@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.},
}

@article {pmid42648135,
year = {2026},
author = {Remelli, S and Ducci, L and Filonzi, L and Pinardi, R and Rizzo, P and Celico, F and Scanferla, E and Pianu, M and Menta, C},
title = {Rethinking ecotoxicological paradigms: microbial-mediated tolerance and life-history trade-offs of Folsomia candida in hydrocarbon-contaminated groundwater.},
journal = {Chemosphere},
volume = {411},
number = {},
pages = {145072},
doi = {10.1016/j.chemosphere.2026.145072},
pmid = {42648135},
issn = {1879-1298},
abstract = {The ecological relevance of soil invertebrates in contaminated groundwater systems remains largely unexplored, particularly under chronic exposure to petroleum-derived compounds. Here, we provide the first evidence of stable colonization and functional persistence of the model collembolan Folsomia candida within a hydrocarbon-polluted aquifer in Gaeta (central Italy). Long-term monitoring (2019-2023) revealed persistent groundwater contamination, with ethyl tert-butyl ether (ETBE) > 10,000 μg/L and total petroleum hydrocarbons (TPH) > 1000 μg/L. Despite these extreme conditions, F. candida populations were consistently detected on the water surface of quiescent piezometers and taxonomically confirmed via COI DNA barcoding. To disentangle tolerance and potential adaptive responses, we performed ecotoxicological bioassays using three populations (laboratory control, native contaminated population, and a depurated lineage) across aqueous and soil exposure scenarios with site-specific groundwater. Survival remained high (>70%) across all treatments which indicates a limited acute toxicity of ETBE-dominated mixtures. In contrast, reproduction was significantly stimulated under contaminated conditions, suggesting a shift from toxic to trophic effects mediated by hydrocarbon-associated microbial communities, including Aeromonas and Sulfuricurvum, likely providing both nutritional subsidy and oviposition substrates. However, under soil conditions, this enhanced reproductive output was coupled with reduced body length, revealing a contamination-driven life-history trade-off between reproduction and somatic growth. These results demonstrate that organism-microbe-contaminant interactions can modulate ecotoxicological outcomes beyond direct toxicity paradigms, enabling persistence and even functional exploitation of polluted environments. Our findings redefine the ecological boundaries of Collembola and support their use as bioindicators of hydrocarbon contamination pathways across terrestrial and groundwater interfaces, with implications for risk assessment frameworks in subsurface ecosystems.},
}

@article {pmid42649521,
year = {2026},
author = {Ji, Q and He, S and Lai, S and Long, S and Jing, X and Lu, Y},
title = {Molecular identification of Hypoderma sinense cutaneous myiasis in a child from a cattle-raising pastoral region of China: a case report.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {42649521},
issn = {1348-8945},
abstract = {BACKGROUND: Human cutaneous myiasis caused by Hypoderma sinense is rarely reported and may be mistaken for common bacterial skin disease.

CASE PRESENTATION: A 3-year-old boy from a livestock-raising pastoral region of China presented with multiple painful subcutaneous nodules that had not responded to topical antibacterial treatment. Marked eosinophilia, elevated total IgE, and linear ultrasonographic structures raised suspicion of parasitic infestation. A larva was removed intact from the posterior neck lesion through a pre-existing punctum under local anesthesia. Whole-genome shotgun sequencing followed by de novo assembly generated a 16,888-bp mitochondrial contig containing a complete COI barcode region, supporting identification of the larva as H. sinense. At the one-month follow-up, the pain and subcutaneous nodules had resolved.

CONCLUSIONS: This case highlights the importance of considering cutaneous myiasis in children from livestock-raising regions with painful, treatment-resistant subcutaneous nodules and demonstrates the diagnostic value of ultrasonography, minimally invasive larval extraction, and molecular identification.},
}

@article {pmid42652432,
year = {2026},
author = {Zafar, MI and Wang, S and Liu, Q and Hassan, J and Shafique, T and Liu, Y},
title = {Habitat-Driven Insect Community Structure in an Arid Agroecosystem of Xinjiang, China: Integrated Light-Trap Monitoring and DNA Barcoding Evidence.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080777},
pmid = {42652432},
issn = {2075-4450},
support = {KH0394//Science and Technology Project of the Fourth Division of the Xinjiang Production and Construction Corps/ ; },
abstract = {Research on insect biodiversity in arid and semi-arid agroecosystems of Central Asia remains limited, hindering the development of effective insect conservation strategies and integrated pest management (IPM) programs. This study examined insect community structure, diversity, and seasonal dynamics across three habitat types in Kekedala City, in the autonomous region of Ili Kazakh, Xinjiang, China. Solar-powered ultraviolet LED light traps (350-420 nm) were used for sampling from April to August 2024. A total of 63,090 individuals of 83 species, 57 families and 72 genera of insects were collected. Diversity indices calculated using the complete species dataset showed highest diversity in the riparian corridor (L3: H' = 3.42, D = 0.962, S = 62), intermediate diversity in the agro-horticultural garden (L2: H' = 3.18, D = 0.948, S = 54), and lowest diversity in the xerophytic shrubland (L1: H' = 2.97, D = 0.935, S = 47). A supplementary analysis targeted a shared core assemblage of 17 species, defined as taxa captured at all three sampling sites with cumulative total abundances ranging from 50 to 100 individuals. This subset exhibited near-uniform diversity metrics across habitats (H' = 2.83, D = 0.941, Pielou's evenness J' ≈ 1.0), a pattern driven by the prevalence of habitat generalists rather than capturing site-specific full community diversity. Two abundant pest species, Helicoverpa armigera (Hübner, 1808) (cotton bollworm, 5209 individuals, 8.3% of total) and Oryctes rhinoceros (Linnaeus, 1758) (rhinoceros beetle, 5206 individuals, 8.2% of total), both peaked in abundance in July-August; O. rhinoceros is associated with local ornamental and date palm plantings in the study area. In total, 15 major pest species were recorded. Mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding confirmed two new national insect records for China: Stethoconus pyri (Mella, 1861) (Hemiptera: Anthocoridae) and Pinacoplus didymogramma (Hampson, 1907) (Lepidoptera: Noctuidae). This study provides the first comprehensive baseline inventory of the insect fauna of Kekedala City. Descriptive ordination analyses suggest that habitat vegetation complexity may exert a stronger filtering effect on insect assemblage composition than the relatively small seasonal variation in temperature and humidity observed during the sampling period. As only a single trap was deployed within each habitat with no within-site replication, all cross-habitat community patterns reported herein are strictly descriptive and require validation via replicated field sampling in future research.},
}

