@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

@article {pmid42483311,
year = {2023},
author = {Ross, E and Cooper, J and O'Reilly, D and Maguire, A},
title = {Data Resource Profile: The Enhanced Prescribing Database (EPD) in Northern Ireland.},
journal = {International journal of population data science},
volume = {6},
number = {1},
pages = {3354},
pmid = {42483311},
issn = {2399-4908},
mesh = {Northern Ireland ; *Databases, Factual ; Humans ; *Drug Prescriptions/statistics & numerical data ; },
abstract = {INTRODUCTION: The Enhanced Prescribing Database (EPD) is a comprehensive electronic database capturing detailed information on all Health and Social Care Northern Ireland (HSCNI) prescriptions dispensed in community pharmacies across Northern Ireland (the publicly funded healthcare system in Northern Ireland, equivalent to the NHS elsewhere in the United Kingdom). Established in 2010 by the Health and Social Care Business Services Organisation (HSC BSO), the EPD provides a valuable resource for monitoring prescribing practices and supporting population-based research.

METHODS: When pharmacies in Northern Ireland submit dispensed prescriptions to the HSC BSO for reimbursement, these forms are scanned, and information is extracted from 2D barcodes. This data is initially stored in the Electronic Prescription and Eligibility System (EPES) for payment processing. The EPD is then created as a separate research database, derived from the EPES but tailored for research purposes. The inclusion of the unique Health and Care Number (HCN) facilitates linkage to other health and social care datasets within approved projects. Direct identifiers (including the HCN) are retained only within the secure environment for linkage, and are replaced with project-specific anonymous identifiers prior to researcher access.

RESULTS: The EPD is held within the Health and Social Care Honest Broker Service (HSC HBS), the Secure Data Environment for Health and Social Care research in Northern Ireland. The database captures prescribing data from January 2010 onwards and is updated monthly, with data available up to December 2025 at the time of manuscript preparation. The EPD contains information on over 44 million prescribed items annually, with detailed information on dispensed items, prescriber information, patient demographics and classification data. Data quality is high, with product codes populated for over 99% of records, HCNs populated for approximately 70-90% of records, and scan rates (the proportion of prescriptions for which patient identifiers are successfully captured) improving from 74.9% in 2018/19 to 91.1% in 2024/25.

CONCLUSION: Researchers can access de-identified data via the HSC HBS following approval from the Health and Social Care Data Access Committee (HSCDAC). The EPD supports a wide range of research, including drug utilisation studies, prescribing practice evaluations, and analyses that use prescribing data as proxy indicators of treated disease. Ongoing system enhancements, including Optical Character Recognition, support incremental improvements in patient information capture and linkage completeness.},
}

Northern Ireland
*Databases, Factual
Humans
*Drug Prescriptions/statistics & numerical data

@article {pmid42486041,
year = {2026},
author = {Zhang, Y and Yuan, Z and Lyu, L and Xu, Z and Feng, B and Zhou, Q and Fan, X and Wang, T},
title = {Comparative and Pan-Chloroplast Genome Reveals Molecular Markers, High Haplotype Diversity, and Geographic Structure in Medicinal Leymus Species (Triticeae, Poaceae).},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {159},
number = {},
pages = {158595},
doi = {10.1016/j.phymed.2026.158595},
pmid = {42486041},
issn = {1618-095X},
abstract = {BACKGROUND: The genus Leymus includes traditional medicinal species. A lack of comprehensive chloroplast genome analyses, coupled with morphological similarities, has impeded advances in Leymus species identification, molecular evolution, and phylogeny. Qinghai Province, the primary habitat of L. secalinus, requires characterization of its chloroplast genome variation for elucidating adaptive mechanisms.

PURPOSE: To elucidate the phylogenetic relationships and genomic features of Leymus chloroplasts, as well as the adaptive variation of Leymus secalinus populations in Qinghai Province.

METHODS: Chloroplast genomes of 28 Leymus secalinus and 2 Leymus flexus individuals from Qinghai were de novo sequenced and analyzed alongside 36 public accessions. Comparative genomic analyses revealed features and evolutionary patterns. We also constructed a L. secalinus pan-plastome atlas for genomic diversity analysis.

RESULT: Leymus chloroplast genomes exhibit a typical Poaceae quadripartite structure and lack ycf1, ycf2, and accD genes. Sequence variation is mainly concentrated in intergenic spacer regions, while coding regions are highly conserved. Phylogenetic analyses indicate that L. secalinus is most closely related to L. flexus. Highly variable regions (petA and trnL-UAA intron) partially resolve phylogenetic relationships, suggesting their potential utility as supplementary DNA barcodes for species identification. Pan-plastome analyses reveal weak phylogeographic structure across saline-alkaline habitats, suggesting that historical dispersal and lineage admixture have played a dominant role in shaping current chloroplast haplotype distributions.

CONCLUSION: Comparative analyses of Leymus chloroplast genomes provide insights into genome evolution and phylogenetic relationships. Pan-plastome analysis further indicates a highly conserved chloroplast genomic background across environmentally heterogeneous populations of L. secalinus.},
}

@article {pmid42486426,
year = {2026},
author = {Hoyos-López, RO and Toro-Cantillo, A and Fernández, N and Gallego-Gómez, JC},
title = {DNA barcoding reveals taxonomic gaps and cryptic diversity in mosquito vectors from arbovirus-active coastal ecosystems of Colombia.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108249},
doi = {10.1016/j.actatropica.2026.108249},
pmid = {42486426},
issn = {1873-6254},
abstract = {BACKGROUND: Mangrove-coastal ecosystems in the Colombian Caribbean combine high mosquito diversity, migratory birds, vertebrate reservoirs, and documented circulation of medically important arboviruses. Reliable vector identification in these systems is limited by morphological complexity and incomplete public barcode reference libraries.

METHODS: Adult mosquitoes collected in coastal rural localities of Córdoba department, Colombia, were morphologically identified and analyzed using COI DNA barcoding. A curated dataset of 181 quality-controlled COI sequences standardized to 696 alignment positions was generated after removal of exact duplicate records and sequences with internal stop codons. K2P distances and Neighbor-Joining trees were estimated in MEGA12. To address the limitations of distance-based inference, maximum-likelihood analysis was performed in IQ-TREE with ModelFinder, SH-aLRT, and ultrafast bootstrap support; Bayesian inference was performed in MrBayes; and maximum parsimony was used as a complementary topology check. Public BOLD searches were used as an independent reference-library check.

RESULTS: The dataset represented 15 mosquito taxa across medically and ecologically relevant genera. Mean intraspecific K2P distances ranged from 0.0000 to 0.0143, with the highest values in An. aquasalis and Ps. confinnis. Mean between-taxon K2P distances ranged from 0.0638 to 0.2542. IQ-TREE selected GTR+F+G4 as the best-fit model and recovered the principal barcode clusters observed in the NJ/K2P tree; Bayesian inference produced a broadly congruent topology with acceptable convergence diagnostics. Public BOLD searches supported several morphology-based identifications but returned genus-level, ambiguous, or discordant placements for difficult groups, especially Culex, Psorophora, Haemagogus, and Culex grupo Salinarius.

CONCLUSIONS: This expanded COI barcode dataset provides a molecular baseline for mosquito surveillance in arbovirus-active coastal ecosystems of Colombia. The results support the operational value of COI while showing that single-marker identifications must be interpreted cautiously in groups affected by incomplete reference libraries, species complexes, and unresolved mitochondrial structure.},
}

@article {pmid42487348,
year = {2026},
author = {Bae, J and Kim, Y and Choe, J and Hong, J and Lee, B and Hashiya, K and Bando, T and Sugiyama, H and Lee, S and Lee, JH and Jo, K},
title = {DOM: Dual Optical Mapping Integrating Sequence-Specific Barcodes and A/T Density Profiles.},
journal = {Small methods},
volume = {},
number = {},
pages = {e70883},
doi = {10.1002/smtd.70883},
pmid = {42487348},
issn = {2366-9608},
support = {SRFC-MA2101-07//Samsung Research Funding Center/ ; RS-2024-00441954//National Research Foundation of Korea/ ; RS-2025-00515166//National Research Foundation of Korea/ ; },
abstract = {Accurate single-molecule optical genome mapping remains challenging due to the limited information content of barcode-only or profile-only strategies. Here, we present Dual Optical Mapping (DOM), which integrates sequence-specific barcode markers with AT frequency-dependent intensity profiles on the same DNA molecules to enhance mapping accuracy. Conventional optical mapping approaches rely either on sequence-specific barcodes generated by restriction endonucleases, nicking enzymes, or methyltransferases, or on dense profile mapping using DNA-binding molecules. By combining these complementary sources of information within a unified dual-channel framework, DOM increases positional specificity and alignment confidence. As a model system, we applied DOM to the E. coli genome (4.6 Mbp), where the combined dual-channel scoring metric (cc_rg2) ranked 172 of 182 molecules (95%) at the correct genomic locus as the top match, while 179 of 182 molecules (98%) could be validated after quality-control review. We further extended DOM to the human genome through genome-wide cross-correlation scanning coupled with placement score ranking. This quantitative framework enables objective evaluation of alignment distinctiveness across the entire genome, demonstrating scalability to large and complex genomic contexts. These results establish DOM as a scalable dual-channel framework for high-accuracy single-molecule genome mapping across both bacterial and human genomes.},
}

@article {pmid42488589,
year = {2026},
author = {Annessi, M and Riccieri, A and Polidori, C and Mei, M and Di Giulio, A},
title = {Cleptoparasitic bees (Apoidea, Anthophila) in rural protected areas in Latium (Italy): a faunistic survey through an integrative taxonomic approach.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e193040},
pmid = {42488589},
issn = {1314-2828},
abstract = {BACKGROUND: Cleptoparasitic bees represent a poorly studied yet ecologically important component of wild bee communities, responding sensitively to environmental heterogeneity and reflecting local wild bee diversity. Despite representing approximately 13% of bee species globally, significant knowledge gaps remain regarding their species distribution, taxonomy, and conservation status, particularly within the Mediterranean region, which is recognized as a global hotspot for bee diversity.

NEW INFORMATION: This work provides a faunistic survey of cleptoparasitic bees collected in rural protected areas within the province of Rome (Latium, central Italy), employing an integrative taxonomic approach combining morphological identification and DNA barcoding (COI-5P gene). A total of 417 individuals belonging to 44 species from 10 genera and three families were collected. Five species are newly recorded for Latium. A total of 98 COI-5P sequences were generated and deposited in BOLD and GenBank, including the first COI-5P record for Nomada nausicaa Schmiedeknecht, 1882. The integrative approach proved particularly valuable for resolving challenging identifications and for highlighting some taxonomic issues - particularly within the genus Melecta - that clearly require further molecular and morphological studies. Our findings provide new distributional data on cleptoparasitic bees in central Italy and expand the availability of COI-5P sequences in public molecular databases.},
}

@article {pmid42489177,
year = {2026},
author = {Brooks, CM and DiBacco, C and McBride, MC and Krumhansl, KA},
title = {Dive surveys and eDNA detect contrasting macroalgal community composition in Nova Scotia, Canada.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70208},
pmid = {42489177},
issn = {1529-8817},
support = {//Fisheries and Oceans Canada/ ; },
abstract = {Morphological identification of macroalgae can be time-consuming and species may be difficult to observe, collect, or identify, preventing detailed study on the distribution and ecology of many species. The use of eDNA in species surveillance and biodiversity assessments has gained considerable traction in studying macroalgae, as it provides an opportunity for increased sampling efficiency and a reduced reliance on taxonomic expertise for morphological identification. However, it is crucial to understand how eDNA tools may bias results of species diversity and detection and how these biases differ from traditional morphological surveys. The present study compared species composition and detection rates of dive quadrat collections with a combination of morphological identification and DNA barcoding (i.e., traditional survey methods) to two types of eDNA tools: quantitative polymerase chain reaction (qPCR) using four species-specific qPCR assays and metabarcoding using two metabarcoding markers. Metabarcoding detected nearly two times more species than traditional surveys; however, species overlap was as low as 19.2%, and some large conspicuous and ecologically important macroalgae were not detected by metabarcoding. This result suggests that metabarcoding uncovers a host of taxa largely distinct from dive surveys. Metabarcoding and qPCR proved capable of detecting target species even at very low abundances, but both showed a high incidence of false negatives. Results presented here support a combined approach leveraging the considerable strengths of eDNA in concert with species validation and abundance metrics provided by tradtional surveys.},
}

@article {pmid42475732,
year = {2026},
author = {Insuk, C and MacDougall-Shackleton, H and Bertolo, S and Lightfoot, H and Humber, J and Xu, J},
title = {DNA Metabarcoding of Myotis lucifugus Guano Reveals Unexplored Arthropod Diversity and Diet Variability in Newfoundland.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2025-0082},
pmid = {42475732},
issn = {1480-3321},
abstract = {All bats in Newfoundland, Canada are insectivores. While the dietary insects of several bat species have been investigated elsewhere in Canada and North America, little is known about the insect prey of Newfoundland bats. Here we use DNA metabarcode sequencing of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to identify insect prey from Myotis lucifugus guano. Among 21 guano samples from six sites in Newfoundland, 346 amplicon sequence variants (ASVs) of arthropods were identified. Among these 346 ASVs, 343 and 330 have not been documented in the barcode of life database from Newfoundland and Canada, respectively. In addition, only 34 and 54 of the 346 ASVs were identified to 19 species and 24 genera respectively with high confidence. Overall, Trichoptera had the highest percentage of COI sequences while Coleoptera had the most ASVs. High arthropod variabilities were observed among guano samples from both within and among sites. In eastern Newfoundland, notable difference in prey arthropod compositions was observed between two sampling times. Together, our results show tremendous undiscovered arthropod diversity in Newfoundland and that bat guano DNA metabarcoding can be an effective tool to help reveal this biodiversity. The implications of this research to bat conservation were discussed.},
}

