@article {pmid40787725,
year = {2025},
author = {Puillandre, N and Zuccon, D and Abdelkrim, J and Lemarcis, T and Ratti, C and Van Weddingen, M and Zaharias, P and Farhat, S},
title = {The CODEX Approach: High-Throughput Sequencing of the Cox-1 Barcode Fragment in Neogastropods (Mollusca, Gastropoda).},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70031},
doi = {10.1111/1755-0998.70031},
pmid = {40787725},
issn = {1755-0998},
support = {865101//H2020 European Research Council/ ; },
abstract = {DNA barcoding traditionally relies on Sanger sequencing but faces limitations with degraded samples. High-throughput sequencing (HTS) offers a cost-effective alternative, enabling rapid barcode generation for extensive datasets. The advantage of HTS is its ability to employ multiplexing strategies, allowing thousands of samples to be processed simultaneously in a single sequencing run. This study presents the CODEX approach, a double-indexed HTS method designed to sequence overlapping cox-1 barcode fragments, suitable for samples with degraded DNA. The approach was applied to neogastropods, a diverse lineage of marine molluscs, using specimens (both recently collected and relatively older) from the Muséum national d'Histoire naturelle (MNHN) collections. The pipeline was used to process 15,076 samples, yielding 10,905 cleaned and assembled sequences, achieving a success rate of 72.33%. The CODEX method demonstrated advantages over Sanger sequencing by enabling the recovery of barcodes from samples previously deemed unsuitable, with significantly reduced costs (€0.5 per sequence vs. €4.5). Notably, DNA quality and sequencing success were strongly correlated with collection date, emphasising the impact of preservation methods and storage conditions. Sequencing success rates varied among families but were not correlated with phylogenetic relationships or specimen size, indicating the robustness of the primers designed for neogastropods. This study highlights the efficiency of the CODEX approach for large-scale DNA barcoding projects, especially when handling degraded samples. The CODEX pipeline and associated resources are publicly accessible, offering a scalable solution for molecular systematics and beyond.},
}

@article {pmid40787158,
year = {2025},
author = {Juhász, A and Makaula, P and Cunningham, LJ and Archer, J and Cowlishaw, R and Jones, S and LaCourse, JE and Kayuni, SA and Musaya, J and Stothard, JR},
title = {Notes on the threadworm Strongyloides fuelleborni (Nematoda: Strongyloididae) in vervet monkeys (Chlorocebus pygerythrus) and zoonotic strongyloidiasis in southern Malawi.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {28},
number = {},
pages = {101121},
pmid = {40787158},
issn = {2213-2244},
abstract = {We sought to ascertain whether zoonotic strongyloidiasis occurred in vervet monkeys (Chlorocebus pygerythrus), a non-human primate (NHP) species becoming increasingly common in Southern Malawi. Faecal collection took place in four locations: Nyala Park, a private wildlife reserve adjacent to a sugarcane plantation in Chikwawa District, and three public locations, each near tourist lodges in Mangochi District. Our sampling took place during July 2023, when 32 faecal samples were inspected with parasitological methods. After faecal culture, threadworm larvae were noted in both districts that were confirmed by molecular identification methods as Strongyloides fuelleborni, a first report for Malawi. Given the close spatial proximity of vervets with people, our findings affirm prior disease surveillance concerns of local zoonotic potential. We therefore encourage future targeted helminthological surveys for better local monitoring of strongyloidiasis in NHPs and people.},
}

@article {pmid40785988,
year = {2025},
author = {Neuhaus, J and de Wilt, ME and Rossel, S and Brix, S and Etter, RJ and Jennings, RM and Linse, K and Martínez Arbizu, P and Schwentner, M and Peters, J},
title = {High Connectivity at Abyssal Depths: Genomic and Proteomic Insights Into Population Structure of the Pan-Atlantic Deep-Sea Bivalve Ledella ultima (E. A. Smith, 1885).},
journal = {Ecology and evolution},
volume = {15},
number = {8},
pages = {e71903},
pmid = {40785988},
issn = {2045-7758},
abstract = {Phylogeographic analyses have advanced our understanding of evolutionary processes in the deep sea, yet patterns of genetic variation and population divergence at abyssal depths remain poorly understood. The bivalve Ledella ultima is one of the most abundant protobranchs in the abyssal Atlantic, making it a valuable model organism for studying phylogeographic patterns and population connectivity. However, evidence for sex-specific heteroplasmic mtDNA challenges the assessment of genetic structure using mitochondrial markers alone. To address this, we used mtDNA (COI, 16S), single-nucleotide polymorphisms (SNPs) from 2b-RAD, and proteomic profiles to examine the population structure of L. ultima across seven Atlantic basins spanning over 10,000 km in latitude. Five mitochondrial lineages with a lack of geographic structure were consistently identified by COI and 16S. Conversely, SNP and proteomic data did not mirror these findings, denoting that heteroplasmic mtDNA inflates intraspecific genetic divergence in this gonochoric species. Despite the SNP data revealing overall low genetic divergence, subtle genetic structure was detected by admixture analyses supporting two source populations: one in the north and central Atlantic, and a second in the south Atlantic, with moderate admixture in the Brazil and Cape basins. Proteomic fingerprinting revealed two basin-separated groups with patterns distinct from the nuclear data, suggesting environmentally driven shifts in protein expression. Our findings underscore the value of integrating nuclear genomic and proteomic tools to decipher population connectivity at abyssal depths, where minimal genetic differentiation necessitates fine-scale analyses.},
}

@article {pmid40785415,
year = {2025},
author = {Williamson, R and Dusek, N and Lopez-Echartea, E and Ramsett, MKT and Geddes, BA},
title = {Evaluation of Engineering Potential in Undomesticated Microbes With VECTOR.},
journal = {Microbial biotechnology},
volume = {18},
number = {8},
pages = {e70215},
pmid = {40785415},
issn = {1751-7915},
support = {//Richard and Linda Offerdahl Faculty Fellowship/ ; FF-NIA21-0000000061m//Foundation for Food and Agriculture Research/ ; },
mesh = {*Genetic Vectors ; Plasmids/genetics ; *Bacteria/genetics ; *Genetic Engineering/methods ; Green Fluorescent Proteins/genetics/analysis ; },
abstract = {Genetic engineering research has predominantly focused on well-characterised organisms like Escherichia coli and Bacillus subtilis, with methods that often fail to translate to other microorganisms. This limitation presents a significant challenge, particularly given the increasing isolation of large microbial collections through high-throughput culturomics. In response, we developed a scalable, high-throughput pipeline to evaluate the engineerability of diverse microbial community members we named VECTOR (Versatile Engineering and Characterisation of Transferable Origins and Resistance). We utilised a library of vectors with the Bacterial Expression Vector Archive (BEVA) architecture that included combinations of three antibiotic resistance genes and three broad host-range origins of replication (pBBR1, RK2 and RSF1010) or the restricted host-range R6K with an integrative mariner transposon. We tagged each vector with green fluorescent protein and a unique nucleotide barcode. The resulting plasmids were delivered en masse to libraries of undomesticated microbes from plant microbiomes in workflows designed to evaluate their ability to be engineered. Utilising OD600 and relative fluorescence measurements, we were able to monitor genetic cargo transfer in real time, indicating successfully engineered strains. Next-generation sequencing of plasmid molecular barcodes allowed us to identify specific vector architectures that worked well in particular bacterial strains from a large community. Modifications to the procedure facilitated isolation of engineered microbes.},
}

*Genetic Vectors
Plasmids/genetics
*Bacteria/genetics
*Genetic Engineering/methods
Green Fluorescent Proteins/genetics/analysis

