation of Shandong Province/ ; tsqn202507391//Taishan Scholars Foundation/ ; },
abstract = {Cancer-derived extracellular vesicles (EVs) act as systemic carriers of functional sialic acids and participate in local or distant immune escape via the Siglec pathway. Therefore, assessing the expression of Siglec ligands on EVs can facilitate the exploration of novel cancer biomarkers and enable the evaluation of circulating sialic acid-mediated immunosuppression. However, the structural complexity and functional redundancy of Siglec ligands pose challenges for evaluating their collective role in immune evasion. Here, an adjustable Siglec-DNA barcoding platform is established for multiplexed detection of four Siglec ligands on EVs, thereby enabling the simultaneous profiling of multiple ligand-receptor pairs in a single competitive assay. EV Siglec ligand signatures show statistical differences between cancer and normal groups, as quantified by the Siglec-DNA platform in cell lines and clinical samples, highlighting their potential for pancreatic cancer discrimination. Specific types of Siglec ligands on EVs also inactivate natural killer (NK) cells and T cells in co-culture, demonstrating their immunosuppressive potential. These findings uncover a novel, systemic mechanism of immune inhibition mediated by sialic acids, and also offer new insights into how EVs modulate cancer immunity.},
}

@article {pmid42644667,
year = {2026},
author = {Muñoz-Sánchez, AH and Contreras-Negrete, G and Zaldívar-Riverón, A and Colín, RT and Zakharov, EV and López-Vaamonde, C and Hernández-López, A},
title = {High-Throughput DNA Barcoding Reveals Multi-Trophic Networks of Plants, Leafminers and Parasitoids in a Tropical Dry Forest.},
journal = {Molecular ecology resources},
volume = {26},
number = {6},
pages = {e70183},
pmid = {42644667},
issn = {1755-0998},
support = {58548//Consejo Nacional de Ciencia y Tecnología/ ; //the European Union via the FEDER program FONDS EUROPEEN DE DEVELOPPEMENT REGIONAL - PROGRAMME OPERATIONNEL FEDER - FSE 2014-2020 CONSEIL REGIONAL CENTRE-VAL DE LOIRE/ ; CBF 2025 G576//SECIHTI/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Forests ; Tropical Climate ; Mexico ; Sequence Analysis, DNA ; Plant Leaves/parasitology ; *Insecta/classification/genetics/physiology ; *Plants/genetics/classification/parasitology ; },
abstract = {Tropical dry forests host highly diverse insect communities and complex trophic interactions, yet these networks remain difficult to resolve using conventional molecular or rearing-based approaches. Here, we integrate long-read DNA barcoding, non-target sequence co-amplification, and host plant taxonomy to reconstruct tri-trophic interactions among leaf-mining insects, their host plants, and associated parasitoids in a Mexican tropical dry forest. Using Single Molecule, Real-Time (SMRT) sequencing on the PacBio Sequel IIe platform, we generated high-fidelity barcodes from individual leaf-miner larvae and from parasitoid larvae and pupae recovered from leaf mines. From 253 specimens, we obtained 214 sequences, and identified 83 operational taxonomic units including leaf-mining Lepidoptera, Diptera, Coleoptera, and their hymenopteran parasitoids, plus 31 non-target sequences. Of the 214 sequences, 69 were parasitoid wasps (32.2%). Of these, 40 were obtained from parasitoids dissected directly from leaf mines, while 29 were co-amplified from leaf-miner samples, demonstrating that SMRT-based co-amplification allows detection of parasitism without rearing. Our analysis revealed 156 trophic interaction types and 247 interaction events. Network analyses showed a highly modular tripartite network, with module structure primarily driven by host plant identity and a reduced set of influential leaf-miner and parasitoid taxa. Bipartite networks supported the hypothesis that interactions are more strongly compartmentalized between leafminers and host plants than at higher trophic levels. These results demonstrate that long-read DNA barcoding with co-amplification detection provides a scalable framework for reconstructing multi-trophic interactions from individual specimens, overcoming key limitations of rearing-based methods and enabling robust biodiversity and ecological network assessments in species-rich ecosystems.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Forests
Tropical Climate
Mexico
Sequence Analysis, DNA
Plant Leaves/parasitology
*Insecta/classification/genetics/physiology
*Plants/genetics/classification/parasitology

@article {pmid42646098,
year = {2026},
author = {Wei, S and Mi, Y and Zhang, X and Qi, B and Wang, W and Wang, Q and Shi, D and Li, Y},
title = {Exploration of the Potential Suitable Distribution Range of the Lyophyllum decastes Complex in High-Altitude Cold Regions of Southwest China.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
pmid = {42646098},
issn = {2309-608X},
abstract = {Climate change may alter the abiotic conditions associated with macrofungal occurrence, but projections for taxonomically unresolved species complexes require cautious interpretation. Here, we used an AICc-optimized MaxEnt model to characterize the climate-defined aggregate suitability envelope of records assigned to the Lyophyllum decastes (Fr.) Singer complex in Sichuan, Yunnan, and Xizang, Southwest China, under current conditions and four RCP scenarios for the 2050s and 2070s. After spatial thinning, 70 occurrence records compiled from field surveys and published sources were modeled with correlation-filtered bioclimatic variables. The optimized model showed high discrimination for the pooled occurrence dataset (mean AUC > 0.95), and mean temperature of the coldest quarter had the largest contribution (50.8%). Projected changes differed between scenarios, with increasing fragmentation and reductions in highly suitable climate space under several futures. These outputs do not represent a lineage-resolved species distribution, as the occurrence records were not uniformly verified by molecular barcodes, and the model omits host availability, vegetation, soil, land use, dispersal, and other biotic processes. We therefore interpret the maps as a hypothesis-generating, aggregate climatic envelope for the complex that can guide stratified field surveys, molecular sampling, and habitat monitoring rather than as direct evidence of taxon-specific physiological tolerances or realized distributions.},
}