@article {pmid42475748,
year = {2026},
author = {Pantoja, JDSL and Corrêa, LDC and Díaz, XFG and Melo, NFAC and Hamoy, IG and Campos, PN and Durand, JD and Sá, A},
title = {DNA barcoding of the Amazon Continental Shelf ichthyoplankton: fish larvae assemblages inside and outside of the Amazon River plume.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2026-0015},
pmid = {42475748},
issn = {1480-3321},
abstract = {The Amazon River plume (ARP) impacts the Amazon Continental Shelf's (ACS) marine ecosystem, but its effect on fish larvae remains uninvestigated. To investigate the influence of the ARP on the ichthyoplankton community, MIDI Multinet net integrative tows were carried in the ACS (September 2021) and samples were identified and separated into morphotypes for molecular analysis. Morphological assessment of 343 fish larvae initially suggested 30 families, but subsequent DNA barcoding revealed a 42% discrepancy, highlighting the limitations of traditional taxonomy for larvae identification. Eighty-three fish larvae, representatives of identified morphotypes were successfully assigned to 58 BINs, including sequences new to global databases and possibly five new occurrences in the region. The assemblage displayed a heterogeneous mix of neritic, oceanic, and estuarine taxa. However, no clear pattern emerged between species life-history traits and their distribution across the plume-generated hydrographic habitats. Although species composition varied across the plume's influence gradient, our sampling design cannot identify the underlying environmental drivers, underscoring the need for broader seasonal and spatial surveys in the region. These findings reveal the complexity of the ACS ecosystem and demonstrate the necessity of integrating molecular tools to accurately characterize biodiversity gaps and support conservation strategies in this dynamic region.},
}

@article {pmid42478011,
year = {2026},
author = {Farzali, S and Saglam, N},
title = {COI mtDNA barcodes of freshwater leeches (Hirudinea) from Azerbaijan reveal lineage structure within taxa.},
journal = {Journal of genetics},
volume = {105},
number = {},
pages = {},
pmid = {42478011},
issn = {0973-7731},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Phylogeny ; *DNA, Mitochondrial/genetics ; Azerbaijan ; *Electron Transport Complex IV/genetics ; Fresh Water ; Genetic Variation ; },
abstract = {We present a COI-based assessment of freshwater leeches in Azerbaijan's Lankaran-Astara region. Between 2019 and 2021, we sampled 136 individuals from 33 wetlands across six districts and generated 15 new COI sequences, which were combined with curated GenBank records. Four species were confirmed in three families: Dina lineata (Erpobdellidae), Helobdella stagnalis (Glossiphoniidae), Hirudo orientalis (Hirudinidae), and Trocheta sp. (Erpobdellidae). Azerbaijani D. lineata populations occur as two distinct clades, one that includes an individual from Iraq (Lineage A) and one that includes an individual from Iran (Lineage B). These Asian lineages are separated from European D. lineata. An Azerbaijani Trocheta sp. specimen (FSM20) clusters with one from Iran on a distinct branch that is > 8% divergent from its closest congeners. We suggest this is likely a new species. Our results validate COI barcoding for resolving species boundaries in Caucasian leeches, and highlight the South Caucasus as a promising region for Trocheta diversity and discovery.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Phylogeny
*DNA, Mitochondrial/genetics
Azerbaijan
*Electron Transport Complex IV/genetics
Fresh Water
Genetic Variation

@article {pmid42472257,
year = {2026},
author = {Pérez-Del-Olmo, A and Kostadinova, A},
title = {DNA barcoding Diplostomum (Digenea: Diplostomidae) through the lens of taxonomy: Status and issues.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {10},
number = {},
pages = {100406},
pmid = {42472257},
issn = {2667-114X},
abstract = {Molecular barcoding is causing fundamental changes in our understanding of the species diversity in a large number of digenean families. Yet, after 16 years of barcoding, we are still far from reaching a global coverage and a clearer picture of the taxonomic diversity of Diplostomum, the most species-rich genus of the digenean family Diplostomidae, comprising important fish pathogens. Here, focusing on taxonomy, we provide an overview of the important developments during this period (2009-2025), an update of Diplostomum taxonomy and nomenclature for 49 species and species-level lineages barcoded to date, an assessment of the progress in several specific areas of current interest, such as species richness and taxonomic diversity, geographical distribution, life cycles, host specificity, and the status of barcode libraries, and identify problems with the use and interpretations of the new data gathered that may affect future work.},
}

@article {pmid42473110,
year = {2026},
author = {Madeira, FP and de Jesus, AC and Ribeiro, MAL and de Freitas, FHS and Lima, JD and Menezes, ALR and de Oliveira, J and da Rosa, JA and Santana, JKS and de Paiva, VF and Dos Reis, YV and Camargo, LMA and Alevi, KCC and Correia, JPSO and Galvão, C and de Oliveira Meneguetti, DU},
title = {Cavernicola pilosa Barber (Hemiptera, Reduviidae, Triatominae) infected by Trypanosoma cruzi marinkellei Baker et al. (Kinetoplastida, Trypanosomatidae): Household invasion and risk in the state of Acre, Western Brazilian Amazon.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70094},
pmid = {42473110},
issn = {1365-2915},
support = {//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; //Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; //Fundação de Amparo à Pesquisa do Estado do Acre/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {The genus Cavernicola belongs to the subfamily Triatominae, which includes insect vectors of Chagas disease. This study reports the occurrence of Cavernicola pilosa Barber infected with Trypanosoma cruzi marinkellei Baker et al. (Kinetoplastida: Trypanosomatidae) in the state of Acre, Brazil. The triatomine bug was collected inside a house by a resident of Cruzeiro do Sul, Acre. Specimen identification was based on the morphological characters described by Galvão (2014). Trypanosomatid identification was performed through DNA extraction from the abdominal contents of the specimen, followed by fluorescent fragment length barcoding and phylogenetic analyses using the V7-V8 region of the SSU rRNA and the gGAPDH gene. The insect was identified as a male Cavernicola pilosa infected with Trypanosoma cruzi marinkellei. This record increases the known number of triatomine species in the state of Acre from 11 to 12 and the number of genera from four to five. Furthermore, it represents the first documented occurrence of a Triatominae species infected with T. c. marinkellei in Acre, highlighting the need for further studies to elucidate the distribution, ecology and vectorial potential of C. pilosa in the region.},
}

@article {pmid42474104,
year = {2026},
author = {Zhang, C and Gao, Z and Wang, H and Zhou, W and Deng, Y and Yang, R and Chen, H and Chen, J and Zhu, S},
title = {Comparative plastome analyses and genomic resource development for five Neoporphyra haitanensis and two Neopyropia yezoensis cultivars based on genome skimming data.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70205},
pmid = {42474104},
issn = {1529-8817},
support = {2024S130//Ningbo Public Welfare Science and Technology Program Project/ ; 32373099//NSFC/ ; //Ningbo Yongjiang Talent Program/ ; 2021Z004//Major Scientific and Technological Project of Ningbo/ ; 2021Z103//Major Scientific and Technological Project of Ningbo/ ; //China Agriculture Research System of MOF and MARA/ ; 2021C02069-9//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural (Aquaculture) Varieties/ ; },
abstract = {Neoporphyra haitanensis and Neopyropia yezoensis are two economically important seaweeds in Asia, yet their germplasm identification is often hindered by high phenotypic plasticity and limited molecular resources. To address this, we utilized a genome skimming strategy on five No. haitanensis and two Ny. yezoensis cultivars to retrieve their plastome information (including whole plastome sequences, plastome-divergent hotspots, and plastome-derived SSRs) and to identify genome-wide polymorphic nuclear SSRs. The plastomes of No. haitanensis (201,110-201,310 bp) were markedly larger than those of Ny. yezoensis (191,974 bp), a difference largely driven by expansions in intergenic regions. Gene annotation identified 253 genes in No. haitanensis and 256 in Ny. yezoensis, with the latter uniquely containing two additional hypothetical ORFs (ORF33 and ORF35) and an extra rRNA gene (rrfB). Further comparative analysis revealed seven hypervariable regions (π > 0.1), five of which-apcE-tatC, psbW-trnR, psbX-accD, trnW-rpl11, and ycf32-rpl32-are intergenic spacers with strong potential as species-discriminatory barcodes. We also characterized 26-30 chloroplast-derived SSRs and identified notable interspecific variations in their repeat-type profiles. Importantly, we developed 230 and 505 high-quality polymorphic nuclear SSRs for No. haitanensis and Ny. yezoensis, respectively, predominantly trinucleotide repeats, offering a robust toolset for fine-scale genetic analyses. Phylogenetic reconstruction using 201 shared plastid protein-coding genes clearly separated the two species into distinct clades, supporting their independent evolutionary trajectories, and further revealed intraspecific genetic differentiation, particularly with the cultivar ZD-1 forming a distinct branch within No. haitanensis. This study provides comprehensive genomic resources-including complete plastomes, hypervariable regions, and polymorphic SSR markers-that will facilitate germplasm identification, phylogenetic studies, and molecular breeding in Porphyra sensu lato.},
}

@article {pmid42466118,
year = {2026},
author = {Chapuma, C and Bondwe, P and Singini, G and Chamanga, R and Nkosi, P and Ghobede, E and Maphosa, T},
title = {Potential of integrated national laboratory information management system in enhancing early HIV care for infants in Malawi: a report.},
journal = {BMJ innovations},
volume = {},
number = {},
pages = {},
pmid = {42466118},
issn = {2055-642X},
abstract = {BACKGROUND: Initiating and retaining HIV-exposed infants (HEI) on antiretroviral therapy (ART) before 12 weeks of age remains a pressing public health concern in Malawi and other sub-Saharan African countries. Despite its known benefits in reducing mortality and morbidity, challenges persist, including long turnaround times (TAT) for DNA-PCR results, negative caregiver perspectives, and healthcare-worker barriers. This report discusses the potential of integrating different data collection methods in laboratory information systems to reduce TAT between testing and ART initiation.

METHODS: To address delays in the Malawi National Laboratory Information Management System (NLIMS), we integrated NLIMS into the electronic medical records(EMRs). We conducted this activity between November 2022 and June 2023 at the Elizabeth Glaser Paediatric Aids Foundation (EGPAF) in Malawi.

RESULTS: The integrated NLIMS featured offline capabilities, barcode standardization, and efficient order pulling from previously independent workflows. Electronic transmission to EMRs improved the efficiency of transmitting test statuses online. The average TAT decreased by 65 days (from 77 to 12 days) during months with both lower and higher testing volumes ranging from 2,595 to 5,349 samples.

CONCLUSIONS: Integrating data collection workflows significantly reduced TAT, demonstrating a non-random variation and overall improvement. Future studies should explore algorithms, workflows, and modules that alert healthcare providers and caregivers of the critical therapeutic point before 12 weeks.},
}

@article {pmid42469622,
year = {2026},
author = {Odo, CV and Ojua, EO and Agbatutu, A and Onaebi, CN and Oyediran, OT and Egedigwe, UO and James, OV and Anyadike-Ezeonwumelu, MC and Ubochi, KC and Momoh, ME and Abu, NE},
title = {Molecular identification of some wild macrofungi from Southeastern Nigeria.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-026-01470-2},
pmid = {42469622},
issn = {2730-6844},
abstract = {Mushrooms are grossly under exploited and efforts to domesticate them are not yielding enough results as over 95% of mushrooms consumed in Africa and most parts of the world are still collected from the wild. However, the utility and commercialization of wild mushrooms has been hampered by incorrect morphological identifications. Molecular markers, including the internal transcribed spacer (ITS) region, have proven to be efficient in mushroom diversity studies. This research aimed to investigate the diversity of wild mushrooms indigenous to southeast Nigeria. Fifty (50) samples of wild growing mushrooms were collected using opportunistic sampling method in 5 states of the region. Zymo Research Quick-DNA Plant/Seed Miniprep kit was used for DNA extraction, the ITS region was amplified using PCR and subsequently sequenced with Sanger sequencing technology. BLASTn search in Genbank databases were conducted to determine the identity of the sampled mushrooms. Genomic DNA was successfully extracted and amplified, although with varying band quality. Forty-one (41) out of the 50 mushroom samples were successfully sequenced and identified. The identified mushroom species were classified into 11 families with family Polyporaceae (13), Agaricaceae (9), Omphatotaceae (7) and Ganodermataceae (4), topping the list. Trametes (7) and Lentinus (6) were the most abundant genera followed by Neonothopanus (5), and Ganoderma (4). Barcode marker (ITS region) was effective in identifying the wild mushrooms of Southeastern Nigeria.},
}

@article {pmid42470839,
year = {2026},
author = {Urbisz, AZ and Chajec, Ł and Yadav, S and Verma, A and Masłowska, M and Świątek, P},
title = {Insights into ovary micromorphology and oogenesis in Drawida pellucida earthworm (Moniligastridae).},
journal = {Micron (Oxford, England : 1993)},
volume = {207},
number = {},
pages = {104081},
doi = {10.1016/j.micron.2026.104081},
pmid = {42470839},
issn = {1878-4291},
abstract = {Moniligastrids are regarded as the most primitive group of earthworms; unlike Crassiclitellata, they lack a multilayered clitellum and produce yolky (mesolecithal) eggs, with some peculiarities in their reproductive systems not seen in other earthworms or Clitellata. While Moniligastridae have undergone classical morphological studies on reproductive organ localization and gross morphology, no reports detail ovary histology and ultrastructure. Here, using light and electron microscopy, histochemistry, and DNA barcoding, we analyzed Drawida pellucida from India to describe the ovary micromorphology and follow oogenesis. In the species studied, paired ovaries are feathery with multiple elongated lobes surrounding the intestine in segment XI. No ovarian chamber is present. Proximal lobe parts connect to the septum, housing oogonia and early meiotic cells (till diplotene), united into small germline cysts (≤10 cells). The cysts feature crassiclitellate-like architecture: a few cells interconnected by ring canals to a thin reticular cytophore. Distal regions contain growing oocytes appearing individual, lacking ring canals or cytophore. Notably, no nurse cells were observed, which is surprising as they occur in all studied clitellates to date. We propose to term these ovaries "Drawida" type due to substantial morphological and organizational differences from other earthworms. As oogenesis progresses, oocytes detach from ovarian lobes and gather in large, sac-shaped and irregularly thickened ovisacs, where they finalize yolk uptake. Oocytes are small (∼100 µm diameter), mesolecithal, rich in proteinaceous yolk and lipids. We also provide molecular markers for the studied species and compare the ovary/oogenesis with Crassiclitellata, aiding the debate on moniligastrid phylogeny.},
}

@article {pmid42472253,
year = {2026},
author = {Situmorang, T and Xhekaj, B and Unterköfler, MS and Schlamadinger, L and Sekulin, K and Hoxha, I and Obwaller, AG and Walochnik, J and Kniha, E and Muja-Bajraktari, N and Sherifi, K and Fuehrer, HP},
title = {Pathogen diversity in mosquitoes (Diptera: Culicidae) from the Republic of Kosovo: a two-year cross-sectional study.},
journal = {New microbes and new infections},
volume = {72},
number = {},
pages = {101806},
pmid = {42472253},
issn = {2052-2975},
abstract = {BACKGROUND: Mosquitoes (Diptera: Culicidae) are important vectors of human and animal pathogens. Balkan countries in the southeastern part of Europe exhibit a diverse mosquito fauna and can act as a crossway for both natural and anthropogenic introduction. Some countries however lack data on mosquito fauna distribution, diversity, and pathogen circulation.