@article {pmid40783800,
year = {2025},
author = {Urumarudappa, SKJ and Bommuluri, V and J, S and Chaturvedi, S and Mittal, AK and Zhang, Y and Chang, P and Swanson, G},
title = {Authentication Methods for Phytochemicals (Botanicals) in Plant Extracts and Dietary Supplements.},
journal = {Journal of dietary supplements},
volume = {},
number = {},
pages = {1-42},
doi = {10.1080/19390211.2025.2538487},
pmid = {40783800},
issn = {1939-022X},
abstract = {Demand for high-quality and standardized phytochemicals (botanicals) and plant extracts if rising in both the food and dietary supplement industries. Ensuring the authenticity of the plant raw materials used in botanical and dietary supplement manufacturing is an important step before processing raw materials. However, authenticating phytochemicals (botanicals) are challenging due to their unique characteristics, including geographical location, seasonal variations, environmental conditions, and plant diversity. These factors cause variability in properties, making consistent authentication methods difficult to establish. The current review is centered on the utilization of multisource and qualitative methods for authenticating the identity of botanical and food ingredients. This review highlights the integral role of various botanicals and plant extracts authentication methods such as micro/macroscopy, chromatography, and spectroscopy technology, including DNA-based approaches. Further summarizing the current state of knowledge and importance its potential contributions to the field of botanical ingredient authentication system. This study also highlights the plants used in dietary supplement categories of weight management, memory enhancement and blood sugar regulation and their adulteration/admixture. Furthermore, discusses considerations for selecting appropriate methods and optimization steps in the implementation and standardization of botanical and plant extract authentication. In addition, we discussed the challenges and opportunities associated with the implementation and standardization of botanical and plant extracts authentication system. The future of botanical authentication will be shaped by advances in molecular diagnostics such as targeted DNA barcoding, Next-Generation Sequencing (NGS), and chemometric integration with spectroscopic techniques which are set to greatly enhance accuracy, traceability, and global compliance in botanical product safety and quality.},
}

@article {pmid40781841,
year = {2025},
author = {Li, CJ and Jiang, YZ and Li, DZ and Wu, QZ},
title = {Test Species Discrimination in Codonopsis (Campanulaceae) Using Genome Skimming Data.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70025},
doi = {10.1111/1755-0998.70025},
pmid = {40781841},
issn = {1755-0998},
support = {BS202211//Shenyang Normal University Ph.D., Introduced Talents Scientific Research Project Startup Fund/ ; JYTQN2023418//Liaoning Provincial Department of Education University Fundamental Research Project/ ; XDB31000000//Chinese Academy of Sciences/ ; 2024-BS-104//Liaoning Provincial Doctoral Research Startup Fund/ ; },
abstract = {To overcome the limitations of conventional barcoding loci, plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences recovered from genome skimming, proposed as 'super-barcodes' have been suggested as candidates for delimitating recently diverged species or complex plant groups. DNA super-barcodes must be further assessed for their effectiveness in other diverse plant groups. This research focused on the genus Codonopsis, a medicinally significant yet taxonomically complex group characterised by morphological similarity and high phenotypic plasticity in response to environmental conditions. We analysed standard DNA barcodes and super-barcodes across 81 individuals from 36 of the 42 species of Codonopsis from Asia. Our work provides a comprehensive DNA barcode library for Codonopsis species identification. Our findings demonstrated that super-barcodes significantly improved the phylogenetic resolution and the discriminatory power compared to standard DNA barcodes. Since mitochondrial sequence variation is generally low in plant species, few studies have assessed its effectiveness as super-barcodes. We screened the mitochondrial protein-coding sequences (CDS) using genome skimming and evaluated the identification capacity of their combination. Unexpectedly, the discriminatory power of mitochondrial DNA with high nucleotide variation was comparable to that of the concatenated plastid CDS. However, the organelle genome cannot wholly determine the species boundaries of Codonopsis, which might be related to their rapid evolutionary radiation, ILS, hybridisation and strong natural selection. Future multi-locus nuclear markers will likely be developed in plants for additional discriminatory power. Our study provides new knowledge and insights into species discrimination of recently evolved Codonopsis taxa in a biodiversity hotspot.},
}

@article {pmid40777731,
year = {2025},
author = {Shao, KT and Ko, HL and Chiu, YC and Huang, HK and Chen, YF and Chang, YW},
title = {Establishing a COI DNA barcoding reference database for Taiwanese coastal fish species from egg and larvae specimens.},
journal = {ZooKeys},
volume = {1247},
number = {},
pages = {207-216},
pmid = {40777731},
issn = {1313-2989},
abstract = {Fish eggs and larval stages are essential components of marine ecosystems and play important roles in sustaining marine food webs. However, the egg and larval stages often lack distinct diagnostic characteristics, making it challenging to identify species solely based on their morphology. In this study, we applied a DNA barcoding approach targeting the cytochrome c oxidase subunit I gene to establish a comprehensive reference for fish eggs and larval material in coastal waters off Taiwan. A total of 7602 records of fish eggs and larvae were collected from marine coastal waters surrounding Taiwan between 2004 and 2023 and identified using a DNA barcoding approach. By comparing our newly generated DNA barcoding sequences with records from public reference databases, we identified 1112 different fish taxa encompassing 24 orders, 158 families, 500 genera, and 844 fish species. This DNA barcoding referencing effort will facilitate future studies on the early life stages of Taiwanese coastal marine fish communities. In addition, it will also provide an important baseline for the development of new methods, such as eDNA and DNA metabarcoding diet analysis. This database provides comprehensive spatial and temporal distribution data of fish eggs and larvae in the waters surrounding Taiwan, contributing to a better understanding of fish spawning seasons, spawning grounds, and resource fluctuations. This database enhances the accuracy of species identification and serves as a scientific foundation for biodiversity conservation and fishery resource management.},
}

@article {pmid40777057,
year = {2025},
author = {Peñaherrera, E and Sarmiento-Pacurucu, J and Santos-Ordóñez, E and Kachatryan, A and Cuzco, N and Vanegas, D and Calle-López, J and Villao-Uzho, L and Heyden, YV and Wilches, I and León-Tamariz, F},
title = {Desmodium molliculum (Kunth) DC., an Andean medicinal plant: DNA barcoding and HPLC fingerprint for species discrimination and evaluation of its pharmacological potential.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1612556},
pmid = {40777057},
issn = {1664-462X},
abstract = {In the Ecuadorian traditional medicine, two species of the Desmodium genus, D. adscendens and D. molliculum, are used interchangeably for the treatment of various ailments, particularly those related to inflammatory processes, wound healing, stomach ulcers and liver disorders. Despite the extensive knowledge and characterization of D. adscendens, there is limited information regarding D. molliculum. This highlights the necessity for the development of analytical tools that facilitate the differentiation between these two species and the characterization of the latter. The tools were developed and evaluated at two distinct levels: genetically, using the DNA barcoding technique, and analytically, using chromatographic fingerprinting. Additionally, the antioxidant potential of the samples was evaluated through the establishment of the RACI index, based on various in vitro evaluation techniques. De novo genetic DNA barcodes were obtained for D. molliculum and the phylogenetic analysis separated them from those obtained from D. adscendens, demonstrating that the trnH-psbA, matK, and ITS1 markers are the most effective for differentiating between the species. Additionally, the antioxidant potential of D. molliculum was found to be higher than that of D. adscendens. The apigenin 8-C-glucoside (vitexin), together with tannic and chlorogenic acids have been pointed by HPLC fingerprinting analysis as responsible for this pharmacological activity.},
}

@article {pmid40776713,
year = {2025},
author = {Cassim, N and Buthelezi, EP and Sarang, S and Moodly, S and Hans, L and Coetzee, LM},
title = {Assessing laboratory specimen losses for the city of Johannesburg, South Africa.},
journal = {African journal of primary health care & family medicine},
volume = {17},
number = {1},
pages = {e1-e8},
doi = {10.4102/phcfm.v17i1.4907},
pmid = {40776713},
issn = {2071-2936},
mesh = {South Africa ; Humans ; Retrospective Studies ; *Specimen Handling/standards ; Primary Health Care ; *Clinical Laboratory Information Systems ; *Laboratories ; },
abstract = {BACKGROUND: Specimen losses across the pathology value chain (PVC) result in missed diagnostic opportunities. It is difficult to fully assess these due to the current paper-based systems, with tracking of specimens only possible on the laboratory information system (LIS).

AIM:  This study aimed to assess specimen losses using the paper-based register.

