@article {pmid42581346,
year = {2026},
author = {Shehata, FA and El-Demerdash, MM and Elsehely, HH and Saad-Allah, KM and Gad, D},
title = {Taxonomic delineation of four Zygophyllum simplex L. (Zygophyllaceae) morphotypes using morphoanatomical, molecular (SCoT) and chemotaxonomic evidence.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42581346},
issn = {1471-2229},
mesh = {Phylogeny ; *Zygophyllum/genetics/classification/anatomy & histology/chemistry ; Egypt ; Plant Leaves/anatomy & histology/chemistry ; },
abstract = {BACKGROUND: This study presents a comprehensive taxonomic adjustment of Zygophyllum simplex (L.) four constituent varieties in Egypt, integrating morphological, anatomical, palynological, molecular, and phytochemical analyses to evaluate their infraspecific differentiation. Samples were collected from the eastern part of Egypt and subjected to detailed morphological, anatomical, and palynological analyses with SCoT molecular genotyping and HPLC phytochemical profiling.

RESULTS: Four distinct morphological groups (informally designated as "cylindrica", "retusa", "orbicularis", and "lanceolata") were distinguished by significant differences in growth habit, leaf and stem anatomy, floral morphology, and fruit architecture. SCoT molecular marker analysis revealed a genetic similarity range of 0.825-0.881, with phylogenetic clustering strongly compatible with the morpho-anatomical groupings. HPLC profiling further identified group-specific accumulation patterns of key phenolic and flavonoid compounds, such as chlorogenic acid and catechin. While palynological analysis showed limited diagnostic value, the collective data from multiple disciplines provide robust evidence for the recognition of these four distinct morphotypes.

CONCLUSIONS: Morphological, anatomical, and fruit architectural traits, together with group-specific phytochemical profiles and SCoT molecular markers, provided robust evidence for the differentiation of four distinct morphotypes within the Z. simplex complex. However, given the moderate resolution of SCoT markers (37.77% polymorphism), formal varietal status is not proposed at this stage. We recommend that future studies employ higher-resolution molecular approaches, such as single nucleotide polymorphism (SNP) analysis and DNA barcoding, to validate whether these morphotypes represent genetically distinct and reproductively coherent varieties. Pending such validation, these taxa should be treated as morphotypes, thereby establishing a preliminary integrative framework for their identification.},
}

Phylogeny
*Zygophyllum/genetics/classification/anatomy & histology/chemistry
Egypt
Plant Leaves/anatomy & histology/chemistry

@article {pmid42581425,
year = {2026},
author = {Hebenstreitová, K and Mahlerová, K and Vaňková, L and Vaněk, D},
title = {Species Determination Within the Felidae Family Using mtDNA Minibarcoding.},
journal = {Animal genetics},
volume = {57},
number = {4},
pages = {e70181},
pmid = {42581425},
issn = {1365-2052},
support = {VJ01010026//Ministerstvo Vnitra České Republiky/ ; },
mesh = {*Felidae/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA Primers ; Electron Transport Complex IV/genetics ; Animals ; },
abstract = {Wildlife forensic analysis frequently deals with highly degraded DNA samples, including those from tanned hides, processed products of traditional Chinese medicine, and specimens stored in preservation fluids. These samples present significant challenges for traditional DNA barcoding due to the difficulty of amplifying sufficiently long DNA fragments. To overcome this limitation, we designed five primer pairs to amplify short mitochondrial DNA (mtDNA) fragments (~100 base pairs). When aligned collectively, these fragments span approximately 500 bp of the cytochrome C oxidase subunit I (COI) gene, which is one of the most common species-barcoding targets. We subjected the primers to a comprehensive validation process, including in silico analysis and experimental verification using various non-degraded and degraded samples of animal tissues. Here, we demonstrate the efficacy and reliability of our DNA minibarcoding method. By addressing the limitations of traditional DNA barcoding, this method improves the accuracy and success of species identification, thereby supporting wildlife conservation, management, and forensic investigations.},
}

*Felidae/classification/genetics
*DNA Barcoding, Taxonomic/methods
DNA Primers
Electron Transport Complex IV/genetics
Animals

@article {pmid42582359,
year = {2026},
author = {Liu, Y and Shen, X and Liang, J and Tian, L and Huang, Y and Tian, W and Zhuge, F and Jiang, D},
title = {Comparative chloroplast genomics clarifies the taxonomic status and supports molecular identification of Viburnum keteleeri 'Sterile' and Viburnum keteleeri.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1908462},
pmid = {42582359},
issn = {1664-462X},
abstract = {Viburnum keteleeri 'Sterile' and V. keteleeri are traditional ornamental plants in China and are highly valued for their large, spherical inflorescences. However, due to long-term artificial selection and morphological similarity, the taxonomic boundary between V. keteleeri 'Sterile' and V. keteleeri has remained controversial. Conventional morphological identification and conventional barcodes have proven insufficient for accurately resolving their taxonomic relationship. In this study, V. keteleeri 'Sterile', V. keteleeri, and their closely related species were investigated using complete chloroplast genome (CPG) data. Comparative genomic analyses were subsequently performed using additional CPGs of Viburnum species retrieved from public databases. The results showed that both CPGs exhibited the typical quadripartite structure of angiosperms, each with a total length of 158,662 bp and containing 133 annotated genes. Simple sequence repeat analysis revealed that T/A-type repeats were the most abundant SSR category, while codon usage analysis indicated a strong preference for synonymous codons ending in A/U. Comparative analyses of 49 Viburnum CPGs demonstrated extremely low genetic divergence between V. keteleeri 'Sterile' and V. keteleeri. Phylogenetic reconstruction consistently placed the two taxa within the same terminal clade, suggesting a very close relationship. Based on the available chloroplast genome evidence, V. keteleeri 'Sterile' is unlikely to represent the nominal species and is more appropriately regarded as a horticultural cultivar or cultivated form derived from V. keteleeri. In addition, 293 lineage-specific single nucleotide polymorphism (SNP) loci were identified, and the ycf1 genes of both V. keteleeri 'Sterile' and V. keteleeri were found to be significantly longer than those of the other examined Viburnum species. These genomic features provide valuable candidate markers for rapid and accurate molecular identification. Overall, this study provides valuable genomic resources for clarifying taxonomic relationships, supporting germplasm conservation, facilitating cultivar authentication, and strengthening plant variety protection and nursery stock quality control in Viburnum.},
}

@article {pmid42584226,
year = {2026},
author = {Liu, Y and Zhao, S and Ren, Z and Li, S},
title = {Photonic fingerprint barcodes mediated by microsphere WGM lasing.},
journal = {Nanoscale},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6nr01349j},
pmid = {42584226},
issn = {2040-3372},
abstract = {Optical encoding technologies have emerged as promising tools for biomedical sensing and single-cell tracking, offering unparalleled opportunities for high-precision biological analysis. However, conventional optical barcoding systems suffer from limited coding capacity, poor biocompatibility, and low signal-to-noise ratios. Here, we report a photonic fingerprint barcode platform mediated by biocompatible microsphere lasers, which leverages whispering gallery mode (WGM) lasing to generate unique, fingerprint-like optical signatures. By engineering the structural parameters and excitation conditions of biocompatible polymer microspheres, we generate six distinct photonic fingerprint barcodes, mirroring the arch, tented arch, left loop, right loop, double loop, and whorl patterns of human fingerprints. Each generated barcode is characterized by a unique barcode-like intensity spectrum and waveform profile, enabling high-throughput, label-free biological identification with exceptional specificity. This work establishes a versatile, biocompatible optical encoding strategy, offering a promising tool for precision medicine, single-cell tracking, and multiplexed biosensing.},
}

@article {pmid42586759,
year = {2026},
author = {Su, Q and Zhou, X and Long, Y and Duan, F and Lian, Q},
title = {Pattern-Filter structural validation of single-cell RNA-seq reads reduces artifactual barcodes and improves biological resolution.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.281717.125},
pmid = {42586759},
issn = {1549-5469},
abstract = {Single-cell RNA sequencing (scRNA-seq) pipelines rely on the assumption that sequencing reads possess correct structural architecture, a premise we show is incomplete. Standard quantification tools treat errors exclusively as base mismatches, failing to identify structural aberrations arising from off-target priming or nonspecific amplification. We demonstrate that these pervasive artifacts, reads lacking essential anchor motifs like poly(T) tracts, linkers, or template-switching oligos, generate large numbers of spurious barcodes, artificially inflate cell counts, and substantially affect biological interpretation. To resolve this, we developed Pattern-Filter, a universal preprocessing tool that systematically validates read integrity before alignment. It functions by detecting platform-specific anchor sequences and applying strict base-composition filtering to ensure barcodes and UMIs contain only canonical nucleotides. When applied across diverse platforms, including 10x Genomics, Drop-seq, BD Rhapsody, and SPLiT-seq, Pattern-Filter systematically removes 2%-18% of total reads yet reduces spurious barcode diversity by up to 80%. This asymmetric reduction confirms that a small fraction of invalid reads drives the majority of technical noise, compromising cluster stability. Consequently, this targeted removal enhances data reproducibility and recovers biologically relevant cell types, such as dopaminergic neurons in mouse striatum, which were previously obscured by artifact-induced noise. These findings establish structural validation as an essential prerequisite for analysis, positioning Pattern-Filter as a useful standard for ensuring molecular fidelity and reliable biological discovery in single-cell transcriptomics.},
}

@article {pmid42239442,
year = {2026},
author = {Oikonomou, P and Calvary, L and Du, D and Polansky, J and Gattoni, G and Lynch, C and Shi, L and Mayer, C and McFaline-Figueroa, J and Nerurkar, NL},
title = {An endodermal subpopulation gives rise to neuromesodermal progenitors in the posterior chick embryo.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.726401},
pmid = {42239442},
issn = {2692-8205},
abstract = {Embryogenesis occurs through a progressive narrowing of cell fate potential, initiating with the segregation of three distinct germ layers during gastrulation. Although classically, each germ layer contributes to distinct tissue types as development proceeds, this view has been revised with the discovery of neuromesodermal progenitors (NMPs) - a bipotent progenitor population in the posterior embryo that gives rise to traditionally ectodermal and mesodermal tissues after gastrulation has concluded. However, until now the notion of lineage restriction of the endoderm to gastrointestinal, respiratory, and endocrine tissues has largely remained intact. Here, we describe a unique subpopulation in the chick endoderm that initially lines the ventral surface of Hensen's node (the amniote organizer). As posterior regression of the node ends with termination of the primitive streak, these cells undergo an FGF-dependent epithelial-to-mesenchymal transition, erasing their endodermal identity as they invade the tailbud and subsequently differentiate into a remarkably broad range of cell types including paraxial, lateral plate, and intermediate mesoderm, and to a lesser extent, notochord and neural tube. Disrupting ingression of node endoderm reduced embryonic axis elongation - a process attributed to mesoderm - by 50%. Through lineage barcoding, single-cell RNA sequencing, and fate mapping experiments, we conclude that the endodermal compartment of Hensen's node harbors a mixed population of fate restricted and multipotent progenitor cells that give rise to clonal populations spanning traditional germ layer boundaries. These findings illustrate a surprising example of germ layer plasticity and fate convergence across distant progenitor populations during amniote development.},
}

@article {pmid42571322,
year = {2026},
author = {Huang, JF and Liao, YC and Chan, TY and Chen, HM and Smith, DG},
title = {The congrid eel genus Gnathophis in Taiwan (Anguilliformes, Congridae), with descriptions of three new species.},
journal = {ZooKeys},
volume = {1287},
number = {},
pages = {11-46},
pmid = {42571322},
issn = {1313-2989},
abstract = {The genus Gnathophis differs from other genera of Congridae in having a moderately blunt and rounded tail tip and a slightly hardened tail extremity. The fleshy tip of the snout extends distinctly forwards beyond the intermaxillary teeth. A longitudinal fleshy keel is present on the ventral surface of the snout tip. Currently, two species of Gnathophis have been recorded from Taiwan, G. heterognathos and G. asanoi, whereas G. xenica has subsequently been determined to be a misidentification. In this study, three new species of the congrid eel genus Gnathophis Kaup are described from deep-sea waters off northeastern and southwestern Taiwan, based on 130 specimens. Gnathophis kbalanensis sp. nov. is diagnosed by the combination of blackish dorsal, caudal, and anal fins; 34-36 preanal vertebrae, 42-43 precaudal vertebrae, and 134-137 total vertebrae; 32-35 preanal lateral line pores; and elevated lateral line pores above the pectoral fin. Gnathophis melanurum sp. nov. is distinguished from its congeners by having whitish dorsal and anal fins and a blackish caudal fin; 28-32 preanal vertebrae, 37-41 precaudal vertebrae, and 98+-125 total vertebrae; 29-32 preanal lateral line pores; and elevated lateral line pores above the pectoral fin. Gnathophis nanhaiensis sp. nov. is separable from other species of Gnathophis in possessing whitish dorsal, caudal, and anal fins; 40-42 preanal vertebrae, 47-48 precaudal vertebrae, and 139-143 total vertebrae; 37-41 preanal lateral line pores; and lateral line pores above the pectoral fin that are not elevated. The validities of G. kbalanensis sp. nov. and G. melanurum sp. nov. are further supported by DNA barcoding analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Molecular comparisons additionally indicate that specimens of G. heterognathos (Bleeker) from waters off Taiwan exhibit a maximum intraspecific COI sequence divergence of 1.4%.},
}

@article {pmid42571425,
year = {2026},
author = {Pförtner, F and Briem, E and Enard, W and Richter, D},
title = {Increasing usable reads in RNA-seq protocols.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116984},
pmid = {42571425},
issn = {2589-0042},
abstract = {Bulk and single-cell RNA-seq are powerful tools for transcriptomic analysis, providing insights into molecular and cellular phenotypes. Costs constrain the biological insights obtainable within a given budget, and as sequencing prices decline, efficient library protocols have become a decisive factor. In this study, we introduce an approach to systematically optimize the number of usable reads generated by RNA-seq protocols. We applied this "funnel strategy" to prime-seq, an early-barcoding bulk RNA-seq protocol, by systematically testing critical protocol steps totaling 1,256 samples in 65 libraries. This resulted in the optimized prime-seq2 protocol that increases the number of usable reads by 60% and improves one of the most cost-efficient bulk RNA-seq protocols available. Our study also suggests that monitoring usable reads can serve as a valuable quality control for many RNA-seq protocols and sheds light on the complex interplay of experimental conditions that shape RNA-seq library composition and their interpretation.},
}

@article {pmid42573597,
year = {2026},
author = {Laux, M and Jardelino, AC and Vasconcelos, S and Pires, ES and Bernard, E and Oliveira, G and De-Souza, C and Nunes, GL},
title = {The shared performance of different COI regions increases the niche breadth detectable from bat guano eDNA.},
journal = {Genetics and molecular biology},
volume = {49},
number = {3},
pages = {e20250080},
pmid = {42573597},
issn = {1415-4757},
abstract = {The cytochrome c oxidase subunit I (COI), widely adopted as a DNA barcode for Metazoa, exhibits distinct variation levels in different regions within the gene. We investigated the efficacy of combining three arthropod-specific primers to enhance the detection of dietary niches, as opposed to relying on a single primer. This study utilized bat guano collected in bat caves from the Amazon and Caatinga biomes in Brazil. The UEA2-UEA3, UEA3-UEA4, and UEA5-UEA6 primer pairs recovered distinct proportions of Arthropoda (10%, 57%, and 42%, respectively) and exhibited considerable levels of unassigned reads (29%, 33%, and 42%, respectively) and non-target sequences (61%, 10%, and 16%, respectively). The UEA2-UEA3 primarily recovered Chiroptera (57%) but demonstrated the highest taxonomic coverage and richness for Arthropoda. On the other hand, UEA3-UEA4 and UEA5-UEA6 showed the highest α-diversity for Arthropoda; however, UEA5-UEA6 predominantly recovered Lepidoptera (40%) with the highest number of unique Arthropoda genera (45%), while UEA3-UEA4 mostly assigned to Lepidoptera and Diptera. Our results suggest the use of more than one primer pair and show that the analysis of only one primer pair can generate biased outputs. The choice primer is a crucial step in eDNA studies, especially for complex samples such as bat guano.},
}

@article {pmid42575597,
year = {2026},
author = {Rafuna, G and Sherifi, K and Ahmeti, S and Lindhorst, ZTL and Cvetkovikj, A and Kniha, E and Fuehrer, HP and Xhekaj, B},
title = {PCR-based screening for vector-borne pathogens reveals different Mycoplasma species in cats from Kosovo.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {73},
number = {},
pages = {101515},
doi = {10.1016/j.vprsr.2026.101515},
pmid = {42575597},
issn = {2405-9390},
mesh = {Animals ; *Mycoplasma/isolation & purification/genetics/classification ; Cats ; *Cat Diseases/epidemiology/microbiology/parasitology ; Polymerase Chain Reaction/veterinary ; Female ; Kosovo/epidemiology ; *Mycoplasma Infections/veterinary/epidemiology/microbiology ; Prevalence ; Male ; *Vector Borne Diseases/veterinary/epidemiology/microbiology ; },
abstract = {Vector-borne pathogens (VBPs) comprise a diverse range of pathogens, including viruses, bacteria, protozoa, and helminths, that are transmitted to vertebrate hosts by various species of arthropod vectors. The present study aimed to report the first data on the prevalence of VBPs in domestic cats in Kosovo and investigate associations with potential risk factors. Blood samples were collected from 107 domestic cats between April and October 2024 and preserved on filter papers. Samples were screened for VBPs, including Anaplasma spp., Ehrlichia spp., Babesia spp., Hepatozoon spp., Cytauxzoon spp., Bartonella spp., Filarioidea, Mycoplasma spp., Rickettsia spp., and Trypanosoma spp., using polymerase chain reaction (PCR), followed by sequence analysis. Haemotropic mycoplasma DNA was detected in 9 cats (8.4%, 95% CI: 4.2-15.8). Of the sequences obtained, three were identified as Mycoplasma haemofelis and six as Candidatus Mycoplasma haematominutum. The samples resulted negative for the presence of DNA from other VBPs. Significant variations in infection prevalence were associated with age, sex, outdoor access, and health status. This study provides the first molecular detection of Mycoplasma spp. infection in domestic cats from the capital region, Prishtina, and contributes to a better understanding of the epidemiology of this pathogen in the local feline population, which is essential for the development of effective preventive and control strategies.},
}

Animals
*Mycoplasma/isolation & purification/genetics/classification
Cats
*Cat Diseases/epidemiology/microbiology/parasitology
Polymerase Chain Reaction/veterinary
Female
Kosovo/epidemiology
*Mycoplasma Infections/veterinary/epidemiology/microbiology
Prevalence
Male
*Vector Borne Diseases/veterinary/epidemiology/microbiology

@article {pmid42581006,
year = {2026},
author = {Rosen, JD and Vasanthakumari, AD and Salomon, K and de Lange, N and Dash, PM and Keukeleire, P and Hassan, A and Barrera, A and Krupkin, B and Oualline, G and Kircher, M and Love, MI and Schubach, M},
title = {Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.281462.125},
pmid = {42581006},
issn = {1549-5469},
abstract = {As researchers and clinicians seek to identify human genomic alterations relevant to traits and disorders, identifying and aggregating evidence providing mechanistic support for associations between alterations and phenotypes remains challenging. In particular, the study of noncoding genomic variation remains a major challenge because of the lack of accurate functional annotation for activity in a given context and across alleles. Experimental evidence is critical for prioritizing and interpreting functional effects of genetic alterations. Massively parallel reporter assays (MPRAs) have emerged as a powerful high-throughput approach, enabling quantification of regulatory element activity and allelic effects, as well as systematic dissection of gene regulatory logic and variant effects across different contexts. However, the diversity of MPRA designs, lack of standardized formats, and many potential processing parameters hamper data integration, reproducibility, and meta-analyses across studies. To address these challenges, the Impact of Genomic Variation on Function (IGVF) Consortium established an MPRA focus group to develop community standards, including harmonized file formats, and robust analysis pipelines for a wide range of library types and experimental designs. Here, we present these formats and comprehensive computational tools, MPRAlib and MPRAsnakeflow, for uniform processing from raw sequencing reads to counts, processing, and visualization. Using diverse MPRA data sets, we investigated technical variability sources including barcode sequence bias, outlier barcodes, and delivery method (episomal vs. lentiviral). Our results establish best practices for MPRA data generation and analysis, facilitating robust, reproducible research and large-scale integration. The presented tools and standards are publicly available, providing a foundation for future collaborative efforts in regulatory genomics.},
}

@article {pmid42581234,
year = {2026},
author = {Jang, B and Zenhausern, R and Lian, L and Gentry, K and Abbas, AM and Rudden, S and Shin, YJ and Doan, J and Loughrey, D and Curran, EH and Wood, JS and Stammen, RL and Johnson, RP and Kim, H and Dahlman, JE},
title = {Non-invasive nanoparticle barcoding in nonhuman primates.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42581234},
issn = {1546-1696},
abstract = {The clinical relevance of a lipid nanoparticle (LNP)-mRNA drug candidate is often dictated by its behavior in nonhuman primates. Yet, evaluating how chemically distinct LNPs behave in nonhuman primates remains difficult, in part because nanoparticle barcoding assays require euthanasia and difficult downstream tissue processing. Here we report non-invasive nanoparticle barcoding, which quantifies functional mRNA delivery mediated by several LNPs in a single nonhuman primate using 30 µl of serum. This method is enabled by snapCodes, benzylguanine-modified DNA barcodes that covalently bind an mRNA-encoded nanoluciferase-SNAP-tag fusion protein in vivo. The resulting DNA-fusion protein complexes are exported from cells, isolated from serum and sequenced. After validating snapCode and fusion protein activity, we intravenously administer six snapCoded LNPs to mice and nonhuman primates, thereby comparing LNP delivery across species. Measuring mRNA delivery from multiple LNPs using a low-volume blood draw reduces animal use and may help identify promising nanoparticle formulations.},
}

@article {pmid42570715,
year = {2026},
author = {Felizardo, ACC and Catipon, AVT and Fontanilla, IKC and Leonardo, LR and Moendeg-Mamades, K and de Cadiz, AE and Fornillos, RJC and Lv, S and Tabios, IKB},
title = {Molecular identification of Haplorchis taichui and other trematodes infecting thiarid freshwater snails from Southern Philippines.},
journal = {Parasitology international},
volume = {116},
number = {},
pages = {103361},
doi = {10.1016/j.parint.2026.103361},
pmid = {42570715},
issn = {1873-0329},
abstract = {Fish-borne zoonotic trematodiases (FZT) are neglected parasitic infections of global public health significance, persisting in communities where there is a cultural practice of consuming raw or undercooked freshwater fish. In the Philippines, FZT surveillance efforts remain largely focused on human stool-based diagnostics, leaving intermediate host transmission stages poorly characterized. In this study, we provide molecular characterization of the zoonotic trematode cercariae infecting thiarid snails from five FZT-endemic barangays in New Corella, Davao del Norte, Southern Philippines. Of 387 thiarid snails collected in freshwater near human settlements, 26 (6.72%) were infected with three cercarial morphotypes. DNA barcoding and phylogenetic analyses using partial 28S and cox1 sequences identified parapleurolophocercous cercariae from Melanoides tuberculata as Haplorchis taichui, the most prevalent fish-borne zoonotic fluke species reported in the Philippines. The other two morphotypes represented lineages with distinct, non-fishborne transmission routes. Megalurous cercariae confirmed as Philophthalmus gralli, an ocular trematode of birds capable of aberrant human infection, were recovered from Stenomelania sp., representing a putative new first intermediate host record for this species. Virgulate xiphidiocercariae recovered from M. tuberculata were assigned to family Lecithodendriidae, though limited reference sequence coverage precluded genus- or species-level resolution. These findings characterize co-occurring trematode diversity in thiarid snails from Southern Philippines and corroborate active transmission of H. taichui in areas with documented human heterophyid infections. Future work integrating molecular surveillance of both snail and fish intermediate hosts into FZT monitoring may provide a more complete assessment of FZT transmission and human infection risk in these endemic areas.},
}

@article {pmid42566945,
year = {2026},
author = {Wu, Z and Bai, J and Chang, A and Wang, T and Liu, Y and Yu, H},
title = {Intercellular mitochondrial exchange shapes tumor evolution, microenvironment adaptation, and therapeutic vulnerabilities.},
journal = {Translational oncology},
volume = {72},
number = {},
pages = {102913},
doi = {10.1016/j.tranon.2026.102913},
pmid = {42566945},
issn = {1936-5233},
abstract = {Mitochondrial transfer has emerged as a previously underappreciated mode of intercellular communication with major implications for tumor biology. Beyond their cell-autonomous roles in bioenergetics and signalling, mitochondria can be exchanged between cells as intact organelles or as mitochondrial cargo, thereby reshaping the metabolic state, stress tolerance and therapy responsiveness of recipient cells. In tumors, mitochondrial transfer can buffer oxidative stress, compensate for mtDNA damage and restore oxidative phosphorylation, enabling metabolic plasticity and contributing to immune dysfunction within the tumor microenvironment. This review synthesized current evidence for the structural routes and regulatory logic of mitochondrial exchange in cancer, spanning actin-based tunneling nanotubes, extracellular vesicle-mediated export and uptake, and other contact-dependent mechanisms. We highlight actionable "gatekeepers" that constrain transfer efficiency, including conduit biogenesis programs, MIRO1/2-TRAK-motor coupling that licenses mitochondrial trafficking, and EV biogenesis/uptake modules, as well as microenvironmental triggers such as hypoxia and redox stress. We also evaluate emerging methodological standards required to distinguish bona fide organelle transfer from dye leakage or indirect cargo exchange, and discuss how orthogonal validation (genetic reporters, mtDNA barcoding and functional rescue assays) can improve rigor and comparability across studies. By integrating current findings, this article aims to provide a theoretical foundation and strategic guidance for targeting tumor metabolic regulation and improving precision oncology approaches.},
}