METHODS: mosquitoes were trapped in all seven districts of Kosovo in July and August of both 2022 and 2023, then were investigated for the presence of pathogens using PCR-based methods. A total of 144 different locations were surveyed using up to three CDC miniature light traps. Individual trapped mosquitoes were morphologically identified, then pooled, and DNA/RNA was isolated. Identification was confirmed by cytochrome oxidase I (COI) barcoding, and PCR-based pathogen screening was performed, targeting the medically relevant Filarioidea, Plasmodium and trypanosomatid protozoans as well as arboviruses (West Nile, Dengue and Zika virus).

RESULTS: Altogether 6491 mosquitoes belonging to 18 species in six genera were trapped, identified, and screened in 1122 pools. Of 986 female pools, 21 pools (2.1%) tested positive for DNA of filarioid helminths (Dirofilaria immitis and D. repens), 52 pools (5.3%) tested positive for avian Plasmodium DNA, and 82 (8.3%) tested positive for trypanosomatid DNA.

CONCLUSION: This study thus presents the most extensive survey of mosquitoes and their parasites in Kosovo to date, providing data on the prevalence of the animal and human pathogens, Filarioidea, Plasmodium and Trypanosoma.},
}

@article {pmid42461315,
year = {2026},
author = {Al-Solami, HM and Al-Rashidi, HS and Shaher, FM and Alkuriji, MA and Munawar, K and Almutairi, MF and Alghamdi, AG and ALyahya, HS and Al-Farga, A and Fouad, MR and Mahyoub, JA},
title = {Molecular Characterization of Mosquito Species and Confirmation of First Record of Aedes aegypti in Buraydah City, Kingdom of Saudi Arabia.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {15303667261469036},
doi = {10.1177/15303667261469036},
pmid = {42461315},
issn = {1557-7759},
abstract = {Mosquitoes are a source of concern because they transmit many infectious diseases, including Zika virus, chikungunya, and malaria. Accurate and rapid identification of mosquitoes is essential for disease surveillance and control. Genetic diversity in mosquito species, resulting from adaptation to different environments, leads to many differences in morphological characteristics. Traditional identification methods relying on morphology can be time-consuming and unreliable. The study aimed to identify medically and veterinary significant adult mosquito species throughout 2021 in Buraydah City, Kingdom of Saudi Arabia (KSA). We collected adult mosquitoes using Black Hole light traps in the city. The mosquitoes were morphologically identified using traditional identification keys and characterized by using the mitochondrial cytochrome oxidase c subunit I (COI) barcode regions. Although the genetic sequences we discovered do not necessarily represent new records, they do represent species with a long history of evolutionary independence, at least among adult mosquito species in KSA, especially in Buraydah city. Both morphological and molecular data identified five mosquito species: Culex pipiens (Linnaeus, 1758), Cx. sitiens (Wiedemann, 1828), Aedes aegypti (Linnaeus, 1762), Ae. caspius (Pallas, 1771), and Anopheles dthali (Patton, 1905). These species correspond to those from Kenya, India, KSA, and Iran with genetic variation. Aedes aegypti was confirmed for the first time in Buraydah city. DNA barcoding is a useful tool that can overcome inefficiencies and difficulties and complement traditional taxonomy.},
}

@article {pmid42464363,
year = {2026},
author = {Daniel, IK and Kelly, MA and Ramos, RAN and Hakimi, H and Kattoor, JJ and Wilkes, RP and Sidouin, MK and Nare, RNB and Oaukou, PT and Saleh, MN and Haynes, E and Cleveland, CA and Yabsley, MJ and Garabed, R and Tritten, L and Verocai, GG},
title = {Vector-borne pathogen profiling and phylogeny of ticks infesting domestic dogs in Chad, Africa, using targeted next-generation sequencing and DNA barcoding.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07566-z},
pmid = {42464363},
issn = {1756-3305},
abstract = {BACKGROUND: Understanding the range of vectors and pathogen diversity in sub-Saharan Africa is crucial for efficient disease prevention and control efforts. Domestic dogs are susceptible to many vector-borne pathogens (VBPs) and serve as sentinels for several human pathogens. Yet, critical surveillance gaps in canine VBPs persist in Central Africa, where the tropical climate and pastoral agro-livelihoods create unique transmission risks.

METHODS: We conducted a cross-sectional survey from September to October 2021, collecting 4238 ticks from 1254 domestic dogs across 56 villages in Chad, Africa. All ticks were identified morphologically and/or by sequence analysis of 16S rDNA, 12S rDNA, and cytochrome c oxidase subunit I (COI) gene regions. A representative subset (n = 618) was subsequently screened for comprehensive, simultaneous detection of 21 VBPs using a targeted next-generation sequencing (tNGS) assay. Logistic regression models were used to assess associations between potential risk factors and pathogen detection.

RESULTS: Five tick species belonging to four genera were identified: Rhipicephalus linnaei (89.8%; 3805/4238), Rhipicephalus muhsamae (9.4%; 400/4238), Amblyomma variegatum (0.6%; 26/4238), Haemaphysalis leachi (0.1%; 4/4238), and Hyalomma truncatum (0.1%; 3/4238). Overall, 59.1% (365/618; 95% CI 55.1 - 62.9%) of the ticks were positive for at least one pathogen. We detected 14 pathogens, with the most prevalent being Hepatozoon canis (47.6%, n = 294/618), followed by Ehrlichia canis (8.4%, n = 52/618), Coxiella-like endosymbionts (5.3%, n = 33/618), Rickettsia spp. (4.7%, n = 29/618), Anaplasma platys (4.4%, n = 27/618), Anaplasma spp. (3.7%, n = 23/618), hemotropic Mycoplasma spp. (1.5%, n = 9/618), and Anaplasma phagocytophilum (1.1%, n = 7/618). Babesia caballi, Hepatozoon felis, Rickettsia conorii, and Rickettsia massiliae were each identified in < 1% of the ticks. The highest pathogen diversity was detected in R. linnaei, although R. muhsamae harbored the highest diversity of zoonotic Rickettsia species. Independent predictors for VBP infections included tick species for E. canis (P = 0.02) and H. canis (P = 0.001), and geographic region for E. canis (P = 0.01).

CONCLUSIONS/SIGNIFICANCE: This study provides a comprehensive molecular characterization of canine VBPs in ticks from Central Africa using deep sequencing. The high pathogen prevalence and diversity highlight the need for expanded surveillance and control strategies in Chad, including educating dog owners on ectoparasite prevention.},
}

@article {pmid42460795,
year = {2026},
author = {Romero Martínez, ML and Abreu, J and Queirós, JP and Xavier, JC and Hollyman, PR and Fitzcharles, E and Collins, MA},
title = {DNA barcoding reveals the presence of Whitson's grenadier, Macrourus whitsoni, in sub-Antarctic waters of South Georgia, Southern Ocean.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70577},
pmid = {42460795},
issn = {1095-8649},
support = {SFRH/BD/144320/2019//Universidade de Coimbra/ ; 2020.07291.BD//Universidade de Coimbra/ ; UIDB/04292/2020//MARE/ ; UIDP/04292/2020//MARE/ ; LA/P/0069/2020//Associate Laboratory ARNET/ ; UIDP/04004/2025//Centre for Functional Ecology - Science for the People & the Planet/ ; },
abstract = {Macrourid species constitute the main bycatch in Southern Ocean toothfish longline fisheries. We report the first confirmed record of Whitson's grenadier, Macrourus whitsoni, in the South Georgia toothfish fishery. Mitochondrial cox1 DNA barcoding confirmed its presence in bycatch samples collected around South Georgia and the northern South Sandwich Islands, with approximately 1% divergence from its congener, M. caml. Haplotype network analysis revealed a single dominant haplotype and two peripheral haplotypes, indicating a well-connected Southern Ocean stock. These findings highlight the need for accurate species-level identification to inform effective fisheries management.},
}

@article {pmid42456979,
year = {2026},
author = {Bullows, JE and Castro, CJ and Meade, C and Poston, K and Jorba, J},
title = {Performance comparison of rapid and native barcoding methods for Oxford Nanopore sequencing of Poliovirus Viral Protein 1 (VP1) amplicons.},
journal = {Journal of virological methods},
volume = {346},
number = {},
pages = {115436},
doi = {10.1016/j.jviromet.2026.115436},
pmid = {42456979},
issn = {1879-0984},
abstract = {Accurate and timely sequencing of poliovirus is critical for global eradication efforts, particularly for molecular epidemiology based on the typing region of the genome, viral protein 1 (VP1). While Oxford Nanopore Technologies (ONT) sequencing has expanded capabilities for poliovirus surveillance, the relative performance of different ONT library preparation methods, including ligation-based (Native Barcoding) and transposase-based (Rapid Barcoding) approaches, has not been systematically evaluated. In this study, we compared rapid barcoding and native barcoding workflows for sequencing VP1 amplicons from 17 type 2 poliovirus-positive samples, each processed in triplicate. Native barcoding generated significantly more sequencing output, producing approximately 2.3-fold greater total read yield than rapid barcoding, and demonstrated higher run-to-run reproducibility (R[2] = 0.979-0.998 vs. 0.847-0.929, respectively; p < 0.001). In addition, native barcoding generated 80% of the total yield achieved by rapid barcoding within approximately 7 h, whereas rapid barcoding required approximately 40 h to reach the same output. Despite these differences, both methods produced identical VP1 consensus sequences across all samples, with comparable read quality (median per-base Q-scores of approximately Q17-Q18). Rapid barcoding provided substantial practical advantages, reducing hands-on library preparation time (55 vs. 200 min) and per-sample cost ($12.82 vs. $16.54), while simplifying workflow and reducing technical complexity. These findings indicate that sequencing yield may not be a determinant of downstream analytical outcomes for poliovirus VP1 ONT sequencing. Rapid barcoding therefore represents a cost-effective and efficient approach for routine poliovirus surveillance, whereas native barcoding remains advantageous in applications requiring rapid data generation or maximal sequencing depth.},
}

@article {pmid42459740,
year = {2026},
author = {Tombers, N and Vasilița, C and Richling, I},
title = {Preserving Shell Integrity of Microgastropods With the Nondestructive HotSHOT DNA Extraction Method.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e74031},
pmid = {42459740},
issn = {2045-7758},
abstract = {Gastropods rank among the most species-rich animal classes, accounting for 5% (4-8) of all described animal species with about 1/3 of microgastropods (< 5 mm in size). DNA extraction from preserved microgastropods retracted into their shells is challenging because established methods usually damage the shell. This study tests the HotSHOT alkaline lysis method as a nondestructive protocol for small ethanol-preserved gastropods. Using a brief lysis step at high pH and temperature, we achieved effective DNA extraction suitable for COI barcode amplification while preserving shell integrity and fragile periostracal structures. High-quality full-length sequences were obtained from 76% of the samples, and 85% of the sequences were suitable for species identification. The remaining samples (15%) did not yield usable sequence data, possibly due to poor preservation, insufficient buffer access in tightly closed shells, or potential PCR problems. Specimens with fully closed opercula showed reduced success unless buffer access was facilitated. Our results show that HotSHOT is a fast and inexpensive method for DNA extraction that preserves shell vouchers, making it ideal for large-scale barcoding of retracted microgastropods and valuable when working with rare specimens. By its low cost and high speed, it has a high potential to accelerate species discovery and delimitation, diversity assessments and monitoring and thus support conservation.},
}

@article {pmid42459996,
year = {2026},
author = {Filippova, N and Bulyonkova, TM and Zvyagina, E and Ageev, D and Rudykina, E and Mingalimova, A},
title = {Cortinarius barcoding database of Western Siberia and adjacent areas.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e196734},
pmid = {42459996},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Cortinarius (Pers.) Grays. is a highly diverse and ecologically crucial group of ectomycorrhizal fungi in boreal forests. Despite a long history of mycological study in Russia, a comprehensive, molecularly validated inventory of its diversity in Western Siberia has been lacking. Global genetic resources are essential for modern fungal research, yet such a curated, regional dataset for this complex genus has not been previously available for this region.

NEW INFORMATION: This paper describes a curated database of 624 Cortinarius specimens from Western Siberia and adjacent regions, resulting in 624 high-quality ITS sequences. The dataset includes detailed collection metadata, morphological descriptions and photographic documentation, all standardised and linked to DNA sequence data originally managed in Specify 7. The sequences were processed through a rigorous bioinformatics pipeline with strict quality controls and assigned provisional taxonomy using a defined BLAST protocol against international reference databases. The complete dataset, including raw sequences, specimen data and collection images, has been deposited in international repositories (Global Biodiversity Information Facility (GBIF) (https://doi.org/10.15468/4v8km8), Sequence Reads Archive (SRA) and GenBank), providing a foundational resource for future taxonomic, phylogenetic and ecological studies on this key fungal genus in Western Siberia.},
}

@article {pmid42449954,
year = {2026},
author = {Almerekova, S and Yermagambetova, M and Turemuratova, S and Anuarbek, S and Yessimbekova, M and Sakuma, S and Turuspekov, Y},
title = {Chloroplast Genome Characterization, Comparative Analysis, and Phylogenetic Insights into Five Aegilops Species.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135680},
pmid = {42449954},
issn = {1422-0067},
support = {AP23490217//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {*Genome, Chloroplast ; *Phylogeny ; *Aegilops/genetics/classification ; Microsatellite Repeats ; Evolution, Molecular ; Sequence Analysis, DNA ; Base Composition ; },
abstract = {The genus Aegilops comprises important wild relatives of cultivated wheat and represents a valuable genetic resource for wheat improvement. In this study, the complete chloroplast genomes of five Aegilops species (Ae. crassa, Ae. cylindrica, Ae. juvenalis, Ae. tauschii, and Ae. triuncialis) collected from Kazakhstan and Uzbekistan were sequenced, assembled, and comparatively analyzed. The chloroplast genomes exhibited a conserved quadripartite structure consisting of a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IR) regions. Genome sizes ranged from 135,612 to 136,840 bp, with an identical GC content of 38% across all species. Comparative analyses revealed high structural conservation among chloroplast genomes, particularly within IR regions, whereas greater sequence divergence was observed in the non-coding regions of the LSC and SSC. Sliding-window analysis identified several highly polymorphic regions, including rpl32-trnL(UAG), ndhF-rpl32, trnC(GCA)-rpoA, psbA, and ndhD, which may serve as potential DNA barcodes and informative markers for phylogenetic studies. A total of 850 chloroplast simple sequence repeats (SSRs) were detected, predominantly A/T-rich mononucleotide repeats. Codon usage analysis demonstrated a conserved preference for A/U-ending codons across all species. Ka/Ks analysis indicated that most chloroplast protein-coding genes are under strong purifying selection, although relatively elevated evolutionary rates were detected in rpoA and ycf4. Phylogenetic analyses based on complete chloroplast genomes strongly supported sectional relationships within Aegilops and confirmed close maternal relationships among several species. Overall, this study provides chloroplast genome resources for Aegilops and contributes to understanding chloroplast genome evolution, phylogeny, and molecular marker development.},
}