@article {pmid42652433,
year = {2026},
author = {Zhao, J and Xu, Q and Chi, G and Zhang, S and Yu, R and Zhao, S and Gao, Q and Yang, Z and Xu, G},
title = {Species-Specific COI Primers for Rapid Molecular Identification of Leucoptera malifoliella.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080778},
pmid = {42652433},
issn = {2075-4450},
support = {2026KJCXZX-SGS-9//Hebei Academy of Agriculture and Forestry Sciences/ ; HBCT2024150208//Science and Technology Innovation Project of Hebei Agriculture Research System/ ; },
abstract = {Leucoptera malifoliella (Lepidoptera: Lyonetiidae) is a quarantine pest of apple and other Rosaceae fruit trees whose range is expanding into new territories. Its minute size and morphological overlap with closely related Lyonetiidae make routine identification unreliable, especially for larvae and damaged specimens. We compared COI sequences from six common small Lepidoptera species found in orchards and designed the species-specific primer pair SXW-F/SXW-R. The resulting polymerase chain reaction (PCR) assay amplifies an ~500 base pairs (bp) fragment exclusively from L. malifoliella; no product was detected in any of five non-target species. The reaction tolerates annealing temperatures of 50-58 °C and consistently detects the target across all life stages (first- to third-instar larvae, pupae, adults) and all adult tissues tested (antennae, head-thorax, abdomen, wings, legs). Detection sensitivity reaches 0.03 ng/μL-approximately one-thousandth of the DNA content of a single adult. This is the first species-specific COI (SS-COI) method reported for L. malifoliella. It furnishes a rapid, specific, and sensitive diagnostic tool for quarantine inspection, field monitoring, and integrated pest management (IPM) programs.},
}

@article {pmid42652468,
year = {2026},
author = {Xie, TY and Zhang, Y and Chen, YZ and Liu, Z and Lin, XL},
title = {DNA Barcoding Reveals Hidden Genetic Diversity and Environmental Correlates of Lineage Differentiation in Neozavrelia Goetghebuer & Thienemann, 1941 (Diptera: Chironomidae).},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080814},
pmid = {42652468},
issn = {2075-4450},
support = {12110600000018003910//the Ministry of Natural Resources' High-Level Scientific and Technological Innovation Talent Cul-tivation Program/ ; 41502021//National Natural Science Foundation of China/ ; 12111300000018001-14//the Innovative Research Project on the Laboratory of Geo-Specimens Study and Testing at the Ge-ological Museum of China/ ; },
abstract = {Species delimitation and biodiversity assessment in Chironomidae are frequently hindered by morphological conservatism and widespread cryptic diversity. Neozavrelia (Diptera: Chironomidae), a genus inhabiting specialized freshwater microhabitats such as springs and hygropetric seepages, remains poorly understood with respect to its genetic diversity and the environmental processes underlying lineage differentiation. Clarifying lineage diversity is a prerequisite for evaluating the ecological factors associated with genetic differentiation. In this study, we compiled a global COI DNA barcode dataset comprising 137 sequences from newly generated specimens and publicly available records in the Barcode of Life Data Systems (BOLD). Genetic diversity was evaluated using neighbor-joining (NJ) analysis and Automatic Barcode Gap Discovery (ABGD), whereas environmental and geographic drivers of genetic differentiation were assessed using Mantel tests, distance-based redundancy analysis (db-RDA), variation partitioning, and hierarchical partitioning. A total of 26 molecular operational taxonomic units (MOTUs) were identified, with most lineages forming well-supported clades in the NJ tree. Genetic differentiation was significantly associated with both environmental and geographic distances, although environmental variables explained a substantially greater proportion of the observed variation. Hierarchical partitioning identified slope, annual cloud cover, mean precipitation amount of the coldest quarter, and frost frequency as the principal environmental predictors of lineage differentiation. Our findings reveal substantial COI genetic diversity within Neozavrelia and suggest that environmental heterogeneity, particularly variation in water availability and thermal conditions, is significantly associated with lineage differentiation. This study expands the global COI DNA barcode reference library for Neozavrelia and provides new insights into ecological and evolutionary factors associated with diversification in freshwater chironomids.},
}

@article {pmid42652502,
year = {2026},
author = {Santiago-Calvo, Y and de Paz, V and Bastin, S and Fusu, L and Baños-Picón, L and Flores-Pérez, D and Pozo-Romero, MI and Asensio-S-Manzanera, MC},
title = {Parasitoid Diversity and Biological Control of Bactericera tremblayi and Bactericera trigonica (Hemiptera: Psylloidea) in Horticultural Crops in Spain.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080848},
pmid = {42652502},
issn = {2075-4450},
support = {ASOPROFIT 001 - PDRCYL (2014-2022) Sub. 16.2//ASOPROFIT 001/ ; HORTICCROP 013 - PPAC (2023-2027) Int. CYL7162//HORTICCROP 013/ ; },
abstract = {Biological control using parasitoids is a key strategy for managing psyllid pests in horticultural crops. This study investigated the parasitoid complex associated with Bactericera tremblayi and Bactericera trigonica, two economically important psyllid pests of leek and carrot, respectively, in Castile and León (Spain). Nymphs of both psyllid species were collected and reared to assess parasitism; emerging parasitoids were identified morphologically and by DNA barcoding. A total of 969 parasitized nymphs were collected, from which 291 parasitoids emerged, including Tamarixia pronomus, Tamarixia tremblayi, Syrphophagus herbidus, Syrphophagus cf. taeniatus, Cheiloneurus sp. and Encyrtidae sp. Tamarixia pronomus is reported here for the first time as parasitoids of B. tremblayi while T. tremblayi, S. herbidus, and S. cf. taeniatus are newly recorded as parasitoids of B. trigonica. Moreover, the two Syrphophagus species represent the first records of this genus for Spain. The COI barcode sequences were generated for T. pronomus, T. tremblayi and S. cf. taeniatus. The parasitism rate of S. herbidus on B. trigonica reached a maximum of 23.18%. No significant differences in parasitism by Tamarixia species were observed between the two Bactericera hosts. Maximum parasitism rates recorded were 32.43% for T. pronomus on B. trigonica, and approximately 11-12% for T. tremblayi on both host species. Total parasitism of B. tremblayi in leek crops reached up to 70%, whereas parasitism of B. trigonica in carrot remained generally low and poorly synchronized with pest population dynamics. These results highlight a diverse parasitoid complex with substantial natural control of B. tremblayi and variable but lower impact on B. trigonica, underscoring the relevance of habitat and temporal factors for conservation biological control in these agroecosystems.},
}