@article {pmid42568342,
year = {2026},
author = {Tedersoo, L and Prous, M and Chen, M and Anslan, S and Saar, I and Dubois, B and Mikryukov, V},
title = {Benchmarking Full-Length ITS Metabarcoding Across Illumina 2 × 500, PacBio, and Oxford Nanopore Sequencing Using Mock and Soil Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {6},
pages = {e70189},
pmid = {42568342},
issn = {1755-0998},
support = {101200758//HORIZON EUROPE European Research Council/ ; TK200//Estonian Ministry of Education and Research/ ; 362828//Research Council of Finland/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods/standards ; *Soil Microbiology ; *Metagenomics/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; DNA, Ribosomal Spacer/genetics/chemistry ; Benchmarking ; Biodiversity ; },
abstract = {Metabarcoding is a powerful tool for biodiversity comparisons, where standard-size DNA barcodes (> 500 bases) offer better taxonomic resolution than shorter ones. Still, the choice of sequencing platforms and bioinformatics pipelines may strongly affect inferred diversity due to various technical biases. We assessed the relative performance of Illumina MiSeq i100 (2 × 500 paired-end), PacBio Revio and Oxford Nanopore MinION sequencing and bioinformatics pipelines, using full-length ITS amplicon sequencing datasets from a 103-species mock community and 45 composite soil samples. Despite numerous low-quality reads, PacBio yielded the lowest overall error rate and highest number of taxa. Illumina revealed the highest proportion of chimeric and index-switched reads, along with a strong bias towards shorter amplicons. MinION data analysed using PRONAME and Minovar-a bioinformatics pipeline presented here-had the largest proportion of low-quality data, and rare taxa were lost during data filtering and read polishing steps. Although Minovar enabled amplicon sequence variant (ASV) level precision for common taxa, we recommend clustering ASVs into OTUs. For PacBio, standard filtering approaches outperformed the ASV approach because they retained rare taxa. For Illumina, a stringent ASV approach or removal of rare OTUs would limit artefacts. Across all platforms, excess PCR cycles promoted chimeric and low-quality reads and lost quantitativity in biodiversity assessments. With moderate differences in effect sizes, all analytical approaches supported the conclusion that sampling design determines how we see soil biodiversity responses to land use. For biodiversity surveys based on the full-length ITS metabarcoding, we recommend using PacBio sequencing with standard, non-ASV pipelines.},
}

*DNA Barcoding, Taxonomic/methods/standards
*Soil Microbiology
*Metagenomics/methods
Computational Biology/methods
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
DNA, Ribosomal Spacer/genetics/chemistry
Benchmarking
Biodiversity

@article {pmid42565232,
year = {2026},
author = {Protić, N and Jadrná, I and Škaloud, P and Knotek, P and Čertnerová, D},
title = {Linking variation in genome size to cyst size in chrysophytes.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70217},
pmid = {42565232},
issn = {1529-8817},
support = {23-05546O//Grantová Agentura České Republiky/ ; },
abstract = {Genome size varies tremendously across eukaryotes, which often contain far more DNA than expected from their biological complexity. To explain this paradox, selection-based hypotheses propose that genome size evolves through selection acting on life-history traits correlated with the phenotypic effects, independent of its genic content. To test the association between genome size and resting cyst size-a structure with morphology that may reflect overall body size-we selected chrysophyte algae (Chrysophyceae) producing siliceous stomatocysts as a model. In this study, we obtained and identified 85 chrysophyte strains representing 31 Mallomonas species using nuclear ITS rDNA region barcoding and estimated their genome sizes using propidium iodide flow cytometry. Within this genus, we observed more than a 75-fold variation in genome size (0.15-11.25 pg) and frequent substantial intraspecific variation, in some cases consistent with whole-genome doubling (polyploidization). By summarizing the published genome size records, adding our new measurements and combining them with published cyst sizes, we assembled a data set for 54 chrysophyte species to examine the relationship between genome size and cyst volume. Linear regression on log-transformed data revealed a strong positive correlation (R adj 2 = 0.626, p < 0.001), showing that species with larger genomes tend to produce larger stomatocysts. In chrysophytes, this relationship is considerably stronger than the widely documented genome size-cell size correlation observed across eukaryotes. Our findings suggest that stomatocyst size is a more informative predictor of genome size in this group and highlight the potential for using stomatocyst sizes to infer ancestral genome sizes from the fossil record.},
}

@article {pmid42565653,
year = {2026},
author = {Ugalde, J and Janzen, D and Hallwachs, W and Kohlmann, B and Hebert, P and Brown, B and Whitfield, J and Fernández-Triana, J and Ugalde, R and Rodriguez, E and Zúñiga, R and Smith, M and Steinke, D and Sharkey, M and Quicke, D and Manjunath, R and Puschendorf, R},
title = {Large-scale DNA barcoding reveals highly distinct insect distribution patterns across Costa Rican ecosystems.},
journal = {Genome},
volume = {69},
number = {},
pages = {1-26},
doi = {10.1139/gen-2025-0128},
pmid = {42565653},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Costa Rica ; Biodiversity ; *Ecosystem ; *Insecta/genetics/classification ; Phylogeny ; },
abstract = {Although insects are fundamental to understanding and conserving global biodiversity, they are vastly understudied. Here, we present a national inventory of Costa Rican insects based upon 3.78 million DNA barcodes representing 152 891 Barcode Index Numbers (BINs, proxies for species) from 28 localities sampled from 2017 to 2023 through the national BioAlfa program of Costa Rica. Although only 3.6% of BINs are linked to Linnean species, barcode-based community analyses revealed strong, consistent ecogeographic structure. Clustering of BIN data using bootstrapped Jaccard distances revealed seven distinct mainland assemblages and a distinct island cluster, shaped primarily by Costa Rica's mountain ranges, elevation, and slope orientation. Separate analyses for Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera coupled with analyses focused on some of their largest families (e.g., Braconidae, Cecidomyiidae, Cicadellidae, Erebidae, and Staphylinidae) confirmed these patterns and further revealed extremely high species turnover with most BINs being exclusive to a single region or locality. Our results reveal limited overlap of insect communities across ecosystems, implying that each life zone harbors unique taxonomic assemblages. Large-scale DNA barcoding has detected fine-grained spatial structure, providing a genomic framework for biodiversity monitoring and conservation in diverse tropical regions undergoing rapid environmental change.},
}

Animals
*DNA Barcoding, Taxonomic
Costa Rica
Biodiversity
*Ecosystem
*Insecta/genetics/classification
Phylogeny

@article {pmid42564840,
year = {2026},
author = {Etebari, K and Furlong, MJ},
title = {Interpreting molecular evidence for biosecurity decision-making: Lessons from coconut rhinoceros beetle incursions in the Pacific.},
journal = {Current research in insect science},
volume = {10},
number = {},
pages = {100131},
pmid = {42564840},
issn = {2666-5158},
abstract = {Molecular and genomic tools are increasingly used in biosecurity to support early detection, diagnostics and reconstruction of invasion pathways. However, selecting an appropriate marker for the question being addressed is critical, and translating molecular evidence into operational decisions can be challenging. Over-interpretation of commonly used markers may lead to misleading conclusions about population structure, invasion history and management priorities. DNA barcoding remains valuable for species identification and initial haplotype assignment, but questions concerning invasion pathways, admixture and phenotypic variation require additional molecular and ecological evidence. Here, we use coconut rhinoceros beetle (Oryctes rhinoceros) incursions in the Pacific as a case study to highlight interpretive pitfalls and lessons for applying molecular and genomic tools in biosecurity and biological control. We synthesise evidence on the strengths and limitations of mitochondrial markers, particularly CoxI, for haplotyping and inference of population relationships, and show how incomplete sampling and simplified assays can obscure cryptic diversity and bias interpretation. We then examine factors that complicate interpretation of OrNV-based biocontrol outcomes, including diagnostic sensitivity, study design and environmental modulation of host-pathogen interactions. Overall, these examples show that molecular evidence is most informative when marker choice, biological validation and phenotypic data are aligned with the biosecurity question.},
}

@article {pmid42564887,
year = {2026},
author = {Ngo, NP and Lee, MS and Chiang, P and Huang, JY and Hung, HL and Wu, KC},
title = {Integrated chemical and genetic authentication of Polygoni Multiflori Caulis: Refuting diameter restrictions and exposing market adulteration.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21561},
pmid = {42564887},
issn = {2167-8359},
mesh = {Chromatography, High Pressure Liquid ; Polymorphism, Single Nucleotide ; *Fallopia multiflora/genetics/chemistry/classification ; Emodin/analogs & derivatives/analysis ; *Drug Contamination ; Plant Stems/chemistry/genetics ; Genetic Variation ; *Drugs, Chinese Herbal/chemistry/standards ; Glucosides/analysis ; *Polygonaceae/genetics/chemistry/classification ; },
abstract = {BACKGROUND: Polygoni Multiflori Caulis (PMC), the dried stem of Pleuropterus multiflorus (Thunb.) Turcz. ex Nakai (PM), is a fundamental traditional Chinese medicine utilized for treating sleep disorders. Despite its medicinal importance, species confusion exists due to the taxonomic synonymy of Polygonum multiflorum var. hypoleucum (PMH) and Pleuropterus angulatus (PA) with PM. Furthermore, conventional quality standards often restrict PMC collection to specific stem diameters. This study evaluatedthe chemical and genetic diversity of PMC and its related taxa and assessed the authenticity of commercial PMC products.

METHODS: Authenticated samples of PM, PMH, and PA were analyzed using high-performance liquid chromatography (HPLC) to quantify three key markers, including 2,3,5,4'-tetrahydroxystilbene-2-O-β-D-glucoside (THSG), emodin, and physcion. The ITS2 region was sequenced to evaluate genetic diversity and identify single nucleotide polymorphisms (SNPs). We examined the impact of stem diameter (2.0 to 25.1 mm) on constituent levels in PM and surveyed eleven commercial PMC samples from Taiwanese markets.

RESULTS: Chemical analysis revealed that PMC samples across the entire diameter range (2.0 to 25.1 mm) consistently fulfilled the regulatory standards of the Taiwan Herbal Pharmacopoeia (THP), Chinese Pharmacopoeia (CP), and Hong Kong Chinese Materia Medica Standards (HKCMMS), effectively challenging the previously recommended 4 to 7 mm limit. In contrast, authenticated PMH samples lacked both the characteristic marker THSG and the enlarged tuberous roots typical of PM, and PA stem samples exhibited variable chemical phenotypes, with only a small subset meeting official standards. ITS2 sequencing successfully resolved the three taxa by identifying 13 SNPs and 16 distinct SNP genotypes. Notably, the market survey revealed that 82% of commercial samples were substituted with PA, of which 72% contained undetectable levels of the required analytes.

CONCLUSIONS: The findings demonstrate that PMH and PA represent distinct chemotypic lineages and should not be considered interchangeable botanical sources for PMC. The integration of HPLC quantification and ITS2 SNP barcoding provides a robust, multifaceted framework for quality control. Furthermore, our findings suggest that stems across the 2.0-25.1 mm diameter range can meet current pharmacopoeial requirements, providing preliminary evidence that the traditional 4-7 mm restriction may be unnecessarily narrow.},
}

Chromatography, High Pressure Liquid
Polymorphism, Single Nucleotide
*Fallopia multiflora/genetics/chemistry/classification
Emodin/analogs & derivatives/analysis
*Drug Contamination
Plant Stems/chemistry/genetics
Genetic Variation
*Drugs, Chinese Herbal/chemistry/standards
Glucosides/analysis
*Polygonaceae/genetics/chemistry/classification

@article {pmid42555814,
year = {2026},
author = {Cocchi, S and Talijanovic, M and Høgdall, EV and Lopacinska-Jørgensen, J},
title = {Assessing the Impact of Patient Selection and Analytical Methods on mRNA Biomarker Identification in Ovarian Cancer Using TCGA Data.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {33},
number = {},
pages = {10732748261468094},
pmid = {42555814},
issn = {1526-2359},
mesh = {Humans ; Female ; *Ovarian Neoplasms/genetics/drug therapy/pathology ; *Biomarkers, Tumor/genetics ; *Patient Selection ; *RNA, Messenger/genetics ; Retrospective Studies ; Gene Expression Profiling/methods ; Drug Resistance, Neoplasm/genetics ; Gene Expression Regulation, Neoplastic ; },
abstract = {IntroductionThe Cancer Genome Atlas (TCGA) data has been extensively used for differentially expressed genes (DEGs) discovery and validation in high-grade serous ovarian cancer (HGSOC), however platinum-sensitivity biomarkers have not yet reached clinical application. We aimed to propose a robust analytical framework for TCGA platinum sensitivity studies and systematically demonstrate how patient characteristics influence DEG analyses between platinum-sensitive and resistant groups, while also considering experimental platforms and analysis pipelines, as their impact is recognized but not comprehensively evaluated.MethodsThis retrospective TCGA cohort study used publicly available microarray and RNA-seq gene expression data. TCGA-derived datasets were identified through a literature review, including only studies enabling unambiguous patient identification. Three TCGA-based cohorts were assembled-two directly from published studies and one curated through own selection-differing in patient numbers (230, 201 and 142 patients, respectively) and stage distribution. Data were analyzed using DESeq2, edgeR, limma-voom, and Wilcoxon rank-sum test to compare the impact of patient selection and pipeline choice on DEGs outcome. Genes with an adjusted p-value < 0.05 and an |log2 fold change| > 2 were considered differentially expressed.ResultsThe three cohorts showed partial overlap of DEGs across platforms and pipelines. Both patient selection and analytical workflow influenced which genes were identified, highlighting findings variability even when using the same TCGA dataset. We establish a robust analytical framework for TCGA HGSOC biomarker studies, including the provision of patient barcodes and openly shared workflows that enable straightforward replication of our analyses from data download to DEG analysis.ConclusionsReproducibility of TCGA studies is limited by variability in patient selection, platinum sensitivity definitions, data sources, and analysis pipelines. We addressed these factors by providing a robust framework that can serve as a template for data analysis and transparent reporting when identifying and validating predictive signatures of platinum sensitivity in HGSOC patients.},
}

Humans
Female
*Ovarian Neoplasms/genetics/drug therapy/pathology
*Biomarkers, Tumor/genetics
*Patient Selection
*RNA, Messenger/genetics
Retrospective Studies
Gene Expression Profiling/methods
Drug Resistance, Neoplasm/genetics
Gene Expression Regulation, Neoplastic

@article {pmid42558731,
year = {2026},
author = {Chaunzwa, M and McElfresh, GW and Morrow, D and Boggy, GJ and Kaza, M and Benjamin, S and Feltham, S and Ojha, S and Swarbrick, GM and Rott, KH and Gilbride, RM and Labriola, CS and Axthelm, MK and Joag, V and Kain, D and Plessis, ND and Walzl, G and Lewinsohn, DA and Lewinsohn, DM and Hansen, SG and Picker, LJ and Bimber, BN},
title = {T cell antigenic recognition sequencing (TAR-seq) enables precise characterization of vaccine-elicited cellular immunity ex vivo and in vivo.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1823042},
pmid = {42558731},
issn = {1664-3224},
mesh = {Animals ; *Receptors, Antigen, T-Cell/genetics/immunology ; *Immunity, Cellular ; Lymphocyte Activation/immunology ; *Vaccines/immunology ; Macaca mulatta ; *T-Lymphocytes/immunology ; *Simian Immunodeficiency Virus/immunology ; Single-Cell Analysis ; Humans ; Single-Cell Gene Expression Analysis ; },
abstract = {INTRODUCTION: The functional responses of antigen (Ag) specific T cells are complex, clonotype-specific, context-dependent, and incompletely captured by dominant analytic approaches. Here we present T Cell Antigenic Recognition Sequencing (TAR-seq), a two-part process that uses single-cell RNA + T cell receptor sequencing (scRNA/TCR-seq) to provide a precise and comprehensive characterization of the differentiation state and functional response of T cells specific to a given antigen, ex vivo and in vivo.

METHODS: Many approaches use stimulation and activation-induced markers to identify Ag-specific T cells. We extend this by adding an scRNA/TCR-seq readout to identify the responding TCRs for each subject. We performed rigorous validation using tetramer-sorted T cells and developed a reusable probabilistic model to differentiate TCR-stimulated cells from bystander activation. These TCRs provide molecular barcodes to identify Ag-specific cells from unsorted scRNA/TCR-seq data, irrespective of stimulation, enabling a comprehensive view of their activity.

RESULTS: We applied this method to a cohort of SIV-vaccinated rhesus macaques (RMs). We performed SIV-infected cell recognition assays to identify the SIV-specific TCRs for each RM. We used these TCRs to subset SIV-specific cells and perform precise contrasts. Despite identical vaccination, we identified clone- and subject-level variability in their cytotoxic differentiation and cytokine production after incubation with SIV-infected targets. Per clonotype, the percentage of cells that responded after antigen exposure varied widely. Finally, we used TCRs as barcodes to precisely map the in vivo activity of CD8+ T cells 48-120H after SIV challenge. Precise TCR-based identification separated Ag-specific and bystander effects, measuring tissue-specific responses of SIV-specific T cells within 48 hours of infection.

DISCUSSION: Together, our data validate a powerful method to comprehensively understand T cell activity, with relevance to infectious disease, cancer, and autoimmunity, across species.},
}

Animals
*Receptors, Antigen, T-Cell/genetics/immunology
*Immunity, Cellular
Lymphocyte Activation/immunology
*Vaccines/immunology
Macaca mulatta
*T-Lymphocytes/immunology
*Simian Immunodeficiency Virus/immunology
Single-Cell Analysis
Humans
Single-Cell Gene Expression Analysis

@article {pmid42559103,
year = {2026},
author = {Wang, W and Shen, M and Su, Z and Yu, L and Ma, Z},
title = {Comparative plastome analyses and phylogenetic insights of Stellaria (Caryophyllaceae).},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1902479},
pmid = {42559103},
issn = {1664-462X},
abstract = {Stellaria (Caryophyllaceae) comprises approximately 112 species globally, with China serving as a significant center of diversity hosting about 64 species. Despite its taxonomic importance, the genus remains insufficiently studied in China. Previous phylogenetic studies relying on limited DNA barcodes produced weakly supported inferences, while those based on chloroplast genomes are currently lacking. Here, we characterize the chloroplast genome structure and reconstruct its highly resolved infrageneric phylogeny using 60 newly sequenced plastomes. All plastomes displayed a conserved quadripartite structure, with lengths varying from 147,205 bp to 149,409 bp, GC contents ranging from 36.6% to 36.7%, and gene counts spanning 128 to 129 genes. Codon usage patterns were highly conserved with leucine encoded by UUA exhibiting the highest relative synonymous codon usage. A total of 55-74 simple sequence repeats and 42-64 long repeats were detected. Three hypervariable regions-petN-psbM, trnP-rpl33, and ycf1 were identified as promising candidate DNA barcodes. Phylogenomic analysis resolved Stellaria into three strongly supported major clades and 15 well-defined subclades. The results are largely consistent with the established phylogeny of Stellaria. However, we observed certain discrepancies within specific clades. We propose some suggestions for these clades and species based on morphological and molecular evidence. This study provides the first comprehensive phylogenetic framework for Stellaria based on the chloroplast genome, establishing a robust foundation for future taxonomic revisions and evolutionary studies.},
}

@article {pmid42560383,
year = {2026},
author = {Dos Reis, JC and de Melo-Ximenes, AA and Nunes, R and Baptista, LAM and Silva, LCF and de Campos Telles, MP},
title = {DNA barcode markers for birds of the genus Sporophila: advances in species identification.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42560383},
issn = {1573-4978},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Female ; Phylogeny ; *Birds/genetics/classification ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers/genetics ; Species Specificity ; Male ; NADH Dehydrogenase/genetics ; Haplotypes ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Accurate identification of Sporophila is crucial for conservation and combating trafficking. Due to morphological similarity among females, molecular tools are essential. Although cytochrome c oxidase subunit 1 (COI) is the standard animal barcode, its limited resolution in recently diverged species necessitates more informative regions, such as cytochrome b (CYTB) and NADH dehydrogenase 2 (ND2), which are effective for Thraupidae. The aim of this study was to provide molecular mitochondrial markers to support species identification and development of tools that contribute to conservation of Sporophila.

METHODS AND RESULTS: The markers were validated using 62 adult males (13 species) and applied to 47 unidentified females from the Centro de Triagem de Animais Silvestres (CETAS). DNA was amplified via PCR, targeting CYTB and ND2, using genus-specific primers for all samples. COI was amplified exclusively for males, using primers based on literature. Sequences were analyzed using an ABI3500.Maximum likelihood trees and haplotype networks compared each studied region. Nearest-neighbor and barcode gap analyses confirmed marker efficiency for species identification, with CYTB and COI demonstrating the highest reliability. Among the 13 species evaluated, five showed barcode gaps across all markers, while two depended on the marker used. Female samples achieved a 100% amplification rate, with 74.47% showing high identity (> 98%); conclusively, 52.13% were identified with high confidence, whereas the remainder belonged to species falling outside our markers' current discrimination efficiency.

CONCLUSIONS: This study provides efficient tools for future research and conservation initiatives targeting Sporophila species.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Female
Phylogeny
*Birds/genetics/classification
Cytochromes b/genetics
Electron Transport Complex IV/genetics
Genetic Markers/genetics
Species Specificity
Male
NADH Dehydrogenase/genetics
Haplotypes
Polymerase Chain Reaction
Sequence Analysis, DNA/methods

@article {pmid42560944,
year = {2026},
author = {Padhye, SM and Ballesteros-Mejia, L and Agda, J and Agda, J and Hebert, PDN and Ratnasingham, S},
title = {BOLDconnectR: An R package for streamlined retrieval, transformation, and analysis of DNA barcode data on BOLD.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0355496},
pmid = {42560944},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Biodiversity ; Information Storage and Retrieval ; },
abstract = {DNA barcode data are essential infrastructure for biodiversity science as they enable scalable species identification and integrative analyses that link sequences to specimens, taxonomy, and geography. The Barcode of Life Data System (BOLD) is a centralized bioinformatics workbench that supports the full barcode data lifecycle: including acquisition, storage, validation, analysis, and dataset publication within a secure collaboration model. While BOLD's web interface is optimized for interactive dataset assembly and publication, many researchers require programmatic access to both public data and permissioned private records to build reproducible pipelines for curation and analysis prior to release. We introduce BOLDconnectR, an R package that provides authenticated access to BOLD, returns records in the Barcode Core Data Model (BCDM), performs automated transformation into commonly used R data structures, and enables customizable analytic workflows that generate publication-ready outputs.},
}

*DNA Barcoding, Taxonomic/methods
*Software
*Computational Biology/methods
Biodiversity
Information Storage and Retrieval

@article {pmid42563049,
year = {2026},
author = {David Wegner, K and Resch-Genger, U},
title = {Synthesis of Environmentally Friendly Heavy-Metal-Free AgInS2/ZnS Quantum Dots Using Microwave Heating.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3025},
number = {},
pages = {37-47},
pmid = {42563049},
issn = {1940-6029},
mesh = {*Quantum Dots/chemistry ; *Microwaves ; *Sulfides/chemistry ; *Zinc Compounds/chemistry ; *Indium/chemistry ; *Green Chemistry Technology/methods ; Metals, Heavy/chemistry ; },
abstract = {Luminescent semiconductor nanocrystals, also known as quantum dots (QDs), have had a major impact on applications of optical techniques in the life sciences, such as biosensing and bioimaging. Their unique optical properties, such as broad absorption bands with high molar extinction coefficients, together with their narrow size-dependent photoluminescence (PL) bands, high PL quantum yields (QYs), and a high photostability, are unique advantages for QDs as optical reporters in immunoassays, theranostics, in vitro/in vivo imaging, and flow cytometry. This also laid the foundation for numerous applications of optical multiplexing and barcoding. The most popular QD element compositions are based on heavy-metal elements, such as cadmium or lead, which pose a high toxic risk and are meanwhile restricted in Europe by REACH regulation. Increasing environmental concerns and the growing interest in and need for nanomaterials accessible by sustainable synthesis routes triggered the search for more eco-friendly QDs in the last years. Promising heavy-metal free candidates are ternary AgInS2 QDs, which can be synthesized with high-quality optical properties using aqueous synthesis methods. However, the use of conventional heating mantles or oil baths to heat the reaction mixture to the desired reaction temperature can lead to significant batch to batch variations caused by an inhomogeneous heat diffusion influencing the nucleation and growth of the QDs. A solution to this problem is the use of microwave-assisted heating. This enables a fast and homogeneous heat distribution throughout the entire reaction vessel, resulting in high-quality nanomaterials prepared with high batch-to-batch reproducibility. In this chapter, we will describe the synthesis steps for the preparation of AgInS2/ZnS QDs using microwave-assisted heating. The influence of the stabilizing ligands, variation of precursor concentrations, and the pH of the reaction solution will be detailed in the note section.},
}

*Quantum Dots/chemistry
*Microwaves
*Sulfides/chemistry
*Zinc Compounds/chemistry
*Indium/chemistry
*Green Chemistry Technology/methods
Metals, Heavy/chemistry

@article {pmid42564452,
year = {2026},
author = {Csuzdi, C and Razafindrakoto, M and Hong, Y},
title = {A new and interesting earthworm species from Madagascar (Crassiclitellata, Kynotidae) with an updated key to the Kynotus Michelsen, 1891 species.},
journal = {ZooKeys},
volume = {1286},
number = {},
pages = {251-263},
pmid = {42564452},
issn = {1313-2989},
abstract = {A new effort in 2025 to collect earthworms in northern Madagascar resulted in the discovery of a new species of Kynotus, a genus belonging to the endemic family Kynotidae, as well as the rediscovery of K. darwinii, the type species of Kynotus. The latter species had not been collected since its original reports in the late 19[th] century. With the description of the new species, Kynotus insularis sp. nov., the family Kynotidae now has 23 species. New DNA barcode sequences were generated for both species, confirming their distinctness and further demonstrating the high efficiency of the COI barcode region in identifying Kynotus species. An identification key to the currently known kynotid species is also presented.},
}

@article {pmid42564565,
year = {2026},
author = {Gumbau, M and Marteil, C and Groussier, G and Cruaud, A and Nidelet, S and Warot, S and Fernandez-Triana, J and Penet, L and Blazy, JM and Rasplus, JY},
title = {A synopsis of neotropical parasitoid wasps of Diaphania hyalinata (Lepidoptera, Crambidae), with new records from Guadeloupe.},
journal = {ZooKeys},
volume = {1286},
number = {},
pages = {293-336},
pmid = {42564565},
issn = {1313-2989},
abstract = {Diaphania hyalinata Linnaeus, 1767 (Lepidoptera, Crambidae), commonly known as the melonworm, is a major pest of cucurbits in the Neotropics. Yet, a comprehensive review of the parasitoid wasps that may act as biocontrol agents of this pest is still lacking. An extensive literature review was conducted to compile the current knowledge on the identity, distribution, and biology of parasitoid wasps associated with D. hyalinata across its range. Eggs, larvae, and pupae of D. hyalinata were collected in Guadeloupe and reared to document the local parasitoid diversity. Among the 37 parasitoids identified in our review, eight were recovered during our field survey, all of which are new records for the island. These parasitoids were photographed and DNA-barcoded to facilitate their potential use in future biological control programs targeting D. hyalinata. The species Trichogramma pretiosa Riley, 1879 (Trichogrammatidae; egg parasitoid) and Schoenlandella montserratensis Kang, 2021 (Braconidae; larval parasitoid) appear to be promising candidates for the biological control of D. hyalinata in Guadeloupe. It may be also worth evaluating the effectiveness of two additional larval parasitoids, Eiphosoma dentator Fabricius, 1804 (Ichneumonidae) and Apanteles impiger Muesebeck, 1958 (Braconidae), while assessing possible non-target effects on local fauna. However, it is important to consider that the presence of the hyperparasitoid Aphanogmus fijiensis Ferrière, 1933 (Ceraphronidae) could undermine biocontrol efforts. Overall, it would be valuable to gain a better understanding of the biological and environmental factors (such as agricultural practices and landscape features) that enhance the natural regulatory activities of this parasitoid community.},
}

@article {pmid42564774,
year = {2026},
author = {Salgado, J and Mariño-Brito, E and Mosquera-Yuqui, F and Ruales Guerra, A and Acebo Arcentales, JJ},
title = {First clinical isolation of Purpureocillium lilacinum in a pediatric oncological patient in Ecuador.},
journal = {Oxford medical case reports},
volume = {2026},
number = {8},
pages = {omag129},
pmid = {42564774},
issn = {2053-8855},
abstract = {BACKGROUND: Purpureocillium lilacinum is a ubiquitous environmental fungus widely utilized as an agricultural biocontrol agent, but it is increasingly recognized as an opportunistic human pathogen. While invasive fungal infections caused by this microorganism have been documented globally, disseminated systemic presentations in pediatric oncology remain exceptionally rare and carry high mortality rates.