*Genome, Chloroplast
*Phylogeny
*Aegilops/genetics/classification
Microsatellite Repeats
Evolution, Molecular
Sequence Analysis, DNA
Base Composition

@article {pmid42450087,
year = {2026},
author = {Li, H and Chu, X and Xiao, W and Jiang, J and Xia, R and Chen, M and Di, Y and Liu, Y and Liu, X},
title = {Forensic Species Identification: A Case Involving Trafficked Fish Maws and Shark Fins.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135813},
pmid = {42450087},
issn = {1422-0067},
support = {LJ2024051//Shanghai Leading Talent Program of Eastern Talent Plan/ ; GY2025T-1//Ministry of Finance of the People's Republic of China/ ; GY2024G-3//Ministry of Finance of the People's Republic of China/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Wildlife Trade ; Phylogeny ; *Sharks/genetics/classification ; *Fishes/genetics/classification ; *Animal Fins ; Endangered Species ; Electron Transport Complex IV/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Illegal wildlife trade and other forms of wildlife crime pose significant threats to global biodiversity. Accurate species identification of wildlife products is crucial for effectively combating illegal wildlife trade. In recent years, forensic species identification using molecular methods has gained increasing attention. Here, we report a case involving 1777 trafficked fish maws and 18,170 trafficked shark fins. We employed DNA barcoding for forensic species identification and a large-sample inference strategy for population estimation. A total of 325 samples (197 fish maws and 128 shark fins) were randomly selected for DNA testing based on their pre-classified morphological categories. Two DNA barcodes (COI and 16S) were used, and sequence alignment was conducted using the NCBI GenBank and BOLD systems. Phylogenetic analyses were performed based on sequences detected from the samples and reference sequences, with results consistent with the sequence alignment. Consequently, seven species were identified, four of which, corresponding to approximately 17,351 to 18,170 specimens, are listed in Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).},
}

Animals
*DNA Barcoding, Taxonomic/methods
Wildlife Trade
Phylogeny
*Sharks/genetics/classification
*Fishes/genetics/classification
*Animal Fins
Endangered Species
Electron Transport Complex IV/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid42455624,
year = {2026},
author = {Signorelli, T and Walker, M and Robertson, J and Quizon, K and Zhang, Y and Reimer, AR and Eagle, SHC},
title = {Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001738},
pmid = {42455624},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Benchmarking ; *DNA, Bacterial/isolation & purification/genetics ; Humans ; Microbiota/genetics ; Feces/microbiology ; Nanopores ; *DNA/isolation & purification ; },
abstract = {Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.},
}

*Metagenomics/methods
*Nanopore Sequencing/methods
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
Benchmarking
*DNA, Bacterial/isolation & purification/genetics
Humans
Microbiota/genetics
Feces/microbiology
Nanopores
*DNA/isolation & purification

@article {pmid42455889,
year = {2026},
author = {Wu, YC and Schwartz, D and Khalil, EA and Upadhye, A and Rehman, J and Lee, SS},
title = {NicheProt: Cell-type-resolved proteomics of tissue compartments.},
journal = {Science advances},
volume = {12},
number = {29},
pages = {eaee6237},
doi = {10.1126/sciadv.aee6237},
pmid = {42455889},
issn = {2375-2548},
mesh = {Animals ; *Proteomics/methods ; Mice ; *Dendritic Cells/metabolism ; Spleen/metabolism/cytology ; *Proteome ; Laser Capture Microdissection ; Mass Spectrometry ; },
abstract = {Spatial proteomics uncovers the molecular basis of cellular function in intact tissues. Laser capture microdissection coupled with mass spectrometry enables comprehensive proteomic profiling of selected tissue regions but typically does not support cell-type-specific proteomic analysis. We present NicheProt, a 3D optical microscopy-guided and photobleaching-mediated cell barcoding approach for isolating intact, specific cell types from defined microanatomical tissue compartments or niches. Using sequential bottom-up proteomic analysis, we defined two distinct phenotypes of CD11c[+] dendritic cells based on their spatial locations in the inflamed mouse spleen. These two compartment-specific dendritic cell populations were characterized by proteomic signatures differing in the levels of 54 proteins. This 3D tissue microscopy-guided method offers cell-type and microregion-resolved proteomic analysis, facilitating the proteomic discovery of previously unrecognized cell subtypes and their functional roles in distinct tissue compartments.},
}

Animals
*Proteomics/methods
Mice
*Dendritic Cells/metabolism
Spleen/metabolism/cytology
*Proteome
Laser Capture Microdissection
Mass Spectrometry

@article {pmid42445498,
year = {2026},
author = {Alouadi, Y and Hassen, B and Jaouani, I and Mraouna, R and Ben Souissi, J and El Bour, M},
title = {Marine biofilms as reservoirs of antimicrobial bacteria: molecular identification and functional characterization of epibiotic culturable communities from biofouling invertebrates in northern Tunisia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1802528},
pmid = {42445498},
issn = {1664-302X},
abstract = {Marine biofouling communities constitute a rich reservoir of microbial diversity and represent a promising source of bioactive metabolites. In this study, we investigated culturable epibiotic bacteria associated with fouling invertebrates from the Marina in northern Tunisia, with a focus on their enzymatic activities, antimicrobial potential, and antibiotic resistance profiles. A total of 52 bacterial isolates were recovered from 23 fouling invertebrate hosts and characterized using DNA barcoding and molecular identification. The epibiotic culturable bacterial community was dominated by members of the genera Vibrio, Photobacterium, Halomonas, and Pseudomonas. Enzymatic screening revealed a high hydrolytic potential, with DNase (71.2%), lipase (65.4%), and gelatinase (59.6%) being the most prevalent activities. Antimicrobial assays showed that a substantial proportion of isolates exhibited inhibitory activity against at least one pathogenic indicator strain, whereas antibiotic susceptibility testing revealed frequent resistance, particularly to fosfomycin and cefoxitin. Together, these findings highlight the dual nature of epibiotic culturable bacteria in the Marina in northern Tunisia, acting both as a reservoir of biotechnologically valuable antimicrobial producers and as potential carriers of antibiotic resistance, underscoring their ecological relevance and public health significance in Mediterranean coastal ecosystems.},
}

@article {pmid42445829,
year = {2026},
author = {Shi, Y and Lu, Y and Zhou, Y and Chen, R and Li, Z and Liu, H and Cao, J},
title = {Precision Nanomedicine for Renal Tubular Injury: From Passive Accumulation to Subcellular Targeting.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {616742},
pmid = {42445829},
issn = {1178-2013},
mesh = {Humans ; Animals ; *Nanomedicine/methods ; *Kidney Tubules/injuries/metabolism/drug effects ; Drug Delivery Systems ; *Precision Medicine/methods ; *Kidney Diseases/drug therapy/metabolism ; },
abstract = {Renal tubular epithelial cell injury is a central pathogenic feature of kidney diseases, yet precise therapeutic interventions remain elusive. Conventional nanomedicines relying on passive accumulation lack the specificity required to treat complex tubular pathologies. This review elucidates the evolution of renal nanotherapeutics from non-specific organ accumulation to active, biologically informed targeting. We examine strategies utilizing specific surface receptors and injury-associated microenvironmental signals to engineer ligand-directed and stimuli-responsive nanocarriers. Furthermore, we highlight biomimetic platforms, such as engineered extracellular vesicles. Crucially, to achieve the ultimate goal of precision intervention, we emphasize the necessity of subcellular targeting. With a primary focus on mitochondria, we delineate hierarchical delivery strategies designed to restore cellular bioenergetics and metabolic homeostasis. Finally, we provide a forward-looking perspective on overcoming translational barriers by integrating DNA barcoding and artificial intelligence to accelerate the discovery of clinically translatable, precision nanomedicines.},
}

Humans
Animals
*Nanomedicine/methods
*Kidney Tubules/injuries/metabolism/drug effects
Drug Delivery Systems
*Precision Medicine/methods
*Kidney Diseases/drug therapy/metabolism

@article {pmid42447203,
year = {2026},
author = {Caixeta, HC and Oliveira, C and Melo, MRS},
title = {Molecular diversity of deep-sea fishes (Actinopterygii: Teleostei) in the western South Atlantic: A high diversity and new findings revealed by DNA barcoding.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0347925},
doi = {10.1371/journal.pone.0347925},
pmid = {42447203},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Fishes/genetics/classification ; *Genetic Variation ; Atlantic Ocean ; *Biodiversity ; Phylogeny ; Brazil ; Electron Transport Complex IV/genetics ; Species Specificity ; },
abstract = {The deep sea hosts approximately 15% of all fish species, but the difficulty of sampling limits our knowledge, causing large gaps in geographic distribution, and many deep-sea fish groups still require taxonomic revisions. Herein, the deep-sea fishes collected in the southern Brazil, western South Atlantic, are studied through DNA barcoding resulting in a better understanding of the biodiversity and genetic diversity of the region. The samples were obtained during oceanographic cruises aboard the Brazilian R/V Alpha Crucis, focusing on the continental slope off southern Brazil at depths of 200-1,500 meters. A total of 170 sequences of actinopterygian fishes from 102 different species of 49 families and 19 orders were generated. The DNA barcoding identified 84 sequences at the species level, with the remaining being identified at least to the genus level. A high level of genetic divergence between species was observed, ranging from 3.9% to 36.7%. We provided the first COI sequences for 13 species that, to date, were not represented in databases. Among the species already represented in online databases with COI sequences, we expanded the geographic coverage of existing data. As a result, we increased representation for 16 species in the Atlantic, 26 species in the South Atlantic, and 28 species in the western South Atlantic. Our efforts revealed a diverse deep-sea fish fauna in the region, highlighting new occurrences and demonstrating a high genetic divergence between some taxa.},
}

Animals
*DNA Barcoding, Taxonomic
*Fishes/genetics/classification
*Genetic Variation
Atlantic Ocean
*Biodiversity
Phylogeny
Brazil
Electron Transport Complex IV/genetics
Species Specificity

@article {pmid42448786,
year = {2026},
author = {Filgueiras, CC and Kim, Y and Gluesenkamp, D and Willett, DS},
title = {Digital phenotyping accelerates soil biodiversity discovery.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61754-6},
pmid = {42448786},
issn = {2045-2322},
abstract = {Soils are among the most biodiverse ecosystems on the planet, home to staggering amounts of small organisms. Many of these organisms are not known to science. This biodiversity 'dark matter' remains largely unexplored because identifying small soil organisms requires either specialized taxonomic expertise or expensive molecular methods, creating a throughput bottleneck that restricts ecosystem-scale monitoring. To explore this dark matter, we developed a high-throughput digital phenotyping approach using multispectral flow cytometry to create digital 'fingerprints' of soil organisms. Analyzing 2318 organisms spanning nematodes, collembola, mites, and tardigrades, we show that these digital fingerprints distinguish taxonomic groups with high accuracy and capture phylogenetic signal that explains 91% of variance in DNA barcode relationships. Machine learning alignment enables us to assess genetic similarity based solely on digital fingerprints, allowing prediction of relationships without sequencing. Smart sampling strategies guided by these projections achieve 6-fold improvements in species discovery efficiency compared to traditional approaches, with advantages that compound as sampling increases. Our smart sampling approach has applications across domains and provides a scalable pathway for rapid biodiversity assessment with immediate applications in agriculture, conservation, and ecosystem monitoring.},
}

@article {pmid42448940,
year = {2026},
author = {Mussmann, SM and Saltzgiver, MJ and Diver, TA and Gilbert, EI and Farrington, MA and Schleicher, BJ},
title = {Semipermeable species boundaries permit gene flow but prevent a hybrid swarm among sympatric catostomids of a desert ecosystem.},
journal = {Heredity},
volume = {},
number = {},
pages = {},
pmid = {42448940},
issn = {1365-2540},
support = {R20PG00102//Bureau of Reclamation/ ; },
abstract = {Interspecific hybridization can reshape patterns of genetic variation and alter evolutionary trajectories, but the implications of naturally occurring hybridization for endangered species remain uncertain. Understanding how species boundaries are maintained or eroded in the presence of hybridization is therefore essential for managing endangered species in altered ecosystems. In the San Juan River, three native catostomids (bluehead sucker Catostomus discobolus, flannelmouth sucker C. latipinnis, and the endangered razorback sucker Xyrauchen texanus) form a hybridizing assemblage in an ecosystem transformed by anthropogenic disturbance. Despite annual reproduction, razorback sucker recruitment is exceptionally rare, whereas adult flannelmouth x razorback sucker hybrids are regularly encountered. We applied double digest restriction site-associated DNA sequencing and mitochondrial DNA barcoding to characterize hybridization dynamics and evaluate whether introgression threatens razorback sucker persistence. Analysis of 30,774 loci from 1128 individuals revealed that 98.8% of hybrids involved crosses between flannelmouth and razorback sucker. F1 (68.4%) and third-generation (28.4%) hybrids were most prevalent, while second-generation hybrids were rarely detected (3.2%). All second and third-generation hybrids resulted from backcrossing. Razorback sucker mitochondrial haplotypes occurred in 92.7% of hybrids, suggesting asymmetric mating or potential mitonuclear incompatibilities. Genomic cline analyses identified loci with non-neutral introgression patterns, including a large chromosomal region consistent with overdominance and others reflecting potential Dobzhanzky-Muller incompatibilities or genetic drift. These patterns, combined with a scarcity of later-generation intermediate hybrids, suggest that disruption of co-adapted gene complexes limits hybridization beyond the F1 generation. Although hybridization occurs regularly, introgression appears constrained, and formation of a hybrid swarm remains unlikely under current conditions.},
}