@article {pmid42652511,
year = {2026},
author = {Xie, T and Chai, L and Zhang, N and Wang, N and Ge, X and Yan, C},
title = {A DNA Barcode Reference Library for Trichoptera of Jingpo Lake: Taxonomic Diversity and Molecular Identification Basics.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080857},
pmid = {42652511},
issn = {2075-4450},
support = {32400357//National Natural Science Foundation of China/ ; },
abstract = {Jingpo Lake in Northeast China is a vital aquatic ecosystem, yet it lacks baseline molecular data for its insects. Trichoptera (caddisflies) are excellent ecological bioindicators, but their accurate identification is often hindered by morphological similarities, life-stage limitations, and insufficient DNA barcode records. To address this gap, this study combined morphological identification with DNA barcoding to establish a local reference database. From 285 collected adult caddisflies, 105 representative specimens were selected for genetic analysis. The survey identified 22 species across 9 families, revealing four new records for China and six for Heilongjiang Province. Analyses confirmed the high efficacy of the COI marker, demonstrating low intraspecific genetic divergence (0.78%) and high interspecific divergence (17.80%), with a clear barcode gap separating all examined species. Species accumulation curves indicated robust sampling of the main genera, although expanded collection efforts could still uncover additional species. In conclusion, this study provides a valuable DNA barcode reference library for Trichoptera in the Jingpo Lake region. It establishes foundational data for regional biodiversity inventories and future ecological monitoring based on environmental DNA (eDNA) or metabarcoding approaches.},
}

@article {pmid42633069,
year = {2026},
author = {Duffy, GA and Wainwright, JA and Gonzalez, BC and Bond, T and Jamieson, AJ},
title = {Two new species of Princaxelia (Crustacea, Amphipoda, Pardaliscidae) from hadal depths of the Tonga and Mariana trenches (Pacific Ocean).},
journal = {ZooKeys},
volume = {1289},
number = {},
pages = {303-334},
pmid = {42633069},
issn = {1313-2989},
abstract = {Princaxelia Dahl, 1959, is a genus containing predatory pardaliscid amphipods, typically captured in small numbers from hadal trenches (> 6,000 m ocean depth). Here, two new species, Princaxelia malohi Duffy & Wainwright, sp. nov. and Princaxelia kahat Duffy & Wainwright, sp. nov., are added to the genus based on key morphological features to bring the total number of species of Princaxelia to seven. DNA barcodes at the 16S and COI region are also provided for all type specimens where possible to add to the limited but growing number available. Princaxelia malohi sp. nov. was described from five specimens captured using baited landers between 8,200-8,350 m water depth in the Tonga Trench. They exhibit the first identified record of Princaxelia from this hadal feature. Key diagnostic features include the presence of two plumose setae on the inner plate of maxilla 1 and one projection near the base of the dactylus in gnathopods 1 and 2. The second species, Princaxelia kahat sp. nov., is described from between 8,000-8,964 m in the Mariana Trench, and is the second species described from this hadal feature. Key diagnostic features for this species include the presence of six plumose setae on the inner plate of maxilla 1, and three to four projections near the base of the dactylus in gnathopod 1, and four to five projections on the base of the dactylus in gnathopod 2. A morphological matrix and key to the genus is updated to aid in future identification of species of Princaxelia and notes on in situ observations are also included.},
}

@article {pmid42633071,
year = {2026},
author = {Likhitrakarn, N and Golovatch, SI and Srisonchai, R and Thi, S and Chhin, S and Lou, V and Sinovas, P and Jirapatrasilp, P and Sutcharit, C and Panha, S and Seesamut, T},
title = {Integrated taxonomy of two new species of the millipede genus Plusioglyphiulus Silvestri, 1923 from Cambodia (Diplopoda, Spirostreptida).},
journal = {ZooKeys},
volume = {1289},
number = {},
pages = {237-269},
pmid = {42633071},
issn = {1313-2989},
abstract = {Two new sympatric cavernicolous species of the millipede genus Plusioglyphiulus Silvestri, 1923, are described from Battambang Province, northwestern Cambodia: Plusioglyphiulus parviserratus Likhitrakarn & Seesamut, sp. nov. and Plusioglyphiulus battambangensis Likhitrakarn & Seesamut, sp. nov. Both new taxa are diagnosed based on an integrated taxonomic approach combining morphological features and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences from a previous study. Plusioglyphiulus parviserratus sp. nov. is distinguished from all congeners by having the male leg 1 telopodite distinctly 2-segmented with a rudimentary, knob-like second telopoditomere, the anterior gonopod coxosternal processes long, slender, and regularly curved anteriorly, resembling a bird's head, and a unique micro-serrate upper margin of the broad flagellum process. In contrast, P. battambangensis sp. nov. is characterized by a distinct carinotaxic formula of the collum, a significantly smaller second telopoditomere on the male leg 1, a slender, elongated, paramedian coxal process of the posterior gonopod, and a narrow, smooth-margined flagellum process. The two new species are separated from each other by an interspecific COI p-distance of 10.3% and show divergences of 9.6-9.9% from their closest known relatives, all lying well within the stable range observed for species boundaries in the Cambalopsidae and therefore strongly supporting their independent specific status. Beyond traditional descriptions, this study evaluates the resolution efficiency and practical limitations of multiple imaging modalities, including the standard transmission light photography, traditional line drawings, scanning electron microscopy, and micro-computed tomography scanning. While 3DµCT reconstructions provide powerful, non-destructive visualizations of external somatic architectures, we demonstrate that current in-situ tomographic data remain insufficient for resolving the highly condensed, tightly appressed gonopodial microscopic characters, thereby emphasizing the continued necessity of physical dissection and SEM in cambalopsid taxonomy. These findings increase the number of Plusioglyphiulus species currently known to occur in Cambodia to six, highlighting the significant, yet severely understudied, cavernicolous diplopod diversity in the country's extensive karst systems. An updated identification key to all six Cambodian Plusioglyphiulus species is provided. These discoveries underscore the critical need for continued taxonomic exploration and the implementation of conservation strategies for the imperiled limestone karst ecosystems in the region.},
}

@article {pmid42633869,
year = {2026},
author = {Hong, O and Mayor, T and Joshi, J},
title = {Peptide barcoding: an alternative to the phenotype-genotype problem.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2026.08.007},
pmid = {42633869},
issn = {1876-4347},
abstract = {Barcoding methods are powerful tools for screening large libraries and have successfully been employed using DNA-centric approaches for over two decades. Yet despite the central role of proteins in most biological processes, protein-based barcoding methods have only recently emerged as a viable alternative. In this review we summarize recent advances in peptide barcoding and highlight its diverse applications, including screening of binding affinity, lipid nanoparticles, mRNA untranslated regions, and designed protein libraries. We discuss key challenges in barcode design, library construction, and mass spectrometry methods for accurate, scalable, and high-throughput screening. We propose that peptide barcoding represents a conceptual shift in genotype-phenotype mapping and will play an increasingly important role in AI-driven protein engineering, delivery technologies, and synthetic biology.},
}