CASE DESCRIPTION: We report the case of an 11-year-old female patient with a high-grade osteosarcoma who developed high-risk febrile leukopenia during chemotherapy. Blood cultures from both a subcutaneous port and peripheral blood turned positive for both yeast-like and hyphal structures, which were further identified by DNA barcoding (ITS and EF1a regions) as P. lilacinum. The patient exhibited concurrent multiorgan dissemination, including hyperchromic scaling skin lesions in the perianal region and limbs, as well as diffuse bilateral pulmonary micronodules confirmed via video-thoracoscopy biopsy. Despite initial treatment with amphotericin B and fluconazole, clinical resolution was successfully achieved only after optimizing the antifungal regimen with oral voriconazole. The patient fully recovered and remains stable.

CONCLUSIONS: To our knowledge, this represents the first clinical isolation and reported case of disseminated systemic P. lilacinum infection in a pediatric oncological patient in Ecuador. This case highlights the aggressive nature of this pathogen in immunosuppressed children, the challenge of its diagnosis due to the lack of specialized infrastructure for antifungal susceptibility testing, and the critical importance of a multidisciplinary approach and prompt, targeted first-line therapy with voriconazole to ensure survival.},
}

@article {pmid42553576,
year = {2026},
author = {Schilthuizen, M and Boomsma, R and Faes, S and Jousma, M and Buisman, J and Lankenau, DH and Kountouras, S and van den Broek, M and Hemelaar, EM and Noomen, J and de Vries, R and Lopatriello, G and Limongi, AR and Maestri, S and Kamchev, P and van Manen, S and Khalik, MZ and Delledonne, M and Đokić, J and Mićanović, A and Popović, J and Njunjić, I and Zallot, E},
title = {Two new Cochlostoma species from the Durmitor and Komarnica regions of northern Montenegro (Caenogastropoda, Cochlostomatidae).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e196955},
pmid = {42553576},
issn = {1314-2828},
abstract = {BACKGROUND: Slow-migrating gastropods are key indicators of habitat continuity, i.e. areas of relatively long-term ecological stability. The gastropod genus Cochlostoma (Architaenioglossa, Cochlostomatidae) is a common and widespread component of karst communities throughout the countries surrounding the Mediterranean. Recent work has taken into account genetic and reproductive-anatomical diversity and has revealed that the uniform shell morphology hides surprisingly rich and deep divergences.

NEW INFORMATION: Here, we describe two species of the subgenus Turritus, C. (Turritus) dobrido sp. nov. and C. (Turritus) komarnica sp. nov. They were collected, studied and described as part of citizen-science expeditions to the threatened Komarnica Canyon and to Durmitor National Park, two adjoining regions in Montenegro. The new species were found sympatrically and, in some cases, syntopically with Cochlostoma scalariniforme (A. J. Wagner, 1906), as well as with each other.},
}

@article {pmid42553627,
year = {2026},
author = {Tippery, NP and Larkin, DJ and Bohnen, J and Wendell, DL and Anderson, NO and Galatowitsch, SM and Abbey, M and Smith, AG and Noyszewski, AK},
title = {Molecular methods for differentiating Phragmites australis subspecies and identification of hybrid stands in the Upper Midwestern United States.},
journal = {Applications in plant sciences},
volume = {},
number = {},
pages = {e70073},
pmid = {42553627},
issn = {2168-0450},
abstract = {PREMISE: In North America, Phragmites australis (common reed) has drawn a great deal of research attention. Non-native P. australis subsp. australis is a noxious weed that has locally displaced native P. australis subsp. americanus in some areas. Although morphological features can distinguish the two subspecies, molecular tools often are required to confirm identifications. Additionally, the existence of natural intrasubspecific hybrids presents novel management challenges. Hybrid Phragmites is difficult to detect, and it has become standard practice to apply molecular tools to survey for hybrids.

METHODS: We applied several molecular techniques-microsatellite, DArTseq (a type of genotyping-by-sequencing), restriction fragment length polymorphism (PCR-RFLP), and next-generation sequencing-to characterize P. australis at the landscape scale in Minnesota and Wisconsin and to search for hybrids.

RESULTS: We obtained molecular data for Phragmites plants sampled from 341 stands, ultimately characterizing 98 stands as native and 236 as non-native. Plants from two adjacent stands in Washington County, Minnesota, were confirmed to be hybrids.

DISCUSSION: These are the first confirmed hybrids from the Upper Midwest/western Great Lakes region. We also discuss the relative cost and effectiveness of the various molecular methods and offer recommendations for future studies.},
}

@article {pmid42553711,
year = {2026},
author = {Duong Nguyen Xuan, L and Tran Thi Van, A and Thai Hong, D and Le Thi Tuyet, A and Vo Ngoc Linh, G},
title = {Characterization of the complete plastid genome and 45S nrDNA sequences of Murdannia medica (Lour.) D.Y. Hong (Commelinaceae) and its phylogenetic analysis.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {11},
number = {9},
pages = {1003-1007},
pmid = {42553711},
issn = {2380-2359},
abstract = {Murdannia medica is a Vietnamese traditional medicinal herb. Here, we report DNA super‑barcodes comprising the complete plastid genome (plastome, 177,455 bp) and 45S nuclear ribosomal DNA (45S nrDNA, 5,741 bp) of M. medica. The plastome has a large single‑copy (LSC, 100,132 bp), a small single‑copy (SSC, 21,125 bp), and a pair of inverted repeats (IRs) of 28,099 bp each. It contains 115 annotated genes and has an overall A/T content of 68.2%. Plastome‑based phylogenetic analyses show that M. medica sister with M. edulis. These new genomic resources provide a valuable foundation for future cultivation, conservation, and systematic investigations of M. medica.},
}

@article {pmid42555226,
year = {2026},
author = {Nitta, M and Uchiyama, M and Hayashi, T},
title = {Redescription of the Larval Trematode Taxon Monilicaecum ventricosum (Hemiuroidea: Didymozoidae) from Type Host Cololabis saira, with Inference of the Definitive Host Based on DNA Analysis.},
journal = {Zoological science},
volume = {43},
number = {4},
pages = {417-425},
doi = {10.2108/zs260004},
pmid = {42555226},
issn = {0289-0003},
mesh = {Animals ; *Trematoda/genetics/classification/anatomy & histology ; Larva/classification/genetics ; *Trematode Infections/parasitology/veterinary/epidemiology ; DNA, Helminth/genetics ; Phylogeny ; *Fish Diseases/parasitology ; Host-Parasite Interactions ; Japan ; },
abstract = {The larval trematode taxon Monilicaecum ventricosum Yamaguti, 1942 (Didymozoidae) was redescribed from its type host, the Pacific saury Cololabis saira (Brevoort, 1856), collected from the North Pacific off Eastern Hokkaido, Japan. Because didymozoid larvae and adults differ markedly in morphology, linking these two stages using morphological data alone has traditionally been difficult. Consequently, the monotypic genus Monilicaecum Yamaguti, 1942 is currently regarded as a collective group, similar to genera established solely on larval forms of other trematodes. However, recent advances in molecular studies have enabled researchers to link larval and adult stages, clarify life cycles, and undertake more robust taxonomic evaluations. In this study, newly collected larval specimens were examined morphologically, and DNA barcodes (28S, ITS, and cox1) were generated to confirm their identity as M. ventricosum through morphological comparisons with type materials. These sequences were compared with those available in public databases to determine the corresponding adult stages and definitive hosts. Although no identical adult sequences were detected, M. ventricosum showed a close genetic relationship with four didymozoid species parasitizing the Australian yellowfin tuna, Thunnus albacares (Bonnaterre, 1788), suggesting that its definitive host is likely a species of Thunnus South, 1845. These findings provide essential molecular data for M. ventricosum, contribute to the taxonomic stability of Didymozoidae, and offer a foundation for future studies aimed at elucidating species boundaries and life-cycle connections within this group.},
}

Animals
*Trematoda/genetics/classification/anatomy & histology
Larva/classification/genetics
*Trematode Infections/parasitology/veterinary/epidemiology
DNA, Helminth/genetics
Phylogeny
*Fish Diseases/parasitology
Host-Parasite Interactions
Japan

@article {pmid42546145,
year = {2026},
author = {Ascensao, JA and Yu, Q and Hallatschek, O},
title = {The evolution of genetic drift over 50,000 generations.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyag199},
pmid = {42546145},
issn = {1943-2631},
abstract = {Random variation in reproductive success-genetic drift-profoundly shapes genetic diversity and evolutionary trajectories. The strength of drift depends on the variance in descendant number, σ2d, which governs key evolutionary outcomes: for instance, the establishment probability of a beneficial mutation scales inversely with σ2d. However, whether σ2d itself evolves over long timescales has remained unclear, because allele-frequency fluctuations depend on drift only through the effective population size, Ne = N/σ2d, which blends census population size with descendant-number variance. Here, we disentangle these components by using model-based Bayesian inference combined with joint tracking of (i) frequency fluctuations of neutrally barcoded lineages and (ii) census population sizes across growth cycles in the E. coli Long-Term Evolution Experiment (LTEE). Analyzing 33 clones spanning the ancestor through 50,000 generations in two replicate populations (Ara-2 and Ara+2), we find that the strength of genetic drift evolved markedly-and divergently-between the two replicate populations. Both census size and σ2d changed substantially through time, with most variation in Ne driven by shifts in σ2d rather than census size. After approximately 2,000 generations, the σ2d of the two populations diverged sharply: Ara+2 generally remained close to a bottleneck-only null expectation, whereas Ara-2 exhibited 1.5-5× stronger drift, consistent with an evolved increase in stochasticity during growth. These results imply that mutations can alter both the mean and the variance of the descendant-number distribution, and we show that the joint distribution of mutational effects on fitness and on σ2d can substantially modulate the rate of adaptation. The key parameter governing genetic drift can therefore itself evolve in the LTEE, with direct consequences for adaptation.},
}

@article {pmid42548531,
year = {2026},
author = {Jamdade, R and Al Jasmi, M and Alsallani, M and Al Shaer, K and Al Harthi, E and Gairola, S and Shabana, HA and Mahmoud, T and Mosa, KA and El-Keblawy, A},
title = {An integrative multi-locus DNA barcode library of selected medicinal plants from the United Arab Emirates.},
journal = {3 Biotech},
volume = {16},
number = {8},
pages = {368},
pmid = {42548531},
issn = {2190-572X},
abstract = {UNLABELLED: A multi-locus DNA barcode reference library was developed for 55 medicinal plant species from the 56 collected in the United Arab Emirates using rbcL, matK, and ITS2 markers, generating 397 high-quality sequences from 146 specimens. The rbcL marker showed the highest amplification (82.71%) and sequencing success (94.41%), while ITS2 and matK exhibited greater sequence variability with nucleotide diversities of 20.35 and 27.88, respectively. Genetic divergence analyses revealed minimal within-species variation for rbcL (mean 0.03%) and higher divergence within genera and families for matK (mean up to 10.12%) and ITS2 (mean up to 22.20%), confirming their complementary resolution across taxonomic levels. Barcode-gap assessments identified persistent delimitation challenges within Zygophyllum and Suaeda, where intra- and interspecific distances overlapped across all three markers. Species delimitation using Assemble Species by Automatic Partitioning (ASAP) correctly classified up to 94.9% of specimens with rbcL, while ITS2 and matK achieved 82.2-82.6% accuracy. Support Vector Machine (SVM) classification substantially improved resolution, achieving 96.82% accuracy for rbcL and 100% for both matK and ITS2. Logical consensus evaluation across marker combinations without sequence concatenation further demonstrated that SVM-based pairwise combinations resolved up to 100% of evaluable species, with rbcL+matK, matK+ITS2, and rbcL+matK+ITS2 all achieving perfect resolution, outperforming ASAP-based combinations for identical marker sets. The reference library provides validated DNA barcodes that support molecular identification, herbal-product authentication, biodiversity assessment, and conservation planning, and contributes to the Arabian Barcode of Life initiative.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04946-1.},
}

@article {pmid42548659,
year = {2026},
author = {Du, Q and Zhang, Z and Li, R},
title = {Pan-chloroplast genomes of Hordeum reveal insights into chloroplast evolution in the Poaceae family.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1881945},
pmid = {42548659},
issn = {1664-462X},
abstract = {Chloroplast genomes are widely used in phylogenetic and evolutionary studies due to their conserved structure and maternal inheritance. However, a comprehensive pan-chloroplast analysis across the genus Hordeum remains lacking. In this study, we assembled and annotated 43 chloroplast genomes representing 12 Hordeum species, together with 18 chloroplast genomes from other Poaceae species, to investigate structural variation, repeat sequences, codon usage, RNA editing, selective pressure, and nucleotide diversity. All chloroplast genomes exhibited the typical quadripartite structure with genome sizes ranging from 136,461 bp to 137,149 bp in Hordeum. The lengths of LSC and IR regions showed strong positive correlations with chloroplast genome size (r = 0.853 and 0.857, respectively). IR boundaries were highly conserved within Hordeum, whereas three distinct boundary types were identified across Poaceae. Pentanucleotide simple sequence repeats (SSRs) were universally present in Hordeum but absent in some other Poaceae species, representing a candidate Hordeum-enriched marker pending broader validation. Based on the newly assembled chloroplast genomes of Hordeum, the phylogenetic relationships were reappraised. A total of 66 protein-coding genes contained RNA editing sites, with ndhB harboring the most edits in Hordeum. All examined protein-coding genes showed Ka/Ks values below 1, while ribosomal subunit genes exhibited the highest interspecific variation in Ka/Ks. Hordeum bulbosum displayed the highest intraspecific nucleotide diversity and haplotype diversity, whereas cultivated Hordeum vulgare showed extremely low diversity. Several hypervariable regions were identified as candidate DNA barcodes. This pan-chloroplast genome study provides new insights into the structural and evolutionary dynamics of Hordeum chloroplast genomes and offers valuable genomic resources for phylogeny, germplasm identification, and adaptive evolution in the genus.},
}

@article {pmid42550841,
year = {2026},
author = {Jung, JL and Haderlé, R and Cosnier, K and Al Musallami, M and Al Mehairbi, S and Perumal, P and Al Hammadi, S and Valentini, A and Ung, V and Prazuck, C and Chaveneau, C and Adam, O},
title = {First eDNA-based monitoring of marine vertebrates in the urban marine ecosystem of Abu Dhabi: Mangrove and seagrass beds as biodiversity reservoirs?.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0352249},
pmid = {42550841},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *DNA, Environmental/genetics/analysis ; *Ecosystem ; *Vertebrates/genetics/classification ; *Environmental Monitoring/methods ; Wetlands ; *Aquatic Organisms/genetics/classification ; United Arab Emirates ; },
abstract = {The Arabian Gulf is a semi-enclosed sea with shallow waters. Its marine fauna must cope with extreme and recurring environmental conditions (high summer temperatures, hypersalinity, hypoxia). In addition, local human activities are very significant and have a marked impact on coastal areas, particularly in urban marine ecosystems (UME). Taken together, the Arabian Gulf's low species richness, its exposure to multiple human-induced stressors, and the proximity of many taxa to their environmental tolerance limits create a particularly concerning situation. Monitoring marine wildlife must be a priority in this context, particularly with respect to marine vertebrates, difficult to study using integrative approaches. The present study aimed to generate relevant data on marine vertebrate biodiversity in the UME of Abu Dhabi, and to provide evidence-based information to inform conservation policy. In addition, investigating marine biodiversity in the world's warmest sea in summer, the Arabian Gulf, will provide us with information of general interest in terms of the adaptation and evolution of marine fauna in the current period of global climate change. We conducted the first environmental DNA (eDNA)-based survey of marine vertebrate diversity in Abu Dhabi's UME. Using a standardized process of water sampling, eDNA metabarcoding using a ~ 97 bp fragment of the mitochondrial 12S rRNA gene as barcode, and taxonomic assignment, we studied vertebrate biodiversity at four urban sites, including a marina, a newly developed area, a seagrass bed, and a protected urban mangrove. We identified 83 distinct taxa, including five birds, two elasmobranchs, one marine mammal, and 75 teleosts. The specific taxonomic richness did not vary significantly between sites. In contrast, phylogenetic diversity metrics revealed lower diversity than expected for the newly developed area, while the mangrove and, to a lesser extent, the seagrass bed exhibited a phylogenetic structure consistent with their species richness. This approach provides a powerful, non-invasive and integrative framework for long-term monitoring and supports evidence-based conservation planning for marine biodiversity in the Arabian Gulf.},
}

Animals
*Biodiversity
*DNA, Environmental/genetics/analysis
*Ecosystem
*Vertebrates/genetics/classification
*Environmental Monitoring/methods
Wetlands
*Aquatic Organisms/genetics/classification
United Arab Emirates

@article {pmid42551976,
year = {2026},
author = {An, SH and Myagmarsuren, T and Heo, GB and Jeong, H and Kang, YM and Dondog, U and Tsogbadrakh, U and Lee, YJ and Tseren-Ochir, EO and Lee, KN},
title = {Clade 2.3.4.4b H5N1 highly pathogenic avian influenza detected in wild bird feces, Eastern Mongolia, 2024.},
journal = {Journal of veterinary science},
volume = {27},
number = {4},
pages = {e38},
doi = {10.4142/jvs.25274},
pmid = {42551976},
issn = {1976-555X},
support = {I-1543418-2021-25-01/QIA/Animal and Plant Quarantine Agency/Korea ; },
mesh = {Animals ; *Influenza A Virus, H5N1 Subtype/isolation & purification/genetics/pathogenicity/classification ; Mongolia/epidemiology ; *Influenza in Birds/virology/epidemiology ; Feces/virology ; Phylogeny ; Birds ; Animals, Wild/virology ; },
abstract = {IMPORTANCE: Despite ongoing intercontinental spread of clade 2.3.4.4b H5N1 highly pathogenic avian influenza (HPAI), surveillance data from Mongolia -- a critical junction between Central and East Asian migratory flyways -- remain scarce, leaving a gap in understanding how viruses move between northern breeding areas and southern wintering grounds.

OBJECTIVE: We aimed to detect and genetically characterize HPAI viruses in wild bird populations in Mongolia and assess their relationship with viruses circulating in East Asia.

METHODS: Active surveillance was conducted at Ganga Lake, Mongolia, in October 2024. A total of 352 wild bird fecal samples were collected and tested for AIVs. Viral isolates were subtyped, whole-genome sequenced, and phylogenetically analyzed. Host species was identified using c oxidase I barcoding.

RESULTS: Sixteen AIVs were isolated, including one clade 2.3.4.4b H5N1 HPAI virus (M9-3) from whooper swan feces. Genomic analysis revealed M9-3 had > 99% similarity with Korean and Japanese H5N1 isolates reported in late 2024 and undergone recent reassortment and disseminated through migratory flyways.