@article {pmid42437077,
year = {2026},
author = {Thomas-Cabianca, A and Jordaens, K and Buenaventura, E and Rytter-Jensen, A and Martínez-Sánchez, A and Goergen, G and Rojo, S and Cerretti, P and Pape, T},
title = {DNA barcoding of Afrotropical nose flies (Diptera, Calliphoridae, Rhiniinae): species identification, female-male morphotype association, and reference library development.},
journal = {ZooKeys},
volume = {1284},
number = {},
pages = {149-183},
pmid = {42437077},
issn = {1313-2989},
abstract = {DNA barcoding offers a practical approach to species identification, especially in morphologically complex taxa such as Rhiniinae (Diptera, Calliphoridae). The most extensive COI barcode dataset for the subfamily to date was assembled, combining 216 newly generated sequences with more than 1,150 publicly available records from BOLD Systems and GenBank, with emphasis on Afrotropical taxa. Distance-based analyses, Neighbour-Joining (NJ) and Maximum Likelihood (ML) clustering, were evaluated, as well as automated barcode clustering approaches (ABGD and ASAP), for identifying morphospecies within this group. These analyses recognized 79 putative Afrotropical species, with most morphospecies forming well-supported barcode clusters congruent with morphological identifications. Several lineages, however, including species of Fainia, Rhinia, Cosmina, Stomorhina, and Rhyncomya, displayed low interspecific COI divergence, indicating that COI alone offers limited resolution. Yet, NJ and ML clustering helped highlight problematic taxa and identify previously unrecognized lineages. Public data on BOLD Systems comprised 957 BINs identified to subfamily level. Integrating ML, ABGD, ASAP, and voucher-based assessment allowed the assignment of 749 unnamed BINs to 11 species names, 193 BINs to eight genus names within 24 morphospecies, 12 BINs remain as Rhiniinae, and three represent non-Rhiniinae. The analyses also allowed linking 31 Afrotropical female morphotypes to their conspecific male morphotypes. This study establishes the first quality-controlled COI reference library for Afrotropical Rhiniinae and provides a framework for future taxonomic, ecological, and molecular investigations.},
}

@article {pmid42439713,
year = {2026},
author = {Nisar, S and Jan, N and Hassan, I and Andleeb, L and Shabir, PA},
title = {Chemotypic diversity and neuroactive potential of Valeriana jatamansi Jones: a systematic review on phytochemistry, pharmacology and standardisation challenges.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/14786419.2026.2697332},
pmid = {42439713},
issn = {1478-6427},
abstract = {Valeriana jatamansi (Indian valerian), a vital but endangered Himalayan plant, exhibits extreme chemical heterogeneity that undermines its clinical reliability and current pharmacopoeial standards. This systematic review (1979-May 2026; 312 studies) delineates five distinct chemotypes (OPLS-DA > 92%) defined by compositional extremes of patchouli alcohol (0.4-63.7%), maaliol (2.9-53.8%), valepotriates (1.8-2.4% Dry Weight), bornyl esters (10-20%) or sesquiterpenes (50-80%), driving 15-35% batch bioactivity variability. Mechanistically, valepotriates positively modulate GABA_A receptors (EC50 3-10 μM), while 6-methylapigenin targets the benzodiazepine site (IC50 0.3 μM). A meta-analysis of 12 Randomized Controlled Trials (RCTs) (n > 1500) confirms clinically meaningful improvements in insomnia (PSQI Δ3.8 ± 1.2 > MCID) and anxiety (SMD = -0.72). Crucially, this chemical diversity is therapeutically exploitable. We propose a chemotype-directed multi-marker bioactivity index combined with DNA barcoding to reduce batch variability below 10%, addressing IUCN 'Vulnerable' status (40-70% population decline) and transforming a conservation crisis into a foundation for evidence-based, sustainable phytomedicine.},
}

@article {pmid42440792,
year = {2026},
author = {Kumano, S and Tanaka, K and Nojima, A},
title = {Use of the Peptide Barcode Method for Efficient Screening of mRNA Expression Control Sequence.},
journal = {Mass spectrometry (Tokyo, Japan)},
volume = {15},
number = {1},
pages = {A0196},
pmid = {42440792},
issn = {2187-137X},
abstract = {The precise control of specific protein expression in target cells remains a critical challenge for the advancement of messenger RNA (mRNA) therapeutics. While incorporating regulatory sequences, such as microRNA-responsive RNA switches, is a promising approach for cell-type-specific targeting, optimizing these sequences requires extensive and time-consuming screening using conventional evaluation methods. In this study, we applied a multiplexed evaluation methodology utilizing peptide barcodes coupled with liquid chromatography-mass spectrometry (LC-MS) to improve the screening and design efficiency of mRNA expression control sequences. We designed mRNAs equipped with cell-specific expression control sequences and fused unique peptide barcodes to the encoded target proteins. By comparing conventional individual transfections with simultaneous co-transfections, we demonstrated that our LC-MS-based method can successfully distinguish and quantify protein expression derived from individual mRNA candidates within a single mixed sample. The simultaneous evaluation using peptide barcodes yielded results equivalent to the individual evaluations but required a reduced number of samples. This multiplexed technology would accelerate the screening process for regulatory sequences and is expected to enhance the development of mRNA therapeutics with high targeting specificity.},
}

@article {pmid42441075,
year = {2026},
author = {Hamraoui, A and Onfroy, A and Sénamaud-Beaufort, C and Coulpier, F and Lemoine, S and Jourdren, L and Thomas-Chollier, M},
title = {A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag070},
pmid = {42441075},
issn = {2631-9268},
mesh = {*Computational Biology/methods ; *Single-Cell Analysis/methods ; Benchmarking ; *RNA-Seq/methods ; Single-Cell Gene Expression Analysis ; Gene Expression Profiling/methods ; Humans ; *Sequence Analysis, RNA/methods ; Alternative Splicing ; *Nanopore Sequencing/methods ; Spatial Transcriptomics ; Animals ; },
abstract = {Alternative splicing plays a crucial role in transcriptomic complexity, yet remains difficult to resolve at the single-cell level due to the limitations of short-read technologies. Coupling single-cell with long-read sequencing offers full-length transcript coverage, enabling more accurate isoform detection. Diverse computational tools tailored for single-cell and spatial long-read transcriptomics have been developed. To compare the effectiveness of these approaches, we generated paired short-read and Nanopore long-read single-cell datasets, tailored for benchmarking bioinformatics tools. We evaluated ten state-of-the-art methods, spanning four analytical dimensions: barcodes and unique molecular identifiers (UMI) detection, demultiplexing and UMI clustering, gene-level expression profiling, and isoform detection and quantification. Using real and simulated datasets across different protocols, sequencing depths and chemistries, we assessed the accuracy, robustness, and scalability of each tool. Our results revealed method-specific trade-offs, and highlight the importance of sequencing quality and UMI correction strategies. This benchmark provides a practical resource for optimizing isoform analysis and accurate gene expression profiling in single-cell and spatial transcriptomics using long-read sequencing. The workflow employed for benchmarking is designed to be reusable, thereby enabling method developers to compare their own approaches against the set of reference methods evaluated in this work.},
}

*Computational Biology/methods
*Single-Cell Analysis/methods
Benchmarking
*RNA-Seq/methods
Single-Cell Gene Expression Analysis
Gene Expression Profiling/methods
Humans
*Sequence Analysis, RNA/methods
Alternative Splicing
*Nanopore Sequencing/methods
Spatial Transcriptomics
Animals

@article {pmid42442603,
year = {2026},
author = {Gatzios, A and Stinckens, M and Verhoeven, A and Rombaut, M and De Win, D and Heymans, A and Loosen, A and Van Goethem, F and De Kock, J and Rodrigues, RM and Boeckmans, J and Vanhaecke, T},
title = {Human stem cell-derived hepatic cells recapitulate polygenic risk in MASLD development and highlight CD36 as a key mediator.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124587},
doi = {10.1016/j.lfs.2026.124587},
pmid = {42442603},
issn = {1879-0631},
abstract = {Several genetic variants have been identified that impact outcomes in patients with metabolic dysfunction-associated steatohepatitis (MASH), but cellular platforms to identify molecular targets for treatment remain scarce. This study aims to employ a polygenic risk score for hepatic fat content (PRS-HFC) in a human-based in vitro model to identify potential druggable targets related to a genetic risk for MASH. Ninety-two human skin-derived precursor (hSKP) cell lines were genotyped and classified according to their PRS-HFC. Per risk category, five cell lines were selected and differentiated to hepatic progenitor-like cells (hSKP-HPCs) before being exposed to MASH-related triggers or control medium. Lipid accumulation, fatty acid uptake, generation of oxidative stress, secretion of inflammatory mediators, and alterations of the transcriptome were assessed. Potential drug targets were modulated using siRNA. hSKP-HPCs displayed a positive correlation between lipid accumulation and PRS-HFC, both in the control and 'MASH' condition. hSKP-HPCs with high PRS-HFC exhibited increased secretion of interleukin 6 and enhanced fatty acid uptake. Bulk RNA barcoding and sequencing revealed distinct gene expression profiles depending on genetic predisposition and predicted increased CD36-signalling as potential upstream regulator thereof. Silencing of CD36 effectively reduced lipid accumulation in cultures with high PRS-HFC and attenuated expression of genes related to de novo lipogenesis, lipolysis and inflammation. hSKP-HPCs recapitulate the effect of the PRS-HFC on lipid accumulation and inflammation. CD36 appeared to at least partially mediate these effects, and its silencing further substantiated its role in conferring high genetic risk for MASH, highlighting CD36 as a potential therapeutic target for genetically-driven MASH. ABBREVIATIONS.},
}

@article {pmid42427407,
year = {2026},
author = {Sultana, E and Mamun, MSA},
title = {Toward point-of-care cancer diagnostics: gold nanoparticle-based colorimetric sensors.},
journal = {RSC advances},
volume = {},
number = {},
pages = {},
pmid = {42427407},
issn = {2046-2069},
abstract = {Nowadays, cancer has become one of the major causes of mortality all over the world, irrespective of age and gender. The early detection of cancer can markedly enhance patient survival outcomes. Cancer cells are analyzed by comparing the optimum concentration of different types of biomarkers, including alpha-fetoprotein (AFP), prostate-specific antigen (PSA), microRNA-21, and carcinoembryonic antigen (CEA), in biological samples. These biomarkers play a crucial role in the early detection, screening and treatment of cancer. Novel colorimetric assays based on modified AuNPs are discussed in this review, which have opened a new avenue for the facile, point-of-care diagnosis of cancer. Due to their unique characteristics such as surface plasmon resonance (SPR), AuNPs provide a selective, trustworthy and simple strategy to detect cancerous cells by visualizing a color change when used in colorimetry. The principles of the sensing methods (aggregation, anti-aggregation, etching, and enzyme-mimetic activity) are illustrated in this review. Besides, some portable devices, such as paper-based devices (PADs), barcodes, and lateral flow assays (LFTs), are mentioned, which have made this complicated detection process as convenient as a pregnancy strip test. However, these devices are primarily limited by their low sensitivity and inadequate capability for accurate quantitative analysis. This review highlights the progress of paper-based colorimetric sensing devices for the detection of cancers, such as breast cancer, prostate cancer, pancreatic cancer, and bladder cancer. Furthermore, we outline the key advantages of these devices and emphasize their major limitations. Finally, we have also mentioned some perspectives that may improve the sensitivity of these colorimetric devices as biosensors.},
}

@article {pmid42427866,
year = {2026},
author = {DeGolier, KR and DeVoe, S and Abushawish, MA and Prete, A and Fry, TJ and Scott-Browne, JP},
title = {Single-cell genomics links targeted functional manipulations to efficacy-associated chromatin signatures in CAR T cells.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {42427866},
issn = {2693-5015},
abstract = {Chimeric antigen receptor (CAR) T cells produce extraordinary remission rates in some hematologic tumors, results inconsistently replicated across malignancies and/or target antigens. Anti-tumor efficacy can be enhanced by modifying CAR architecture or T cell differentiation state. Pooled screening methods to identify effects of modifications are often restricted to in vitro readouts of abundance or transcriptome, limiting ability to interrogate biology and project long-term T cell fates. We use genetically-encoded barcodes to track the effects of diverse functional manipulations on pooled murine and human CAR T cell chromatin states using scATAC-seq. We report stable and transient transcription factor activities programmed by cytokine concentration during in vitro expansion and altered in vivo effector differentiation programs driven by modifications to CAR antigen binding domain construction. These data establish genetic barcoding to tie targeted functional manipulations to single CAR T cell chromatin profiles in vitro and in vivo, providing insights toward augmented therapeutic efficacy.},
}

@article {pmid42434932,
year = {2026},
author = {Sun, D and Sealy, D and Truong, D and Konforte, D},
title = {Automation of sample preparation workflow for trace elements testing by ICP-MS/MS.},
journal = {Clinical chemistry and laboratory medicine},
volume = {},
number = {},
pages = {},
pmid = {42434932},
issn = {1437-4331},
abstract = {OBJECTIVES: Inductively coupled plasma-mass spectrometry (ICP-MS) is a gold standard for testing trace elements. Despite its wide adoption in clinical laboratories, sample preparation workflows are typically manual and prone to environmental contamination. The objective of this study was to develop an automated sample preparation procedure for quantitation of zinc (Zn), copper (Cu) and selenium (Se) in serum by ICP-MS/MS.

METHODS: Revvity Janus G3 expanded liquid handling workstation was customized to: (1) scan barcodes on specimen collection (primary) tubes and sample preparation (secondary) tubes to verify sample matching; (2) add diluent containing internal standards to secondary tubes; (3) aliquot blanks, calibrators, quality controls and human serum samples from standard rack or primary tubes to secondary tubes. Zn, Cu and Se were quantified by a multiplex ICP-MS/MS method.

RESULTS: The linear regression results between the automated (y) and the manual (x) sample preparation methods were y=1.04x-0.14 (R[2]=0.999, n=264), y=1.04x-0.22 (R[2]=0.998, n=264), and y=1.03x+0.00 (R[2]=0.994, n=264) for Zn, Cu and Se, respectively. A blank batch test was performed to assess the risk of environmental contamination during automated pipetting. Other validation studies including calibration preparation verification, accuracy, precision, and stability of standards, all met the acceptable performance limits.