@article {pmid42635227,
year = {2026},
author = {Noman, AA and Sashittal, P},
title = {Sensitivity analysis of cell fate trajectories from single-cell transcriptomics.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {Supplement_2},
pages = {},
pmid = {42635227},
issn = {1367-4811},
support = {//Virginia Tech/ ; },
mesh = {Single-Cell Gene Expression Analysis ; *Single-Cell Analysis/methods ; *Cell Differentiation/genetics ; Animals ; *Transcriptome ; Gene Regulatory Networks ; Mice ; Sequence Analysis, RNA/methods ; *Computational Biology/methods ; *Gene Expression Profiling/methods ; },
abstract = {SUMMARY: Cell differentiation is a dynamic process in which cells traverse through high-dimensional gene expression space under the influence of gene regulatory networks and environmental cues. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled us to measure high-resolution snapshots of this dynamic process. Several computational methods have been developed to reconstruct cellular flow maps from these snapshots, revealing the trajectories taken by cells in gene expression space. While existing methods provide increasingly detailed descriptions of cellular trajectories, the stability of these trajectories to perturbations is largely unexplored. As such, it remains unclear how robust inferred trajectories are to perturbations, which genes most strongly influence long-term fate outcomes, and where instability arises between competing fate commitments. While sensitivity and stability analysis tools from dynamical systems theory provide a principled way to study the stability of differentiation trajectories, existing approaches are not designed for the high-dimensionality and sparsity of scRNA-seq data. Here, we introduce FateSens, a sensitivity-based computational framework for analyzing gene regulatory dynamics using flow maps derived from scRNA-seq data. FateSens performs sensitivity analysis of differentiation trajectories derived from scRNA-seq data to identify regulatory genes and fate boundaries. To demonstrate its utility, we applied FateSens to study neutrophil-monocyte differentiation using scRNA-seq data of mouse hematopoiesis. While FateSens relies only on transcriptomic measurements, this dataset also contains lineage tracing barcodes that provide ground-truth fate relationships. Our results show that FateSens accurately recovers regulators consistent with known biology and identifies fate boundaries that are supported by lineage tracing data.

We implement FateSens in Python 3, with an open-source implementation available at: https://github.com/sashittal-group/FateSens.},
}

Single-Cell Gene Expression Analysis
*Single-Cell Analysis/methods
*Cell Differentiation/genetics
Animals
*Transcriptome
Gene Regulatory Networks
Mice
Sequence Analysis, RNA/methods
*Computational Biology/methods
*Gene Expression Profiling/methods

@article {pmid42637706,
year = {2026},
author = {He, Q and Zhao, LH and Xu, HE},
title = {Arrestins as programmable integrators of GPCR signaling: structural microstates, spatiotemporal logic, and therapeutic control.},
journal = {Cell discovery},
volume = {12},
number = {1},
pages = {},
pmid = {42637706},
issn = {2056-5968},
support = {32130022, 82495184,82121005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371255, 32071203//National Natural Science Foundation of China (National Science Foundation of China)/ ; 23ZR1475200//Natural Science Foundation of Shanghai (Natural Science Foundation of Shanghai Municipality)/ ; },
abstract = {Arrestins were originally defined as terminators of G protein-coupled receptor (GPCR) signaling, yet structural and mechanistic advances now reveal them as programmable, spatiotemporal integrators of cellular signaling. Recent cryo-electron microscopy studies have revealed a diverse spectrum of GPCR-arrestin engagement modes, including core-, tail-, loop-, side-engaged, and membrane-anchored conformations, across GPCR classes and arrestin isoforms. These structures reveal that arrestin recruitment operates as a conditional, allosterically regulated process rather than a binary on-off switch. The selection of the arrestin microstate is governed by layered regulatory inputs, including GPCR kinase-dependent phosphorylation barcodes, membrane and lipid cofactors, and isoform-specific mechanics, which together define the signaling geometry, duration, and subcellular localization. This structural logic provides a mechanistic foundation for biased signaling, noncanonical endosomal signaling, and GPCR-independent arrestin functions. Importantly, emerging therapeutic strategies, including intracellular allosteric modulators and molecular glues, demonstrate that arrestin signaling can be reprogrammed by directly sculpting transducer assemblies rather than ligand efficacy alone. Here, we synthesize recent structural, biochemical, and physiological insights to outline how arrestins decode regulatory inputs into signaling outcomes and how this knowledge enables the development of next-generation, structure-guided GPCR therapeutics.},
}

@article {pmid42630299,
year = {2026},
author = {Schaub, D and Lessing, A and Meyer, F and Stockinger, P and Estévez-Gay, M and Eichenberger, M and von Haugwitz, G and Gloger, A and Scheuermann, J and Buller, R},
title = {A tailored CoA ligase-N-acyltransferase cascade for on-DNA amide bond formation gives access to broad substrate scope.},
journal = {Nature catalysis},
volume = {9},
number = {8},
pages = {834-847},
pmid = {42630299},
issn = {2520-1158},
abstract = {DNA-encoded chemical library (DEL) technology is a powerful tool in early-stage drug discovery. Although widely applied in industry and academia, challenges persist in generating DELs with high quality and chemical diversity. Low yields in building-block incorporation, limited selectivity and, most importantly, DNA damage from harsh reaction conditions compromise library quality, reduce signal-to-noise in affinity selections and ultimately hinder drug discovery. Here we show that tailored enzymes can be harnessed for the effective construction of molecular diversity on DNA under mild conditions. Targeting amide bond formation, we designed a cascade of complementary coenzyme A ligases and rationally tailored N-acyltransferases to access a broad amide scope on-DNA (>120 examples), identifying structural elements that optimize the biocatalysts' DNA compatibility in the process. Integrating the enzymatic cascade with chemical synthesis led to the construction of a diverse DEL without damage to the DNA barcode, highlighting the biocatalysts' applicability for early scaffold construction and late-stage functionalization.},
}