CONCLUSIONS AND RELEVANCE: This is the first detection of clade 2.3.4.4b H5N1 in Eastern Mongolia in a fecal sample during late autumn. These findings underscore Mongolia's importance as a sentinel location for interregional HPAI dissemination.},
}

Animals
*Influenza A Virus, H5N1 Subtype/isolation & purification/genetics/pathogenicity/classification
Mongolia/epidemiology
*Influenza in Birds/virology/epidemiology
Feces/virology
Phylogeny
Birds
Animals, Wild/virology

@article {pmid42552959,
year = {2026},
author = {Spurgeon, BEJ},
title = {Platelet flow cytometry: An evolving platform for clinical hematology.},
journal = {Cytometry. Part B, Clinical cytometry},
volume = {},
number = {},
pages = {},
doi = {10.1002/cyto.b.70060},
pmid = {42552959},
issn = {1552-4957},
abstract = {Flow cytometry has transformed platelet biology and diagnostics through high-resolution, single-cell analysis of surface markers, activation states, and intracellular signaling. This review traces its evolution from early applications in glycoprotein profiling and immune thrombocytopenia to clinical roles in HIT, VITT, and FNAIT. Advances in spectral cytometry, phosphoflow, and fluorescent barcoding have increased analytical depth and supported development of whole blood-compatible platelet function assays. Flow cytometry now enables characterization of platelet subpopulations, assessment of complement deposition, and functional evaluation across immune and thrombotic disorders. These capabilities support applications in diagnostics, bleeding and cardiovascular risk assessment, drug-induced thrombocytopenia, and platelet product quality control. As these technologies mature, flow cytometry is expanding its role in clinical workflows and may enable more biologically informed and individualized approaches in precision hematology.},
}

@article {pmid42553547,
year = {2026},
author = {Schneider, JA and Salden, T and Moser, M and Peters, RS},
title = {kretschmanni's global relatives: The Aphanogmus species with spiny sternite females (Hymenoptera, Ceraphronidae).},
journal = {ZooKeys},
volume = {1286},
number = {},
pages = {187-225},
pmid = {42553547},
issn = {1313-2989},
abstract = {The Western Palaearctic Aphanogmus kretschmanni Moser, 2023 is unique among all described species of Ceraphronidae in having two distinct rows of spines on the seventh metasomal sternite of the female. In this study, we examined additional Aphanogmus that share this trait and found at least five additional putative species in an integrative taxonomy approach using morphology and publicly available CO1 barcode data on BOLD. Two new species are described herein: A. manta Schneider, Salden & Peters, sp. nov. and A. liceodosriosi Schneider, Salden & Peters, sp. nov. The diagnosis of A. kretschmanni is updated. The remaining putative species are listed but not formally described as reliable diagnoses require additional material. We also describe males, including male genitalia, of species with spiny sternite females for the first time. Males lack the metasomal sternal spines which implies a sex-specific function of the spines, for example, in oviposition. In our morphological diagnoses, we use characters of the Waterston's evaporatorium (WE) present on the sixth metasomal tergite in both males and females in addition to previously established morphological characters and further highlight the value of the WE in delimiting Ceraphronidae species and morphologically matching males and females. The number of putative species and their distribution literally around the globe (Neotropics, Afrotropics, Palaearctic, Australasia, Orientalis) imply the presence of an unexpectedly large number of relatives of A. kretschmanni. Future investigations are necessary to capture the true diversity within the genus Aphanogmus and to unravel the biological and evolutionary background of the intriguing sternal spines.},
}

@article {pmid42539960,
year = {2026},
author = {Bu, Y and Gao, Y},
title = {New species and new records of Tullbergiidae (Arthropoda, Hexapoda, Collembola, Poduromorpha) from Xizang, Southwest China, with genetic distance analysis within the family.},
journal = {ZooKeys},
volume = {1286},
number = {},
pages = {41-62},
pmid = {42539960},
issn = {1313-2989},
abstract = {The Tullbergiidae of Xizang, Southwest China, are studied based on specimens newly collected in 2024. Metaphorura alticola sp. nov., which was discovered in two localities at extremely high altitudes of 4000-5300 m in Shannan City, is described and illustrated. It can be distinguished from the similar M. motuoensis Bu & Gao, 2017 by the dorsal chaetotaxy, number of vesicles on PAO, and the shape of anal spines on Abd. VI, as well as the large genetic distance of the COI gene. Mesaphorura macrochaeta Rusek, 1976, found from several localities in Xizang, is recorded in China for the first time, and Chinese specimens are described and illustrated. In addition, the distributions for M. hylophila Rusek, 1982, M. krausbaueri (Börner, 1901), M. pacifica Rusek, 1976, and M. yosii (Rusek, 1967) in Xizang are updated according to the newly collected material. DNA barcodes of mitochondrial COI gene for Metaphorura alticola sp. nov., M. macrochaeta, and M. hylophila are newly sequenced and analyzed together with 26 sequences of the family extracted from GenBank. The genetic distances of different levels in the family Tullbergiidae are analysed. A key for all tullbergiid species recorded in Xizang and a map of their distributions are also provided.},
}

@article {pmid42540691,
year = {2026},
author = {Inumaru, M and Noda, R and Itokawa, K and Matsumura, R and Kimura, T and Kuwata, R and Nakao, S and Tsuha, O and Takemura, A and Nishiyama, S and Yamauchi, T and Tamatani, H and Yoshikawa, A and Hattori, M and Sasaki, T and Watanabe, M and Sawabe, K and Aboshi, AR and Kobayashi, D and Yang, C and Yamada, A and Isawa, H and Kasai, S and Higa, Y},
title = {National Distribution of Bisexual and Parthenogenetic Haemaphysalis longicornis of Japan, and a Real-Time PCR-Based Method to Distinguish the Two Reproductive Groups.},
journal = {Journal of parasitology research},
volume = {2026},
number = {},
pages = {9395344},
pmid = {42540691},
issn = {2090-0023},
abstract = {The Asian longhorned tick, Haemaphysalis longicornis, is a well-known vector of several zoonoses including SFTS and Japanese spotted fever. This species consists of two different reproductive forms, bisexual and parthenogenetic, which are suggested to have differential roles in disease transmission. In Japan, the distributions of these forms have been suspected from sex bias in each population. Meanwhile, recent insights about the origin of the parthenogenetic form suggest the possibility of individual-level diagnosis using mitochondrial phylogeny. To reassess the current distribution of those reproductive forms and potential changes over time in Japan, 1750 H. longicornis collected across 23 prefectures of Japan were investigated. The COI barcoding region was used to distinguish the mitochondrial haplogroup of each individual. Additionally, we developed real-time PCR probes to distinguish the two mitochondrial haplogroups representing each reproductive form. As previous studies have suggested, the parthenogenetic mitochondrial haplogroup was present throughout the country, while the bisexual mitochondrial haplogroup was found only in central and western Japan. Interestingly, populations consisting of either one or both haplogroups were found in neighboring areas, highlighting the need for more detailed and fine-scaled investigations in order to fully reveal the distribution of the reproductive groups. The newly developed real-time PCR method successfully differentiated all tested haplotypes. Furthermore, alignment of 173 COI haplotypes revealed that the diagnostic nucleotide selected for the method was consistent across all haplotypes, including those outside of Japan. This suggests that this method can accurately distinguish between the two haplogroups of H. longicornis in both Japan and other countries. This one-step method will serve as a rapid tool to distinguish bisexual and parthenogenetic H. longicornis, making further investigations, particularly into their role in disease transmission and shifts in distributions, possible.},
}

@article {pmid42541285,
year = {2026},
author = {Aupalee, K and Srisuka, W and Takaoka, H and Rodpai, R and Jones, MO and Charoenvilaisiri, K and Saingamsook, J and Pusawang, K and Saeung, A},
title = {Multiplex PCR for the differentiation of Simulium asakoae and molecular detection of pathogens in the S. asakoae species group in Thailand.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {10},
number = {},
pages = {100414},
pmid = {42541285},
issn = {2667-114X},
abstract = {A human-biting black fly, Simulium (Gomphostilbia) asakoae Takaoka & Davies, 1995, together with certain other members of the S. asakoae species group, is of medical and veterinary importance as a vector of various pathogens. However, accurate species identification remains challenging due to the high morphological similarity among related members and the limitations of cox1 barcoding. To address this challenge, this study developed a multiplex PCR assay based on the cox1 gene to differentiate S. asakoae. In addition, diverse pathogens circulating in the S. asakoae species group collected from Chiang Mai Province, northern Thailand, were molecularly detected. The multiplex PCR assay was developed using two allele-specific forward primers combined with universal cox1 primers as an internal control. This assay demonstrated 100% sensitivity and specificity, successfully differentiating S. asakoae from other Thai-related species in the same species group. Pathogen screening of 100 individual specimens and 20 pooled samples of the S. asakoae species group revealed the highest infection rate for Leucocytozoon (14% in individuals and 8.5% minimum infection rate (MIR) in pools), followed by trypanosomatids (10% in individuals and 4% MIR in pools) and filarial nematodes (5% in individuals and 2.5% MIR in pools). Molecular analysis further confirmed the first detection of Leucocytozoon sabrazesi, Trypanosomatidae spp. (including Leptomonas spiculata), Onchocerca sp. Type I, and a possible new Onchocerca sp. in the S. asakoae species group in Thailand. To the best of our knowledge, this study provides the first multiplex PCR assay for the rapid and correct identification of S. asakoae and confirms the circulation of diverse pathogens in the S. asakoae species group, thereby supporting enhanced surveillance and vector control programmes in Thailand.},
}

@article {pmid42542665,
year = {2026},
author = {Kwawukume, S and Kandula, N and Cui, L and Singh, P},
title = {A rapid rhPCR-lateral flow assay for authenticating royal red and Argentine red shrimp in the U.S. seafood supply chain.},
journal = {Food chemistry. Molecular sciences},
volume = {13},
number = {},
pages = {100434},
pmid = {42542665},
issn = {2666-5662},
abstract = {In the United States, approximately one-third of shrimp sold are misrepresented. DNA barcoding requires robust infrastructure and one to three days to generate results, limiting enforcement utility. We hypothesized that RNase H2-dependent PCR (rhPCR) primers targeting cytochrome oxidase subunit I (COI) sequence-specific sites, coupled with lateral flow detection, could enable rapid species authentication of royal red shrimp (Pleoticus robustus) and Argentine red shrimp (Pleoticus muelleri). Species-specific rhPCR primers labeled with FAM and biotin were designed and evaluated using crude DNA extracts from 65 barcoded shrimp specimens representing seven commercially traded species. The assays were further validated using 20 blinded retail samples marketed as royal red shrimp. Both assays demonstrated high specificity comparable to DNA barcoding results, and an analytical sensitivity of 0.01 ng/μL. Analysis of retail samples revealed 60% of samples were not royal red shrimp. Total time-to-results for 20 samples was approximately 150 min, demonstrating a rapid, simpler, and sequencing-free alternative for regulatory enforcement.},
}

@article {pmid42539220,
year = {2026},
author = {McGee, AV and Biar, CG and Martin, BK and Li, T and Lalanne, JB and Kim, H and Shendure, J},
title = {Locus-Scale Massively Parallel Reporter Assays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42539220},
issn = {2692-8205},
abstract = {Interactions among c is-regulatory elements (CREs) are central to mammalian gene regulation. Long @$$ massively parallel reporter assays (LAMPRAs) integrate combinatorial cloning, molecular barcoding and long- and short-read sequencing, to scalably measure how CRE identities, numbers, spacings, orders, orientations, and interactions shape regulatory output at multi-kilobase length scales. As a proof-of-concept, we assay 36,000 × 5-kb synthetic c is-regulatory loci (sCRLs), each a 5 × 1-kb random combination of enhancers, insulators and spacers, to model how locus composition drives gene expression.},
}

@article {pmid42537001,
year = {2026},
author = {Zolfaghari, A and Fraiture, MA and Vanneste, K and Stuyts, A and Frouin, J and Meunier, AC and Deforce, D and Roosens, NHC and D'aes, J},
title = {RiSpy: a feature selection-based fingerprinting framework for accurate identification of genome-edited rice lines.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {4},
pages = {},
doi = {10.1093/bib/bbag406},
pmid = {42537001},
issn = {1477-4054},
mesh = {*Oryza/genetics ; *Genome, Plant ; *Plants, Genetically Modified/genetics ; *Gene Editing ; *Software ; Computational Biology/methods ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing ; Genomics/methods ; *DNA Fingerprinting/methods ; },
abstract = {The European Union (EU) enforces strict regulations on the traceability and labeling of genetically modified organisms (GMOs), including genome-edited (GE) lines produced through new genomic techniques (NGTs). Identifying GE organisms created by single nucleotide variations (SNVs) is however challenging, as a single SNV alone cannot unambiguously define a GE line. Recently, we introduced the concept of generating a genetic fingerprint to distinguish a specific GE rice line. This proof-of-concept approach integrated whole-genome sequencing (WGS)-based characterization with the Illumina technology, the public 3 K Rice Genomes (3KRG) database, and statistical feature-selection tools, to select and combine key genetic elements, including GE on-target site(s) and cultivar-specific 2-SNV barcodes, into a unique genetic fingerprint. In the present study, we expand this concept into a generalized data-driven framework allowing identification of multiple rice lines. Supported by newly developed bioinformatics and statistical feature-selection-based pipelines, this optimized strategy enables the generation of genetic fingerprints irrespective of a rice cultivar's inclusion in publicly available databases like 3KRG. In addition, this refined strategy can leverage WGS data generated from both Illumina and Oxford Nanopore Technologies (ONT) platforms for fingerprint generation and GE line identification. Using two distinct in-house GE rice lines from different cultivars, along with various publicly available WGS datasets, we demonstrated the robustness, scalability, and specificity of this approach for reliable GE rice line identification. Our findings provide a methodological foundation for data-driven traceability of GE rice lines, reinforcing regulatory compliance, supporting intellectual property (IP) protection, and contributing to the responsible implementation of EU GMO/NGT legislation.},
}

*Oryza/genetics
*Genome, Plant
*Plants, Genetically Modified/genetics
*Gene Editing
*Software
Computational Biology/methods
Polymorphism, Single Nucleotide
Whole Genome Sequencing
Genomics/methods
*DNA Fingerprinting/methods

@article {pmid42533593,
year = {2026},
author = {Świątek, P and Brown, GG and James, S and Urbisz, AZ and Gajda, Ł},
title = {Ovaries of Three Eukerria and Two Kerriona Earthworms (Annelida, Crassiclitellata, Ocnerodrilidae) Are Morphologically Different, but Their Microorganization and Oogenesis Are the Same.},
journal = {Journal of morphology},
volume = {287},
number = {8},
pages = {e70155},
pmid = {42533593},
issn = {1097-4687},
support = {//National Science Center, Poland (2020/37/B/NZ4/00560)/ ; 2020/37/B/NZ4/00560//National Science Center, Poland/ ; },
mesh = {Animals ; Female ; *Oligochaeta/anatomy & histology/ultrastructure/cytology/physiology/genetics ; *Ovary/cytology/ultrastructure/anatomy & histology ; *Oogenesis/physiology ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal/genetics ; Oocytes/cytology/ultrastructure ; RNA, Ribosomal, 18S/genetics ; },
abstract = {The ovaries of five barcoded earthworm species (nuclear 18S rRNA and 28S rRNA, and mitochondrial COI and 12S rRNA gene sequences are provided) from the family Ocnerodrilidae have been analyzed using various microscopic techniques. In both genera studied, ovaries are paired and located in the anterior part of segment XIII. Surprisingly, the ovarian morphology observed in Eukerria differs from that found in Kerriona. Ovaries of Eukerria are flattened, of rectangular or triangular shape, with one or two oocyte rows (egg strings) at the posterior part. Ovaries in Kerriona are fan-shaped, with numerous egg strings. Kerriona's ovaries are of the typical shape found in other representatives of the family Ocnerodrilidae and are similar to the ovaries characteristic of megascolecid earthworms. In contrast, Eukerria ovaries resemble those typical for Lumbricidae. This observation is inconsistent with other reports, which suggested that the ovaries in Ocnerodrilidae are fan-shaped and contain numerous egg strings. Despite the differences in morphology, the internal ovary organization and the course of oogenesis are the same in all studied species and resemble those known from other earthworms. The apical ovary part is composed of a solid mass of germline cells enveloped by thin somatic (follicular) cells. Germline cells are interconnected into syncytial cysts, in which each cell has a single intercellular bridge connecting it to the central cytoplasmic mass, the cytophore. Cysts unite oogonia and early meiotic cells. During diplotene, the future oocyte detaches from the cyst, forms microvilli, and gathers nutrients, whereas the remaining nurse cells do not grow and remain connected to the cytophore. Vitellogenic oocytes finally detach from the ovaries and float freely in the segment lumen. They are 80-90 µm in diameter and are regarded as oligolecithal. Nurse cells probably die within the ovaries; they have never been observed within the coelom.},
}

Animals
Female
*Oligochaeta/anatomy & histology/ultrastructure/cytology/physiology/genetics
*Ovary/cytology/ultrastructure/anatomy & histology
*Oogenesis/physiology
RNA, Ribosomal, 28S/genetics
RNA, Ribosomal/genetics
Oocytes/cytology/ultrastructure
RNA, Ribosomal, 18S/genetics

@article {pmid42534460,
year = {2026},
author = {Zhang, Y and Wu, H and Yang, X and Zeng, Y and Feng, M and Zhang, J and Ye, Y and Liu, P and Wei, J},
title = {Establishment of a two-tiered molecular identification system for Dracaena species - the source plants of dragon's blood.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1851019},
pmid = {42534460},
issn = {1664-462X},
abstract = {BACKGROUND: The unresolved taxonomy of Dracaena species, the botanical sources of the prized traditional medicine Dragon's blood, poses significant challenges to resource conservation, material traceability, and quality control. This study aimed to resolve these taxonomic ambiguities by developing and validating a high-resolution, integrated molecular authentication system. Based on 26 original plant samples from the genus Dracaena, along with relevant DNA barcode loci retrieved from NCBI, five previously reported DNA barcodes were evaluated and assessed. Simple sequence repeat (SSR) sequences from the transcriptome of D. cambodiana were subsequently screened. Finally, the established DNA barcode and SSR molecular marker systems were applied to identify the botanical origin of Dragon's blood.

RESULTS: The trnP-psaJ and psbK-psbI regions were identified as optimal barcodes, effectively distinguishing foreign sources (D. cinnabari and D. draco) from domestic ones. From transcriptomic data, we screened and validated 16 highly polymorphic SSR primers. While DNA barcodes confirmed broad phylogenetic relationships, SSR markers provided superior resolution, clearly delineating the closely related domestic taxa D. cambodiana, D. cochinchinensis, and the "Yanzong" plant into distinct genetic clusters. A key finding was the consistent genetic distinctiveness of Hainan Island populations, supporting the genetic affinity of the Hainan populations with D. cambodiana, indicating that they fall within the genetic variation range of this species based on the available reference samples. Furthermore, cultivation analysis revealed that D. cambodiana is the predominant cultivated species in China; the horticultural variety "Heizhenzhu" was identified as a likely variant of this species, while "Taikongtie" showed ambiguous affinity, possibly involving D. cochinchinensis or Guangxi populations.

CONCLUSIONS: We established a novel, two-tiered molecular identification system that combines the trnP-psaJ barcode for rapid screening with a panel of 16 SSR markers for fine-scale discrimination. This integrated approach successfully clarifies the taxonomy of important Dragon's blood source plants. It provides a reliable, efficient protocol for authenticating Dracaena species and germplasm, offering a critical technical foundation for resource conservation, medicinal material standardization, and targeted breeding programs.},
}

@article {pmid42534551,
year = {2026},
author = {Sterling, MJ and Lees, DC},
title = {A revision of the genus Ptochoryctis Meyrick, 1894 (Lepidoptera, Gelechioidea, Xyloryctidae) with the description of 12 new species.},
journal = {ZooKeys},
volume = {1285},
number = {},
pages = {261-328},
pmid = {42534551},
issn = {1313-2989},
abstract = {The genus Ptochoryctis Meyrick, 1894 is revised and reinstated in the Xyloryctidae (previously treated in Autostichidae) based on molecular and morphological evidence. A fuller description is provided of the morphology of all the species previously described in Ptochoryctis which are not combined elsewhere. The following new species of Ptochoryctis are described: Ptochoryctis blanchella sp. nov., P. caputanatis sp. nov., P. draconella sp. nov., P. flavalbella sp. nov., P. fuscilinea sp. nov., P. kitchingi sp. nov., P. marmorella sp. nov., P. minimella sp. nov., P. persicotincta sp. nov., P. ochraceella sp. nov., P. robinsoni sp. nov. and P. splendidella sp. nov. Deloryctis Meyrick, 1934 is synonymised with Ptochoryctis. The following new combinations are established: Ptochoryctis corticivora (Meyrick, 1934), comb. nov. (which is consequently transferred from Depressariidae to Xyloryctidae), Metathrinca alma (Meyrick, 1908), comb. nov., M. inviolata (Meyrick, 1925), comb. nov., M. ochrograpta (Meyrick, 1923), comb. nov.; and M. perigramma (Meyrick, 1926), comb. nov.},
}

@article {pmid42534578,
year = {2026},
author = {Bhandari, P and Xu, C and Li, BZ and Li, FX and Jiménez-Mejías, P and Zhang, SR and Zhou, SL},
title = {A universal DNA-barcode approach to aid species identification in the family Cyperaceae.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1794327},
pmid = {42534578},
issn = {1664-462X},
abstract = {Cyperaceae, one of the ten largest plant families with a cosmopolitan distribution, presents significant taxonomic challenges due to its highly reduced and complex floral structures. These complexities make species identification through conventional morphology-based methods difficult. To address these limitations, DNA barcoding was employed for accurate species identification. This study evaluates the universality of DNA barcodes across the entire Cyperaceae family using a total of 6739 sequences. The performance of four DNA barcoding regions ITS, matK, rbcL, and rps16, was explored using three analytical approaches, genetic distance, sequence similarity, and phylogenetic tree methods. Among single-locus barcodes, the nuclear region internal transcribed spacer (ITS) showed higher discriminatory power than the chloroplast regions matK, rbcL, and rps16. Among multi-locus combinations, ITS + matK + rps16 was found to be most effective. These findings provide valuable insights for improving the precise identification of Cyperaceae species. Future efforts should focus on sampling species-rich tribes such as Cariceae, Cypereae, Schoeneae, Rhynchosporeae, and Sclerieae, particularly in poorly sampled regions of Asia and Africa. Expanding these efforts is crucial for building a robust and comprehensive GenBank reference database for Cyperaceae.},
}

@article {pmid42530017,
year = {2026},
author = {Quinlan, A and Kuo, LY and Hu, JM and Huang, YM},
title = {Ferns on ferns: gametophyte assemblages on tree ferns reveal associations with accidentally epiphytic ferns.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcag232},
pmid = {42530017},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Tree ferns are substantial hosts for epiphytes, often hosting distinct communities that are considerably different from other hosts. While previous research has highlighted the prevalence of epiphytic ferns growing on tree ferns, studies have yet to explore this host relationship for the gametophyte generation. This study aims to investigate the epiphytic fern gametophyte communities growing on low trunks of Alsophila spinulosa (Cyatheaceae).

METHODS: A high-throughput DNA barcoding approach was used to identify fern gametophytes collected from tree fern trunks and neighboring angiosperm hosts across six established plots. Co-occurring sporophytes were surveyed along the same trunks. Gametophyte identification was achieved by sequencing multiplexed trnL-F amplicons derived from tissue-direct PCR on an Illumina MiSeq platform.

KEY RESULTS: Tree fern trunks harbored a higher abundance and species richness of fern gametophytes than angiosperm trunks, and hosted more cordiform gametophytes, most of which were otherwise terrestrial ferns considered to be accidentally epiphytic. In comparison, angiosperm hosts were associated with non-cordiform, obligately epiphytic ferns. The humid microclimate of tree fern trunks simulate a terrestrial-like environment, offering an indistinct boundary from the forest floor which provides habitat for fern species that typically establish on the ground. Our survey also recovered three species we interpret as independent fern gametophytes Antrophyum henryi., Callistopteris apiifolia, and Haplopteris yakushimensis, given that their sporophyte phases were not present and are not known from nearby localities.

CONCLUSIONS: DNA barcoding techniques provide an opportunity to study the distribution and habit of fern gametophytes, the life history stage of ferns which is often overlooked. Our results demonstrate that gametophyte growth form and habit are correlated with habitat preference and community structure. Our findings support the importance of incorporating gametophytes into broader studies of fern ecology and distribution.},
}

@article {pmid42531124,
year = {2026},
author = {Wu, JW and Xu, Y and Chen, Y and Yang, JM and Huang, CH},
title = {Protocol for multiplexed quantification of fluorescent biosensor FRET efficiency using barcoded cells.},
journal = {STAR protocols},
volume = {7},
number = {3},
pages = {104756},
doi = {10.1016/j.xpro.2026.104756},
pmid = {42531124},
issn = {2666-1667},
abstract = {Genetically encoded fluorescent biosensors frequently use Förster resonance energy transfer (FRET) between donor and acceptor fluorescent proteins (FPs) as readouts for monitoring molecular activities in live cells. Here, we present a protocol for determining FRET efficiency through the simultaneous imaging of multiple FRET biosensors alongside donor and acceptor FPs using spectrally orthogonal fluorescent cell barcodes. We describe steps for culturing and transfecting cells, acquiring and analyzing images, and calculating FRET efficiency. This approach facilitates simultaneous analysis of multiple FRET biosensors. For complete details on the use and execution of this protocol, please refer to Wu et al.[1].},
}

@article {pmid42531424,
year = {2026},
author = {Pérez-Bielsa, N and Abras, A and Heras, S and Palmada-Flores, M and García-Marín, JL},
title = {Hybridization With a Non-Native Congener Threatens the Catalan Chub (Squalius laietanus): Optimization of a DNA-Based Early Warning Tool.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70154},
pmid = {42531424},
issn = {1749-4877},
support = {AG-2021-686//Inland Fisheries Services of the Autonomous Government of Catalonia/ ; IEC-PR2025-3-REC//Institute for Catalan Studies (IEC)/ ; },
abstract = {Hybridization with non-native congeners represents an increasingly recognized threat to the long-term viability and genetic integrity of endemic freshwater fishes. The Catalan chub (Squalius laietanus), a leuciscid endemic to northeastern Iberian river basins and currently listed as Vulnerable on the International Union for the Conservation of Nature Red List, has recently been exposed to the expansion of other Squalius species within its range, particularly the European chub (Squalius cephalus), raising concerns regarding interspecific hybridization and introgression. Here, we develop and apply a rapid and cost-effective nuclear DNA assay that reliably discriminates native, non-native, and hybrid genotypes. Using this approach, hybridized individuals were consistently detected in known contact zones, as well as in river sections where only S. laietanus had previously been identified based on mitochondrial DNA barcoding. These results provide molecular evidence of spatially widespread hybridization between S. laietanus and non-native S. cephalus across the core distribution of the endemic species. The observed pattern of hybridization adds another threat to S. laietanus, and it is therefore directly relevant for its future Red List assessment.},
}

@article {pmid42531675,
year = {2026},
author = {Tepper, A and Nguyen, T and Falcomatà, C and Brown, BD},
title = {Emerging Principles in Spatial Functional Genomics.},
journal = {Current opinion in immunology},
volume = {102},
number = {},
pages = {102814},
doi = {10.1016/j.coi.2026.102814},
pmid = {42531675},
issn = {1879-0372},
abstract = {Spatial transcriptomic and proteomic atlases have enabled mapping of gene programs within intact tissues, but these measurements remain largely descriptive and do not define the mechanisms controlling tissue biology. Pooled CRISPR screening provides scalable causal interrogation of gene function but remains largely confined to dissociated systems that lack spatial context. In vivo spatial functional genomics (SFG) bridges these approaches by integrating genetic perturbations with in situ transcriptomic and proteomic readouts to measure gene function within intact tissue ecosystems. By preserving spatial organization, SFG enables interpretation of perturbations through effects on cell-cell interactions, diffusible signals, multicellular niches, and tissue architecture. Here, we outline key design axes of SFG: perturbation strategy, barcoding strategy, and phenotypic readout. We discuss computational challenges, including spatial autocorrelation, neighborhood dependence, and context-aware null modeling, and highlight how SFG reveals non-cell-autonomous, architecture-dependent mechanisms of gene function, advancing toward predictive models of tissue organization and gene function.},
}