CONCLUSIONS: An automated sample preparation method was developed and validated for multiplex quantitation of Zn, Cu and Se in human serum using ICP-MS/MS. Since its implementation, we have observed quality improvements and hands-on time savings.},
}

@article {pmid42436282,
year = {2026},
author = {Wang, F and Wu, LL and Yang, GZ and Liu, DX and Zheng, LP},
title = {Comparative chloroplast genomes and phylogenetic analysis of the genus Stephania (Ranunculales: Menispermaceae): implications for molecular marker development.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61351-7},
pmid = {42436282},
issn = {2045-2322},
support = {202301AT070254//Yunnan Provincial Basic Research Project/ ; 202101AZ070001-056//Yunnan Provincial Science and Technology Department-Applied Basic Research Joint Special Funds of Chinese Medicine/ ; 31960103//National Natural Science Foundation of China/ ; },
abstract = {The genus Stephania is a member of the family Menispermaceae within the angiosperms, possesses remarkable species diversity across south of China. To elucidate phylogenetic relationships within the genus Stephania at the chloroplast genome level, we sequenced the complete chloroplast genomes of four Stephania species, namely Stephania longipes, Stephania lincangensis, Stephania longa, and Stephania herbacea, using a combination of second- and third-generation sequencing technologies. The complete chloroplast genomes of four Stephania species sequenced in this study exhibited a conserved quadripartite circular structure, with total lengths ranging from 157,727 bp to 158,138 bp. These genomes comprised 130 functional genes, with a Guanine-cytosine (GC) content ranging from 38.24% to 38.28%. Among these, protein-coding genes displayed a significant A/U preference at the third codon position. Repetitive sequence analysis detected a total of 31 to 43 long repeat sequences and 74 to 96 simple sequence repeats (SSRs), with A/T type mononucleotide repeats constituting the largest proportion. The complete chloroplast genomes of Stephania exhibited a high degree of conservation, with no significant large-scale gene rearrangements or inversions observed, and the boundaries are relatively stable. Nucleotide diversity (Pi) analysis showed that the shared intergenic regions generally exhibited higher nucleotide polymorphism than the shared coding regions, and nine highly variable regions could serve as candidate barcode regions for species identification in Stephania. DNA barcoding analysis showed that the trnK-UUU-matK region could be successfully amplified in all tested samples, and the phylogenetic tree based on this region was highly consistent with that inferred from complete chloroplast genomes, indicating its potential as a candidate DNA barcode for Stephania. Phylogenetic analysis of chloroplast genomes revealed that the genus Stephania formed a distinct monophyletic clade, with S. longipes and S. lincangensis closely related, while S. longa and S. herbacea clustered together in another lineage. The phylogenetic relationships in the genus Stephania reflect the division of subgenera, but do not reveal section division within the genus. It is indicated that inflorescence and fruit morphological characteristics in Stephania are useful for taxonomic identification but may provide limited phylogenetic signal. Additionally, Stephania japonica var. timoriensis and Stephania japonica var. discolor showed a certain degree of differentiation from typical Stephania japonica, suggesting that their taxonomic status warrants further evaluation.},
}

@article {pmid42425638,
year = {2026},
author = {Čadež, N and Košmerl, T},
title = {Microbial communities of artisanal ciders in Slovenia and their role in fermentation.},
journal = {Food microbiology},
volume = {140},
number = {},
pages = {105227},
doi = {10.1016/j.fm.2026.105227},
pmid = {42425638},
issn = {1095-9998},
mesh = {Fermentation ; Slovenia ; *Microbiota ; *Bacteria/isolation & purification/classification/genetics/metabolism ; *Yeasts/isolation & purification/classification/metabolism/genetics ; *Alcoholic Beverages/microbiology/analysis ; Malus/microbiology ; Food Microbiology ; },
abstract = {Traditional cider production relies on spontaneous fermentation driven by complex microbial communities. In this study, we investigated the microbial communities, chemical compositions, and functional interactions underlying artisanal cider production in Carinthia, a subalpine region of northern Slovenia. Samples of spontaneously fermented ciders and swabs from wooden cellar equipment were collected from 11 remote farms using traditional practices to identify potential microbial reservoirs. Yeasts and bacteria were isolated, enumerated, dereplicated, and identified using sequencing of barcoding regions. Chemical parameters, organic acids, and volatile phenols were quantified, and their associations with microbiota were assessed. Despite differences in farm elevation, apple varieties, and equipment, all ciders shared a stable, technologically relevant core microbiota consisting of pellicle-forming yeasts, a diverse Saccharomyces complex dominated by Saccharomyces uvarum, Brettanomyces species, lactic acid bacteria primarily represented by Oenococcus oeni, and acetic acid bacteria. The microbial profiles found on wooden equipment largely overlapped with those in the ciders, indicating that resident microbiota contribute to inoculation and product consistency. Controlled fermentation trials showed that S. uvarum drives alcoholic fermentation, and that O. oeni contributes to lactic acid production. Growth of O. oeni was enhanced by the presence of B. bruxellensis, suggesting metabolic interdependencies. Overall, this study highlights the importance of indigenous microbial communities in determining the composition and characteristics of traditional cider and provides a foundation for preserving and managing distinctive fermentations across regions.},
}

Fermentation
Slovenia
*Microbiota
*Bacteria/isolation & purification/classification/genetics/metabolism
*Yeasts/isolation & purification/classification/metabolism/genetics
*Alcoholic Beverages/microbiology/analysis
Malus/microbiology
Food Microbiology

@article {pmid42422546,
year = {2026},
author = {Sharkey, MJ and Mutanen, M and Baker, A and Brown, BV and Butcher, BA and Dowling, APG and Godfray, HCJ and Hallwachs, W and Hausmann, A and Hebert, PDN and Inclán, DJ and Janzen, DH and Kiljunen, N and Miller, SE and Oliveira, G and Packer, L and Quicke, DLJ and Skevington, JH and Steinke, D and Hernández Ugalde, JA and Vogler, AP and Hartop, E},
title = {Toward scalable species descriptions for dark taxa: the role of molecular data.},
journal = {ZooKeys},
volume = {1283},
number = {},
pages = {297-322},
pmid = {42422546},
issn = {1313-2989},
abstract = {Species descriptions remain the foundation of biodiversity science, but alpha taxonomy faces a twofold challenge: accelerating the pace of species discovery while ensuring that descriptions produce data that are usable, comparable, and reproducible. This is particularly acute for "dark taxa"-small, hyperdiverse, and morphologically challenging groups-for which morphology-based workflows alone often fail to deliver scalable and reliable identifications. As a result, most species remain undescribed, and many described species are difficult or impossible to identify. We argue that species descriptions must be integrative in a way that meets the practical requirements of modern taxonomy, including scalability, reliable identification, reproducibility, and applicability across life stages. At present, standardized molecular data in the form of DNA barcoding is the only approach that consistently satisfies these criteria. Emerging approaches based on robotics, imaging and artificial intelligence may eventually provide complementary frameworks, but currently lack the standardization and interoperability required for routine application at scale. In contrast, barcode data already enable high-throughput species delimitation, straightforward identification, and direct comparability across studies, supported by global reference libraries and standardized protocols. We therefore propose that DNA barcodes be treated as a baseline component of species descriptions for invertebrates. Standardizing molecular data in taxonomy will accelerate species discovery, improve reproducibility and stability, and ensure that newly described taxa remain accessible in an increasingly DNA-based research landscape.},
}

@article {pmid42423472,
year = {2026},
author = {Chu, L and Wang, H and Gao, H and Chen, S and Li, Z and Hao, Z and He, L and Han, D},
title = {Time Resolved DNA Barcodes for Information Encoding and Dynamic Encryption.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76492},
pmid = {42423472},
issn = {2198-3844},
support = {2021YFA0909400//National Key Research and Development Program of China/ ; //Yangtze River Delta Science and Technology Innovation Community Joint Basic Research Project/ ; 22225402//National Natural Science Foundation of China/ ; 22474127//National Natural Science Foundation of China/ ; 32341017//National Natural Science Foundation of China/ ; 2023SDYXS0002//Zhejiang Provincial Jianbing Lingyan Research and Development Project/ ; //Scientific Experiment Center from the Hangzhou Institute of Medicine (HIM) Chinese Academy of Sciences/ ; },
abstract = {The rapid expansion of the information era necessitates molecular information encoding systems that simultaneously offer high capacity and robust security. DNA, characterized by its ultra-high information density, outstanding chemical stability, and inherent programmability, stands out as a promising medium for molecular data storage. Nevertheless, traditional DNA sequence-based information encoding strategy remains intrinsically static, restricting real-time and dynamic manipulation of stored information, and thereby limiting its practical utility in adaptive data processing and dynamic encryption. To overcome these limitations, we present a programmable data encoding and dynamic encryption platform leveraging DNA Temporal Barcodes (DTBs). DTBs consist of DNA strands designed with distinct retention times during high-performance liquid chromatography (HPLC) separation. Through systematic programming of chemical modifications and DNA sequences, we constructed a versatile DTB library capable of encoding a broad diversity of information states. HPLC, while providing time-resolved readout for DTBs, also allows for their efficient recovery and subsequent reuse in information encoding. Notably, to further reinforce data security, we introduce a key-triggered DNA ligation mechanism that generates reconfigurable DTBs, facilitating dynamic encryption at the molecular level. This work establishes a versatile strategy for constructing programmable, high-capacity, and dynamically adaptable molecular information security systems.},
}

@article {pmid42420666,
year = {2026},
author = {Ounjai, S and Liu, H and Zhou, Z and Correia, MP and Creedy, TJ and Andújar, C and Arribas, P and Vogler, AP},
title = {Phylogenetic Authentication of Amplicon Sequence Variants in Single-Specimen Metabarcoding of Tropical Insects.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70178},
pmid = {42420666},
issn = {1755-0998},
support = {//Institute for the Promotion of Teaching Science and Technology/ ; //Biodiversity Initiative of the Natural History Museum/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods/standards ; *Phylogeny ; *Coleoptera/classification/genetics ; Tropical Climate ; *Metagenomics/methods/standards ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA ; Genetic Variation ; DNA, Mitochondrial/genetics ; },
abstract = {High-throughput sequencing (HTS) allows large-scale DNA barcoding of individually tagged specimens ('megabarcoding'), but deep amplicon sequencing produces a mixture of authentic mitochondrial sequences together with nuclear pseudogenes (NUMTs), environmental and cross-sample contaminants, and sequencing artefacts. Standard approaches relying on read clustering or dominant-read selection often fail to classify these types, leading to incorrect taxonomic identifications and species counts. We developed an authentication framework by integrating abundance filtering, phylogenetic placement and taxonomic congruence. The workflow was applied to 18,533 morphospecies of tropical beetles (Coleoptera) from multiple biogeographic regions, which were imaged for family-level identification, prior to individual Illumina barcoding. Sequencing yielded > 36 million reads and 64,544 unique ASVs, which were evaluated against a reference phylogeny of > 13,000 mitogenomes. Authentication succeeded for 86.5% of quality-passing specimens (15,901 ASVs). Non-authentic sequences were technical artefacts (58.0%), environmental contamination including prey DNA (14.2%), intra-individual variants (NUMTs, heteroplasmy; 11.3%) and cross-sample contamination (7.5%). Authentication success and the proportions of failure categories varied markedly across trap types, sampling campaigns, taxonomic groups and sequencing runs. We identified 930 confirmed NUMTs based on consistent co-occurrence patterns and phylogenetic proximity to authenticated haplotypes. Single-specimen HTS data contain substantial biological and technical complexity not resolved by standard filtering methods. Our pipeline-agnostic, phylogenetically informed authentication framework achieves robust recovery of validated barcodes while retaining informative secondary variants, improving the accuracy of molecular ASV data to a standard sufficient for inclusion in barcode reference databases and the phylogenetically informed DNA barcoding of tropical insects.},
}

Animals
*DNA Barcoding, Taxonomic/methods/standards
*Phylogeny
*Coleoptera/classification/genetics
Tropical Climate
*Metagenomics/methods/standards
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA
Genetic Variation
DNA, Mitochondrial/genetics

@article {pmid42422028,
year = {2026},
author = {Wang, X and Mu, K and Xu, C and Zhu, Z and Yang, X and Zhang, J},
title = {Enhanced DNA barcode datasets for Aristida grasses: new whole genome skimming data for the protected species Aristida triseta Keng integrated with public sequences.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {113043},
pmid = {42422028},
issn = {2352-3409},
abstract = {Aristida triseta Keng is a Class II national protected wild plant in China, possessing significant ecological and economic importance. In this study, the complete chloroplast genome of A. triseta was sequenced using the DNBSEQ-T7 platform. The chloroplast genome is a circular molecule with a total length of 138,428 bp, displaying the typical quadripartite structure found in Poaceae. It consists of a large single-copy (LSC) region of 80,413 bp, a small single-copy (SSC) region of 12,517 bp, and a pair of inverted repeat regions (IRa and IRb) of 22,749 bp each. A total of 133 genes were annotated, comprising 87 protein-coding genes (PCGs), 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Meanwhile, we screened and acquired sequence data for six core DNA barcode regions (rbcL, matK, ndhF, rpl16, trnL-trnF, and ITS) from the sequencing data. By integrating these sequences with publicly available Aristida sequences from public databases, we constructed six enhanced DNA barcode datasets for the genus Aristida. Similarity analysis using blastn and phylogenetic analyses showed that each barcode sequence of A. triseta efficiently matched homologous sequences from the genus Aristida, exhibiting heterogeneous phylogenetic signals. The six enhanced DNA barcode datasets enrich the genetic resources of Aristida, providing a foundation for molecular breeding, genetic diversity analysis, and phylogenetic research of A. triseta, while also serving as a useful resource for developing molecular markers for species discrimination and taxonomic studies within the genus Aristida.},
}

@article {pmid42417135,
year = {2026},
author = {Walker, WB and Neven, LG},
title = {eDNA analysis of yard waste samples reveals taxonomical diversity, sequence database limitations, and consistencies across sequencing platforms.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {4},
pages = {},
pmid = {42417135},
issn = {1536-2442},
support = {//Washington State Department of Agriculture Specialty Crops Block/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA, Environmental/analysis ; High-Throughput Nucleotide Sequencing/methods ; Biodiversity ; Sequence Analysis, DNA ; Insecta/genetics/classification ; Extrachromosomal DNA ; },
abstract = {Timely identification of biological species is often needed for various purposes, including economic reasons, and advances in DNA sequencing technologies have greatly augmented the ability to identify species through the application of DNA barcoding. One such method examines environmental DNA (eDNA) to sample the presence of organisms in an environment without necessarily having direct access to the whole organisms. In recent years, multiple high-throughput sequencing platforms have emerged, and there are differences in the efficiency, effectiveness, and economics across these platforms. In this report, we examine the application of two platforms, from PacBio and Oxford Nanopore Technologies, to sequence COI amplicons from nine barcoded yard waste samples that we previously studied for a different purpose. Here, we observed consistencies across the platforms in the identification of operational taxonomical units (OTUs) from broad swaths of life, most prominently including Bacteria, Amoebozoa, Fungi, Arthropoda, Nematoda, Spiralia, and Viridiplantae. Other taxonomical groupings were also tentatively identified. However, limitations in coverage of the diversity of COI sequences in the public databases rendered species-level identification impossible for many of the OTUs. Insect species were the best represented across all barcoded samples, and both sequencing platforms regarding percentage identity to the best BLAST hits in the databases. Following this, we took an in-depth look at the knowledge of the presence of highly matched species in the locality from where the eDNA samples were derived. Strengths and limitations of this approach in the analysis of eDNA are discussed.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*DNA, Environmental/analysis
High-Throughput Nucleotide Sequencing/methods
Biodiversity
Sequence Analysis, DNA
Insecta/genetics/classification
Extrachromosomal DNA

@article {pmid42417433,
year = {2026},
author = {Lu, JY and Bao, YJ and Feng, TZ and Lv, Q and Shi, YL and Wang, XD},
title = {Development and applications of epitaxial heterostructures based on organic nanowires.},
journal = {Chemical Society reviews},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5cs01277e},
pmid = {42417433},
issn = {1460-4744},
abstract = {One-dimensional organic single crystals offer a promising platform for miniaturized photonics, yet their single-component nanowire forms currently lack the functional complexity required for integrated devices. In this review, the systems discussed are described as multicomponent or hierarchical organic nanowire heterostructures with spatially controlled composition, interfaces, topology, and functions. We categorize hierarchical designs into axial, radial, and branch topologies, and discuss the critical roles of noncovalent interactions, lattice engineering, kinetic control, and supramolecular assembly in achieving precise spatial division and high-quality interfaces. We further summarize device-level demonstrations enabled by these heterostructures, including optical anti-counterfeiting, photonic barcoding, exciton cascade control, and logic-like signal processing. Finally, we identify predictive growth and high-density integration as key challenges, and outline strategies toward building programmable, highly integrated organic photonic chips from reproducible low-dimensional modules.},
}

@article {pmid42419401,
year = {2026},
author = {Huang, Q and Jing, X and Chen, G and Jiang, F and Huang, Y},
title = {Identification of biological raw materials in Chinese patent medicine Gejie Dingchuan Wan using high-throughput sequencing.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {122173},
doi = {10.1016/j.jep.2026.122173},
pmid = {42419401},
issn = {1872-7573},
abstract = {Gejie Dingchuan Wan (GDW), a classical prescription comprising fourteen ingredients, including twelve biological materials and two mineral components, is used to nourish yin, clear the lung, and relieve asthma and vulnerable to adulteration, yet a systematic molecular method for simultaneously authenticating all prescribed biological ingredients is lacking.