SETTING:  Randomly selected Primary health care (PHC) facilities, City of Johannesburg, South Africa.

METHODS:  The retrospective descriptive study design was used to scan 1,000 barcodes from facilities in sub-districts A to G. Data was limited to barcodes from the request form and excluded surveillance testing. Matching data from the laboratory repository was extracted. PVC losses were assessed by determining the percentage of scanned barcodes that had a registered, tested, reviewed and/or rejected date. The analysis was stratified according to sub-district, health facility type and test code.

RESULTS:  The dataset analysed included 33 867 barcodes with 121 697 test codes, equating to 3.59 tests per barcode. Matching registered, tested and reviewed dates were detected for 33 107 (97.76%) barcodes. In total, a rejection for one or more test codes was detected for 1,961 barcodes (5.79%). At the sub-district level, between 95.95% (D) and 98.90% (E) of barcodes were reviewed. The rejection rate ranged from 3.27% (F) to 10.93% (D). For community health centres and clinics, 97.37% and 97.97% of the barcodes had a matching reviewed date.

CONCLUSION:  PVC losses reported were 4.05%, excluding rejections (5.79%), with slightly higher levels noted at the sub-district level. Contribution: The continuous audit of PVC losses is recommended.},
}

South Africa
Humans
Retrospective Studies
*Specimen Handling/standards
Primary Health Care
*Clinical Laboratory Information Systems
*Laboratories

@article {pmid40776180,
year = {2025},
author = {Nguyen, HN and Madanian, S and Nguyen, M and Merry, A and Parry, D},
title = {Digital Transformation of Medication Identification: Technological Evolution.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {1684-1685},
doi = {10.3233/SHTI251163},
pmid = {40776180},
issn = {1879-8365},
mesh = {*Medication Errors/prevention & control ; Humans ; *Radio Frequency Identification Device ; *Electronic Data Processing ; },
abstract = {Medication errors pose a significant health challenge, contributing to thousands of deaths annually. This systematic review explores the technological evolution of medication identification: Barcode/Quick Response (QR) Code systems, Radio Frequency Identification (RFID)/Near-Field Communication (NFC), and Computer Vision, used to reduce errors and enhance patient safety. 140 articles from different databases were reviewed to compare their strengths, limitations, and applications. While barcodes offer cost-effective scanning, they require line-of-sight, RFID/NFC provide robust data retrieval yet faces high costs, and Computer Vision excels in flexibility despite computational demands. Combining these technologies could optimize safety.},
}

*Medication Errors/prevention & control
Humans
*Radio Frequency Identification Device
*Electronic Data Processing

@article {pmid40775874,
year = {2025},
author = {Konishi, S and Tanaka, Y and Sugimoto, K and Wada, S and Okada, K and Takeda, T},
title = {GS1 and RFID Integration for Enhanced Medical Device Traceability in Catheterisation Laboratories.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {332-336},
doi = {10.3233/SHTI250856},
pmid = {40775874},
issn = {1879-8365},
mesh = {*Radio Frequency Identification Device/methods ; *Cardiac Catheterization/instrumentation ; Humans ; Systems Integration ; },
abstract = {This study presents a novel system that integrates GS1 barcodes and radio frequency identification (RFID) technology with the objective of enhancing the medical device traceability in catheterization laboratories. The necessity for precise tracking of medical devices, particularly in the context of cardiovascular procedures is underscored by the occurrence of sporadic product recalls. Despite the existence of traceability systems, no solution has effectively combined GS1 and RFID technologies to ensure precise tracking throughout the clinical process. In this study, an apparatus for reading and collecting RFID tags was developed and integrated with the radiology information system and medical device master database. The medical devices delivered to the hospital were linked to RFID tags by means of scanning the GS1 barcodes on their packaging. During the catheterization procedures, the tags of each medical device used were scanned to record the usage in real-time. The new system has already been employed in more than 500 catheterization procedures. In an analysis of 16 percutaneous coronary intervention procedures, the system demonstrated high accuracy in capturing the chronological order of device usage, with a mean Kendall's rank correlation coefficient of 0.95±0.12. While some discrepancies were observed when non-stock devices were used, the system demonstrated an overall robust reliability. The system, which combines GS1 and RFID technologies, enabled real-time recording of medical devices used in catheterization laboratories, thereby enhancing the traceability of medical devices. Potential future applications include the use of generative artificial intelligence to draft preliminary percutaneous coronary intervention reports, enable real-time detection of complications by comparing device usage patterns with an operator's past cases, and support retrospective analyses for educational and procedural improvements.},
}

*Radio Frequency Identification Device/methods
*Cardiac Catheterization/instrumentation
Humans
Systems Integration

@article {pmid40775323,
year = {2025},
author = {Mahgoub, YA and Mahmoud, HA and El-Sebakhy, NA and Abdallah, II},
title = {Unravelling Artemisia species genetic variation via DNA barcoding, ISSR and RAPD with the development of eco-specific SCAR markers.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1034},
pmid = {40775323},
issn = {1471-2229},
mesh = {*Artemisia/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Random Amplified Polymorphic DNA Technique ; *Genetic Variation ; Phylogeny ; Genetic Markers ; *Microsatellite Repeats/genetics ; DNA, Plant/genetics ; Species Specificity ; },
abstract = {BACKGROUND: Genus Artemisia is one of the largest and most globally spread genera, comprising more than 500 species known for their phytochemical diversity and therapeutic properties. This necessitates the accurate authentication and differentiation of its species. Traditional morphological, microscopical and metabolic profiling methods are often insufficient for reliable discrimination. The aim of this study is the authentication and assessment of the genetic diversity of wild Egyptian Artemisia species; A. herba-alba, A. monosperma, A. judaica and cultivated A. annua using a combined molecular approach of DNA barcoding, ISSR, RAPD, and the development of eco-specific SCAR markers.

RESULTS: DNA barcoding targeting both nuclear (ITS2) and plastid (psbA-trnH) spacers revealed that ITS2 is recommended over psbA-trnH as the discriminatory barcode of choice since it accurately identified all species with > 99% identity and phylogenetic clustering with greater genetic distances. ISSR fingerprinting with five primers generated 41 polymorphic bands (100% polymorphism) and displayed genetic diversity among the species. However, the morphologically and chemically similar A. herba-alba and A. judaica remained partly undifferentiated. Therefore, RAPD profiling was implemented as a complementary technique for better and reliable discrimination. RAPD profiling with 27 primers generated 212 bands (99.5% polymorphic). RAPD primers OPA-10 and OPK-07 showed superior differentiation of the Artemisia species, while primers OPG-07, OPB-20, OPS-12 and OPD-15 failed to discriminate between the studied species. The reproducible RAPD banding profiles generated by OPG-02, OPG-04, OPA-09 and OPD-15 primers were targeted for the development of species-specific SCAR markers by isolating, cloning, and sequencing the distinct RAPD bands specific for each species. These putative SCAR markers were assessed and validated confirming the identity of the studied species.