@article {pmid42531990,
year = {2026},
author = {Kotková, L and Vinitzky, S and Loskot, M and Fischer, O and Drábek, J},
title = {Species-origin identification of the deer in the Purtier Placenta Live Stem Cell Therapy by DNA typing.},
journal = {Forensic science international. Genetics},
volume = {86},
number = {},
pages = {103594},
doi = {10.1016/j.fsigen.2026.103594},
pmid = {42531990},
issn = {1878-0326},
abstract = {Purtier Placenta Live Stem Cell Therapy is a food supplement by Riway Singapore Pte. Ltd., claimed to contain living deer placenta stem cells together with 11 other active ingredients. It is also promoted as maintaining health and youthfulness and as being supported by numerous patents and research trials. Individual ingredients are accompanied by many other statements implying that Purtier Placenta can alleviate or cure diseases such as diabetes, cancer, and neurodegenerative diseases. However, none of these claims is traceable in clinical trial registries, and the mechanism allowing stem cells to be alive in the capsule and be effectively delivered to the body via the digestive tract does not seem plausible. Consequently, authorities in the United Arab Emirates, the Philippines, and Singapore have issued public warnings or imposed penalties in relation to misleading claims. Nevertheless, the product has gained popularity among Czech oncological patients, who perceive it as a magic cure. This paper describes a three-stage testing process designed to verify the species origin of the declared main ingredient. Using barcoding primer mixes, melting analysis, and Sanger sequencing with species-specific primers against seven reference species, we tested whether the capsule content corresponded to the red deer (Cervus elaphus) depicted on the official website (https://www.officialpurtier.com). Our analysis identified that DNA extracted from the 6th Edition capsule was primarily Rusa unicolor/timorensis, with minor components of Dama dama and Cervus elaphus. Although the main component was confirmed to be of deer origin, the lack of specific information and the wording of the marketing materials may be misleading.},
}

@article {pmid42524026,
year = {2026},
author = {Stallman, JK and Quijada, L and Aime, MC and Quandt, CA and Raudabaugh, DB and Melie, T and Rimer, I and McAdam, S and Haelewaters, D},
title = {Phylogeny of Gelatinodiscaceae (Leotiomycetes) with emphasis on the taxonomy of Ascocoryne in North America.},
journal = {Persoonia},
volume = {56},
number = {},
pages = {420-456},
pmid = {42524026},
issn = {0031-5850},
abstract = {The family Gelatinodiscaceae and genus Ascocoryne represent diverse lineages in Helotiales (Ascomycota, Leotiomycetes) that lack well-sampled phylogenies and taxonomic study. Our research objectives were to 1) determine whether certain genera that lacked DNA sequence data or had uncertain phylogenetic placement - Clathrosporium, Phaeangellina, Skyathea, and Xerombrophila - belonged to Gelatinodiscaceae, 2) estimate species richness and describe new species in Ascocoryne, 3) determine if morphological characteristics delineate intrageneric clades in Ascocoryne, and 4) test the mitochondrial tricarboxylate transport protein (CTP) as an alternative DNA barcode in Ascocoryne. We made 83 Gelatinodiscaceae collections primarily from the midwestern United States, examined 61 collections previously deposited in herbaria, and generated DNA sequence data for seven loci (18S, ITS, 28S, EF1, RPB1, RPB2, CTP) from these collections. We found that Skyathea, Xerombrophila, and up to four other unnamed, putative genera belong to Gelatinodiscaceae, while Clathrosporium and Phaeangellina are excluded. Up to 37 putative undescribed species-level clades or single isolates are present in Ascocoryne, in addition to the nine previously described species and four newly described ones here: Ascocoryne diminutiva, A. fibrosa, A. neoinflata, and A. wilsoniae. Additionally, descriptions for two unnamed species similar to A. cylichnium are given, a preliminary description of the sexual morph of A. laurisilvae is provided, and A. trichophora is synonymized with A. vinosa. Four main clades are found in the genus Ascocoryne. The size of lipid bodies in living ascospores, the arrangement of conidia borne on ascospores, and the presence of calcium oxalate crystals are the most important morphological characteristics for distinguishing among clades. The CTP and ITS loci successfully identified six of six Ascocoryne species tested. This study provides the best-sampled phylogeny of Gelatinodiscaceae and Ascocoryne and highlights unnamed genus- and species-level diversity in this group. Citation: Stallman JK, Quijada L, Aime MC, Quandt CA, Raudabaugh DB, Melie T, Rimer I, McAdam S, Haelewaters D (2026). Phylogeny of Gelatinodiscaceae (Leotiomycetes) with emphasis on the taxonomy of Ascocoryne in North America. Persoonia 56: 420-456. doi: 10.3114/persoonia.2026.56.07.},
}

@article {pmid42524220,
year = {2026},
author = {Crous, PW and Akram, W and Albuquerque, GMR and Alfenas, AC and Alfenas, RF and Altés, A and Alvarado, P and Amirmijani, AR and Arumugam, E and Asif, M and Bandini, D and Barreto, GG and Barreto, RW and Batista, VEC and Bezerra, JDP and Bilański, P and Bizio, E and Castañeda-Ruiz, RF and Chaves, J and Condé, TO and Costa, MM and Custódio, FA and Courty, PE and Czachura, P and Damm, U and Darmostuk, V and Dearnaley, J and De la Peña-Lastra, S and Delgado, G and de Silva, NI and Dovana, F and Drummond-Herdman, A and Eberhardt, U and Esteve-Raventós, F and Ferisin, G and Ferreira, RJ and Ferro, LO and Firmino, AL and Flakus, A and Fournier, J and Gardiennet, A and Gerbeau-Pissot, P and Ghobad-Nejhad, M and Gruhn, G and Guard, FE and Harms, K and Heilmann-Clausen, J and Hongsanan, S and Hülsewig, T and Inokuti, EM and Jankowiak, R and Kaliyaperumal, M and Kehlet, T and Lacerda, SR and Larsson, E and Leão, AF and Lebel, T and Lima, AA and López-Villalba, Á and Maciá-Vicente, JG and Mateos, A and Mejía, LC and Mendes, DR and Möller, L and Mombert, A and Monteiro, MBN and Moreno, G and Nagy, L and Niskanen, T and Nogueira, PTS and Oliveira, JA and Oliveira, PHF and Ortiz, DA and Pancorbo, F and Paz, A and Pazmiño, DA and Pereira, OL and Piątek, M and Plata, O and Pordel, A and Raaijmakers, JM and Ralaiveloarisoa, AB and Ramos, DO and Ravikumar, S and Rigueiro-Rodríguez, A and Rivas-Torres, GF and Rodrigues, JG and Rodriguez-Flakus, P and Romero, M and Saba, M and Sánchez, A and Sánchez-Dueñas, G and Santana, JS and Serrano, M and Silva, JAS and Stępniewska, H and Stryjak-Bogacka, M and Tennakoon, DS and van 't Hof, P and van Vuuren, NI and Varga, T and Vauras, J and Vieira, BS and Visagie, CM and Wipf, D and Woods, R and Groenewald, JZ},
title = {Fungal Planet description sheets: 1868-1920.},
journal = {Persoonia},
volume = {56},
number = {},
pages = {1-173},
pmid = {42524220},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Marasmius ballator on leaf litter in subtropical rainforest, Marasmius carbinensis on litter and twigs of Hyptis suaveolens, Marasmius clocca on leaf litter of regenerating subtropical rainforest. Bolivia, Aggregatorygma saraanense on trunk of Trichilia inaequilatera. Brazil, Arthropolymorpha endophytica (incl. Arthropolymorpha gen. nov.), from healthy roots of Coffea arabica, Didymella digitariae on Digitaria insularis, Geastrum baseiae on soil, Magnibotryascoma souzamottae as endophyte from cladodes of Tacinga inamoena, Neoleptosporella agapanthi from stalks of Agapanthus praecox, Penicillifer endoradicis as endophyte from roots of Musa acuminata, Sirastachys cavernicola from leaf litter, Toxicocladosporium atratum as root endophyte of Cattleya locatellii. China, Fasciatispora citri on dead twig of Citrus maxima. Denmark, Inocybe leucantheana on wet ground with Alnus, Betula and Picea. Ecuador (Galapagos Islands), Fusarium cristobalense on Scalesia gordilloi, Fusarium scalesiae on Scalesia pedunculata. Finland, Inocybe ranaria on mull soil, near Betula pendula and Abies sp. France, Bullatosporium pinophilum on the bark of Pinus nigra subsp. nigra, Dialonectria eutypellicola on Eutypella prunastri, on branches of Prunus spinosa, Mycobernardia involucriformis on dead Bambusa sp., Pseudocosmospora perforaticola on dead stromata of Hypoxylon perforatum on Fraxinus, Stylonectria colleeniae on Trimmatostroma scutellare, with Lophium mytillinum, on dead branch of Larix decidua. French Guiana, Neocosmospora duolechatii on dead bark of Bauhinia sp. Germany, Inocybe giovannii on soil under Abies alba, Fagus sylvatica and Picea abies, Triseptosporium fallopiae (incl. Triseptosporium gen. nov.) on Fallopia japonica. India, Phylloporia bharatavarsa on living tree of Phyllanthus emblica. Iran, Fusarium phoenicis on roots of Phoenix dactylifera. Italy, Inosperma confusum on soil under Quercus ilex and Pinus halepensis, Inosperma subinodorum on calcareous soil in Picea abies forest. Madagascar, Oudemansiella viscida on dead wood or branches. Netherlands, Colletotrichum urticicola from leaf spots on Urtica dioica. Pakistan, Agrocybe punjabensis on soil on fallen remains of Saccharum officinarum. Panama, Ijuhya panamaensis and Sarcopodium panamaense on twig litter of angiosperm. Poland, Cytospora tatrensis from dead stems of Pinus mugo, Myxotrichum flavum on resin of Picea abies, Symphoricola tarnoviensis (incl. Symphoricola gen. nov.) from sooty mould community on Symphoricarpos albus. Portugal, Hypoxylon azoricum on fallen branch of Laurus azorica, Tuber honstrassii in clayey and calcareous soil under Quercus rotundifolia and Arbutus unedo. South Africa, Paraphaeosphaeria andropogonicola on leaves of Andropogon eucomus, Talaromyces armstrongii from soil. Spain, Geoglossum martinae on soil under Quercus ilex and Cistus ladanifer, Inocybe percastanea on sandy, acidic soils under Cistus ladanifer and Pinus pinaster, Lamproderma stephensonii on twigs of Pinus sylvestris, Ramariopsis alboviolacea on soil under Prunus lusitanica subsp. lusitanica, Russula olivaceopinetorum on acidic sandy soil among Pinus sylvestris needles, Scolecobasidium endophyticum from root-associated soil collected in a grassland, Tuber danielis in acidic soil beneath Cistus ladanifer, Quercus ilex, and Genista scorpius. Sweden, Inocybe adusticans on soil, in snow bed area with Salix herbacea and Bistorta vivipara, Inosperma friesii on soil in mixed deciduous forest. Switzerland, Stylonectria stoeckliana on Cytospora sp. on twigs of Salix sp. Thailand, Neoleptosporella camporesiana on dead branch of unidentified plant. Uganda, Bjerkandera ugandensis on a rotting log. UK (Scotland), Narcissea scotica on decaying dung of Lagopus scotica. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Akram W, Albuquerque GMR, Alfenas AC, Alfenas RF, Altés A, Alvarado P, Amirmijani AR, Arumugam E, Asif M, Bandini D, Barreto GG, Barreto RW, Batista VEC, Bezerra JDP, Bilański P, Bizio E, Castañeda-Ruiz RF, Chaves J, Condé TO, Costa MM, Custódio FA, Courty P-E, Czachura P, Damm U, Darmostuk V, Dearnaley J, De la Peña-Lastra S, Delgado G, de Silva NI, Dovana F, Drummond-Herdman A, Eberhardt U, Esteve-Raventós F, Ferisin G, Ferreira RJ, Ferro LO, Firmino AL, Flakus A, Fournier J, Gardiennet A, Gerbeau-Pissot P, Ghobad-Nejhad M, Gruhn G, Guard FE, Harms K, Heilmann-Clausen J, Hongsanan S, Hülsewig T, Inokuti EM, Jankowiak R, Kaliyaperumal M, Kehlet T, Lacerda SR, Larsson E, Leão AF, Lebel T, Lima AA, López-Villalba Á, Maciá-Vicente JG, Mateos A, Mejía LC, Mendes DR, Möller L, Mombert A, Monteiro MBN, Moreno G, Nagy L, Niskanen T, Nogueira PTS, Oliveira JA, Oliveira PHF, Ortiz DA, Pancorbo F, Paz A, Pazmiño DA, Pereira OL, Piątek M, Plata O, Pordel A, Raaijmakers JM, Ralaiveloarisoa AB, Ramos DO, Ravikumar S, Rigueiro-Rodríguez A, Rivas-Torres GF, Rodrigues JG, Rodriguez-Flakus P, Romero M, Saba M, Sánchez A, Sánchez-Dueñas G, Santana JS, Serrano M, Silva JAS, Stępniewska H, Stryjak-Bogacka M, Tennakoon DS, van 't Hof P, van Vuuren NI, Varga T, Vauras J, Vieira BS, Visagie CM, Wipf D, Woods R, Groenewald JZ (2026). Fungal Planet description sheets: 1868-1920. Persoonia 56: 1-173. doi: 10.3114/persoonia.2026.56.01.},
}

@article {pmid42524280,
year = {2026},
author = {Crous, PW and Akulov, A and Alfenas, AC and Alfenas, RF and Aloi, F and Balashov, S and Barreto, RW and Bensch, K and Cacciola, SO and Cantillo, T and Castillo, R and Conti Taguali, S and Czachura, P and da Silva, NF and Delgado, MA and Denman, S and de Silva, NI and de Vries, RP and Figge, M and Guarnaccia, V and Guterres, DS and Hongsanan, S and Horta Jung, M and Houbraken, J and Hülsewig, T and Jung, T and Jurjević, Ž and La Spada, F and Madrid, H and Mombert, A and Osieck, ER and Pane, A and Parlascino, R and Pereira, CM and Piątek, M and Piattino, V and Riolo, M and Sandoval-Denis, M and Scanu, B and Starink-Willemse, M and Stryjak-Bogacka, M and Tennakoon, DS and van Ingen-Buijs, VA and van Iperen, AL and Verkley, GJM and Lamprecht, SC and Wang, XW and Braun, U and Wingfield, MJ and Groenewald, JZ},
title = {New and Interesting Fungi. 8.},
journal = {Persoonia},
volume = {56},
number = {},
pages = {457-547},
pmid = {42524280},
issn = {0031-5850},
abstract = {Eight new genera, 28 new species, four epitypes, two lectotypes, and 21 interesting new host and / or geographical records are introduced in this study. New genera include: Amesomyces (based on Amesomyces atrobrunneus), Carteromyces (based on Carteromyces arctostaphyli), Scolecofusariella (based on Fusarium peltigerae), Nothoniesslia (based on Nothoniesslia solidaginis), Paraacanthostigma (based on Paraacanthostigma eucalypti), Paraphaeophleospora (based on Paraphaeophleospora tripteridis), Parapolyscytalum (based on Parapolyscytalum minutum) and Subverticillium (based on Subverticillium juncicola). New species include: Bisifusarium duo (from human cornea, India), Capronia parasitica (on Eutypella sorbi on branches of Sorbus aucuparia, Switzerland), Castanediella acericola on dead leaf of Acer cf. pseudoplatanus, Germany), Cladophialophora calamagrostidis (on culm of Calamagrostis arenaria, The Netherlands), Cladophialophora paramycetomatis (on culms of Elegia tectorum, South Africa), Cladophialophora yuccae (on dead leaf of Yucca sp., Germany), Cordana ligni (on dead wood, Germany), Curvularia moniliformis (on leaves of unidentified Poaceae, Chile), Davidhawksworthia rubi (on Rubus stems, Germany), Exophiala ligni (on dead wood, Germany), Fusarium aloetica (on symptomatic leaves of Aloe ferox, South Africa), Harzia cupressicola (on needles of Cupressus sp., The Netherlands), Hoehneliella falsiundulosetulata (on bark of woody host, Germany), Mjuua pseudoclavispora (in association with Fusarium paeoniae and a bacterium, on dead fruit of Alnus glutinosa, Germany), Monilinia yunnanensis (on fruit of Prunus persica, China), Niesslia goniomae (on leaf of Gonioma kamassi, South Africa), Nothoniesslia solidaginis (on dead stems of Solidago sp., Germany), Paraacanthostigma eucalypti (on bark of Eucalyptus globulus, Australia), Phaeococcomyces mesembryanthemi (on Mesembryanthemum schultzii, South Africa), Phialemonium parasulfureum (on algae, Germany), Phytophthora caput-medusae (from rhizosphere soil of Citrus × aurantium, Italy), Pleurophragmium fallopiae (on dead leaf Fallopia sp., Germany), Rhinotrichella carpini (on dead branches of Carpinus betulus, Ukraine), Stagonosporopsis citri (on peel of living fruit of Citrus latifolia, quarantine interception), Subverticillium juncicola (on culms of Juncus effusus, Netherlands), Veronaea parabrunnea (on Eutypella prunastri on twigs of Prunus spinosa, France), Veronaea parasiticola (on Euonymus europaeus, Germany), Verrucocladosporium mesembryanthemi (on Mesembryanthemum schultzii, South Africa). New combinations include: Amesomyces atrobrunneus (based on Chaetomium atrobrunneum), Amesomyces cymbiformis (based on Chaetomium cymbiforme), Amesomyces dreyfussii (based on Chaetomium dreyfussii), Amesomyces gelasinosporus (based on Chaetomium gelasinosporum), Amesomyces hispanicus (based on Amesia hispanica), Amesomyces khuzestanicus (based on Amesia khuzestanica), Amesomyces nigricolor (based on Chaetomium nigricolor), Amesomyces raii (based on Chaetomium raii), Carteromyces arctostaphyli (based on Carteria arctostaphyli), Carteromyces canariensis (based on Carteria canariensis), Capronia americana (based on Cadophora americana), Didymella conyzaphthora (based on Phoma conyzaphthora), Heterotruncatella watsoniae (based on Pestalotia watsoniae), Hoehneliella undulosetulata (based on Paramenisporopsis undulosetulata), Microascus stellatus (based on Humicola stellata), Neoceratosperma marasasii (based on Mycosphaerella marasasii), Paraphaeophleospora tripteridis (based on Septoria tripteridis), Parapolyscytalum minutum (based on Infundichalara minuta), Scolecofusariella peltigerae (based on Fusarium peltigerae) and Veronaea brunnea (based on Exophiala brunnea). Zygophiala is reduced to synonymy under Schizothyrium, Paramenisporopsis and Klebahnopycnis under Hoehneliella, and the descriptions of the order Comminutisporales and family Comminutisporaceae are emended. Citation: Crous PW, Akulov A, Alfenas AC, Alfenas RF, Aloi F, Balashov S, Barreto RW, Bensch K, Cacciola SO, Cantillo T, Castillo R, Conti Taguali S, Czachura P, da Silva NF, Delgado MA, Denman S, de Silva NI, de Vries RP, Figge M, Guarnaccia V, Guterres DS, Hongsanan S, Horta Jung M, Houbraken JA, Hülsewig T, Jung T, Jurjević Ž, La Spada F, Madrid H, Mombert A, Osieck ER, Pane A, Parlascino R, Pereira CM, Piątek M, Piattino V, Riolo M, Sandoval-Denis M, Scanu B, Starink-Willemse M, Stryjak-Bogacka M, Tennakoon DS, van Ingen-Buijs VA, van Iperen AL, Verkley GJM, Lamprecht SC, Wang XW, Braun U, Wingfield MJ, Groenewald JZ (2026). New and Interesting Fungi. 8. Persoonia 56: 457-547. doi: 10.3114/persoonia.2026.56.08.},
}

@article {pmid42524340,
year = {2025},
author = {Morse, DB and Toprakcioglu, Z and Denduluri-Marthi, A and Brenton, JD and Thomas, CJ and Knowles, TPJ},
title = {Transcript Identification Using Arrayed Hydrogels with TrapFISH.},
journal = {Advanced materials technologies},
volume = {10},
number = {18},
pages = {},
pmid = {42524340},
issn = {2365-709X},
support = {ZIA TR000473/ImNIH/Intramural NIH HHS/United States ; },
abstract = {3' single-cell transcriptomics aims to uncover transcript abundance across numerous cells to deepen our understanding of cellular diversity. However, sequencing capacity is often a bottleneck in these experiments, limiting the number of cells that can be profiled. In this study, we introduce trapFISH, a highly scalable proof-of-concept method that extends the capabilities of single-cell transcriptomics by embedding cells in hydrogel beads, arraying these beads in microfluidic chambers, and using probe-hybridization for targeted transcript quantification. This approach mitigates sequencing limitations by focusing on custom gene panels, enhancing throughput and facilitating the discovery of rare cell states. Moreover, microfluidic trapping removes the necessity for cell barcoding by linking transcriptional measurements directly with individual hydrogels. Our findings demonstrate that trapFISH improves scalability while maintaining high accuracy in identifying key cellular transcripts, opening new avenues in large-scale genomic profiling. By prioritizing biologically meaningful gene expression patterns, trapFISH provides a precise and efficient tool for single-cell characterization, expanding the flexibility and applicability of transcriptomics methods.},
}

@article {pmid42527897,
year = {2026},
author = {Javid, M and Ahmad, K and Ilyas, O and Khan, A},
title = {DNA metabarcoding reveals dietary niche partitioning among threatened Himalayan Ungulates based on chloroplast rbcL and nuclear ITS2 markers.},
journal = {BMC ecology and evolution},
volume = {26},
number = {1},
pages = {},
pmid = {42527897},
issn = {2730-7182},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Diet/veterinary ; Himalayas ; Ribulose-Bisphosphate Carboxylase/genetics ; Feces/chemistry ; Ecosystem ; Deer/genetics ; Seasons ; },
abstract = {Diet is the most important axis of niche differentiation in ungulates and mediates coexistence, habitat requirements. Himalaya amplify dietary dynamics because seasonal snow cover and plant phenology decreases resource availability. In this study fecal DNA metabarcoding was used to quantify diet and the dietary niche separation among five sympatric wild ungulates Hangul (Cervus hanglu hanglu), Kashmir markhor (Capra falconeri cashmiriensis), Kashmir musk deer (Moschus cupreus), Himalayan goral (Naemorhedus goral), and Himalayan ibex (Capra sibirica). Fresh fecal samples were collected throughout the Kashmir Valley, western Himalaya across the elevational and habitat gradients. We amplified two plant barcodes (chloroplast rbcL and nuclear ITS2) and sequenced the amplicons using Oxford Nanopore. Diets were analyzed by relative read abundance, functional traits, dietary diversity, niche breadth, and interspecific overlap. Across the seasonal diet profiles, we detected 208 plant species from 174,871 assigned reads. Hangul summer diet exhibits the broadest diet among species (richness = 115 taxa, H' = 4.48, Levins' B = 64.7) with a diffuse core of many co-dominant taxa, indicating generalist mixed feeding during peak plant productivity. Musk deer during autumn showed the narrowest diet (richness = 50, B = 14.3), indicating strong seasonal concentration on a smaller set of plants. Pairwise dietary overlap (Pianka's O) ranged from 0.136 to 0.985, showing both convergence and partitioning among the ungulate species. The results are consistent with a landscape-level coexistence model in which sympatric Kashmir ungulates share a broad forage base but segregate through differences in functional feeding (grazing vs. browsing tendencies), dominance structure, and seasonal shift. The study used composite species-season templates, the results are interpreted as landscape level diet profiles rather than individual or population level variance estimates.},
}

Animals
DNA Barcoding, Taxonomic
*Diet/veterinary
Himalayas
Ribulose-Bisphosphate Carboxylase/genetics
Feces/chemistry
Ecosystem
Deer/genetics
Seasons

@article {pmid42528324,
year = {2026},
author = {Zhang, N and Song, G and Peng, Z and Du, K and Cai, C and Miao, S and Tang, Y and Wang, Y and Li, J},
title = {Profiling Multiplexed Protein-Specific Sialylation in Cancer Drug Resistance Using Proximity Ligation Sequencing.},
journal = {Small methods},
volume = {},
number = {},
pages = {e70912},
doi = {10.1002/smtd.70912},
pmid = {42528324},
issn = {2366-9608},
support = {XDB1020000//Strategic Priority Research Program of the Chinese Academy/ ; 2024SDYXS0003//Pioneer R&D Program of Zhejiang/ ; 2025ZZBS02//Research Program of Hangzhou Institute of Medicine/ ; },
abstract = {Aberrant glycosylation, particularly enhanced sialylation of membrane proteins, acts as a critical regulator of receptor signaling, immune evasion, and therapeutic resistance in cancer. However, systematic and multiplexed interrogation of protein-specific sialylation in living cells remains technically challenging. Here, we report SATP-seq, a next-generation sequencing-based strategy that integrates a sialic acid-reactive probe (SA) with a targeted protein probe (TP) to enable ensemble profiling of protein-specific sialylation. By combining metabolic glycan labeling with nanobody- or aptamer-mediated protein recognition, SATP-seq achieves dual recognition of sialic acids and protein epitopes through DNA-programmed proximity ligation. The resulting ligation products encode sialylation states into unique DNA barcodes, converting glycosylation information into sequencable signals for multiplexed and quantitative analysis within a single sequencing run. Application of SATP-seq to gefitinib-sensitive PC9 and gefitinib-resistant PC9GR cells enables parallel profiling of seven membrane glycoproteins and reveals resistance-associated remodeling of protein-specific sialylation. Notably, differential sialylation of EGFR and CD47 emerges between sensitive and resistant cells, suggesting coordinated reprogramming of proliferative and immune-regulatory pathways. Enzymatic desialylation, EGFR knockdown, and proteomic validation collectively confirm the specificity and biological relevance of these alterations. Together, these findings establish multiplexed protein-specific sialylation profiling as a scalable approach for dissecting glycosylation-driven mechanisms of cancer drug resistance.},
}

@article {pmid42529249,
year = {2026},
author = {Magoga, G and Andreeva, A and Costagliola, P and Cardinale, M and Brunetti, M and Montagna, M},
title = {Contributions to the knowledge of Albanian Chrysomelidae (Coleoptera), with the redescription of Luperus flaviceps Apfelbeck, 1912.},
journal = {ZooKeys},
volume = {1285},
number = {},
pages = {167-185},
pmid = {42529249},
issn = {1313-2989},
abstract = {The Balkan region is among the least-studied areas in Europe with respect to Chrysomelidae, particularly over the last decades. This study aims to contribute new data to the knowledge of the Albanian chrysomelid fauna. Specifically, it aims to: (i) provide new information on the distribution of chrysomelid species within the country; (ii) develop a reference library of DNA barcode sequences for the molecular identification of Albanian Chrysomelidae; and (iii) redescribe Luperus flaviceps Apfelbeck, 1912, a rare chrysomelid found in Albania whose original description is brief and lacks some key diagnostic characters. Chrysomelidae were collected from multiple localities in central and southern Albania. As a result, 12 species are reported from Albania for the first time, together with three additional taxa that likely represent species new to science. Furthermore, updated distributional data for 81 species within the country are provided. A total of 71 DNA barcode sequences representing 57 species were generated; they constitute the only publicly available barcode sequences for Albanian Chrysomelidae, and eight of them represent new taxon records for public reference databases. The redescription of L. flaviceps is provided, including high-quality photographs of both males and females, as well as a detailed description and illustration of the aedeagus morphology, which was previously unknown. The results presented here emphasize the need for further investigations on Albanian Chrysomelidae to improve our understanding of their diversity within the country.},
}

@article {pmid42529905,
year = {2026},
author = {Wei, TY and Paulo, JA},
title = {Implementation of Nonisobaric TMT Analogs for Accurate Precursor-Level Quantification by plexDIA.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {40},
number = {20},
pages = {e70146},
pmid = {42529905},
issn = {1097-0231},
support = {GM156406/GM/NIGMS NIH HHS/United States ; },
mesh = {*Proteomics/methods ; Saccharomyces cerevisiae/chemistry/genetics ; *Saccharomyces cerevisiae Proteins/chemistry/analysis ; *Mass Spectrometry/methods ; Tandem Mass Spectrometry/methods ; Proteome/analysis/chemistry ; },
abstract = {RATIONALE: Multiplexed quantitative proteomics enables simultaneous analysis of multiple biological samples, increasing throughput while reducing instrument time and sample requirements. However, integrating sample multiplexing with data-independent acquisition (DIA) remains challenging. We present a TMTpro plexDIA strategy leveraging MS1-level mass differences between nonisobaric TMTpro reagent variants to enable multiplexed quantification without compromising DIA sensitivity.