AIM OF THE STUDY: To optimize key technical steps, including DNA extraction and barcode selection, for mixed samples containing both animal- and plant-derived medicinal materials; and to establish an HTS-based method for identifying the raw medicinal materials in GDW.

MATERIALS AND METHODS: Total DNA was extracted from three reference and nine commercial GDW samples. An integrated DNA barcoding strategy (16S rRNA for animal-derived materials and ITS2 for plant-derived materials) combined with morphological identification, and all sequences were deposited in GenBank to establish a dedicated reference database. OTUs were assigned taxonomically against custom reference databases. Diversity indices and statistical analyses were calculated.

RESULTS: 41,918,610 high-quality reads were generated, yielding a total of 5,103 operational taxonomic units (OTUs), including 2,798 assigned to animal-derived materials and 2,305 assigned to plant-derived materials. Assessment of potential technical biases showed that all samples had coverage values exceeding 0.9995, while the rarefaction, Shannon-Wiener, and species accumulation curves all reached plateaus, indicating that the sequencing depth was sufficient to capture most of the species diversity. All twelve prescribed biological components were detected in both reference and commercial samples. Gecko was the dominant component, accounting for 50.5%-98.07% relative abundance, while Ophiopogonis Radix was rarely detectable in most samples, with relative abundance ranging from 0.001% to 0.003%. In addition to the prescribed ingredients, HTS also detected sequences corresponding to potential adulterants and contaminants, highlighting the utility of this approach for adulteration surveillance. These non-prescribed taxa included Calotes wangi (a known adulterant of Gecko), Astragalus membranaceus, Bothus robinsi, and various fungal species, including Aspergillus and Penicillium. Notably, some of these taxa were detected not only in commercial samples but also in self-prepared reference samples formulated from raw materials that had been previously authenticated by Sanger sequencing. While 16S rRNA and ITS2 were effective for verifying the identity of individual raw materials, HTS revealed a broader spectrum of DNA sequences present in the finished products, including both prescribed and non-prescribed taxa.

CONCLUSION: The integrated barcoding-HTS pipeline provides a sensitive framework for molecular profiling of complex Chinese patent medicines and highlights the need for empirically defined interpretive criteria before detections of non-prescribed sequences can be translated into regulatory or safety conclusions.},
}

@article {pmid42420376,
year = {2026},
author = {Harris, DJ and Roesch, MA and Vasconcelos, DS and Bernet, C and Rato, C},
title = {Metabarcoding assessment of the diet of an introduced continental lizard to an oceanic island reveals dietary niche conservatism.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59067-9},
pmid = {42420376},
issn = {2045-2322},
abstract = {Invasive species can have devastating effects when introduced into remote island ecosystems, and a fundamental aspect of this concerns the diet of these exotic taxa. Here, we employed a DNA metabarcoding approach to determine the diet of the lizard Agama picticauda on Réunion Island, where it was introduced in 1995. Two separate markers were used to identify dietary components: COI for animals and trnL for plants. The arthropod aspect was notably conservative, with the agama continuing to predominantly consume ants, as they do in their native range. A variety of other invertebrates were also preyed upon, the vast majority being introduced species. For plants, again a wide variety was detected, and while most could not be identified fully, it seems that agamas are deliberately consuming many species, rather than accidentally ingesting them along with targeted invertebrates. Agamas may play a role in seed dispersal of invasive plant species. We also detected some nematode groups, although with limited comparative sequences, these could not be identified to the species level. Several invertebrate records appear to be new for Réunion Island, highlighting how reptiles can be considered as excellent biodiversity samplers, with barcoding diet studies providing novel data on poorly known invertebrate groups. The minimal identification of endemic prey items may reflect the fact that agamas are still predominantly occupying anthropogenically disturbed parts of the island. Our study therefore provides baseline data that can be used to determine the impact of this introduced lizard as it spreads through the ecosystem.},
}

@article {pmid42408950,
year = {2026},
author = {Oh, JI and Ahn, NH and Lee, JY and Kim, SY and Jeong, JH and Song, YG and Cho, KH and Byun, AB},
title = {A new species and a new record of the genus Bucculatrix Zeller, 1839 (Lepidoptera: Bucculatricidae) from Korea.},
journal = {Zootaxa},
volume = {5750},
number = {1},
pages = {139-144},
doi = {10.11646/zootaxa.5750.1.9},
pmid = {42408950},
issn = {1175-5334},
mesh = {Animals ; Republic of Korea ; Female ; Male ; *Moths/classification/anatomy & histology/genetics/growth & development ; Animal Distribution ; Phylogeny ; Animal Structures/anatomy & histology/growth & development ; Organ Size ; Body Size ; DNA Barcoding, Taxonomic ; },
abstract = {In the present study, a new species, Bucculatrix bipuncticosta sp. nov. is described as new to science. Also, B. comporabile Seksjaeva, 1989, is reported for the first time from Korea. The external morphology and genital structures of them are described and illustrated in detail. In addition, mitochondrial COI DNA barcodes were extracted to analyze and compare the genetic information of Bucculatrix species recorded in Korea.},
}

Animals
Republic of Korea
Female
Male
*Moths/classification/anatomy & histology/genetics/growth & development
Animal Distribution
Phylogeny
Animal Structures/anatomy & histology/growth & development
Organ Size
Body Size
DNA Barcoding, Taxonomic

@article {pmid42408985,
year = {2026},
author = {Ding, YH and Li, GZ and Lu, JC and Zhang, F},
title = {New species of Homidia (Collembola: Entomobryidae) from Yunnan, China: morphology, DNA barcodes and first instar characteristics.},
journal = {Zootaxa},
volume = {5787},
number = {3},
pages = {551-571},
doi = {10.11646/zootaxa.5787.3.8},
pmid = {42408985},
issn = {1175-5334},
mesh = {Animals ; China ; *Arthropods/classification/anatomy & histology/genetics/growth & development ; DNA Barcoding, Taxonomic ; Female ; Male ; Phylogeny ; Organ Size ; Body Size ; Animal Structures/growth & development/anatomy & histology ; Animal Distribution ; },
abstract = {This study formally describes a new species of Homidia Börner from Yunnan, China. Homidia quadriporasp. nov. is distinctly characterized by its purple body pigmentation, a V-shaped unpigmented area on the head, a lighter purple patch in the middle on the posterior half of the forth abdominal segment, four M-series mac-chaetae on the head, four pseudopores on the coxae of the mid leg, and a mac-chaeta m5 on the first abdominal segment. Comparative morphological and molecular analyses (using COI sequences) with phenotypically similar Homidia species corroborate its distinctiveness and support its designation as a new species. Furthermore, this research offers a crucial description of its first instar characteristics, comparing them with adult features and early stages of other Homidia species to illustrate developmental changes and differences.},
}

Animals
China
*Arthropods/classification/anatomy & histology/genetics/growth & development
DNA Barcoding, Taxonomic
Female
Male
Phylogeny
Organ Size
Body Size
Animal Structures/growth & development/anatomy & histology
Animal Distribution

@article {pmid42409188,
year = {2026},
author = {Wang, J and Han, J and Pang, X},
title = {DNA mini-barcoding: An innovative solution for degraded DNA and its multidisciplinary application landscape.},
journal = {Biotechnology advances},
volume = {92},
number = {},
pages = {108976},
doi = {10.1016/j.biotechadv.2026.108976},
pmid = {42409188},
issn = {1873-1899},
abstract = {DNA mini-barcoding amplifies short DNA fragments, overcoming the inherent limitations of conventional barcoding that targets longer regions and frequently fails in highly degraded DNA. Capitalizing on its distinct advantages in analyzing highly fragmented and complex-matrix DNA, this technology has emerged as a robust approach across disciplines. This review synthesizes current advances and delineates its expanding application landscape. Specifically, it facilitates biological evidence tracing in forensic science, enables the identification of fossils and archaeological remains, and verifies food authenticity. Furthermore, the technology permits the precise detection of adulteration within the traditional Chinese medicine trade chain and allows for effective species identification from environmental samples for biomonitoring. Importantly, it also shows promise in biodiversity assessment and the regulation of wildlife trade, especially when integrated with complementary techniques for trace DNA detection. This review elucidates the technical principles, evaluates interdisciplinary progress, and provides methodological references. Future research should prioritize optimizing primers for extreme degradation, constructing comprehensive reference libraries, and integrating mini-barcoding with quantitative technologies to enhance diagnostic precision.},
}

@article {pmid42411808,
year = {2026},
author = {Cerqueira, FJ and da Silva, M and Haerter, CAG and Mariotto, S and Centofante, L and Feldberg, E and Filho, OM and Margarido, VP and Blanco, DR and Lui, RL},
title = {DNA barcoding uncovers two putative new species in Trachelyopterus (Siluriformes: Auchenipteridae).},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70540},
pmid = {42411808},
issn = {1095-8649},
support = {//Fundação Araucária de Apoio ao Desenvolvimento Científico e Tecnológico do Paraná (FAPPR)/ ; //Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; },
abstract = {Trachelyopterus is a cryptic genus within the Neotropical catfish family Auchenipteridae with a complex history of taxonomic revisions. Despite the notable morphological and genetic similarities among its species, some studies suggest that the genus harbours greater diversity than is currently recognized, including additional species yet to be formally described. One of the most widely used and effective approaches for investigating species delimitation and assessing biodiversity is DNA barcoding. The application of DNA barcoding has expanded considerably over the past decade, contributing significantly to the understanding of diversity across numerous groups of Neotropical fishes. Thus, in this study, we employed the DNA barcoding approach in both phenetic and phylogenetic contexts to investigate species diversity within the genus Trachelyopterus. Our sampling included four valid species previously identified based on morphology, collected from six hydrographic basins across the Neotropical region: Trachelyopterus galeatus, Trachelyopterus striatulus, Trachelyopterus porosus and Trachelyopterus coriaceus. Our results corroborate the validity of these four species and reveal two distinct lineages: one from the Araguaia River basin and another from the Pantanal in the Paraguay River basin, both of which may represent previously unrecognized species.},
}

@article {pmid42412770,
year = {2026},
author = {Nguyen, DT and Ho, LT},
title = {Correction: Leaf beetle diversity on a Southeast Asian continental island: Taxonomy, DNA barcoding, and preliminary evolutionary insights from Cat Ba Island, Vietnam.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353452},
doi = {10.1371/journal.pone.0353452},
pmid = {42412770},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0351706.].},
}

@article {pmid42416297,
year = {2026},
author = {Tian, L and Wu, J and Ren, T and Duan, M and Tang, S and Hou, R and Gu, W and Jiang, D and Yang, X},
title = {The first complete mitochondrial genome sequences of Neopsylla specialis dechingensis and Neopsylla stevensi sichuanyunnana, with an assessment of their phylogenetic placement.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1865746},
pmid = {42416297},
issn = {2297-1769},
abstract = {Fleas are common blood-sucking external parasites found on mammals; they serve as important vectors for various pathogenic microorganisms and pose a serious threat to human and animal health. Mitochondrial genomes have been widely used in studies such as DNA barcoding for species identification and phylogenetics. Therefore, in this study, we performed sequencing of Neopsylla specialis dechingensis and Neopsylla stevensi sichuanyunnana on the Illumina NovaSeq platform. Genome assembly and gene annotation were subsequently done to obtain their complete mitochondrial genomes. Besides the two newly sequenced specimens, sequence information of 35 extra flea taxa downloaded from the NCBI database was adopted for overall comparative evaluation. The results showed that a significant AT base bias was present in the mitochondrial sequences of all 37 flea species tested. The Ka/Ks values calculated for the 13 PCGs were all lower than 1, which indicates that these genes are subject to persistent purifying selection. The Pi values indicated that ATP8 exhibited the highest variability, while ND5 was the most conserved. Phylogenetic trees were built based on 13 PCGs of 37 species, with Boreus elegans assigned as the outgroup, and both trees share highly identical topological structures. Both N. s. dechingensis and N. s. sichuanyunnana were clustered within the family Ctenophthalmidae. Furthermore, both trees supported the monophyly of the family Pulicidae with auto-expanded support values and posterior probabilities of 100 and 1, respectively. As important disease vectors, fleas pose a substantial risk to both human and veterinary health. However, complete mitochondrial genome data for fleas are currently extremely limited. For this reason, ongoing expansion of the flea mitochondrial genome database is critical to advancing related research efforts.},
}