@article {pmid42629163,
year = {2026},
author = {Chen, Z and Zhang, B and Tang, L and Gong, F and Wan, L and Ma, L},
title = {Bayesian inference of lineage trees by joint analysis of single-cell multimodal lineage-tracing data with BiLinT.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.281460.125},
pmid = {42629163},
issn = {1549-5469},
abstract = {The advent of single-cell lineage-tracing technologies has enabled the simultaneous profiling of gene expression and lineage barcodes. However, accurate, high-resolution reconstruction of cell lineage trees remains challenging because most existing approaches treat these modalities separately and therefore fail to fully exploit their complementary information. Here we present BiLinT, a Bayesian framework that jointly models multimodal single-cell lineage-tracing data for lineage tree reconstruction. BiLinT integrates barcode evolution (a continuous-time Markov chain) with gene expression dynamics (an Ornstein-Uhlenbeck process) within a unified probabilistic model. Across synthetic and real datasets, BiLinT provides accurate lineage-tree reconstruction and reveals differentiation-associated clonal structure and developmental fate biases.},
}

@article {pmid42623401,
year = {2026},
author = {Castillo, AH and Jacobs, S and Steinke, D and Smith, MA},
title = {Assessment of leaf-litter invertebrate biodiversity using high throughput sequencing.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0347811},
pmid = {42623401},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *Plant Leaves ; DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Invertebrates/genetics/classification ; DNA, Environmental/genetics ; Ecosystem ; },
abstract = {Leaf litter ecosystems and their fauna are largely understudied, despite their critical ecological roles. Here, we investigate challenges associated with estimating biodiversity in terrestrial leaf litter. Current methodologies for biodiversity assessment are fraught with limitations; amongst the most significant is a decline in taxonomic expertise, complicating the process of species identification and the significant costs associated with species-level morphological identifications. DNA barcoding employs molecular markers to identify animal species, and the mitochondrial gene cytochrome c oxidase I (COI) is the agreed upon standard for animals. DNA metabarcoding facilitates the identification of multiple species without necessitating taxonomic expertise. Recent studies indicate that environmental DNA (eDNA) may exhibit greater sensitivity compared to taxonomic identifications completed on animals collected using traditional methods (e.g., pitfall traps, pan traps). To test whether eDNA methodology works in a real-world scenario, we sampled leaf litter across a temperate forest/field ecotone. Leaf litter was dried, ground and processed to extract environmental DNA. We evaluated multiple DNA extraction protocols to test their relative efficacy. We found that the Qiagen Blood and Tissue Kit was the most effective at recovering invertebrate diversity and found that there were notable differences in the biodiversity recovered between forest and field habitats. Temperature emerged as a significant factor influencing the composition of the communities observed. Our methodology is applicable across various environments for efficient biodiversity assessment and would be particularly beneficial for monitoring pests and invasive species. Our approach offers a cost-effective and timely alternative to conventional biodiversity assessment methods and underscores the significance of accurate assessment methodologies for leaf litter communities.},
}

Animals
*Biodiversity
*Plant Leaves
DNA Barcoding, Taxonomic/methods
*High-Throughput Nucleotide Sequencing/methods
*Invertebrates/genetics/classification
DNA, Environmental/genetics
Ecosystem

@article {pmid42625985,
year = {2026},
author = {Shankar, M and Moorthy, M and Shetty, A and Gurusiddaiah, SC},
title = {Potential diagnostic role of urinary exosomal microRNAs in immunoglobulin A nephropathy: A case-control study.},
journal = {World journal of nephrology},
volume = {15},
number = {3},
pages = {119882},
pmid = {42625985},
issn = {2220-6124},
abstract = {BACKGROUND: The most common type of primary glomerulonephritis is immunoglobulin A nephropathy (IgAN), which can eventually cause end-stage kidney disease among individuals. A kidney biopsy, which is invasive and has risks of mortality or morbidity, is currently the "gold standard" for diagnosis. Urinary exosomes contain abundant, well-preserved microRNAs (miRNAs), which are small, non-coding endogenous RNAs that may be used as non-invasive biomarkers. Studies on urinary exosomal miRNA profiles for the diagnosis of IgAN are rare.

AIM: To examine the profile of urinary exosomal miRNAs in Indian individuals diagnosed with IgAN.

METHODS: Over a period of 4 years (2020-2024), fifty biopsy-confirmed IgAN patients, fifty healthy controls, and fifty disease controls (DC) were recruited. Urinary exosomes were first discovered and then utilized for miRNA extraction. The nCounter[®] Human v3 miRNA Expression Assay, a digital multiplex technique that evaluates 798 unique miRNA barcodes, was used to further analyze the extracted miRNAs. After the least absolute shrinkage and selection operator feature selection identified candidate miRNAs, logistic regression and the CombiROC algorithm were used.

RESULTS: The average age of patients diagnosed with IgAN was 36.32 years, with a standard deviation of 3.07 years. The average proteinuria was 2.69 ± 0.64 g/day, and the average creatinine level was 2.26 ± 0.318 mg/dL. Nine candidate miRNAs - hsa-miR-4532, hsa-miR-4488, hsa-miR-3158-3p, hsa-miR-151b, hsa-miR-3195, hsa-miR-1289, hsa-miR-20a-5p, hsa-miR-20b-5p, hsa-miR-32-5p, and hsa-miR-525-3p - successfully differentiate IgAN cases from both healthy and DC, exhibiting under the curve values of 0.7, 1, and 0.8 for healthy controls, DC, and IgAN cases, respectively. When compared to healthy and DC, a combination of just two miRNAs - hsa-miR-4532 and hsa-miR-548a-3p - was found to be sufficiently effective for detecting IgAN, with an area under the curve > 0.8.

CONCLUSION: Our investigation involving Indian participants revealed a marked alteration in the urinary exosomal miRNA patterns among individuals with IgAN compared to both healthy subjects and those with other kidney diseases, demonstrating the effectiveness of miRNAs in the non-invasive diagnosis of IgAN.},
}