METHODS: Three Saccharomyces cerevisiae deletion strains (Δmet6, Δpfk2, and Δura2) were labeled with TMTproZero (light), TMTpro16 (standard), and super-heavy TMTpro (heavy), mixed in three permutations, and analyzed by narrow-window DIA (2 m/z isolation, 300 scan events) on an Orbitrap Astral mass spectrometer. Database searching was performed using FragPipe/MSFragger with plex-DIA quantification enabled.

RESULTS: Over 2000 protein groups and over 20 000 precursors were identified per channel per mixture, with closely matched identification rates across all three channels. All nine expected deletion patterns were correctly identified, with channel-specific depletion reproduced consistently across precursor charge states (2+, 3+, and 4+).

CONCLUSIONS: TMTpro plex-DIA enables accurate, multiplexed quantitative proteomics through MS1-level mass separation of the nonisobaric TMTpro isotopologs. The characteristic deletion patterns observed for each knockout strain serve as intrinsic molecular barcodes, validating sample identity and demonstrating the broad utility of plex-DIA for high-throughput, multiplexed proteomics applications.},
}

*Proteomics/methods
Saccharomyces cerevisiae/chemistry/genetics
*Saccharomyces cerevisiae Proteins/chemistry/analysis
*Mass Spectrometry/methods
Tandem Mass Spectrometry/methods
Proteome/analysis/chemistry

@article {pmid42517606,
year = {2026},
author = {Baranowska, P and Lam, T and Herr, AE},
title = {Bead-free deterministic DNA barcoding using vacuum-driven loading of aqueous oligonucleotides to microwell arrays.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6an00352d},
pmid = {42517606},
issn = {1364-5528},
abstract = {Achieving high throughput in experiments requiring sample indexing depends primarily on the precise and reproducible deposition of reagents prior to analysis. Contemporary droplet and microwell systems utilize random deposition of oligonucleotide-coated beads into reaction chambers, requiring costly bead synthesis and offering limited control over the final distribution of barcoded beads. As an alternative, we present deterministic, aqueous barcoding of 512 arrayed microwells using a multi-layer, vacuum-driven microfluidic network. To uniquely barcode each of the 512 microwells, we deposit DNA oligonucleotide solutions designed using a Combinatorial Dual Indexing (CDI) (i5, i7) scheme via deterministic loading. Deterministic fluid loading is achieved by sequentially coupling two bifurcated, orthogonal microchannel networks with a planar microwell array. The microchannel networks actuate fluid flow through a combination of an applied vacuum force and a dead-end channel design. After loading the oligonucleotide solutions, we observed uniform barcode patterning across the arrays of microwells (∼20% CV), reasonable barcode loading times (30-40 min per step), and reduced reagent use (∼8-16 µL at 25 µM oligos vs. 10-50 µL at 100 µM for bead systems). We detected cross-contamination in ∼4% of the microwells. Following DNA barcode delivery, we utilized the platform to generate high-quality ATAC-seq libraries for breast cancer cell line (MCF7) nuclei by integrating tagmentation and on-chip PCR. Overall, we describe a deterministic and bead-free DNA barcoding strategy for efficient barcoding of microwell arrays that are important in single-cell analyses.},
}

@article {pmid42517622,
year = {2026},
author = {Jeon, JH and Ryoo, S and Kang, H and Kim, J and Lim, D-R and Di Nardo, A and Shaw, AE and King, DP and Kim, S-M},
title = {Evaluation of amplicon-based nanopore sequencing for foot-and-mouth disease viruses in clinical and environmental samples.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0079126},
doi = {10.1128/spectrum.00791-26},
pmid = {42517622},
issn = {2165-0497},
abstract = {Foot-and-mouth disease (FMD) causes severe global economic loss, necessitating rapid viral characterization. Nanopore sequencing provides a simple, real-time workflow suitable for on-site outbreak response, addressing the limitations of conventional methods. In this study, we optimized a previously published amplicon-based protocol and used this method to characterize a diverse range of samples (vesicular fluid, epithelium, serum, nasal/oral swabs, and environmental samples) collected during FMD outbreaks in 2025 in the Republic of Korea. Of the 129 samples collected, we successfully recovered complete genomes from 37 samples and VP1 sequences from 85 samples. Amplifying the S-fragment in isolation and separately barcoding each pool of PCR amplicons markedly improved sequence recovery. Furthermore, sequencing success depended on viral load and sample type. Based on comparisons with real-time RT-PCR results, whole-genome sequence (WGS) recovery exceeded 77.3% at cycle threshold (Ct) values ≤25 across all clinical samples. In the Ct > 30 category, serum samples yielded the highest WGS recovery rates (44.4%). This rate was markedly higher than the success rates observed for epithelium (20.0%) and nasal swabs (9.1%), whereas oral swabs and environmental samples failed to yield any sequences (0%). However, VP1 recovery from environmental samples reached 80% at Ct ≤ 30 (8/10), providing an approach to enable non-invasive monitoring. These findings demonstrate that amplicon-based nanopore sequencing is a practical method for the rapid generation of genomic data during FMD outbreaks.IMPORTANCEAlthough rapid detection and genomic data analysis are crucial for effective foot-and-mouth disease (FMD) control, the collection of these data can be challenging for certain sample types and impacted by reduced viral loads that result from nationwide FMD vaccination. This study provides a practical solution through large-scale evaluation of an optimized amplicon-based nanopore sequencing protocol to enhance the sequencing success rates for both clinical and environmental samples. Using a modified protocol to enhance genome recovery, we demonstrated that sequence data could be retrieved from diverse sample types (even with high real-time RT-PCR cycle threshold values). We identified serum as the most suitable sample, with environmental sample sequencing allowing for non-invasive monitoring during outbreaks. These results support the use of nanopore sequencing for rapid genomic analysis, particularly in outbreak responses, such as rapid surveillance, emergency vaccine selection, and epidemiological monitoring.},
}

@article {pmid42517631,
year = {2026},
author = {Pinkevych, M and Docken, SS and Wu, Y and Schlub, T and Harper, JL and Viox, EG and Samer, S and Kulpa, D and Betts, MR and Keele, BF and Paiardini, M and Bar, KJ and Cromer, D and Davenport, MP},
title = {The rebound-initiating viral reservoir (RIVR) in SIV/SHIV infection is dominated by plasma virus sequences present at the time of ART initiation.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0036626},
doi = {10.1128/jvi.00366-26},
pmid = {42517631},
issn = {1098-5514},
abstract = {UNLABELLED: Active human immunodeficiency virus (HIV) replication generates long-lived latently infected cells that persist despite effective antiretroviral therapy (ART). Several studies analyzing proviral DNA sequences sampled during ART have shown that these sequences are closely related to plasma virus present around treatment initiation. However, a large proportion of proviral DNA is defective or difficult to reactivate, suggesting that only a subset of latent proviruses contributes to viral rebound in vivo. Here, we used a barcoded simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV) model to study virus rebounding after antiretroviral treatment interruption (ATI) and its relationship to plasma virus present before ART initiation. We modeled barcode matches between rebound virus and pre-ART plasma virus to estimate the contribution of different time points to subsequent rebound. We estimate that plasma virus sampled immediately before ART contributes approximately 65%-95% of successful rebound lineages. This remains true after re-treatment and re-interruption of ART, with the circulating virus present just before the second ART contributing most to the second rebound. In contrast, analysis of proviral DNA during ART suggests that plasma virus present at the peak of primary infection contributes more substantially to the DNA reservoir (61%-90%), whereas the virus sampled immediately before ART contributes less. These findings suggest that the observable proviral DNA reservoir is established primarily during peak infection and is supplemented throughout untreated infection. However, post-treatment rebound virus originates from only a small subset of the total proviral DNA reservoir, predominantly formed around the time of ART initiation.

IMPORTANCE: Human immunodeficiency virus infection cannot be eliminated because of long-lived, latently infected cells. Understanding when the latent reservoir forms may help identify the timing of interventions to reduce viral rebound. We analyzed data from macaques infected with a barcoded virus that allowed us to track individual viral lineages. Although many lineages were present in plasma during active infection, only a small number rebounded after antiretroviral treatment (ART) interruption. We compared barcode patterns in rebound virus with plasma virus sampled at different times before treatment to identify when rebounding lineages were observed. We found that the rebound virus was most closely related to the plasma virus present at treatment initiation, suggesting that this may be an important time for the formation of the rebound-initiating reservoir. Rebound virus matched pre-treatment plasma virus more closely than proviral DNA detected during ART, suggesting that on-treatment proviral DNA may poorly predict which viruses will re-emerge after treatment interruption.},
}

@article {pmid42519512,
year = {2026},
author = {Fan, Y and Wu, Y and Zeng, H and Zhao, C and Li, C and Chen, L and Hu, J and Li, L},
title = {Complete Chloroplast Genome of Cardamine microzyga and Phylogenetic Analysis.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e73951},
pmid = {42519512},
issn = {2045-7758},
abstract = {Cardamine microzyga (Brassicaceae) is a perennial herbaceous species native to mountainous regions of southwestern China, yet its genomic resources remain poorly characterized. In this study, we assembled and annotated the complete chloroplast (cp) genome of C. microzyga based on Illumina HiSeq 4000 sequencing data, and conducted comprehensive analyses of its genomic structure, repeat sequences, codon usage, nucleotide diversity, and phylogenetic relationships. The cp genome is 154,661 bp in length, exhibiting a typical quadripartite structure comprising a large single-copy (LSC) region (84,261 bp), a small single-copy (SSC) region (17,774 bp), and a pair of inverted repeat (IR) regions (26,313 bp each). A total of 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Fifty-seven mononucleotide and four dinucleotide simple sequence repeats (SSRs) were identified, all of which exhibited a pronounced A/T bias, together with nine complex compound SSRs. Comparative analysis of the IR/LSC and IR/SSC boundaries among 11 Brassicaceae species revealed high structural conservation, with only minor variations. Codon usage analysis indicated that 30 codons had relative synonymous codon usage (RSCU) values > 1, with a strong preference for A/T-ending codons. Nucleotide diversity (Pi) analysis across 106 protein-coding genes identified nine hypervariable regions (Pi > 0.0156), among which trnS-GCU (Pi = 0.03736), rrn4.5S (0.03280), and ycf1 (0.03224) represented promising candidates for DNA barcoding and phylogenetic marker development. Phylogenetic reconstruction based on 45 complete cp genomes using maximum likelihood (ML) method placed C. microzyga within a well-supported clade (bootstrap = 100) comprising C. lyrata, C . fallax , and C. amariformis, with Rorippa as the sister group. This study provides the first complete cp genome of C. microzyga, which not only fills a key genomic gap in an alpine-endemic species but also offers insights into the adaptive evolution of high-altitude plants. These resources will facilitate future taxonomic, evolutionary, and conservation genetics studies in the genus Cardamine and the family Brassicaceae.},
}

@article {pmid42521239,
year = {2026},
author = {Sipiczki, M},
title = {Yeasts on Tree Gum: Taxonomic, Genetic and Phenotypic Diversity.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70393},
doi = {10.1111/1758-2229.70393},
pmid = {42521239},
issn = {1758-2229},
support = {2020-1.1.2-PIACI-KFI-2020-00130//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; 11111//University of Debrecen Programme for Scientific Publication/ ; },
mesh = {Phylogeny ; *Genetic Variation ; *Trees/microbiology/chemistry ; *Yeasts/classification/genetics/isolation & purification/metabolism ; DNA, Fungal/genetics/chemistry ; *Plant Gums/metabolism ; Sequence Analysis, DNA ; DNA, Ribosomal Spacer/genetics/chemistry ; Biodiversity ; Prunus/microbiology ; Molecular Sequence Data ; },
abstract = {Depending on their composition, exudates oozing from trees can support or inhibit the growth of microorganisms. Resins released by conifers have a strong antimicrobial effect. Sugar-rich saps are usually colonised by diverse microorganisms including yeasts. In this study, the yeasts associated with the polysaccharide-containing gums of cherry trees were examined. 227 strains were isolated from gums of 53 abandoned road-side and orchard sour cherry trees in 20 locations. 12 ascomycetous and 19 basidiomycetous species were found among the isolates. All grew very poorly on laboratory media containing gum as the only source of nutrients. The high taxonomic diversity and poor growth of the isolates on gum-based media indicate that the cherry-tree gum is unlikely to be permanently colonised by a characteristic yeast community. Strains of 16 species showed antifungal antagonism. The Metschnikowia pulcherrima isolates killed the cells of the test organisms by releasing pulcherriminic acid. These isolates showed high intragenomic barcode (D1/D2 domain and ITS) diversity due to single-nucleotide dimorphism (ambiguous nucleotides) in many sites. In the D1/D2 domain, the ambiguous sites were concentrated in four segments that correspond to the back-folding strands of the stems of the D1 and D2 loops of the secondary structure of the LSU rRNA.},
}

Phylogeny
*Genetic Variation
*Trees/microbiology/chemistry
*Yeasts/classification/genetics/isolation & purification/metabolism
DNA, Fungal/genetics/chemistry
*Plant Gums/metabolism
Sequence Analysis, DNA
DNA, Ribosomal Spacer/genetics/chemistry
Biodiversity
Prunus/microbiology
Molecular Sequence Data

@article {pmid42523247,
year = {2026},
author = {Karpen, A and Chandrasekaran, AR},
title = {Hexadecimal data encryption in paranemic crossover (PX) DNA.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.17.738806},
pmid = {42523247},
issn = {2692-8205},
abstract = {DNA is highly programmable and efficient for encoding information. In this work, we use the paranemic crossover (PX) DNA structures for a binary-encoded system. As substrates for data storage, we designed a combination of PX and anti-PX structures where the four strands of the PX motif are complementary to those in the anti-PX motif. To write data, we programmed encoding elements in each of the four strands of the PX and anti-PX motifs. The encoded data remains encrypted until the samples are processed at a specific temperature, when the PX and anti-PX motifs reassociate to four distinct duplexes, defined by the encoding elements and retrieved using an electrophoretic readout. We show that the encoded information is stable for several days when stored at 20 °C, 37 °C or outdoors, with the encrypted structures showing higher nuclease resistance compared to the decrypted structures. Using this strategy, we demonstrate hexadecimal encoding using a combination of 4 bits, encrypting specific words and color codes. We envision such systems could find use barcoding, secure messaging and authentication.},
}

@article {pmid42505801,
year = {2026},
author = {Dai, L and Guo, P and Zhang, X},
title = {Integrative Taxonomy Reshapes Palaearctic-Oriental Biogeography: First Discovery of Dicranomyia (Sivalimnobia) (Diptera, Limoniidae) in Mainland China with Two New Species.},
journal = {Insects},
volume = {17},
number = {7},
pages = {},
pmid = {42505801},
issn = {2075-4450},
support = {32470481, 32100356//National Natural Science Foundation of China/ ; XZ202601ZY0095//Science and Technology Projects of Xizang Autonomous Region/ ; QNYCX25067//Graduate Innovation Program of Qingdao Agricultural University/ ; },
abstract = {The crane fly subgenus Sivalimnobia has been taxonomically stagnant for over half a century, with its apparent absence from mainland China representing a major biogeographic anomaly. We address this by integrating detailed morphology and COI DNA barcoding of specimens collected across 14 Chinese provinces. Our study conclusively establishes the presence of Sivalimnobia in mainland China, resolving three species: the newly recorded and continentally widespread Dicranomyia (Sivalimnobia) alticola Edwards, 1916, and two new endemic species-D. (S.) bispinosa sp. nov. (restricted to Yunnan) and D. (S.) inflata sp. nov. (a cryptic lineage within the D. (S.) alticola complex distributed across Chongqing, Sichuan and Yunnan). The discovery of D. (S.) inflata sp. nov. was validated by a discrete male genitalic autapomorphy and a pronounced COI barcode gap (8.7-9.6% divergence). These findings update the global biogeography of the subgenus, identifying India as the primary diversity center and southwestern China as a significant secondary center. The overall pattern suggests a "stepping-stone dispersal and multi-center diversification" model. This work transforms Sivalimnobia from a taxonomic relic into a model for studying Eurasian insect biogeography and highlights the conservation importance of East Asian montane stream habitats.},
}

@article {pmid42505802,
year = {2026},
author = {Lü, H and Zhang, R},
title = {Five New Species of Orthosinus Motschulsky, 1863 from China-Molecular Evidence for Two Species (Coleoptera, Curculionidae, Dryophthorinae).},
journal = {Insects},
volume = {17},
number = {7},
pages = {},
pmid = {42505802},
issn = {2075-4450},
support = {32470456//National Natural Science Foundation of China/ ; },
abstract = {Five new species of Orthosinus Motschulsky, 1863 from China are described: O. borisi sp. nov. (♂♀) and O. urceolatus sp. nov. (♂♀) from Xizang Autonomous Region, O. diaoluoshanensis sp. nov. (♂) from Hainan Province, O. sulcatus sp. nov. (♂♀) from Sichuan Province and O. tengchongensis sp. nov. (♂) from Yunnan Province. Detailed morphological descriptions, diagnostic illustrations, and habitus photographs are provided for each species. An identification key and a distribution map for all known Chinese species of Orthosinus are also provided. With these additions, the number of known Chinese species of Orthosinus is increased from two to seven. Molecular phylogenetic and species delimitation analyses of the COI gene were additionally performed for two of the newly described species, O. urceolatus sp. nov. and O. sulcatus sp. nov., along with other congeneric and outgroup specimens.},
}

@article {pmid42507039,
year = {2026},
author = {Romão, HAA and Corvalán, LCJ and Carneiro, JA and Santos, DDFD and Nunes, R and Dias, RO},
title = {Expanding the mitochondrial genomic toolkit for Polyneoptera: New mitogenomes and evaluation of reduced marker sets for phylogeny and DNA barcoding.},
journal = {Genetics and molecular biology},
volume = {49},
number = {3},
pages = {e20250282},
pmid = {42507039},
issn = {1415-4757},
abstract = {Polyneoptera comprises hemimetabolous insect orders of significant agricultural, ecological, and medical relevance, motivating phylogenetic and molecular research that has nevertheless focused predominantly on canonical mitochondrial markers. Here, we assembled new mitogenomes for Polyneoptera and evaluated the usefulness of genes located in nucleotide-diversity hotspots as markers for species identification and phylogenetic inference. To expand the available mitogenomic resources, raw sequencing data were retrieved from public databases, resulting in the assembly and annotation of 26 complete mitogenomes, all exhibiting the typical insect mitochondrial architecture. These newly assembled genomes were combined with publicly available mitogenomes from Orthoptera, Blattodea, Plecoptera, Mantodea, and Phasmatodea to reconstruct phylogenetic relationships using both complete and reduced datasets comprising nucleotide-diversity hotspot-associated genes. The performance of these hotspot regions was further assessed through barcoding gap analyses and comparisons with the most comprehensive datasets to identify candidate mitochondrial markers for molecular species identification and phylogenetic inference. Across orders, different mitochondrial regions, including the classical markers 16S and COX1, as well as genes from the NADH dehydrogenase complex, emerged as the most informative, although optimal markers varied among lineages. Overall, our findings highlight the value of publicly accessible sequencing data for generating high-quality genomic resources and improving phylogenetic and taxonomic tools.},
}

@article {pmid42507597,
year = {2026},
author = {Maung, HT and Morita, M and Han, SM and Mishima, H and Koga, C and Evangelista, JWC and Girasol, MJ and Suzuki, S and Yoshiura, KI and Kodama, T and Smith, C and Hiyoshi, H},
title = {Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing for Salmonella Typhi genomic surveillance.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
pmid = {42507597},
issn = {2057-5858},
mesh = {*Salmonella typhi/genetics/isolation & purification/classification ; *Nanopore Sequencing/methods ; Genome, Bacterial ; *DNA, Bacterial/genetics ; Whole Genome Sequencing/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Genomics/methods ; Polymorphism, Single Nucleotide ; Typhoid Fever/microbiology ; Sequence Analysis, DNA/methods ; },
abstract = {Pathogen genomic surveillance is essential for monitoring high-risk lineages and antimicrobial resistance in Salmonella enterica serovar Typhi (S. Typhi), yet implementing whole-genome sequencing in sentinel hospital laboratories remains challenging. We evaluated whether mechanically sheared DNA, paired with high accuracy or super accuracy (SUP) basecalling, enables reliable Oxford Nanopore Technologies (ONT)-only sequencing for multiplexed S. Typhi genomic surveillance. Genomic DNA from three benchmark strains (Ty2, Ty42 and Ty43) was either mechanically sheared to ~15 kb or left unsheared and sequenced in a controlled 6-plex run. The optimized workflow was subsequently evaluated in a 24-plex field run that included 3 benchmark strains and 21 clinical isolates from a sentinel hospital in Manila, Philippines. Both runs were performed using the ONT Ligation Sequencing Kit with Native Barcoding 24 V14 (SQK-NBD114.24) and R10.4.1 flow cells (FLO-MIN114). Assembly metrics, single-nucleotide variation (SNV) concordance, core-genome MLST and downstream functional outputs were compared across DNA preparations and basecalling modes. In the 6-plex run, sheared libraries consistently achieved >1,000× pre-filtered coverage across all strains, whereas unsheared libraries showed highly variable depths and reduced stability after downsampling. When paired with SUP basecalling, sheared datasets produced assemblies comparable to Illumina and hybrid references across both structural accuracy and functional outputs. In the 24-plex run, all samples achieved >100× coverage, and 18 of the 22 retained S. Typhi genomes (81.8%) yielded fully circularized assemblies after exclusion of 2 non-S. Typhi isolates. Serotype prediction, genotyping and in silico antimicrobial resistance predictions remained concordant with the corresponding 6-plex benchmark results. These findings demonstrate that mechanical DNA shearing improves coverage uniformity under multiplexed conditions and, together with SUP basecalling, supports ONT-only S. Typhi genome reconstruction for routine genomic surveillance and broad phylogenetic contextualization. However, for fine-scale transmission analysis and high-resolution SNV interpretation, short-read or hybrid sequencing remains important. Overall, this approach provides a scalable framework for high-multiplex S. Typhi genomic surveillance in sentinel laboratory settings.},
}

*Salmonella typhi/genetics/isolation & purification/classification
*Nanopore Sequencing/methods
Genome, Bacterial
*DNA, Bacterial/genetics
Whole Genome Sequencing/methods
High-Throughput Nucleotide Sequencing/methods
Humans
Genomics/methods
Polymorphism, Single Nucleotide
Typhoid Fever/microbiology
Sequence Analysis, DNA/methods