CONCLUSIONS: An integrated molecular approach combining ITS2 barcoding, ISSR, RAPD, and RAPD-derived SCAR markers offered a reliable strategy for the authentication and discrimination of Artemisia species based on their genetic profiles. It is worth mentioning that this is the first report of eco-specific SCAR markers for the Egyptian Artemisia species. The developed SCAR markers allow rapid species identification for quality control of medicinal plants, complementing conventional methods and overcoming their limitations. This provides a reproducible, cost-effective strategy for large-scale authentication of medicinal plants.},
}

*Artemisia/genetics/classification
*DNA Barcoding, Taxonomic/methods
Random Amplified Polymorphic DNA Technique
*Genetic Variation
Phylogeny
Genetic Markers
*Microsatellite Repeats/genetics
DNA, Plant/genetics
Species Specificity

@article {pmid40775299,
year = {2025},
author = {Arias, T and Moreno, JS and Reyes, S and Almario, ML and Serna-Sánchez, A and Iturralde, GA and Valencia, J and Baquero, L and Zuluaga, A},
title = {Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae).},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {79},
pmid = {40775299},
issn = {2730-7182},
mesh = {*Orchidaceae/genetics/classification ; *Phylogeny ; *Genome, Chloroplast ; *Genome, Plastid ; },
abstract = {Well-resolved phylogenetic relationships within the diverse Neotropical orchid genus Lepanthes are presented based on a genome skimming approach that yielded nine newly sequenced chloroplast genomes. We complemented this with 17-86 plastome coding genes for 26 species retrieved from GenBank, alongside amplified matK and rITS regions. The Lepanthes plastomes (157,185-158,260 bp, 37.15% GC content) contained 136 annotated genes, including 86 protein-coding, 42 tRNA, and 8 rRNA genes. We identified six hypervariable regions, including parts of the ycf1 gene, as potential DNA barcodes. Phylogenetic analyses revealed that Carl Luer's subgeneric classifications are non-monophyletic, a finding confirmed by PCA of continuous morphological traits, reflecting significant morphological homoplasy. Six major clades were identified, though resolution for the phylogenetic backbone remains unresolved at two nodes. Subgenus Marsipanthes is not monophyletic as currently circumscribed, with two subclades recovered in distinct positions within the phylogeny. An early-diverging lineage, comprising species restricted to the eastern Andean slopes from southern Colombia to Peru, includes members of both Marsipanthes and Lepanthes. A derived clade, consisting of species from both subgenera, confined to the Chocó biogeographic region, forms an unresolved polytomy. Although only a subset of Lepanthes diversity was sampled, this study captures significant taxonomic, geographic, and morphological variation. It provides foundational insights into the genu's evolutionary history, along with tools and hypotheses that can be expanded upon in future research to further refine our understanding of its biogeographic history.},
}

*Orchidaceae/genetics/classification
*Phylogeny
*Genome, Chloroplast
*Genome, Plastid

@article {pmid40774373,
year = {2025},
author = {Iwaki, T and Sasaki, M and Waki, T and Kurozumi, T},
title = {An unidentified species of Leucochloridium (Trematoda: Leucochloridiidae) found in an Amber snail (Succinea lauta) from Chiba Prefecture, Honshu, Japan.},
journal = {Parasitology international},
volume = {},
number = {},
pages = {103137},
doi = {10.1016/j.parint.2025.103137},
pmid = {40774373},
issn = {1873-0329},
abstract = {Leucochloridium spp. are intriguing parasites due to their colorful, pulsating larval broodsacs in amber snails' eyestalks. The unusual appearance is believed to mimic caterpillars to attract insectivorous birds. Sporocysts of Leucochloridium sp. were discovered in an amber snail (Succinea lauta) in Chiba, located in the central region of Honshu, Japan. The broodsacs displayed a distinctive pattern, characterized by large dark brown spots, bands of the same color at the anterior end, and light brown vertical stripes running through them. Phylogenetic analyses were conducted based on DNA sequences of the nuclear 28S ribosomal RNA gene (28S rDNA) and the mitochondrial cytochrome c oxidase subunit 1 gene (cox1). Although the 28S rDNA sequence of the present species was closely related to that of Leucochloridium problematicum from North America, morphological differences in the broodsacs suggest that it is likely a distinctive species. A ML tree based on the cox1 sequences indicated that the Leucochloridium species analyzed in this study and L. subtilis form a clade separate from other Leucochloridium species in Europe and Asia. However, the p-distance between the cox1 sequences of the present species and L. subtilis was 0.24, supporting their distinction at the species level. Although definitive identification of Leucochloridium sp. was not achieved in this study, the DNA barcodes generated here and in related research may facilitate future direction and identification of adult Leucochloridium sp. in birds residing in or migrating through Japan.},
}

@article {pmid40772542,
year = {2025},
author = {Reddy, S and Wacker, K and Fahmy, M and Hekkala, E and Bates, JM and Goodman, SM and Hackett, SJ and Raherilalao, MJ and Maddox, JD},
title = {VoronaGasyCodes: A Public Database of Mitochondrial Barcodes for Malagasy Birds.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70027},
doi = {10.1111/1755-0998.70027},
pmid = {40772542},
issn = {1755-0998},
abstract = {Molecular tools are increasingly being used to survey the presence of biodiversity and their interactions within ecosystems. Indirect methods, like environmental DNA (eDNA) and invertebrate-derived DNA (iDNA), are dependent on sequence databases with accurate and sufficient taxonomic representation. These methods are increasingly being used in regions and habitats where direct detection or observations can be difficult for a variety of reasons. Madagascar is a biodiversity hotspot with a high proportion of endemic species, many of which are threatened or endangered. Here we describe a new resource, VoronaGasyCodes, a curated database of newly published genetic sequences from Malagasy birds. Our database is currently populated with six mitochondrial genes or DNA barcodes for 142 species including 70% of the birds endemic to the island and will be periodically updated as new data become available. We demonstrate the utility of our database with an iDNA study of leech blood meals where we successfully identified 77% of the hosts to species. These types of resources for characterising biodiversity are critical for insights into species distribution, discovery of new taxa, novel ecological connections and advancing conservation and restoration measures.},
}

@article {pmid40772462,
year = {2025},
author = {Ogiso-Tanaka, E and Ito, MA and Shimada, D},
title = {Nondestructive DNA extraction from specimens and bulk samples preserved in DESS solution for DNA barcoding.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/07366205.2025.2542023},
pmid = {40772462},
issn = {1940-9818},
abstract = {DNA barcoding of small organisms often requires significant damage or destroy specimens. To address this, the development of nondestructive DNA extraction methods that maintain specimen morphology is crucial. Here, we present a protocol using the supernatant of DESS preservation solution (20% DMSO, 250 mM EDTA, saturated NaCl), which conserve both the morphological characteristics and DNA of biological samples long-term. This method successfully conducted nondestructive barcoding of nematodes preserved in DESS and stored 10 years at room temperature. The protocol also applies to bulk environmental samples, where sediment and seagrass collected in the field are immediately preserved in DESS. This enables the subsequent isolation and individual nondestructive barcoding of meiofauna and diatoms from the preserved environmental samples in the laboratory.},
}

@article {pmid40771425,
year = {2025},
author = {Jeffet, J and Hadad, B and Froim, S and Kaboub, K and Rabinowitz, KM and Deek, J and Margalit, S and Dotan, I and Bahabad, A and Ebenstein, Y},
title = {DeepQR: single-molecule QR codes for optical gene-expression analysis.},
journal = {Nanophotonics (Berlin, Germany)},
volume = {14},
number = {15},
pages = {2549-2561},
pmid = {40771425},
issn = {2192-8614},
abstract = {Optical imaging and single-molecule imaging, in particular, utilize fluorescent tags in order to differentiate observed species by color. The degree of color multiplexing is dependent on the available spectral detection window and the ability to distinguish between fluorophores of different colors within this window. Consequently, most single-molecule imaging techniques rely on two to four colors for multiplexing. DeepQR combines compact spectral imaging with deep learning to enable 4 color acquisition with only 3 spectral detection windows. It allows rapid high-throughput acquisition and decoding of hundreds of unique single-molecule color combinations applied here to tag native RNA targets. We validate our method with clinical samples analyzed with the NanoString gene-expression inflammation panel side by side with the commercially available NanoString nCounter system. We demonstrate high concordance with "gold-standard" filter-based imaging and over a four-fold decrease in acquisition time by applying a single snapshot to record four-color barcodes. The new approach paves the path for extreme single-molecule multiplexing.},
}