@article {pmid42408920,
year = {2026},
author = {Birindelli, JLO and Vieira, F and Garavello, JC},
title = {A new species of Leporinus (Characiformes: Anostomidae) from the rio Jequitinhonha, eastern Brazil.},
journal = {Zootaxa},
volume = {5750},
number = {4},
pages = {564-578},
doi = {10.11646/zootaxa.5750.4.6},
pmid = {42408920},
issn = {1175-5334},
mesh = {Animals ; Brazil ; *Characiformes/classification/anatomy & histology/genetics/growth & development ; Phylogeny ; Female ; Male ; Animal Structures/anatomy & histology/growth & development ; Body Size ; Animal Distribution ; Organ Size ; },
abstract = {A new species of Leporinus (Characiformes: Anostomidae) is described from tributaries of the upper rio Jequitinhonha basin, eastern Brazil, based on morphological and molecular evidence. The new species is distinguished from congeners by the unique combination of three premaxillary and four dentary teeth, 12 scale rows around the caudal peduncle, three large dark midlateral blotches on the body, and a conspicuous red spot on the posterior portion of the upper lip. It is further characterized by its reduced body size, with the largest known specimen reaching only 128.6 mm of standard length, an uncommon condition among anostomids. DNA barcoding analyses (COI) revealed genetic divergences ranging from 3.8% to 8.5% from its closest congeners (L. microphthalmus and L. amblyrhynchus) and consistently recovered all specimens of the new species as a distinct Molecular Operational Taxonomic Unit. Phylogenetic analyses placed the new species within the L. melanopleura clade, together with L. amblyrhynchus, L. melanopleura, L. melanopleurodes, and L. microphthalmus. The species is endemic to a restricted area of the rio Jequitinhonha basin, where its populations are likely severely fragmented and threatened by multiple anthropogenic impacts. The discovery of this small-sized anostomid adds to the growing evidence of high levels of endemism and conservation concerns in eastern Brazilian coastal drainages.},
}

Animals
Brazil
*Characiformes/classification/anatomy & histology/genetics/growth & development
Phylogeny
Female
Male
Animal Structures/anatomy & histology/growth & development
Body Size
Animal Distribution
Organ Size

@article {pmid42408924,
year = {2026},
author = {Ricafort, JA and Pelingen, AL and Fontanilla, IKC and Bae, YJ and Uy-Yabut, CJC},
title = {A new stonefly species Neoperla lamesae sp. nov. (Plecoptera: Perlidae) from Quezon City, Philippines, with associated life stages and notes on Neoperla recta Banks, 1913 taxonomy.},
journal = {Zootaxa},
volume = {5750},
number = {3},
pages = {353-370},
doi = {10.11646/zootaxa.5750.3.2},
pmid = {42408924},
issn = {1175-5334},
mesh = {Animals ; Male ; Philippines ; Female ; *Insecta/classification/anatomy & histology/growth & development/genetics ; Animal Distribution ; Animal Structures/growth & development/anatomy & histology ; Body Size ; Organ Size ; Life Cycle Stages ; },
abstract = {A new Plecoptera species Neoperla lamesae sp. nov. Ricafort & Uy-Yabut, 2025 is described and figured from La Mesa Watershed Reservation, Quezon City, Philippines. The description includes all the life stages from egg to adult, confirmed to be from the same species using DNA barcoding. The male adult penis closely resembles a locality morphotype of N. recta. The associated female adult is differentially diagnosed against the N. recta female lectotype by the vaginal sclerites and the polygonal chorion pattern of the egg. The COI data suggest species divergence of two N. recta male penis morphotypes, the Makiling and Imugin morphotypes. The observed COI divergence and previously documented penis variability of N. recta suggest a reevaluation of the species complex.},
}

Animals
Male
Philippines
Female
*Insecta/classification/anatomy & histology/growth & development/genetics
Animal Distribution
Animal Structures/growth & development/anatomy & histology
Body Size
Organ Size
Life Cycle Stages

@article {pmid42398352,
year = {2026},
author = {Rolland, N and Mounier, J and Cadoret, M and Girard, V and Perrin, G and Treguer, S and Cloarec, O and Van Long, NN and Fiabane, L and Deniel, F and Vasseur, V and Jany, JL},
title = {Diversity and source-tracking of spoilage molds in bakery products using MALDI-TOF MS and molecular approaches.},
journal = {International journal of food microbiology},
volume = {459},
number = {},
pages = {111924},
doi = {10.1016/j.ijfoodmicro.2026.111924},
pmid = {42398352},
issn = {1879-3460},
abstract = {Filamentous fungi are significant contributors to global food losses and waste including bakery products. In the baking industry, mold contamination often occurs at the post-baking stage due to exposure to ambient air. The aim of this study was to investigate fungal diversity and to track the environmental sources of spoilage molds in finished products in a French industrial bakery plant, using MALDI-TOF MS and molecular approaches including barcoding and genotyping of microsatellites using next-generation sequencing (SSR-seq). Furthermore, we evaluated MALDI-TOF MS as a rapid tool for the source-tracking of two spoilage molds, i.e., Cladosporium sphaerospermum and Penicillium brevicompactum. Samples from air, food contact surfaces, work clothes and cakes were collected once every four weeks for 42 weeks on 1-4 consecutive days at 2 times. Results showed that areas with uncontrolled air quality such as the pre-baking area, had higher fungal loads compared to air-controlled areas such as post-baking zones. Products not sprayed with ethanol showed significantly higher mold contamination frequency highlighting the importance of surface treatment in reducing spoilage. Cladosporium sphaerospermum and Penicillium brevicompactum, known for their xerophilic and airborne dispersal capabilities, were identified as the main product spoilers. SSR-seq provided insights into the genetic diversity of these species and showed that certain haplotypes, particularly originating from post-baking areas, were more frequently found on spoiled cakes suggesting repeated contamination events from persistent sources. Using both unsupervised and supervised approaches, we showed that there was a good agreement between MALDI-TOF MS and genotyping data analysis at the population level. This study provides new insights into the fungal ecology encountered in the bakery industry.},
}

@article {pmid42399051,
year = {2026},
author = {Goerdeler, F and Narimatsu, Y and Büll, C},
title = {Cell-based mucin arrays.},
journal = {Methods in enzymology},
volume = {732},
number = {},
pages = {177-218},
doi = {10.1016/bs.mie.2026.03.006},
pmid = {42399051},
issn = {1557-7988},
mesh = {Humans ; *Mucins/metabolism/chemistry/genetics/analysis ; Animals ; Polysaccharides/metabolism/chemistry ; HEK293 Cells ; CHO Cells ; Cricetulus ; Glycosylation ; *Protein Array Analysis/methods ; },
abstract = {The cell-based mucin array is a versatile platform for expressing and interrogating recombinant mucin reporter proteins with representative patterning and customizable O-glycan structures. The platform is based on glycoengineered mammalian cell lines (HEK293/CHO), in which the glycosylation machinery is genetically rewritten to enable controlled display of specific O-glycan core structures and terminal epitopes with defined sialylation, fucosylation, and sulfation. Uniquely, the platform presents glycans in their native protein context, enabling investigation of how O-glycan density, clustering, and multivalency influence interactions with mucins. A conceptual framework for recognition of such glycan-context cues is provided by the patterned arrangement of O-glycans within mucin O-glycodomains, often composed of tandem repeat (TR) sequences with distinct O-glycosites resembling molecular barcodes. Mucin reporters mimic the serine-, threonine-, and proline-rich domains of natural mucins and mucin-like proteins or they can be designed as artificial Glycocarriers with model O-glycan cluster motifs. Reporters expressed as membrane-bound forms for cell display or as secreted fusion proteins for production can be applied in diverse bioassays. They have been used to probe glycan/mucin binding by viral and microbial adhesins, as well as human Siglec immune receptors. Moreover, the platform provides defined substrates for functional analyses of mucin and O-glycodomain degradation by microbial O-glycopeptidases or mucinases, revealing information of substrate specificities, cleavage points, and catalytic mechanisms. This chapter describes how the cell-based mucin array can be used to dissect interactions with mucins by glycan- and mucin-binding receptors as well as mucinases. The platform overcomes limitations of contemporary technologies by enabling studies with mimics of natural mucins and O-glycodomains that preserve clustered and patterned O-glycan contexts.},
}

Humans
*Mucins/metabolism/chemistry/genetics/analysis
Animals
Polysaccharides/metabolism/chemistry
HEK293 Cells
CHO Cells
Cricetulus
Glycosylation
*Protein Array Analysis/methods

@article {pmid42399057,
year = {2026},
author = {Gupta, S and Lima, GM and Peng, C and Derda, R},
title = {Exploration of mucin-protein interactions using liquid glycan array.},
journal = {Methods in enzymology},
volume = {732},
number = {},
pages = {391-453},
doi = {10.1016/bs.mie.2026.05.003},
pmid = {42399057},
issn = {1557-7988},
mesh = {*Polysaccharides/chemistry/metabolism ; *Mucins/metabolism/chemistry ; Bacteriophage M13/genetics/metabolism/chemistry ; Protein Binding ; },
abstract = {M13 phage makes it possible to produce DNA-encoded display of any molecules stable in water by prospective DNA-barcoding. For example, chemical conjugation of a glycan to an M13 virion that contains a prospectively introduced DNA barcode in the M13 genome creates a DNA-barcoded glycophage. In this glycophage, there is a 1:1 correspondence between the DNA sequence inside the phage and the structure of the glycan displayed on the surface of the phage. The same construct simultaneously illustrates the concept of DNA-encoded multivalency because there is a one-to-one correspondence between the DNA barcode and the displayed density. In this chapter, we show that a collection of these DNA-barcoded multivalent glycophages, known as Liquid Glycan Array (LiGA), can measure the glycan-recognition profile of mucin-binding proteins. Using DNA-encoded multivalency, we make an intriguing observation that a simple ultra-dense display of D-galactose on M13 "looks like mucin" because it binds to the proteolytically inactive E447D mutant of mucinase StcE (StcE[E447D]). The binding is specific because StcE[E447D] does not bind to the ultra-high-density display of the enantiomer control, L-galactose, nor to the diastereomer controls (D-glucose and D-mannose).},
}

*Polysaccharides/chemistry/metabolism
*Mucins/metabolism/chemistry
Bacteriophage M13/genetics/metabolism/chemistry
Protein Binding

@article {pmid42400034,
year = {2026},
author = {Husin, NA and Low, VL and AbdulRahim, MHS and Abdullah Halim, MR and AbdulHalim, AA and Mohd-Redzuan, MAA and Jiliun, EA and Mohd Kharip Shah, AK and Makepeace, BL and Ya'cob, Z},
title = {Mitochondrial COI and 16S rDNA barcoding improve species delimitation of ixodid ticks in Peninsular Malaysia.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07546-3},
pmid = {42400034},
issn = {1756-3305},
support = {Sub-program MO002A-2021//Dana Langganan Sukuk Pakej Rangsangan Ekonomi Prihatin Rakyat (SUKUK PRIHATIN), Malaysia Ministry of Finance through the Ministry of Higher Education, Malaysia/ ; },
abstract = {BACKGROUND: Hard ticks (Acari: Ixodidae) are major vectors of zoonotic pathogens affecting humans and animals. Accurate species identification is essential for surveillance and disease risk assessment but is often hindered by morphological similarity and intraspecific variation. In Malaysia, tick studies have largely relied on morphology or single-gene barcoding, with limited taxonomic and geographic coverage.

METHODS: This study applied a multilocus mitochondrial approach using cytochrome c oxidase I (COI) and 16S ribosomal DNA (rDNA) to evaluate species boundaries among ixodid ticks from Peninsular Malaysia. Ticks were collected from wild and domestic hosts between 2022 and 2023. A total of 319 specimens representing 14 morphologically defined species were analysed using COI and 16S rDNA sequencing, with additional reference sequences retrieved from GenBank for comparative analyses. Phylogenetic reconstruction, barcode gap assessment, and four species delimitation methods (ASAP, ABGD, bPTP, and GMYC) were employed to assess genetic divergence and identification accuracy.

RESULTS: Molecular analyses were largely congruent with morphological identification. Distance-based delimitation methods (ASAP and ABGD) recovered operational taxonomic units (OTUs) largely consistent with morphologically defined species, whereas tree-based approaches (bPTP and GMYC) inferred substantially higher numbers of OTUs, reflecting sensitivity to intraspecific mitochondrial structuring. These additional subdivisions are interpreted conservatively as population-level genetic differentiation rather than evidence of distinct species. Clear barcode gaps were observed for COI and the concatenated COI + 16S rDNA datasets, whereas partial overlap occurred with 16S rDNA alone. COI demonstrated the highest and most consistent performance for routine species identification, while concatenated datasets improved phylogenetic resolution but reduced assignment clarity under strict barcoding criteria.

CONCLUSIONS: Overall, COI remains the most effective mitochondrial marker for routine species identification of ixodid ticks in Peninsular Malaysia. These findings highlight the value of integrative approaches combining morphology and molecular data to strengthen tick taxonomy and support surveillance of tick-borne pathogens in the region.},
}

@article {pmid42402011,
year = {2026},
author = {Liu, Q and Ma, N and Tang, W and Chen, Q and Tang, D and Zeng, C and Wang, X and Xi, H},
title = {Application of Cell-Free DNA Barcode-Enabled Single-Molecule Test for Non-Invasive Prenatal Testing of α-Thalassemia and β-Thalassemia.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e70298},
doi = {10.1002/jcla.70298},
pmid = {42402011},
issn = {1098-2825},
support = {2025YFC2708200//National Key Research and Development Program of China/ ; 2026JJ81843//Natural Science Foundation of Hunan Province/ ; 2019SK1010//Major Science and Technology Special Project for Collaborative Prevention and Control of Birth Defects in Hunan Province/ ; },
abstract = {PURPOSE: To assess the feasibility of using the cell-free DNA barcode-enabled single-molecule test (cfBEST) for non-invasive prenatal testing (NIPT) of α-thalassemia and β-thalassemia.

METHODS: Seventy two thalassemia carrier families participated in the study. The cfBEST method was employed to identify thalassemia genotypes in fetal cell-free DNA extracted from maternal plasma, targeting four α-thalassemia gene mutations and 13 common β-thalassemia gene mutations. Validation was conducted using gap-PCR and PCR-RDB through invasive prenatal diagnosis. All prenatal diagnosis results were later confirmed for accuracy.

RESULTS: cfBEST successfully identified 94.6% (88/93) of fetal alleles, achieving a sensitivity of 94% (95% CI, 83.45%-98.75%) and a specificity of 95.35% (95% CI, 84.19%-99.43%). All prenatal diagnosis results were followed up, and the follow-up findings were consistent with the prenatal diagnosis results.

CONCLUSION: The findings indicate that cfBEST is a reliable, precise, simple, and cost-efficient method suitable for non-invasive prenatal testing of α-thalassemia and β-thalassemia.},
}