@article {pmid42507747,
year = {2026},
author = {Cortés-Cortés, G and Warner, C and Ellenbach, J and Katz, S and Kim, J and Camps, M},
title = {Long-Read Plasmid Sequencing and Assembly Using Nanopore Sequencing-Based Workflows.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {233},
pages = {},
doi = {10.3791/70202},
pmid = {42507747},
issn = {1940-087X},
mesh = {*Plasmids/genetics ; *Nanopore Sequencing/methods ; *Sequence Analysis, DNA/methods ; Escherichia coli/genetics ; Workflow ; },
abstract = {The present study describes a workflow for nanopore sequencing designed to maximize plasmid DNA yield and sequencing accuracy. Researchers cover each step of the process, which includes plasmid DNA extraction, library preparation with rapid barcoding and adapter ligation, loading of the library onto a flow cell for sequencing, base calling (in real time or post-hoc), and sequence assembly using Autocycler. The authors also specify the computer requirements, which largely depend on whether basecalling is done in real time. The authors sequenced plasmids purified from ten clinical strains using this workflow. To remove host-cell strain differences as a variable, the authors also conjugated these clinical strains with a common recipient strain and sequenced the transconjugants. These experiments produced plasmid assemblies that match plasmid sizes inferred from gel mobility and that, in 2/3 of cases, also match short-read polished assemblies or are within 0.05% pairwise sequence identity. The enrichment of plasmid DNA sequences also maximizes the efficiency of plasmid sequencing, allowing parallel sequencing of up to 24 samples with optimal coverage. This protocol is adequate for plasmids ranging from 4 to 174 kb and tolerates up to 72% chromosomal contamination without affecting accuracy. This protocol is ideal for situations where the chromosomal sequence is already known or of no interest, such as for plasmid sequence verification, improving the accuracy of plasmid sequences already obtained by WGS, or sequencing plasmids captured by conjugation. The organism used to illustrate this work is Escherichia coli, which is representative of hosts used for recombinant gene expression and for plasmid capture through conjugation.},
}

*Plasmids/genetics
*Nanopore Sequencing/methods
*Sequence Analysis, DNA/methods
Escherichia coli/genetics
Workflow

@article {pmid42510895,
year = {2026},
author = {Adorada, DL and Adorada, EE and Gunasinghe, N},
title = {Multilocus Identification of Indigenous Trichoderma Isolates and Their Biocontrol Mechanisms Against Macrophomina in Northern Australia.},
journal = {Current issues in molecular biology},
volume = {48},
number = {7},
pages = {},
doi = {10.3390/cimb48070654},
pmid = {42510895},
issn = {1467-3045},
support = {USQ1907-001RTX//Grains Research and Development Corporation/ ; },
abstract = {Charcoal rot, caused by the pathogen Macrophomina, is becoming an increasing challenge in Australia's northern cropping systems, with few effective management options available. The use of non-indigenous biocontrol agents raises ecological and regulatory concerns, which highlights the need to identify locally adapted microbial antagonists. In this study, indigenous Trichoderma isolates were collected from rhizosphere soils across Queensland and northern New South Wales and characterised using multilocus sequencing (ITS, tef-1α, rpb2) coupled with phylogenetic analysis. Twenty-six isolates were resolved into six species, dominated by T. azevedoi and T. afroharzianum. Dual-culture assays revealed substantial variation in antagonistic capacity, with several isolates achieving >70% inhibition of Macrophomina growth and maintaining consistent performance across pathogen genotypes. Functional screening indicated that enzyme-associated antibiosis was widespread, whereas volatile-mediated inhibition was restricted to a small subset of isolates. These findings demonstrate that biocontrol potential in indigenous Trichoderma populations is highly strain-dependent rather than species-driven. By integrating multilocus identification with functional screening, this study provides a practical framework for selecting locally adapted biocontrol candidates. This work establishes a foundation for developing region-specific biological control strategies and supports a shift toward targeted, strain-level selection for effective management of charcoal rot.},
}

@article {pmid42511154,
year = {2026},
author = {Kyriakos, P and Zoi, G and Athanasia, K and Dimitra, S and Dimitrios, L and Anastasia, I and Thanasis, M and Sofia, GM},
title = {New Records of Isognomon Species from Crete, Greece; Evidence from Adult Specimens and Additional DNA Barcodes.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/ani16142277},
pmid = {42511154},
issn = {2076-2615},
abstract = {During the last two decades, non-indigenous species of the genus Isognomon have been increasingly reported in the Mediterranean Sea, yet their taxonomy and distribution remain poorly resolved because of pronounced shell plasticity and limited molecular reference data. In the present study, Isognomon specimens collected along the coasts of Crete (Greece) were examined, using an integrative approach combining adult morphometric analyses with mitochondrial (COI and 16S rRNA) and nuclear (28S rRNA) genetic markers. The results confirm the establishment of Isognomon bicolor in the eastern Mediterranean and document the presence of specimens morphologically consistent with I. australicus, which clustered within the unresolved I. legumen-I. aff. legumen complex in both mitochondrial and nuclear phylogenetic analyses. Morphometric analyses revealed pronounced shell plasticity, with shell width, hinge length, and nacreous height providing the greatest discriminatory power, although considerable overlap between taxa limited reliable identification based solely on shell morphology. Molecular analyses confirmed the identity of I. bicolor and further supported its eastward expansion within the Mediterranean basin. In contrast, the concordance between mitochondrial and nuclear datasets indicates that the unresolved taxonomy of the I. australicus-I. legumen complex is unlikely to result solely from the use of mitochondrial markers. These findings expand the available morphometric and genetic data for Mediterranean Isognomon populations and highlight the need for integrative taxonomic approaches, incorporating additional nuclear and genomic data to resolve species boundaries.},
}

@article {pmid42516222,
year = {2026},
author = {Vivien, R and Martin, P and Lafont, M and Ferrari, BJD},
title = {DNA Integrity of Chironomids and Oligochaetes Is Maintained During Long-Term Storage in Neutral Buffered Formalin: Implications for Macroinvertebrate Monitoring.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e74047},
pmid = {42516222},
issn = {2045-7758},
abstract = {Oligochaetes and chironomids are valuable bioindicators but ethanol preservation is problematic: it causes oligochaetes to disintegrate and forces a trade-off in insects between DNA integrity and morphological structures. Aiming to develop genetic oligochaete and chironomid indices based on the high-throughput sequencing (HTS) of genetically tagged specimens, we tested whether long-term specimen storage in neutral buffered formalin affects the success rate of subsequent genetic analyses. We performed PCR amplifications of the COI gene on specimens preserved in neutral buffered formalin for periods up to 6 months. For oligochaetes, DNA quantities (amplicon yields) decreased over time but remained sufficient for sequencing at all tested periods; for chironomids, no temporal trend toward degradation was observed. Storing these tissues in neutral buffered formalin for up to 6 months does not prevent subsequent genetic analyses and provides ample time for logistical processing, such as labor-intensive sieving. These results facilitate the implementation of oligochaete and chironomid indices using a single sediment sample for both groups. More broadly, replacing ethanol with neutral buffered formalin as a fixative simultaneously preserves DNA quality, specimen density, community composition, and morphological structures across macroinvertebrate taxa. This integrated preservation allows for: (1) the refinement of macroinvertebrate indices both morphology- and bulk-DNA-based, by ensuring that all taxa, including soft-bodied organisms, are accurately represented; (2) the perfection of insect barcode reference databases by enabling a dual validation approach where high-quality sequences are directly linked to intact morphological vouchers; and (3) the improvement of quality control in bulk-sample HTS by allowing morphological verification of molecular results on the same specimens.},
}

@article {pmid42516991,
year = {2026},
author = {Kubala, A and Mutai, IJ and Mclean, S and Rees, CED},
title = {Viable Spores Can be Obtained and Germinated from Commercially Obtained Dried Morel (Morchella) Mushrooms.},
journal = {Mycobiology},
volume = {54},
number = {4},
pages = {464-471},
pmid = {42516991},
issn = {1229-8093},
abstract = {Morel mushrooms (Morchella sp.) are highly prized edible mushrooms that are still difficult to cultivate despite great interest and advancements made in recent years. Obtaining genetic material of morel mushrooms is necessary to carry out research but may be challenging depending on the region, time of the season, budget, or local legislation. This study assessed whether ascospores could be recovered and germinated from retail dried morel products and whether resulting isolates could be taxonomically identified. Four packets of dried morels from different suppliers were rehydrated, homogenized, and processed to recover spore suspensions. Hemocytometer counts yielded mean spore titers of 1.50 × 10[5] (A), 4.24 × 10[6] (B), 5.86 × 10[6] (C), and 3.51 × 10[5] (D) spores mL[-1]. Aliquots were plated on Sabouraud dextrose agar (SDA) with chloramphenicol and incubated at 24 °C; colony counts indicated cultivable fractions corresponding to c. 2.2% germination for sample A and ∼10-20% for samples B-D. Representative colonies were subcultured, DNA was extracted, and ITS barcodes were generated by Sanger sequencing. Isolates from samples A, B, and D matched Morchella sextelata, while isolates from sample C matched Morchella eximia. The findings demonstrate that viable Morchella ascospores can persist through commercial drying and that dried products constitute a low‑cost source of cultivable material. Discrepancies between sequencing results and product labels highlighted possible country of origin concerns but were considered outside the scope of this work and were not exhaustively investigated.},
}

@article {pmid42500985,
year = {2026},
author = {Andrews, B and Ranganathan, R},
title = {BCAR: A fast and indel-tolerant barcode-sequence mapper.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag557},
pmid = {42500985},
issn = {1367-4811},
abstract = {MOTIVATION: DNA barcodes are commonly used as a tool to distinguish genuine mutations from sequencing errors in sequencing-based assays. In the presence of indel errors, utilizing barcodes requires accurate alignment of the raw reads to distinguish genuine indels from indel errors. Existing strategies to do this generally rely on aligners built for homology comparison and do not fully utilize quality scores. We reasoned that developing an aligner purpose-built for error correction could yield higher quality barcode-sequence maps.

RESULTS: Here, we present BCAR, a fast barcode-sequence mapper for correcting sequencing errors. BCAR considers all of the evidence for each base call at each position both during alignment and during final consensus generation. BCAR creates high-accuracy barcode-sequence maps from simulated reads across a broad range of error rates and read lengths, outperforming existing methods. We apply BCAR to two experimental datasets, where it generates high-quality barcode-sequence maps.

BCAR source code, documentation, and test data are available from: https://github.com/dry-brews/BCAR or https://doi.org/10.5281/zenodo.20088816.},
}

@article {pmid42501335,
year = {2026},
author = {Zhao, S and Li, Y and Peng, H and Liu, Y},
title = {Multiscale symbolic morpho-barcoding reveals region-specific and scale-dependent neuronal organization.},
journal = {Cell reports},
volume = {45},
number = {8},
pages = {117712},
doi = {10.1016/j.celrep.2026.117712},
pmid = {42501335},
issn = {2211-1247},
abstract = {Neuronal morphology shapes circuit organization, yet its multiscale complexity has hindered systematic brain-wide analysis. Here, we introduce multiscale morpho-barcoding (MMB), a framework that encodes whole-brain neuronal morphology into symbolic barcodes spanning cellular geometry, axonal tract routing, arbor organization, and predicted presynaptic distributions. Applying MMB to 1,876 fully reconstructed mouse neurons, comprising 3,776 arbors, and 2.63 million predicted presynaptic sites, we identified distinct multiscale morpho-patterns that help reveal two organizational principles. First, neuronal morphology is region specific: regional identity arises from distinct combinations of shared and region-biased morpho-motifs. Second, organization is scale dependent: different morphological scales contribute differentially to the neuronal classification and circuit architecture. Within this mouse dataset, MMB discriminates major anatomical divisions and resolves canonical thalamic circuit classes, exceeding the resolution of projection strength-based representations. MMB provides an interpretable and scalable framework for integrating morphology with connectivity and function. This framework could further be applicable to analyze disease-oriented structural phenotypes.},
}

@article {pmid42502292,
year = {2026},
author = {Bartos, M and Włodarczyk, R and Paszkowska, A and Rewicz, T and Kamiński, M and Rapczyński, J and Fiutek, P and Minias, P},
title = {Chewing Lice From the Wings of Migrating Shorebirds: Diversity, Host Specificity, and Associations With Host Body Condition.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e74013},
pmid = {42502292},
issn = {2045-7758},
abstract = {Ectoparasites may negatively affect their hosts throughout life, especially during breeding and other energetically demanding periods. In birds, feather-feeding ectoparasites may reduce host condition and performance during seasonal migrations. This study aimed to investigate the diversity of wing-collected chewing lice (Phthiraptera) and their associations with two groups of avian hosts, Charadriidae and Scolopacidae. We examined 1403 individuals from 20 migratory shorebird species to estimate louse prevalence and abundance, and a subsample of lice was identified using microscopic examination and DNA barcoding. In total, 26 lice species were identified across all hosts. Measures of louse prevalence and abundance varied widely among host species (9%-94% infested individuals and 0.2-26.4 lice per individual). Infestation differed significantly between age classes (higher in first-year than in adult birds) and between habitats used by birds during migration (higher at an artificial reservoir than in a natural river valley). Notably, louse abundance was negatively associated with condition (fat load and size-corrected body mass) in a time-constrained long-distance migrant, the wood sandpiper Tringa glareola, whereas no such pattern was found in a short-distance migrant with fewer time constraints during migration, the common snipe Gallinago gallinago. Our findings suggest that chewing lice may negatively influence avian hosts during critical stages of the annual cycle, such as migration, but these effects may be modulated by host behavior, particularly migration strategy.},
}

@article {pmid42502630,
year = {2026},
author = {Djagbaré, P and Tibiri, EB and Nadembèga, WMC and Name, PE and Traoré, L and Sampo, E and Ouédraogo, M and Tiendrebéogo, F and Simporé, J},
title = {Whole genome dataset of bacterial strains isolated from urine analysed by Oxford Nanopore sequencing technologies in Ouagadougou, Burkina Faso.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {113049},
pmid = {42502630},
issn = {2352-3409},
abstract = {A collection of 21 bacterial isolates recovered from urine specimens collected between September 2018 and February 2019 at Saint-Camille and SCHIPHRA hospitals in Ouagadougou, Burkina Faso, is presented. Isolates were identified using the API 20E system and tested for antibiotic susceptibility according to CASFM 2018 guidelines. Genomic DNA was extracted, barcoded with the SQK-RBK114.96 Rapid Barcoding Kit, and sequenced on an Oxford Nanopore MinION Mk1C using an R10.4.1 flowcell. Basecalling was performed with Dorado, and reads were quality filtered prior to de novo assembly with Flye, followed by polishing with Racon and Medaka. Assemblies were evaluated with QUAST, taxonomically assigned with Kraken2, and annotated with Bakta. The dataset comprises 21 barcode-specific raw read sets (1.5 million reads; 4.9 Gb), polished genome assemblies, per-isolate metadata including collection site, collection date, and antibiotic susceptibility measurements, and quality assessment outputs including read statistics, assembly metrics, and functional annotation completeness estimates. All data are available under NCBI BioProject PRJNA1307828. These data provide a useful resource for long-read bacterial genome assembly benchmarking, comparative genomics, and analyses integrating phenotypic and genomic antimicrobial resistance information.},
}

@article {pmid42503162,
year = {2026},
author = {Thomas, JE and Lurgi, M and Davies, CE and Rowley, AF and Coates, CJ},
title = {Hematodinium sp. infection alters haemolymph bacteriome composition and function in shore crabs, carcinus maenas.},
journal = {Virulence},
volume = {},
number = {},
pages = {2709259},
doi = {10.1080/21505594.2026.2709259},
pmid = {42503162},
issn = {2150-5608},
abstract = {Hematodinium sp. is a parasitic dinoflagellate that infects and causes disease in a large fraction of decapod crustaceans in the Northern Hemisphere. The shore crab Carcinus maenas is susceptible to this parasite in its native range of European coastlines and along its invasive fronts. The parasite enters the host from the surrounding water, and fueled by the hemolymph (blood) resources, proliferates until host tissues are overrun. To improve our knowledge of the shore crab-Hematodinium pathosystem, we profiled the hemolymph microbiome of control and Hematodinium-positive crabs with low (early clinical) and high (late clinical) parasite levels through bacterial 16S rRNA V3-V4 meta-barcoding (n = 64). Concurrently, we assessed hemolymph condition through quantification of circulating hemocytes (immune cells) and bacterial colony forming units. Progression of Hematodinium sp. infection coincided with gradual changes in bacterial community composition. These changes were driven by shifts in relative abundances of specific taxa, e.g. Corynebacterium, Flavobacterium. Furthermore, alterations in bacterial communities were accompanied by marked shifts in metabolic signatures from stress and virulence dominated (including biofilm formation) to catabolism, peptide transport and tissue putrefaction at the terminal stage of parasitemia. We present the first account of microbiome dynamics in healthy shore crabs and those overcome by Hematodinium sp. Our experiments reveal a clear link between bacterial community structure-function and the advancing disease state.},
}

@article {pmid42499385,
year = {2026},
author = {Mazur, AM and Starshin, AS and Bogush, NV and Prokhortchouk, EB},
title = {Selection and evaluation of DNase I hypersensitive sites for prenatal screening of trisomy 21 in the fetus.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {30},
number = {4},
pages = {669-675},
doi = {10.18699/vjgb-26-67},
pmid = {42499385},
issn = {2500-0462},
abstract = {This study introduces a novel approach for noninvasive prenatal testing (NIPT) of chromosomal abnormalities, based on analysis of epigenetic features in circulating cell-free DNA (cfDNA). The core innovation of our method leverages fundamental differences in chromatin organization between maternal and fetal cells. Specifically, we focused on genomic regions that exhibit open chromatin configuration in maternal blood cells but remain tightly packed in fetal tissues (DNase I hypersensitive sites or DHSs). These epigenetic differences create distinct cfDNA fragmentation signatures that allow selective identification of fetal DNA within the maternal cfDNA pool. The study workflow comprised several key steps: performing genome-wide screening to identify differentially accessible chromatin regions, selecting the most informative markers using a machine learning algorithm, and targeted sequencing of the selected epigenetic markers using molecular barcodes. Subsequently, a LASSO regression model was constructed and validated. As a proof of concept, the study demonstrates the method's efficacy in identifying trisomy 21 (Down syndrome), though the underlying principles can be readily adapted to other abnormalities. Complementing its robust performance, the technique offers practical advantages in terms of platform compatibility - the same epigenetic markers can be assessed using either next-generation sequencing or simpler, more cost-efficient methods like digital PCR. With further refinement, the approach could be extended to screen for additional aneuploidies (trisomies 13 and 18) and microdeletion syndromes. Therefore, this approach offers new opportunities for developing cost-effective testing systems suitable for widespread routine clinical implementation, combining high diagnostic accuracy with reduced analysis costs.},
}

@article {pmid42500350,
year = {2026},
author = {Xu, P and Zhang, Y and Shu, X and Han, D and Zhao, H},
title = {A new earthworm species of the genus Eisenia Malm, 1877 (Oligochaeta, Lumbricidae) from the Ili River valley, northwestern China.},
journal = {ZooKeys},
volume = {1285},
number = {},
pages = {21-40},
pmid = {42500350},
issn = {1313-2989},
abstract = {The present study focuses on the taxonomy of the earthworm genus Eisenia Ealm, 1877 in China. The taxonomic framework for this genus in China has long been ambiguous, with studies in the northwestern region being particularly scarce. Prior to this research, only four subspecies within the Eisenia nordenskioldi (Eisen, 1879) complex, distributed across northeastern and northern China, had been described. Based on detailed morphological characteristics and molecular data, this paper describes a new species, E. ilensis sp. nov., collected from the Ili River valley in northwestern China. The key diagnostic characteristics of this new species include a medium body length (37-103 mm); two pairs of small, spherical spermathecae without ducts, located at the inter-segmental furrows 9/10 and 10/11; a pair of small, circular tubercula pubertatis on the clitellum situated between the ab setae; the first of dorsal pore beginning at the 4/5 inter-segmental furrow; and a pair of slit-like male pores on segment XV. Phylogenetic analyses based on the mitogenomic protein coding genes indicate that E. ilensis sp. nov. forms a distinct clade with E. balatonica Pop, 1943 supporting its status as an independent species and a basal evolutionary status. The discovery of the new species of E. ilensis sp. nov. not only enriches the species diversity of the genus Eisenia in China but also provides a crucial taxonomic foundation for subsequent research into the evolution and dispersal history of this genus in Eurasia.},
}

@article {pmid42500352,
year = {2026},
author = {Ampuero-Vega, J and Campos-Soto, R and Vargas, HA},
title = {A new genus of Gnorimoschemini (Lepidoptera, Gelechiidae, Gelechiinae) from the Atacama and Sechura deserts.},
journal = {ZooKeys},
volume = {1285},
number = {},
pages = {41-59},
pmid = {42500352},
issn = {1313-2989},
abstract = {Sexually dimorphic Gnorimoschemini moths (Lepidoptera, Gelechiidae, Gelechiinae) were reared from leaf mines collected on Tessaria absinthioides (Hook. & Arn.) DC. (Asteraceae) in the coastal Atacama Desert of northern Chile. Detailed examination revealed a combination of morphological characters not assignable to any known genus of the tribe, including 1) a scale tuft on the male hindwing, 2) an uncus with a triangular postero-medial projection, and 3) a U-shaped gnathos. COI sequences obtained from a male and a female showed minimal intraspecific divergence (0.6%), whereas interspecific divergences with representatives of other Gnorimoschemini genera ranged from 8.1% to 11.8%. Phylogenetic analyses based on COI sequences further confirmed the Atacama moths as a strongly supported, isolated clade, corroborating its morphological distinctiveness and supporting its recognition as a separate evolutionary lineage. The combined evidence justifies the establishment of Azaptilia azapensis Vargas, gen. nov. et sp. nov. Furthermore, based on the remarkable similarity in genitalia morphology, the Peruvian moth Scrobipalpula trichinaspis (Meyrick, 1917) from the Sechura Desert, originally described in Phthorimaea Meyrick, 1902, is also included in the new genus as Azaptilia trichinaspis (Meyrick, 1917), comb. nov. This discovery expands the known diversity of Gnorimoschemini in arid South American ecosystems of the Atacama and Sechura deserts and highlights the importance of integrating rearing, morphology, and DNA barcoding for uncovering hidden diversity in Neotropical Gelechiidae.},
}

@article {pmid42494839,
year = {2026},
author = {Zhang, C and Xing, Y and Zhong, Y and Yu, H},
title = {Huntsman spiders of the genus Sinopoda (Araneae, Sparassidae, Heteropodinae) from the Honghe Hani and Yi Autonomous Prefecture, southwestern China, with descriptions of two new species.},
journal = {ZooKeys},
volume = {1280},
number = {},
pages = {301-320},
pmid = {42494839},
issn = {1313-2989},
abstract = {Spiders of the genus Sinopoda Jäger, 1999 from Honghe Hani and Yi Autonomous Prefecture, Yunnan Province, China are studied. A total of four species are reported and illustrated of which two, Sinopoda honghe Yu & Zhong, sp. nov. and Sinopoda kuan Yu & Zhong, sp. nov., are described as new to science. The other two previously described species from this region: S. tengchongensis Fu & Zhu, 2008 and S. tumefacta Zhong, Jäger, Chen & Liu, 2019 are also illustrated. Detailed descriptions, diagnoses, illustrations and DNA barcodes of the two new species are given. A distribution map of these four species in Honghe is provided.},
}

@article {pmid42494981,
year = {2026},
author = {Wang, J and Li, Z and Chen, J and Li, H and Chen, F and Tan, L and Chen, X and Liu, S and Zhang, W and Shao, H},
title = {The development of single-cell lineage tracing technology and its application in immunotherapy.},
journal = {Molecular therapy. Advances},
volume = {34},
number = {3},
pages = {201802},
pmid = {42494981},
issn = {3117-387X},
abstract = {Immunotherapy stands as one of the most promising approaches in cancer treatment, with engineered T cell therapies, particularly chimeric antigen receptor T cell (CAR-T), leading the charge. However, relapse in some patients post-treatment suggests that research in this field remains incomplete. Tumor heterogeneity and the complexities of the immune microenvironment hinder a comprehensive understanding of the changes engineered T cells undergo once introduced into the human body. Single-cell lineage tracing (SCLT) technology facilitates the investigation of cellular development by monitoring the fate and differentiation of individual cells and their descendants within an organism. Employing methodologies such as CRISPR-based labeling and mitochondrial DNA tracking, SCLT allows for dynamic analysis of T cell clonal evolution, exhaustion mechanisms, and memory cell generation. This approach offers single-cell resolution data that contribute to resolving pertinent clinical challenges. This article provides a comprehensive review of recent developments and characteristics of the SCLT multi-omics approach. It elucidates the manner in which SCLT addresses the conventional constraints associated with spatiotemporal resolution and introduces a novel methodology for generating DNA barcodes to monitor CAR-T cells via CRISPR technology. These contributions offer valuable perspectives for the enhancement of cell therapy strategies.},
}