@article {pmid40770058,
year = {2025},
author = {Khosrowshahli, R and Kheiri, F and Asilian Bidgoli, A and Tizhoosh, HR and Makrehchi, M and Rahnamayan, S},
title = {Enhancing image retrieval through optimal barcode representation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28847},
pmid = {40770058},
issn = {2045-2322},
abstract = {Data binary encoding has proven to be a versatile tool for optimizing data processing and memory efficiency in various machine learning applications. This includes deep barcoding, generating barcodes from deep learning feature extraction for image retrieval of similar cases among millions of indexed images. Despite the recent advancement in barcode generation methods, converting high-dimensional feature vectors (e.g., deep features) to compact and discriminative binary barcodes is still an urgent necessity and remains an unresolved problem. Difference-based binarization of features is one of the most efficient binarization methods, transforming continuous feature vectors into binary sequences and capturing trend information. However, the performance of this method is highly dependent on the ordering of the input features, leading to a significant combinatorial challenge. This research addresses this problem by optimizing feature sequences based on retrieval performance metrics. Our approach identifies optimal feature orderings, leading to substantial improvements in retrieval effectiveness compared to arbitrary or default orderings. We assess the performance of the proposed approach in various medical and non-medical image retrieval tasks. This evaluation includes medical images from The Cancer Genome Atlas (TCGA), a comprehensive publicly available dataset, as well as COVID-19 Chest X-rays dataset. In addition, we evaluate the proposed approach on non-medical benchmark image datasets, such as CIFAR-10, CIFAR-100, and Fashion-MNIST. Our findings demonstrate the importance of optimizing binary barcode representation to significantly enhance accuracy for fast image retrieval across a wide range of applications, highlighting the applicability and potential of barcodes in various domains.},
}

@article {pmid40766630,
year = {2025},
author = {Semwal, A and Morrison, J and Beddows, I and Palmer, T and Majewski, MF and Jang, HJ and Johnson, BK and Shen, H},
title = {Tranquillyzer: A Flexible Neural Network Framework for Structural Annotation and Demultiplexing of Long-Read Transcriptomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40766630},
issn = {2692-8205},
abstract = {Long-read single-cell RNA sequencing using platforms such as Oxford Nanopore Technologies (ONT) enables full-length transcriptome profiling at single-cell resolution. However, high sequencing error rates, diverse library architectures, and increasing dataset scale introduce major challenges for accurately identifying cell barcodes (CBCs) and unique molecular identifiers (UMIs) - key prerequisites for reliable demultiplexing and deduplication, respectively. Existing pipelines rely on hard-coded heuristics or local transition rules that cannot fully capture this broader structural context and often fail to robustly interpret reads with indel-induced shifts, truncated segments, or non-canonical element ordering. We introduce Tranquillyzer (TRANscript QUantification In Long reads-anaLYZER), a flexible, architecture-aware deep learning framework for processing long-read single-cell RNA-seq data. Tranquillyzer employs a hybrid neural network architecture and a global, context-aware design, and enables precise identification of structural elements - even when elements are shifted, partially degraded, or repeated due to sequencing noise or library construction variability. In addition to supporting established single-cell protocols, Tranquillyzer accommodates custom library formats through rapid, one-time model training on user-defined label schemas, typically completed within a few hours on standard GPUs. Additional features such as scalability across large datasets and comprehensive visualization capabilities further position Tranquillyzer as a flexible and scalable framework solution for processing long-read single-cell transcriptomic datasets.},
}

@article {pmid40766425,
year = {2025},
author = {Chambwe, N and Kennedy, SR and Kohrn, BF and Lazarchuk, P and Leutert, M and Qin, G and Tercan, B and Sanchez-Contreras, M and Tang, W and Graber, JJ and Paddison, PJ and Villén, J and Shmulevich, I and Monnat, RJ},
title = {Cellular heterogeneity and therapeutic response profiling of human IDH+ glioma stem cell cultures.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.29.667532},
pmid = {40766425},
issn = {2692-8205},
abstract = {UNLABELLED: Glioblastoma stem cell (GSC) cultures are initiated from glioblastoma (GBM) surgical resection tissue. They can capture and propagate key GBM primary tumor molecular and cellular features. We have deeply characterized four isocitrate dehydrogenase (IDH)-expressing (or IDH+) GSC cultures from unrelated adults to serve as cellular models for the majority of adult primary GBM. We demonstrate that GSC cultures can be continuously propagated in defined, serum-free media and 5% oxygen without requiring specialized growth substrates; have well-defined genomic and mtDNA variants and gene/protein expression profiles; and highly reproducible dose-survival curves when treated with the GBM standard-of-care therapies of ionizing radiation (IR) and temozolomide (TMZ). We also illustrate how expressed lentiviral barcodes, mtDNA variants and single cell gene expression profiling can be used to define and track cellular heterogeneity over 40 days after IR treatment. These well-characterized IDH+ GSC cultures can support many high throughput in vitro assay formats, including xenograft, organoid and other GBM disease modeling protocols. They should prove a useful resource to better understand GBM biology, and to identify new and more effective GBM therapies and treatment regimens.

HIGHLIGHTS: Glioblastoma (GBM)-derived IDH-expressing Glioma Stem Cell (GSC) cultures can capture and propagate GBM genomic variants, gene and protein expression programs.Mitochondrial DNA (mtDNA) variants identified by high accuracy Duplex DNA sequencing are abundant and sub-clonally organized in GSC cultures.GSC cultures have highly reproducible dose-survival curves for ionizing radiation and temozolomide, the GBM standard-of-care therapies.GSC culture cellular heterogeneity can be captured, characterized and tracked by using expressed lentiviral barcodes, mtDNA variants and scRNA sequencing.

ETOC BLURB: IDH-expressing glioma stem cell cultures (GSCs) are experimentally tractable and versatile glioblastoma (GBM) cellular disease models. Deeply characterized GSC cultures can enable new work to understand GBM biology, and help identify new and more effective GBM therapies and treatment regimens.},
}

@article {pmid40765263,
year = {2025},
author = {You, L and Zhang, J and Deng, Y and Shi, X and Liu, C and Zhong, L and Ye, Z and Zhang, Z and Peng, X and Zhou, C and Cao, Z and Li, C and Hu, H and Zheng, L and Zhang, Y},
title = {Multi-Omics Analyses Reveal Metabolic Regulatory Networks in Salinity and Drought Adaptation of Basil QF, a Chinese Cultivar.},
journal = {Physiologia plantarum},
volume = {177},
number = {4},
pages = {e70437},
doi = {10.1111/ppl.70437},
pmid = {40765263},
issn = {1399-3054},
support = {HBMUPI202104//Hubei University of Medicine/ ; 2022BMXKQT4//Hubei University of Medicine/ ; 32200680//National Nature Science Foundation of China/ ; 2060302//Key Project at Central Government Level/ ; T2023016//Science Research Program of Hubei Provincial Department of Education/ ; //Young Top-Notch Talent Cultivation Program of Hubei Province/ ; 222102110380//Science and Technology Development Programs of Henan Province/ ; //the Joint supported by Hubei Provincial Natural Science Foundation and Shiyan-of China [2025AFD172, 2025AFD179, 2025AFD205]/ ; },
mesh = {Droughts ; *Ocimum basilicum/genetics/physiology/metabolism ; Salinity ; Adaptation, Physiological ; Gene Expression Regulation, Plant ; *Metabolic Networks and Pathways ; Stress, Physiological ; Metabolomics ; Plant Leaves/physiology ; China ; Plant Roots/physiology ; Multiomics ; },
abstract = {The Ocimum genus, valued for its culinary, medicinal, and aromatic uses, is often cultivated in regions affected by drought and salinity. This study investigates the adaptive responses of QingFeng (QF), a newly identified basil cultivar locally known as vegetable "jingjie" in China, to high salinity and drought stress. DNA barcoding, mucilaginous seed analysis, flow cytometry, and karyotyping confirmed QF's identity, revealing a chromosome number of 2n = 76 and a 1C genome size of 2962 ± 36 Mb. Phenotyping, transcriptomic and metabolomic profiling, and hormone monitoring showed drought primarily suppressed leaf growth, while salinity inhibited root elongation. Notably, convergent and divergent responses to salinity and drought were observed, including stress-specific remodeling of core metabolic pathways such as the GS-GOGAT cycle, photorespiration, TCA cycle, and pyrimidine metabolism. Secondary metabolite profiling further demonstrated stress-specific patterns in the accumulation of flavonoids and alkaloids. These findings provide a theoretical foundation for deciphering abiotic stress adaptation mechanisms in basil and offering practical approaches to enhance local cultivation of the QingFeng cultivar.},
}