@article {pmid42627892,
year = {2026},
author = {Zhang, Y and Zhu, Y and Zhang, Y and Peng, S and Wu, D and Li, W and Ji, T and Chen, S and Lin, Y and Yang, H and Guo, Y and Li, B and Liu, C and Situ, B and Yan, X and Zheng, L},
title = {Orthogonal DNA barcoding enables subpopulation-resolved extracellular vesicle miRNA profiling.},
journal = {Science advances},
volume = {12},
number = {34},
pages = {eaef8133},
pmid = {42627892},
issn = {2375-2548},
mesh = {Humans ; *MicroRNAs/genetics/metabolism ; *Extracellular Vesicles/genetics/metabolism ; Gene Expression Profiling ; *DNA Barcoding, Taxonomic/methods ; *Stomach Neoplasms/genetics/pathology/metabolism ; ErbB Receptors/genetics ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Biomarkers, Tumor/genetics ; },
abstract = {Extracellular vesicle-associated microRNAs (EV-miRNAs) hold promise for liquid biopsy, but their clinical utility is hindered by EV heterogeneity. Here, we report DEEPER, a DNA-encoded orthogonal recognition platform for selective barcoding of tumor-derived EV subpopulations and in situ miRNA profiling. DEEPER uses four aptamers targeting Cluster of Differentiation 44 (CD44), Epidermal Growth Factor Receptor‌ (EGFR), Human Epidermal Growth Factor Receptor 2‌ (HER2), and ‌Programmed Death-Ligand 1(PD-L1) to generate orthogonal barcodes that distinguish 15 EV subpopulations. Barcoded EVs then undergo targeted membrane fusion with liposome probes, enabling sensitive in situ analysis of subpopulation-specific miRNAs. In a 60-sample cohort of patients with gastric cancer (GC) and healthy donors (HDs), DEEPER identified a high-performing signature, GC-EV miRNA Prime, comprising EGFR[+], EGFR[+]HER2[+], and EGFR[+]HER2[+]CD44[+] EVs, which achieved 98.3% diagnostic accuracy. The same profiling framework also assessed tumor invasiveness with 95.5% accuracy. Mechanistic studies further showed that these EV-miRNAs contribute to tumor progression. In summary, DEEPER not only confirmed the clinical application value of EV-miRNA-based liquid biopsy but also provided unique insights through the EV subpopulations into the mechanisms driving cancer development.},
}

Humans
*MicroRNAs/genetics/metabolism
*Extracellular Vesicles/genetics/metabolism
Gene Expression Profiling
*DNA Barcoding, Taxonomic/methods
*Stomach Neoplasms/genetics/pathology/metabolism
ErbB Receptors/genetics
Cell Line, Tumor
Gene Expression Regulation, Neoplastic
Biomarkers, Tumor/genetics

@article {pmid42623365,
year = {2026},
author = {Bouchet, VMP and Francescangeli, F and Sousa, SHM and de Jesus, MSDS and Pawlowski, J and Frontalini, F},
title = {Taxonomy-free approach overcomes the gaps in ecological knowledge: The case of foraminiferal metabarcoding applied to environmental impact assessment.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0356357},
pmid = {42623365},
issn = {1932-6203},
mesh = {*Foraminifera/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Geologic Sediments/chemistry ; DNA, Environmental/genetics ; *Environmental Monitoring/methods ; Ecosystem ; Zinc/analysis ; Ecology ; },
abstract = {Environmental DNA (eDNA) metabarcoding has emerged as a cost- and time-efficient alternative to traditional morpho-taxonomic methods for benthic foraminiferal inventories. However, the prevalence of soft-walled monothalamous taxa of unknown ecology, which are largely underrepresented in the barcode reference database, limits the accuracy of eDNA studies. Taxonomy-free approaches, which bypass species-level assignment, may overcome these constraints. Here, we use the case study of the Armida gas platform to confirm the potential of the taxonomy-free framework for ecological quality assessment. As highlighted in a PCA, stations located near the platform (i.e., from 0 to 125 m) exhibited significantly higher concentrations of Zn and Ba in the sediment, while stations farther away appeared unpolluted. Molecular indices based on diversity, e.g., ecological quality ratio (EQR) calculated from exp(H'bc), and a taxonomy-free adaptation of Foram-AMBI (Foram-gAMBI) were applied, with barium serving as an independent indicator for ecological group assignment. The indices EQR (morphology), gEQR and Foram-gAMBI (eDNA) were significantly correlated with Zn and/or Ba, while Foram-AMBI (morphology) did not show any significant meaningful correlation. These results are confirmed by the inferred ecological quality statuses which revealed a clear improvement in benthic habitat quality with increasing distance from the platform when assessed with molecular indices (poor to good for gEQR and moderate to good for Foram-gAMBI), while morphological indices, particularly Foram-AMBI, failed to capture this trend. The weak agreement between morphological and molecular indices is likely due to the greater number of Molecular Operational Taxonomic Units (275) than morphospecies (31), including abundant soft-walled monothalamous foraminifera detected only by eDNA. By adopting a taxonomy-free approach to compute Foram-gAMBI, we can fully exploit the metabarcoding dataset without relying on prior taxonomic or ecological knowledge. Our findings demonstrate the robustness and accuracy of taxonomy-free metabarcoding approaches for monitoring benthic ecosystem health using benthic foraminifera in impacted marine environments.},
}

*Foraminifera/genetics/classification
*DNA Barcoding, Taxonomic/methods
Geologic Sediments/chemistry
DNA, Environmental/genetics
*Environmental Monitoring/methods
Ecosystem
Zinc/analysis
Ecology

@article {pmid42620142,
year = {2026},
author = {Solanky, D and Low, C and Hathaway, CL and Cherne, S and Brown, E and Palanee-Phillips, T and Barnabas, RV and Bhattacharyya, RP and Berdy, B and Livny, J},
title = {Phased amplicon multiplex sequencing for cost-effective detection of high-risk human papillomavirus from cervical samples.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.27.26359029},
pmid = {42620142},
abstract = {Access to accurate cost-effective technologies for typing high-risk human papillomaviruses (hrHPV) is critical to expand cervical cancer screening and inform vaccination strategies. Compared with clinical-standard quantitative polymerase chain reaction (qPCR) assays, HPV genotyping by next-generation sequencing (NGS) provides greater flexibility, scalability, and genotype specificity. We have developed a method for HPV genotyping, HPV Phased Amplicon Multiplex Sequencing (PhAM-Seq), that uses combinatorial barcoding of amplicons with short, variable-length inline sequences to enable higher throughput and lower per-sample costs than conventional amplicon sequencing approaches. We evaluated HPV PhAM-Seq using degenerate and type-specific primers targeting the L1 and E6-E7 gene loci in a blinded cohort of 170 cervical samples previously typed by the Seegene Anyplex II HPV28 Detection qPCR assay. Across eight common hrHPV types (HPV16, 18, 31, 33, 35, 45, 52, and 58), HPV PhAM-Seq demonstrated >80% overall agreement with qPCR using degenerate L1-targeting primers, with the highest sensitivity for HPV16, 31, 33, and 58. Sensitivity for HPV35, 45, and 52 improved to 85% or greater with type-specific primers targeting genes E6/E7. Parallel processing and sequencing enables a single technician to assay hundreds of samples per week at a reagent cost of around $10 USD per sample, with laboratory automation and sequencing on higher-output platforms enabling further scaling and cost reduction to a scale amenable to population-level surveillance. We include a detailed SOP; tools for primer design, sequencing library construction, and sample tracking; and all scripts needed for data analysis to ensure HPV PhAM-Seq can be readily implemented for scalable, cost-effective hrHPV genotyping or extended to other similar applications.},
}