@article {pmid42495720,
year = {2026},
author = {Ralston, E and Haskayne, C},
title = {Cell line authentication: a commercial service provider perspective.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1843943},
pmid = {42495720},
issn = {2296-634X},
abstract = {Cell line misidentification and cross contamination continue to undermine research quality despite improved laboratory practices. Short Tandem Repeat (STR) profiling remains the primary method for human cell line authentication and is increasingly required by journals, funders, and regulatory bodies. Analysis of authentication data generated at NorthGene™ in 2024-2025 demonstrates that misidentification and contamination remain prevalent, with 4.7% of lines misidentified and 1.8% contaminated in 2024, and 2.4% misidentified with 1.6% contaminated in 2025. Primary cell lines present additional challenges, as none submitted during this period met ASN 0002 standards for full traceability, posing risks to reproducibility and downstream biological interpretation. Mixture analysis proved essential for resolving inconclusive STR results and identifying specific contaminants, although progress is hindered when reference STR profiles are not publicly available. While STR profiling is highly discriminatory for human cells, complementary methods-such as species specific PCR and CO1 barcoding-may be required to detect interspecies contamination or authenticate non human lines. Overall, these findings highlight the ongoing need for rigorous authentication workflows and complete traceability to ensure scientific integrity and prevent invalid research outcomes.},
}

@article {pmid42498665,
year = {2026},
author = {Magaña, Y and Wang, S and Torreblanca-Zanca, A and Wei, L and Castle, MJ},
title = {Small RNA barcodes for sensitive labeling of AAV transcripts.},
journal = {eNeuro},
volume = {},
number = {},
pages = {},
doi = {10.1523/ENEURO.0034-26.2026},
pmid = {42498665},
issn = {2373-2822},
abstract = {Adeno-associated virus (AAV) vectors are widely used for neuroscience research. Labeling AAV mRNA by in situ hybridization can track AAV transduction with high sensitivity and without the need for reporter genes. However, it is challenging to detect similar mRNA transcripts when multiple AAVs are injected into the same animal, or when a single AAV produces multiple distinct transcripts. To address these challenges, we developed methods for sensitive labeling of small barcodes on AAV mRNA at single-transcript resolution. These small RNA barcodes (ranging from 40 to 44 bases) can be easily added to any AAV vector genome. We provide detailed step-by-step protocols for sensitive and flexible labeling of barcoded AAV mRNA by BaseScope in situ hybridization. We validated these labeling methods in male and female mice, and in a female rhesus macaque. RNA barcoding can improve the reliability of multiplexed in vivo screening: by adding one barcode to half of the AAVs in a pooled library and a second barcode to the other half, barcode labeling can identify cells that receive multiple AAVs without the need for reporter proteins. This approach is also useful for intersectional experiments that combine multiple AAV vectors: multiple unique barcodes can track the spatial distribution of each AAV and can separately label transcripts from different AAV genome conformations, such as before or after Cre-Lox recombination. These new methods for sensitive multiplexed labeling of AAV mRNA will support greater rigor and reliability in neuroscience research.Significance Statement AAV vectors are commonly used in neuroscience research. Modern experimental designs are increasingly complex, often injecting two or more AAVs into different regions, or screening a library of many unique AAVs injected together into a single animal. In such complex experiments, it is challenging to track spatial distribution and rates of co-infection among multiple AAV vectors, especially if the AAVs do not carry reporter genes. To address these challenges, we developed small RNA barcodes and methods for highly sensitive labeling of barcoded AAV mRNA. These small barcodes can be easily added to any AAV genome without altering the experimental design, supporting the assessment of injection targeting and co-infection rates among multiple AAVs without the need for reporter genes.},
}

@article {pmid42498932,
year = {2026},
author = {Almutairi, ZM and Abd-Elgawad, ME},
title = {Integrated ecological, anatomical, phytochemical and genetic characterization of Peganum harmala L. along a soil salinity gradient in the Taif Region, Saudi Arabia.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42498932},
issn = {1471-2229},
support = {PSAU/2024/01/31574//Prince Sattam bin Abdulaziz University/ ; },
mesh = {Saudi Arabia ; *Peganum/genetics/anatomy & histology/chemistry ; *Salinity ; *Soil/chemistry ; Ecosystem ; Genetic Variation ; },
abstract = {BACKGROUND: Peganum harmala L. is a medicinal shrub that tolerates harsh, dry conditions, but the links between its habitat, structure, chemistry, and genetics are still not well understood. In this study, we investigated five geo‑referenced natural populations from the Taif region in Saudi Arabia, using an integrated ecological, anatomical, phytochemical, and molecular approach.

RESULTS: All soils samples were slightly alkaline (pH 7.61-7.79), and fell within the non-saline to slightly saline range based on electrical conductivity (EC) classifications, but they differed in salinity. Sites P1 (Al Ahlam Park) and P2 (C36) had lower EC values, while P3 (Ashayra), P4 (As Sayl al Kabir), and P5 (Al Sir) showed relatively higher EC values within this overall low salinity range. In all locations, P. harmala L. formed well-established, low, spreading to dense dome-shaped shrubs on sandy-stony substrates. Multivariate analysis of soil variables (pH, EC, CaCO₃, major anions and cations) set P3 apart from the other sites, and both clustering and principal component analysis (PCA) grouped P1, P2, P4, and P5 together, with P3 forming its own distinct cluster. Anatomically, most populations had stem cross sections with well-organized vascular cylinders. By contrast, stems from P3 displayed an irregular outline, a compact multilayered cortex, and scattered vascular strands with visibly reduced secondary xylem. Total alkaloid content ranged from 3.208 to 4.106%, with the highest values at P1 and P2 and the lowest at P3. Molecular analyses using SCoT markers (10 primers; 121 bands, 54 polymorphic) and IRAP markers (10 primers; 130 bands, 76 polymorphic) revealed moderate to high nuclear genetic diversity (expected heterozygosity up to 0.50; Shannon's index up to 0.69). Overall genetic similarity among populations was high, but their structure was non-random: populations 2, 4, and 5 consistently clustered together, whereas populations 1 and especially 3 were more divergent. Chloroplast barcodes (matK: PX089557; rpoC1: PV942406) from a representative voucher from Population 1 were consistent with its identification as P. harmala L. and clearly separated this sequence from those of related species in phylogenetic trees. In combination with morphological identification, this supports assignment of all sampled populations to P. harmala L.

CONCLUSIONS: Among the studied populations, P3 emerges as an ecologically and genetically distinct unit within P. harmala L. in the Taif region, characterized by its unique nuclear genetic profile, modified stem anatomy, and reduced total alkaloid content associated with higher soil salinity and altered major-ion composition. This integrative framework-combining soil characterization, quantitative anatomy, total alkaloids, SCoT/IRAP markers, and plastid barcodes illustrate how fine-scale edaphic heterogeneity is associated with anatomical, chemical, and genetic variation in this key desert medicinal shrub.},
}

Saudi Arabia
*Peganum/genetics/anatomy & histology/chemistry
*Salinity
*Soil/chemistry
Ecosystem
Genetic Variation

@article {pmid42489757,
year = {2026},
author = {Anguiano Constante, MA and Rodríguez, A},
title = {The Lycianthes plastome and its comparison with Capsicum (Capsiceae, Solanaceae).},
journal = {Genetica},
volume = {154},
number = {1},
pages = {},
pmid = {42489757},
issn = {1573-6857},
support = {855486/2020-000026-02NACF-19054//Secretaria de Ciencias, Humanidades, Tecnología e Inovación (SECIHTI)/ ; },
mesh = {Phylogeny ; *Capsicum/genetics/classification ; Evolution, Molecular ; *Solanaceae/genetics ; *Genome, Plastid ; *Genome, Chloroplast ; Sequence Analysis, DNA ; },
abstract = {Solanaceae is an important crop plant family and its plastomes have been extensively studied to understand evolution and breeding. Capsicum (chili peppers) includes five domesticated species and worldwide are important economic resources. Lycianthes is the third most species rich genus within the family. Capsicum and Lycianthes are closely related genera and form the Capsiceae. While plastomes are available in public databases for some species of Capsicum, no plastomes for Lycianthes have been published. We anticipate that the plastomes of Lycianthes and Capsicum will be similar. In addition, point sequence variation will generate robust phylogenetic hypotheses. We newly sequenced, assembled and annotated the plastomes of six species of Lycianthes to investigate their genomic characteristics. Also, we carried out comparative and phylogenetic analysis within Capsiceae. Lycianthes presented the typical circular quadripartite structure and organization. Plastomes range from 156,108 to 156,721 bp. All contained 133 genes, divided into 84 Coding DNA Sequence, four pseudogenes, 37 tRNAs and eight rRNAs. Plastomes of Capsiceae were highly conserved, were similar in size and showed the same structure and organization. Comparative analyses revealed that 17 genes made the Capsicum plastome longer than the plastome of Lycianthes. However, the variable regions did not match with the length of the genes. Based on plastome sequences, phylogeny recovered the monophyly of Capsiceae. Also, Capsicum and Lycianthes formed monophyletic genera and had a sister group relationship with each other. The plastome of Lycianthes and Capsicum were similar. Phylogenomics supported the monophyly of both genera and a sister group relationship.},
}

Phylogeny
*Capsicum/genetics/classification
Evolution, Molecular
*Solanaceae/genetics
*Genome, Plastid
*Genome, Chloroplast
Sequence Analysis, DNA

@article {pmid42490671,
year = {2026},
author = {Diekmann, I and Choi, YJ and Supali, T and Alfian, R and Destani, Y and Iskandar, E and Sugianto, N and Mutalip, MHA and Aziz, NAA and Ibrahim, K and Fischer, K and Mitreva, M and Fischer, PU},
title = {Diverse Onchocercidae from Malaysian cats and Indonesian macaques: Morphological and molecular analysis of individual microfilariae using mitochondrial genomes, 28S rRNA, and Wolbachia endosymbiont sequences.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {7},
pages = {e0014015},
doi = {10.1371/journal.pntd.0014015},
pmid = {42490671},
issn = {1935-2735},
abstract = {During an investigation of animals as reservoirs for the filarial parasite Brugia malayi, three molecularly undescribed filarial species were co-detected. Individual microfilariae (Mf) were isolated and analyzed from blood samples of crab-eating macaques (Macaca fascicularis) from Belitung, Indonesia, and from pet dogs and cats in Sabah, Malaysia. Among 163 macaques, 33 (20.2%) were positive for large Mf (mean length 498.9 µm) similar to Dirofilaria ('Belitung I'). One macaque was infected with small Mf (mean length 150.4 µm) ('Belitung II'), with a high density of 17,150 Mf/mL. In two cats co-infected with B. malayi, Mf of a Dirofilaria species ('Sabah') with an average length of 299.1 µm were detected. Morphometric analysis of Mf showed distinct differences between these three species and other Mf described in the area. Whole genome amplification and genome sequencing of 24 individual Mf enabled phylogenetic analysis of mitochondrial genomes, and analysis of specific mitochondrial and nuclear barcode regions. The three Mf groups formed distinct clusters and could not be identified by comparison with available reference sequence. Cluster 'Belitung I' from macaques formed a sister group to other characterized Dirofilaria. Cluster 'Belitung II' included bird filariae and primate filariae of the genus Mansonella as close relatives. The cluster 'Sabah' formed a monophyletic group with the zoonotic species Dirofilaria asiatica and Dirofilaria sp. 'Thailand'. DNA of Wolbachia endobacteria was detected in Mf of 'Belitung I' and 'Sabah', but not in 'Belitung II'. These findings highlight the limited understanding of filarial diversity in macaques and cats in Asia and underscore the need for a more comprehensive approach that combines morphological and molecular data to identify and assess the pathogenicity and zoonotic potential of these parasites.},
}

@article {pmid42491421,
year = {2026},
author = {Jin, YL and Bu, Y},
title = {Two new species of Symphylella (Symphyla, Scolopendrellidae) from North China, with an analysis of genetic divergence in Chinese species.},
journal = {ZooKeys},
volume = {1284},
number = {},
pages = {251-270},
pmid = {42491421},
issn = {1313-2989},
abstract = {Symphylans from Liaoning Province, the Inner Mongolia Autonomous Region, and Shanxi Province, North China, were investigated and studied for the first time. Two new species of the Symphylella isabellae group, S. hylophila sp. nov. and S. rotundata sp. nov., are identified and described. Symphylella hylophila sp. nov. is characterized by having blunt ends of the processes, long, subconical styli each with a blunt apex, and the absence of long, erect setae on the cerci. Symphylella rotundata sp. nov. is characterized by having noticeably roundish ends of the tergal processes, short, subconical styli each with a pointed apex, and long, erect setae on the outer and ventral sides of the cerci. These new species are carefully delimited from similar species. Morphological analyses were supported by DNA barcodes, which were used to analyse the genetic divergence of Chinese species of the genus Symphylella.},
}

@article {pmid42492119,
year = {2026},
author = {Cabrera, R and Zapata, S and Durango-Manrique, Y and López, L and Gómez, GF and Gutiérrez, LA},
title = {Molecular detection of Coxiella spp. and characterization of blood-feeding sources in tick species parasitizing domestic animals in cattle farms from Magdalena Medio, Colombia.},
journal = {Veterinary microbiology},
volume = {320},
number = {},
pages = {111156},
doi = {10.1016/j.vetmic.2026.111156},
pmid = {42492119},
issn = {1873-2542},
abstract = {Coxiella burnetii is a globally distributed zoonotic bacterium responsible for Q fever in humans, with domestic ruminants serving as primary reservoirs. In Colombia, while livestock production is a vital economic sector, the dynamics of C. burnetii circulation among ticks and domestic animal hosts remain poorly understood. This study aimed to identify C. burnetii in hosts and ticks from two cattle farms in the Magdalena Medio region. Ticks were collected directly from domestic animal hosts through physical inspections and the use of the dragging technique on pasture vegetation and identified via morphological keys and COI barcoding as Rhipicephalus microplus s.l., predominating on cattle, Dermacentor nitens on equines, and Rhipicephalus sanguineus s.l. on dogs. Blood-meal analysis using PCR-HRM and sequencing identified feeding sources in equines, bovines, and humans, with human DNA detected in all larval pools. Following tick characterization, Coxiella spp. were screened by qPCR targeting the IS1111 insertion sequence, revealing a frequency of 10.5% in domestic animal hosts and 1.36% in ticks. Finally, phylogenetic analysis of 16S rRNA and rpoB genes confirmed the coexistence of C. burnetii (Clade A) in hosts and ticks, alongside Coxiella-like endosymbionts (Clade C), primarily in R. microplus s.l. These findings reveal complex tick-host interactions and confirm the molecular circulation of Coxiella spp. in tropical livestock systems. The results underscore the need to use multigene markers to differentiate pathogens from endosymbionts and suggest a potential human exposure risk, highlighting the importance of One Health surveillance in these agroecosystems.},
}

@article {pmid42492875,
year = {2026},
author = {Rodrigues, BL and Pinto, IS and de Oliveira, AG and Moreno, ES and Baton, LA and Lopes, TA and Shimabukuro, PHF and Galati, EAB},
title = {Cryptic taxa in the morphospecies Bichromomyia flaviscutellata uncovered by expanded geographic sampling and COI DNA barcodes.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108250},
doi = {10.1016/j.actatropica.2026.108250},
pmid = {42492875},
issn = {1873-6254},
abstract = {The Neotropical sand fly species Bichromomyia flaviscutellata is widely distributed and the main vector of Leishmania amazonensis. Previous molecular studies suggested that it comprises at least two morphologically cryptic taxa, but sampling has remained geographically limited. In this study, we expanded specimen collection across 12 Brazilian municipalities spanning the Amazon, Cerrado, and Atlantic Forest biomes, generating 62 new sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and combining them with publicly available data. A phylogenetic gene tree, and distance- and coalescent-based delimitation methods, were used to evaluate lineage structure and assess potential species boundaries. Our results consistently revealed two deeply divergent and well‑supported mitochondrial lineages within B. flaviscutellata. One lineage (PS1) occurs across the Amazon basin, Cerrado, and an inland fragment of the western region of the Atlantic Forest, while the other (PS2) is restricted to the coastal Atlantic Forest. Additional internal structure was recovered within both lineages. Pairwise genetic distances were high between PS1 and PS2 (14%-15.7%) but remained comparatively low (< 5%) within each lineage. Other species included in the analysis, such as B. bicolor and B. olmeca, each formed a single, cohesive molecular cluster. The pronounced COI divergence observed here indicates long‑term isolation, but confirmation of these candidate species will require multilocus nuclear data. This study provides the most comprehensive molecular assessment of the B. flaviscutellata complex to date and highlights the need for integrative taxonomic approaches to formally evaluate species boundaries.},
}

@article {pmid42494632,
year = {2026},
author = {Koch, MA and Kiefer, C and Bergmann, E and Stein, RE and Barfuss, MHJ},
title = {The different routes of parallel evolution in epiarenic growth in a hyperarid desert environment.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1822909},
pmid = {42494632},
issn = {1664-462X},
abstract = {The Atacama Desert, one of the driest and oldest regions on Earth, represents an extreme environment that has driven remarkable adaptive evolution over millions of years. Within this setting, the genus Tillandsia comprises specialists capable of surviving at the dry limit of plant life. These species exhibit crassulacean acid metabolism (CAM), lack functional roots, and possess trichomes adapted for water and nutrient absorption. Of the more c. 750 known Tillandsia species, nine occur in the Chilean-Peruvian Atacama Desert, where they colonize bare sand surfaces (epiarenic growth) under hyperarid conditions without significant rainfall, relying solely on nocturnal fog for moisture. Despite their striking adaptations, the evolutionary mechanisms and timing underlying the emergence of epiarenic growth remain poorly understood. Here, we reconstructed a maximum-likelihood phylogeny based on 278 plastome sequences of Tillandsioideae and other Bromeliaceae subfamilies to study respective sister species relationships. Further, divergence time estimates for the origin of epiarenic Tillandsia were estimated using Bayesian inference in BEAST2. In addition, we analyzed variation in orthologous copies of the nuclear-encoded Agt1 gene to test for interspecific and interploidal gene flow among epiarenic taxa and their closest relatives. This gene has been previously established as a barcoding marker in bromeliads. The results indicate that epiarenic Tillandsia evolved multiple times independently from the Late Pliocene through the Pleistocene, consistent with a long-term hyperarid evolutionary arena promoting extreme adaptations. Moreover, evidence for frequent interspecific hybridization and gene flow suggests that hybridization may have also contributed to the long-term success of epiarenic Tillandsia species and is reflecting also the spatio-temporal dynamics of the Atacama's hyperarid landscapes during the Pleistocene.},
}

@article {pmid42479329,
year = {2026},
author = {Ascunce, MS and Booher, DB and Stoll, AC and San Juan, A and Lee, A and Porter, SD},
title = {First Records and Expanding Distribution of a Small Big-Headed Ant, Pheidole parva, in Florida, USA.},
journal = {Neotropical entomology},
volume = {55},
number = {1},
pages = {},
pmid = {42479329},
issn = {1678-8052},
support = {Imported Fire Ant//Agricultural Research Service/ ; Household Insects (IFAHI) Unit//Agricultural Research Service/ ; },
mesh = {Animals ; Florida ; *Ants/genetics ; *Animal Distribution ; },
abstract = {Pheidole parva Mayr (1865) is a small ubiquitous ant native to the Indomalayan region where it is considered a pest in healthcare facilities. This tramp ant was first reported outside its native range more than 100 years ago in the Seychelles Islands. Since then, it has been found in other areas of the Old World, where it was likely accidentally introduced via trading ships. In the 2000s, this ant was detected in Japan (2001), the Arabian Peninsula (2009), and recently in the Mediterranean island of Cyprus (2023) and Lebanon (2025). Here, we describe its first occurrence in North America, in the state of Florida where both Nearctic and Neotropical realms meet. Our findings are based on recent Pheidole parva specimens collected throughout the state, curated iNaturalist observations, Antweb data, and DNA barcoding based on the mitochondrial cytochrome oxidase subunit I (COI) gene. Among the 26 P. parva specimens analyzed from Florida, we found three different COI haplotypes. Two of them were also found in other introduced areas; however, one of the haplotypes has only been detected in a native population. The three haplotypes were distributed throughout the state with no clear geographical structure, consistent with multiple introductions and broad establishment of this non-native ant in Florida.},
}

Animals
Florida
*Ants/genetics
*Animal Distribution

@article {pmid42480010,
year = {2026},
author = {Urumarudappa, SKJ and Bommuluri, V and J, S and Mittal, AK and Faller, A and Lu, Z and Chang, P and Swanson, G},
title = {Authentication of Alpinia galanga extracts using DNA barcoding, HPTLC and HPLC analysis.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/14786419.2026.2704039},
pmid = {42480010},
issn = {1478-6427},
abstract = {Alpinia galanga (Linn.) Willd, commonly known as greater galangal, is a perennial rhizomatous plant of the Zingiberaceae family valued in Ayurveda and Traditional Chinese Medicine for its therapeutic properties. Rising demand in the nutraceutical sector requires reliable authentication methods. This study integrates DNA barcoding, HPTLC, and HPLC to authenticate A. galanga rhizomes and extracts. DNA was successfully extracted from all samples, and the rbcL and trnL-trnF regions amplified effectively, proving highly reliable for species-level identification. Complementary chemical analyses supported molecular findings. HPTLC fingerprinting showed consistent banding patterns across botanical reference material, rhizome, and extract samples, with a prominent RF 0.90 band serving as a major marker compound. HPLC profiling confirmed the presence of galangin in all samples, with retention time matching the reference standard. Together, molecular and chemical profiling provide a robust approach to authenticate A. galanga and ensure quality standards while reducing risks of adulteration in plant-based products.},
}

@article {pmid42482167,
year = {2026},
author = {Broft, M and Scheper, W and Schubert, M},
title = {pepitope facilitates TCR-neoantigen screen analysis in the R language.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag542},
pmid = {42482167},
issn = {1367-4811},
abstract = {MOTIVATION: Functional screening of patient-derived T cell receptor (TCR)-neoantigen pairs via co-culture experiments is a way to design personalised immunotherapy or to investigate its mechanism of action. Current computational toolkits can either generate and prioritise candidate epitopes from tumour variants or count barcodes in sequencing data. However, they lack modules to support experimental screening, such as sample demultiplexing, construct quality control, and downstream analysis. To bridge these gaps, we present pepitope, an R package that integrates minigene library generation, sequencing-based quality control (QC), and differential abundance analysis of co-culture screens into a single software package within the accessible R/Bioconductor ecosystem.

RESULTS: pepitope workflows include the extraction of mutant and reference peptides with customisable flanking regions from tumour variant calls using Bioconductor annotation resources; demultiplexing and barcode counting for construct QC; and negative-binomial-based differential testing built on DESeq2 to identify immunogenic epitopes in TCR co-culture assays. By remaining within R, pepitope lowers the barrier for lab-based biologists familiar with R and Bioconductor to perform end-to-end co-culture screen analyses without needing dedicated computational support.

AVAILABILITY: pepitope (R ≥ 4.5.0) is freely available on GitHub under the GPL-3.0 license, with detailed vignettes hosted at https://mschubert.github.io/pepitope/. Installation is facilitated via the remotes package in R.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42483197,
year = {2026},
author = {Ding, N and Sun, J and Zhu, A and Li, J and Sun, J and Yan, H and Ma, Y and He, X and Zhang, T and Yao, Q and Su, B},
title = {Proteomic profiling of single extracellular vesicles reveals association of CD31[+] EV subpopulation with immune dysregulation in people living with HIV.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1871641},
pmid = {42483197},
issn = {1664-3224},
mesh = {Humans ; *HIV Infections/immunology/metabolism ; *Extracellular Vesicles/metabolism/immunology ; *Proteomics/methods ; Female ; Male ; Adult ; Protein Interaction Maps ; Middle Aged ; },
abstract = {BACKGROUND: HIV remains globally prevalent, and the long-term complications experienced by people living with HIV (PLWH) have increased interest in the functional heterogeneity of extracellular vesicle (EV) subpopulations. Defining these EV subsets may help clarify HIV-associated immune dysregulation and inform future diagnostic and therapeutic strategies.

METHODS: Plasma samples were obtained from three PLWH (HIV[+] group) and three healthy controls (HC group). Single-EV surface membrane proteins were profiled using the proximity barcoding assay (PBA), and EV subpopulations were identified by FlowSOM clustering with t-SNE visualization. Functional enrichment analysis, protein-protein interaction (PPI) network analysis, and database-based annotation were used to infer putative subpopulation functions and cellular origins. Differentially expressed EV proteins (DEPs) were screened using limma, and ligand-receptor interaction networks were constructed with CellPhoneDB and cross-referenced with publicly available single-cell RNA sequencing data.

RESULTS: HIV infection did not appear to alter overall EV abundance but was associated with selective remodeling of EV heterogeneity and expansion of distinct EV subpopulations. CD31[+] EVs (cluster 2), inferred to be endothelial-derived, were markedly enriched in PLWH. Ligand-receptor analysis suggested that CD31[+] EVs may communicate with CD16[+] monocytes through F11R-ITGAL/ITGB2 and with plasmablasts through CD31-CD38 interactions; these interactions were associated with inflammatory, leukocyte transendothelial migration, and metabolic pathways. In addition, HIV-enriched B2M[+] EVs (clusters 3) and MUC16[+] EVs (clusters 9) showed predicted interactions with CD4[+] T cells and with CD8[+] effector memory T and NK cells, respectively, suggesting potential effects on reservoir-related and cytotoxicity-related programs.

CONCLUSIONS: These exploratory findings suggest that EV heterogeneity may encode cell-type-specific immune regulatory information in HIV infection and highlight CD31[+] EVs as a candidate EV subset associated with HIV-related immune dysregulation. Larger cohorts and functional validation are required before these EV populations can be considered therapeutic targets for HIV cure strategies.},
}

Humans
*HIV Infections/immunology/metabolism
*Extracellular Vesicles/metabolism/immunology
*Proteomics/methods
Female
Male
Adult
Protein Interaction Maps
Middle Aged