Droughts
*Ocimum basilicum/genetics/physiology/metabolism
Salinity
Adaptation, Physiological
Gene Expression Regulation, Plant
*Metabolic Networks and Pathways
Stress, Physiological
Metabolomics
Plant Leaves/physiology
China
Plant Roots/physiology
Multiomics

@article {pmid40763587,
year = {2025},
author = {Azirakhmet, Z and Shchepin, O and Inoue, M and Kussainova, A and Bersimbaev, R and Schnittler, M},
title = {First records of nivicolous myxomycetes (Amoebozoa) from Kazakhstan.},
journal = {European journal of protistology},
volume = {100},
number = {},
pages = {126161},
doi = {10.1016/j.ejop.2025.126161},
pmid = {40763587},
issn = {1618-0429},
abstract = {We present the first survey of nivicolous myxomycetes (plasmodial slime molds, Amoebozoa) conducted in Kazakhstan, specifically from the Ile-Alatau mountain range near Almaty. A total of 82 specimens were collected, and 16 species were identified using a comparative morphological approach. Except for Didymium dubium, all identified species represent first records for Kazakhstan. DNA barcoding confirmed the morphology-based identification of 70 specimens, revealing 26 distinct barcode sequence variants. Among these, nine 18S rDNA barcode variants were novel and have not been previously reported in the GenBank database.},
}

@article {pmid40761132,
year = {2025},
author = {Bu, A and Wu, G and Hu, L},
title = {Revealing the Heterogeneity of Extracellular Vesicles: From Population to Single Particle Level.},
journal = {Proteomics},
volume = {},
number = {},
pages = {},
doi = {10.1002/pmic.70024},
pmid = {40761132},
issn = {1615-9861},
support = {22374056//National Natural Science Foundation China/ ; 22374056//National Natural Science Foundation China/ ; 22374056//National Natural Science Foundation China/ ; },
abstract = {Extracellular vesicles (EVs) are secreted by cells and enclosed within lipid bilayers. These vesicles contain diverse biomolecular components, including proteins, nucleic acids, lipids, and metabolites. They serve critical roles in intercellular communication and regulate multiple physiological and pathological processes, such as immune modulation, angiogenesis, and tumorigenesis and metastasis. Notably, EVs exhibit marked heterogeneity in both physical characteristics and biomolecular composition. This article will systematically characterize the multidimensional heterogeneity of EVs at the population level through comprehensive analysis of their biogenesis origins, size distribution, surface protein, surface glycan chains, and surface lipid. Conventional population-level analyzes yield averaged molecular profiles that obscure subtype-specific functional correlations, thereby limiting mechanistic insights into EV subpopulation biology. To further understand EV heterogeneity, it is necessary to enhance our understanding about molecular characteristics of EVs from the population to the single particle level. Current single EVs analysis techniques mainly include super-resolution microscopy (SRM), atomic force microscopy (AFM), nanoparticle tracking Analysis (NTA), flow cytometry (FCM), surface enhanced Raman spectroscopy (SERS), mass spectrometry (MS), and proximity barcoding assay (PBA). In this review, we systematically examine population-level EV heterogeneity; evaluate single-particle detection methodologies; and discuss emerging technologies (e.g., click chemistry, Olink proteomics, and molecular imprinting) for resolving single EV heterogeneity.},
}

@article {pmid40758964,
year = {2025},
author = {Molina, L and Williams, G and de Errasti, A and Hadziabdic, D and Pildain, MB},
title = {Diversity of fungi cultured from galleries and bodies of ambrosia beetles (Gnathotrupes spp.) and carpenter moths (Chilecomadia valdiviana) in lenga (Nothofagus pumilio) forests in Patagonia.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/00275514.2025.2522019},
pmid = {40758964},
issn = {1557-2536},
abstract = {Wood-boring insects play an important role in turnover of trees and biomass in temperate forests and interact with a functionally diverse mycobiome. However, the diversity and dynamics of ambrosia beetles, other wood-boring insects, and their fungi remain relatively poorly understood in the forests of temperate South America. Baseline knowledge of insect and fungal diversity is therefore needed to provide a foundation for understanding the potential future dynamics of these critically important ecosystems in the context of global change. This study aimed to document fungal diversity that could be obtained in culture from larvae, adults, and galleries of ambrosia beetles (Gnathotrupes spp.) and a carpenter moth (Chilecomadia valdiviana) from lenga (Nothofagus pumilio) in northwest Patagonia, Argentina. Long molecular barcodes from fungal cultures isolated from galleries, larvae, and adult insects were obtained using nanopore sequencing. Fungal assemblages associated with Gnathotrupes spp. (32 unique taxa) and C. valdiviana (17 unique taxa) differed in structure and composition but shared 11 distinct taxa. Differences were found between fungal assemblages associated with C. valdiviana gut tracts and galleries. Fungal assemblages found in galleries and insect bodies of Gnathotrupes varied among species, seasons, and health conditions of the host crown. Our results also showed that the ophiostomatoid fungi Raffaelea spp. and yeast Cyberlindnera sp. were commonly found with Gnathotrupes spp. whereas Ambrosiozyma angophorae and Oidiodendron sp. were found with C. valdiviana. Species of the blue stain fungi Ophiostoma patagonicum, O. nothofagi, an unidentified Sporothrix sp. and Huntiella decorticans were found with both beetles and moths, and O. patagonicum was the most frequently isolated species. This is the first comprehensive study of microbiota isolated from Gnathotrupes spp. and C. valdiviana.},
}

@article {pmid40758764,
year = {2025},
author = {Edge, RJ and Marriott, AE and Keen, M and Xie, T and Crittenden, EP and Dawson, CA and Wilkinson, MC and Wüster, W and Casewell, NR and Ainsworth, S and Menzies, SK},
title = {Preclinical evaluation of the neutralising efficacy of three antivenoms against the venoms of the recently taxonomically partitioned E. ocellatus and E. romani.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {8},
pages = {e0013371},
pmid = {40758764},
issn = {1935-2735},
mesh = {Animals ; *Antivenins/pharmacology ; Mice ; *Viperidae/classification ; *Viper Venoms/antagonists & inhibitors/toxicity ; *Snake Bites/drug therapy ; Male ; Female ; },
abstract = {Snakebite is a significant public health concern in Africa, with the viperid species Echis ocellatus being responsible for the majority of snakebite deaths in West Africa. Recently E. ocellatus underwent taxonomic revision and was split into two species, E. ocellatus sensu stricto and E. romani, leading to questions regarding differences in venom bioactivities and the efficacy of antivenoms indicated for treatment of 'E. ocellatus' envenoming against the two redefined species. Using a range of in vitro assays we compared the toxin activities of the two species and the venom-neutralising efficacy of three antivenoms (EchiTAbG, SAIMR Echis and Echiven) raised against 'E. ocellatus'. We then used murine preclinical assays to compare the in vivo efficacy of these antivenoms against E. romani and E. ocellatus s. str venoms. Mitochondrial barcoding of snake skins and venom revealed that E. romani, and not E. ocellatus, is used in the manufacture of several antivenoms raised against 'E. ocellatus'. There were also a number of differences in specific toxin activity between the venoms of the two species in the three in vitro assays utilised in this study.; E. ocellatus (Ghana) had the strongest phospholipase A2 (PLA2) activity, followed by weak PLA2 activity for E. romani (Cameroon) and insignificant activity by E. romani (Nigeria). E. ocellatus (Ghana) and E. romani (Nigeria) demonstrated comparable snake venom metalloproteinase activity, whilst E. romani (Cameroon) had reduced, albeit still significant, activity in comparison. However no differences were observed in a plasma clotting assay measuring coagulopathy between the venoms and localities. Venoms from E. ocellatus (Ghana) and E. romani (Cameroon and Nigeria) were all recognised comparably by the three antivenoms, and there were only modest differences between antivenoms in neutralising the various in vitro toxin effects. In murine preclinical assays, each antivenom could neutralise the lethal effects of E. romani (Nigeria), but differences were seen in their comparative potency when the same antivenom doses were tested against E. romani (Cameroon) and E. ocellatus (Ghana). In these comparative potency assays, all three antivenoms were unable to confer 100% survival when tested against E. romani (Cameroon), but SAIMR Echis provided the best protection with 80% survival. When tested against E. ocellatus (Ghana), the comparative doses of SAIMR Echis and Echiven provided 100% protection whereas EchiTAbG failed to prevent lethality beyond three hours. This represents the first detailed analysis of differences between E. ocellatus and E. romani venom bioactivities and the efficacy of existing antivenoms against these two species. Our findings demonstrate that EchiTAbG, SAIMR Echis and Echiven antivenoms are preclinically efficacious against the lethal effects of E. ocellatus and E. romani venom across a number of localities.},
}