@article {pmid42621361,
year = {2026},
author = {Hsu, YF},
title = {Sun moths in the genus Epicroesa (Lepidoptera, Heliodinidae) associated with Ceodes umbellifera, with description of a new species from Taiwan.},
journal = {ZooKeys},
volume = {1289},
number = {},
pages = {203-214},
pmid = {42621361},
issn = {1313-2989},
abstract = {The association of two heliodinid moths with Ceodes umbellifera is documented for the first time: Epicroesa thiasarcha Meyrick, 1907 from Australia and E. bellatula sp. nov. from Taiwan. The two share similar wing patterns and genitalia, but they can be separated by diagnostic features of adults and immatures. The p-distance of COI barcodes was over 9% between samples of the two taxa, lending support to their recognition as distinct species. The considerable geographical separation between these morphologically similar yet genetically diverged species suggests that either both may have broader distributions than currently recognized, or additional undescribed species may occur in the large gap between Australia and Taiwan.},
}

@article {pmid42622428,
year = {2026},
author = {Baker, CS and Colpus, M and Gentry, J and Hall, A and Roghi, E and Webster, H and Drummond, B and Cooper, R and Thai, H and Westhead, J and Turner, R and Peto, TEA and Fowler, PW and Morgan, M and Crook, DW},
title = {Validation of an optimized Oxford Nanopore sequencing workflow versus Illumina for mycobacteria from primary MGIT culture.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0140226},
doi = {10.1128/spectrum.01402-26},
pmid = {42622428},
issn = {2165-0497},
abstract = {UNLABELLED: Illumina short-read sequencing of primary Mycobacterial Growth Indicator Tube (MGIT) cultures is an established approach for mycobacterial genomic characterization but relies on labor-intensive workflows and centralized sequencing facilities. Oxford Nanopore Technologies (ONT) offers long-read sequencing and is increasingly being explored for in-house implementation in diagnostic laboratories; however, low DNA yields from primary MGIT cultures frequently limit standard PCR-free ONT workflows, restricting routine implementation. We developed and evaluated a semi-automated DNA extraction and Rapid PCR Barcoding workflow for ONT sequencing and compared its performance with Illumina for species identification and Mycobacterium tuberculosis complex (MTBC) single-nucleotide polymorphism (SNP) detection. A platform-agnostic bioinformatics pipeline was used for human read removal, taxonomic assignment, and MTBC genomic characterization. The time required to achieve reliable species identification was assessed by subsampling ONT data at 1, 6, and 72 h. Concordance between ONT and Illumina for species classification was 98.3% (95% CI: 95.8%-99.5%), with all discordant classifications attributable to potential mixed infections. MTBC SNP concordance was high, with a mean of 0.3 and a median of 0 SNP differences between platforms after masking. Reliable species identification was achieved for 233/237 (98.3%) samples within 6 h of sequencing, with no incorrect primary species assignments. These findings demonstrate that an optimized PCR-amplified ONT workflow provides a practical approach for routine in-house genomic characterization of primary MGIT cultures, achieving high concordance with Illumina while addressing a major barrier to ONT implementation in diagnostic laboratories.

IMPORTANCE: Rapid genomic characterization of mycobacterial infections is important for timely patient management, infection control, and public health surveillance. However, many diagnostic laboratories rely on referral of positive cultures to regional reference centers for sequencing, introducing delays associated with transport, batching, and processing. Although Oxford Nanopore Technologies (ONT) can support local sequencing, implementation has been limited by the low DNA yields typically obtained from primary Mycobacterial Growth Indicator Tube (MGIT) cultures and the absence of practical workflows suitable for routine diagnostic laboratories. In this study, we developed and validated a semi-automated DNA extraction and PCR-based ONT workflow designed to support implementation in routine diagnostic laboratories. The workflow generated genomic results highly concordant with Illumina sequencing while overcoming a major barrier to ONT implementation by enabling reliable sequencing from low-yield MGIT-derived DNA. This approach supports routine in-house genomic characterization of mycobacterial cultures and has the potential to reduce turnaround times and dependence on external sequencing services.},
}

@article {pmid42608964,
year = {2026},
author = {Hey, L and Chen, C and Xu, T and Cowell, E and Langlet, D and Methou, P},
title = {Widespread Association of Ciliates Colonizing Gills of Shrimps Inhabiting Vents and Seeps Across the Pacific Ocean.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {5},
pages = {e70115},
pmid = {42608964},
issn = {1550-7408},
support = {ANR-17-EURE-0015//ISblue project, Interdisciplinary Graduate School for the Blue Planet/ ; ANR-22-POCE-0007//National Research Agency/ ; 23K05942//Japan Society for the Promotion of Science/ ; 16309324//General Research Funds (GRFs) & Collaborative Research Fund (CRF) of the Hong Kong SAR government/ ; 16100425//General Research Funds (GRFs) & Collaborative Research Fund (CRF) of the Hong Kong SAR government/ ; C2013-22G//General Research Funds (GRFs) & Collaborative Research Fund (CRF) of the Hong Kong SAR government/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability of The Hong Kong University of Science and Technology/ ; 2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; YK23-16S//Cooperative Research Program of Atmosphere and Ocean Research Institute/ ; SIP//Council for Science, Technology, and Innovation (CSTI), Japan/ ; FKt231024//Schmidt Ocean Institute/ ; NSF OCE 1635219//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Gills/parasitology ; Pacific Ocean ; *Ciliophora/classification/genetics/isolation & purification/physiology/ultrastructure ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Symbiosis ; Microscopy, Electron, Scanning ; DNA, Ribosomal/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Bacterial symbiosis is well-documented in chemosynthesis-based ecosystems, but associations with microeukaryotes remain overlooked. In this study, using scanning electron microscopy and 18S rDNA barcoding, we investigate the presence, diversity, and biogeographic patterns of ciliate epibionts associated with two deep-sea caridean families: Alvinocarididae and Thoridae. We identified a widespread lineage of ciliates colonizing the gills of different alvinocaridid species, extending their previously known distribution in freshwater and coastal habitats to deep ocean down to 3388 m. These ciliates form a distinct clade related to coastal Chonotrichia, but show clear genetic divergence from the previously described species. Geographic divergence of these ciliate populations was observed across the Pacific Ocean, with no evident structure related to their host species. These chonotrichian ciliates exhibited variation in occurrence across host species, individuals, and regions, indicating a facultative association with their hosts. In contrast, the thorid shrimps harbored rare and phylogenetically diverse ciliates. More rarely, we found ciliates related to known parasitic lineages hosted by both shrimp families, with signs of immune response (black gills) in some individuals colonized by these ciliates. Our results reveal previously overlooked protist-crustacean associations in chemosynthetic ecosystems and highlight the ecological and biogeographic importance of this group in the deep ocean.},
}