Animals
*Antivenins/pharmacology
Mice
*Viperidae/classification
*Viper Venoms/antagonists & inhibitors/toxicity
*Snake Bites/drug therapy
Male
Female

@article {pmid40758432,
year = {2025},
author = {Baker, SS and Carmona-Galindo, V and Hoque, M and Ali Edriss, F and Alrayyashi, A and Al-Shaghdari, A and Al-Wakeel, A and Ali, N and Alkuhali, A and Allen, A and Bangurah, S and Bazoun, W and Benford, H and Doss, D and Eady, A and Dourra, M and Guirgis, H and Hamade, I and Hamo, R and Jamal Iddin, J and Jarbo, J and Kawtharani, S and Kunnummyalil, K and Markos, B and Nistor, R and Obeid, H and Sema, R and Shelton, S and Riachi, L and Rodriguez, J and Saahir, T and Sareini, S and Scheys, C and Sterling, X and Vosbigian, G},
title = {Advancing Integrative Pollinator Biology Education with Course-based Undergraduate Research Experiences.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf145},
pmid = {40758432},
issn = {1557-7023},
abstract = {The next generation of pollination researchers faces unprecedented environmental change during the Anthropocene and must develop cross-disciplinary research skill sets. Course-based Undergraduate Research Experience (CURE) pedagogy is one instructional approach that can expose students to integrative biology research while introducing them to technologies that will become increasingly important in pollination system studies. CUREs offer additional advantages, including the potential of crowdsourcing research and strategies that can increase retention of underrepresented minorities in science, technology, engineering, and mathematics (STEM). In this perspective, we present CUREs that utilize pollinator research as exemplars of how undergraduates can gain experience with integrative research approaches while providing valuable data on the effects of human activity on pollination systems. At the University of Detroit Mercy, a metabarcoding CURE was developed that utilized nanopore sequencing technology to evaluate pollen profiles in urban apiaries. Another CURE involving the solitary leafcutter bee, Megachile rotundata, is being used to evaluate pollinator habitat restoration efforts in an urban park. The instructional approach involved students integrating classical field biology research techniques with DNA barcoding to determine the success of the restoration efforts. Another example is Bee the CURE, a curriculum at Pima Community College, where students conduct barcoding experiments by uploading bee DNA sequences to a barcoding database. This CURE uses a place-based pedagogy, which has been shown to have a positive impact on Hispanic students' perceptions of STEM. These examples demonstrate that pollinator-centered CUREs can integrate multiple approaches and technologies, contribute to scientific knowledge, and can be successfully implemented in diverse institutions. To expand its impact, the pollinator research community should collaborate to develop scalable programs that train future integrative biologists in emerging technologies, such as high-throughput DNA sequencing, DNA barcoding, and advanced computational methods.},
}

@article {pmid40758411,
year = {2025},
author = {Li, W and Chen, X and Wen, N and Chen, Z and Yang, W and Guo, W and Zhang, Q and Wang, Z and Zhai, X and Qiu, L and Tan, W},
title = {Precision Mapping of Direct Membrane Protein Interactions via Binding-Induced DNA Barcode Transfer Labeling.},
journal = {Nano letters},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.nanolett.5c03014},
pmid = {40758411},
issn = {1530-6992},
abstract = {Cell-cell communication is governed by dynamic membrane protein interactions. Precise tracking of direct protein binding and its functional outcomes across cellular engagements is essential for decoding complex biological processes. While proximity-based labeling techniques convert transient interactions into stable signals, they often fail to distinguish direct binding from nonspecific associations. In this work, we developed a binding-induced labeling strategy for 1:1 DNA barcode transfer between interacting proteins at the cellular interface. Using the PD1/PD-L1 immune checkpoint as a model, we designed functionalized aptamer probes targeting PD-L1 on cancer cells, which upon PD1/PD-L1 binding were covalently transferred to PD1 on T cells via click chemistry. By incorporating barcoded primer sequences and programmable DNA signal amplification, we achieved sensitive and sequential tracking of individual PD1/PD-L1 binding events across multiple cellular interactions. Furthermore, with the integration of single-cell transcriptional profiling, this platform revealed the progressive impact of iterative PD1/PD-L1 binding on T-cell reprogramming.},
}

@article {pmid40757888,
year = {2025},
author = {Berkem, R and Özyol Atkaya, T},
title = {[Are Ureaplasma Species Being Disregarded in Urinary Tract Infections?].},
journal = {Mikrobiyoloji bulteni},
volume = {59},
number = {3},
pages = {292-306},
doi = {10.5578/mb.20250326},
pmid = {40757888},
issn = {0374-9096},
mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis/epidemiology ; *Ureaplasma Infections/microbiology/diagnosis/epidemiology ; *Ureaplasma/isolation & purification/genetics/classification ; Female ; Real-Time Polymerase Chain Reaction ; Ureaplasma urealyticum/isolation & purification/genetics ; Male ; Adult ; Middle Aged ; },
abstract = {Ureaplasma parvum ve Ureaplasma urealyticum, üriner ve genital sistemde kolonize olabilmekte ve çeşitli enfeksiyonlara neden olmaktadır. Bu etkenler, zor üreme özellikleri nedeniyle rutin laboratuvar tanı yöntemleriyle tanımlanamamaktadır. Bu nedenle toplumdaki insidansı, direnç özellikleri ve klinikte neden oldukları enfeksiyonlarla ilgili daha ayrıntılı çalışmalara ihtiyaç duyulmaktadır. Bu çalışmada üriner sistem enfeksiyonu şüphesi olan hastalarda üreaplazmaların varlığının gösterilmesi amaçlanmıştır. Hedefleri arasında U.urealyticum ve U.parvum olan ticari gerçek zamanlı kantitatif polimeraz zincir reaksiyon [real-time quantitative polymerase chain reaction (Rt-qPCR)] panel kiti kullanılmış ve PCR sonuçlarının doğruluğu sekans analiziyle gösterilmiştir. Üriner sistem enfeksiyonu şüphesiyle laboratuvara gönderilen 603 orta akım idrar örneği, idrar yolu enfeksiyonları qPCR panel kiti (Bioeksen, Türkiye) ile çalışılmıştır. U.urealyticum ve/veya U.parvum pozitif bulunan 195 örneğin, örnek miktarı yeterli olan 130 adedine, -20 °C'de saklanmalarının ardından MinION™ (Oxford Nanopore Technologies®, Birleşik Krallık) sisteminde rapid barcoding kit (SQK-RBK110.96) (Oxford Nanopore Technologies®, Birleşik Krallık) ile üretici firma önerilerine uygun olarak yeni nesil dizileme [next generation sequencing (NGS)] analizi yapılmıştır. qPCR ile pozitif bulunan 195 (%32.33) örneğin; 138 (%70.76)'inde U.parvum, 46 (%23.58)'sında U.urealyticum, 11 (%5.64)'inde U.urealyticum ve U.parvum birlikte bulunmuştur. qPCR pozitifliği bulunan 195 örneğin; örnek miktarı yeterli olan 130'una NGS ile sekans analizi çalışılmıştır. Bu 130 örneğin 17'sinde elektroforezde pozitif bant (amplifikasyon ürünü) ve beş örnekte yeterli sekans (< 10 coverage) verisi elde edilememiştir. Dolayısıyla 22 örnekte sekans analiz sonucu elde edilememiş, 108 örnekte ise elde edilmiştir. Yüz sekiz örneğin; 102 (%94.44)'sinde qPCR ve NGS sonuçları uyumlu, altısında (%5.56) ise uyumsuz bulunmuştur. Uyumsuz altı örneğin biri qPCR ile U.urealyticum olarak tanımlanırken, sekans analizinde U.parvum olarak tanımlanmış, diğer beş örnekte qPCR'de birlikte bulunan U.urealyticum ve U.parvum'dan sadece biri NGS ile gösterilebilmiş diğeri gösterilememiştir; beş örneğin üçünde sekans analiziyle sadece U.parvum, ikisinde ise sadece U.urealyticum gösterilebilmiştir. Çalışmada orta akım idrar örneklerinde %32.33 oranında U.parvum ve/veya U.urealyticum pozitifliği bulunmuştur. Bu çalışmada, yüksek pozitiflik oranları nedeniyle bu mikroorganizmaların olası bir üriner sistem enfeksiyonu etkeni olabileceğine ve göz ardı edilmemeleri gerektiğine dikkat çekilmek istenmiştir.},
}