Animals
*Gills/parasitology
Pacific Ocean
*Ciliophora/classification/genetics/isolation & purification/physiology/ultrastructure
Phylogeny
RNA, Ribosomal, 18S/genetics
Symbiosis
Microscopy, Electron, Scanning
DNA, Ribosomal/genetics/chemistry
Sequence Analysis, DNA

@article {pmid42610891,
year = {2026},
author = {Tian, R and Kang, Q and Dai, X and Ding, Y and Chen, A and Zhang, P and Yang, C},
title = {Ortho-Fusion Metaboliprobe for Sensitive and Specific In Situ Detection of Metabolites in Tumor-Derived Exosomes.},
journal = {Analytical chemistry},
volume = {98},
number = {32},
pages = {23572-23583},
doi = {10.1021/acs.analchem.6c01961},
pmid = {42610891},
issn = {1520-6882},
support = {SHSMU-ZLCX20212601//Innovative Research Team of High-level Local University in Shanghai/ ; 22374028//National Natural Science Foundation of China/ ; 22374097//National Natural Science Foundation of China/ ; 2022YFA1305200//National Key Research and Development Program of China/ ; },
mesh = {*Exosomes/metabolism/chemistry ; Humans ; *Prostatic Neoplasms/metabolism/diagnosis ; Tetraspanin 30/metabolism/chemistry ; Male ; Aptamers, Nucleotide/chemistry/metabolism ; Cell Line, Tumor ; *Biomarkers, Tumor/metabolism ; *Adenosine Triphosphate/analysis/metabolism ; Epithelial Cell Adhesion Molecule/metabolism ; Liposomes/chemistry ; },
abstract = {Small molecule metabolites carried by exosomes have emerged as promising biomarkers for cancer liquid biopsy. However, their clinical application is hindered by the complexity of blood components, the difficulty in distinguishing tumor-derived exosome subpopulations, and the low abundance of metabolites. Here, we develop an Ortho-Fusion Metaboliprobe for the in situ detection of small molecule metabolites in tumor-derived exosomes with high specificity and sensitivity. The Ortho-Fusion Metaboliprobe employs a dual allosteric aptamer system targeting CD63 and EpCAM to form an orthogonal labeling barcode on the surface of tumor-derived exosomes, enabling precise discrimination of tumor exosome subpopulations from complex biological backgrounds. Following orthogonal labeling, liposomes functionalized with complementary DNA tags recognize this barcode via zipper hybridization, triggering targeted membrane fusion between the liposome and the exosome. This fusion event delivers the encapsulated Au NFs-based metabolite detection probes into the exosomal lumen, where they react with target metabolites and generate amplified fluorescent signals for sensitive and specific in situ detection. Using this assay, we successfully detected ATP and spermine in exosomes derived from prostate cancer cell lines and clinical plasma samples. Both metabolite markers effectively distinguished prostate cancer patients from benign controls, demonstrating the clinical potential of this assay. This strategy offers a powerful tool for the analysis of small molecule metabolites in tumor-derived exosomes and holds significant promise for early cancer diagnosis and screening.},
}

*Exosomes/metabolism/chemistry
Humans
*Prostatic Neoplasms/metabolism/diagnosis
Tetraspanin 30/metabolism/chemistry
Male
Aptamers, Nucleotide/chemistry/metabolism
Cell Line, Tumor
*Biomarkers, Tumor/metabolism
*Adenosine Triphosphate/analysis/metabolism
Epithelial Cell Adhesion Molecule/metabolism
Liposomes/chemistry

@article {pmid42611350,
year = {2026},
author = {Karendi, MG and Ndungu, CN and Mbadi, EM and Wanga, VO and Nyamvula, HM and Kaigongi, MM and Hu, GW},
title = {Comparative chloroplast genomics and phylogenomic insights into the genus Zehneria (Cucurbitaceae).},
journal = {Genetica},
volume = {154},
number = {1},
pages = {},
pmid = {42611350},
issn = {1573-6857},
support = {32270228, 31970211//National Natural Science Foundation of China,/ ; ZL202203601//Survey of Wildlife Resources in Key Areas of Tibet,/ ; 2019QZKK0502//Tibetan Plateau Scientific Expedition and Research (STEP) program,/ ; 151853KYSB20190027//nternational Partnership Program of Chinese Academy of Sciences,/ ; },
mesh = {*Phylogeny ; *Genome, Chloroplast ; *Cucurbitaceae/genetics/classification ; Codon Usage ; Genomics ; Evolution, Molecular ; Microsatellite Repeats ; },
abstract = {The genus Zehneria (Cucurbitaceae) presents significant taxonomic challenges due to morphological similarities among species and a lack of resolution in molecular studies. In this study, we sequenced and assembled the chloroplast genomes of seven African Zehneria species collected from Kenya, complementing a previously published accession (Zehneria sp. MZ427944.1), to establish a comprehensive plastome-based framework for the genus. The plastomes ranged from 157,150 to 157,365 bp and exhibited a conserved quadripartite structure, with 130-132 annotated genes, including 86-87 protein-coding genes, 36-37 tRNAs, and 8 rRNAs. Structural variation, particularly in non-coding regions and inverted repeat boundaries, was observed, with eight hypervariable loci providing potential targets for molecular marker development. Simple sequence repeat (SSR) analysis revealed a predominance of A/T mononucleotides across species. Codon usage analysis revealed a strong AT-bias across all species, with codons ending in A or U accounting for 72.2% of synonymous codon preferences. Selective pressure analysis identified eight protein-coding genes with Ka/Ks ratios exceeding 1.0, including psaJ and rps8, proposed as candidate molecular barcodes pending further validation. Phylogenomic analysis of 79 protein-coding genes strongly supported the monophyly of Zehneria (ML bootstrap = 96-100%; PP = 1.0), with one node showing slightly reduced support (BS = 96%), and enhanced resolution of interspecific relationships compared to prior studies using fewer loci. This work offers novel insights into genomic diversity and evolutionary history of sampled Zehneria species, providing a critical molecular resource for future taxonomic and phylogenetic studies within Cucurbitaceae. Broader taxon sampling, particularly from Asian lineages, will be necessary to fully resolve interspecific relationships across the genus.},
}

*Phylogeny
*Genome, Chloroplast
*Cucurbitaceae/genetics/classification
Codon Usage
Genomics
Evolution, Molecular
Microsatellite Repeats