Humans
*Urinary Tract Infections/microbiology/diagnosis/epidemiology
*Ureaplasma Infections/microbiology/diagnosis/epidemiology
*Ureaplasma/isolation & purification/genetics/classification
Female
Real-Time Polymerase Chain Reaction
Ureaplasma urealyticum/isolation & purification/genetics
Male
Adult
Middle Aged

@article {pmid40757278,
year = {2025},
author = {Kossatz, P and Mezhov, A and Andresen, E and Prinz, C and Schmidt, W and Resch-Genger, U},
title = {Assessing the Applicability of Lanthanide-Based Upconverting Nanoparticles for Optically Monitoring Cement Hydration and Tagging Building Materials.},
journal = {ACS omega},
volume = {10},
number = {29},
pages = {31587-31599},
pmid = {40757278},
issn = {2470-1343},
abstract = {Chemically stable, lanthanide-based photon upconversion micro- and nanoparticles (UCNPs) with their characteristic multicolor emission bands in the ultraviolet (UV), visible (vis), near-infrared (NIR), and short-wave infrared (SWIR) are promising optical reporters and barcoding tags. To assess the applicability of UCNPs for the monitoring of early stage cement hydration processes and as authentication tags for cementitious materials, we screened the evolution of the luminescence of self-made core-only NaYF4:Yb,Er UCNPs and commercial μm-sized Y2O2S:Yb,Er particles during the first stages of cement hydration, which largely determines the future properties of the hardened material. Parameters explored from the UCNP side included particle size, morphology, surface chemistry or coating, luminescence properties, and concentration in different cement mixtures. From the cement side, the influence of the mineral composition of the cement matrix was representatively examined for ordinary Portland cement (OPC) and its constituents tricalcium aluminate (C3A), tricalcium silicate (C3S), and gypsum at different water to cement ratios. Based on reflection and luminescence measurements, enabling online monitoring, which were complemented by XRD and isothermal heat-flow calorimetric measurements to determine whether the incorporation of these particles could impair cement hydration processes, well suited lanthanide particle reporters could be identified as well as application conditions. In addition, thereby the reporter influence on cement hydration kinetics could be minimized while still preserving a high level of information content. The best performance for the luminescence probing of changes during early stage cement hydration processes was observed for 25 nm-sized oleate (OA)-coated UCNPs added in a concentration of 0.1 wt %. Higher UCNP amounts of 1.0 wt % delayed cement hydration processes size- and surface coating-specifically in the first 24 h. Subsequent luminescence stability screening studies performed over a period of about one year support the applicability of UCNPs as optical authentication tags for construction materials.},
}

@article {pmid40756339,
year = {2025},
author = {Jang, EY and Yang, SB and Chun, J and Kwack, KH and Kang, SW and Lee, JH and Moon, JH},
title = {Single-cell RNA sequencing using split-pool barcoding reveals transcriptional heterogeneity in Porphyromonas gingivalis with implications for periodontal pathogenesis.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2540827},
pmid = {40756339},
issn = {2000-2297},
abstract = {BACKGROUND: Porphyromonas gingivalis is a keystone pathogen in periodontitis, associated with dysbiosis and chronic inflammation. While its virulence mechanisms are well characterized, its transcriptional heterogeneity at the single-cell level remains unexplored.

MATERIALS AND METHODS: We applied split-pool barcoding-based single-cell RNA sequencing to profile gene expression in 1,942 individual P. gingivalis W83 cells cultured under anaerobic conditions. Clustering and differential expression analyses were conducted to identify distinct transcriptional subpopulations.

RESULTS: We identified six transcriptionally distinct clusters, with the two largest accounting for 72.7% of the population. Minor clusters exhibited signatures related to stress responses, metabolism, membrane transport, and DNA regulation. Sub-clustering of major populations revealed rare subgroups, including one enriched for genes involved in iron acquisition, proteolysis, and transport.

CONCLUSIONS: This study presents the first single-cell transcriptomic map of P. gingivalis, revealing rare but functionally significant subpopulations. Such diversity may support bacterial adaptability, virulence, and immune evasion, informing future strategies for targeted periodontal therapy.},
}

@article {pmid40755798,
year = {2025},
author = {Carletti, M and Viñuela Rodríguez, N and Rossetti, G and Rossi, V and Tan, BGP and Reimer, JD},
title = {The tip of the iceberg: extraordinarily high diversity while examining two infralittoral nematode communities on Okinawa-jima Island, Japan, using morphology and DNA barcoding.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19757},
pmid = {40755798},
issn = {2167-8359},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Japan ; *Nematoda/genetics/classification/anatomy & histology ; *Biodiversity ; Islands ; Ecosystem ; Coral Reefs ; Geologic Sediments/parasitology ; Phylogeny ; },
abstract = {BACKGROUND: Nematodes are among the most diverse and abundant metazoans in aquatic habitats, contributing significantly to global biodiversity. Despite their abundance and importance, the presumed number of undescribed species is high and their diversity is often underestimated.

METHODS: In this research, sediment samples were collected from three microhabitats (bare sand, seagrass, coral) in two sites around Okinawa-jima Island in subtropical southern Japan. Nematode specimens were obtained by filtering the sediment and were then used to determine meiofaunal assemblages with morphology and molecular methods at the two sites and to compare them with environmental variables.

RESULTS: The results showed an overwhelmingly high biodiversity of nematofauna with both methods. The morphological identification of free-living nematodes was partly supported by molecular analyses, with the results varying more regarding less common taxa. The discrepancies between different methods may be due to low success of DNA amplifications, high nucleotide variability, and overestimation of congeneric specimens. We observed that coral reef habitats clearly differed from nearby sand and seagrass beds in terms of nematode genus-level assemblages. We identified at least 10 orders and 38 genera of nematodes from our samples that only span two different sites, and it is highly likely these samples include undescribed taxa. Our results strongly suggest that coral reefs and neighboring areas are hot-spots for nematode diversity, at least around Okinawa-jima Island if not also in other coral reef regions.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Japan
*Nematoda/genetics/classification/anatomy & histology
*Biodiversity
Islands
Ecosystem
Coral Reefs
Geologic Sediments/parasitology
Phylogeny

@article {pmid40755785,
year = {2025},
author = {Abuassaf, RA and Al-Jamal, FF and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD},
title = {Evaluating the antibacterial properties of deep-sea sponges Dactylospongia elegants, Stelletta fibrosa, and Haliclona manglaris from the Jordanian Gulf of Aqaba.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19735},
pmid = {40755785},
issn = {2167-8359},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Porifera/chemistry/genetics ; *Gram-Positive Bacteria/drug effects ; *Haliclona/chemistry ; *Gram-Negative Bacteria/drug effects ; Tandem Mass Spectrometry ; },
abstract = {Marine sponges are known for their rich variety of secondary metabolites, many of which show potential for pharmaceutical applications. In this study, three deep-sea sponge species-Stelletta fibrosa, Dactylospongia elegans, and Haliclona manglaris-were identified using DNA barcoding, and their ethanolic extracts were tested for antibacterial activity. The extracts were evaluated against Gram-positive (e.g., Bacillus pumilus, Staphylococcus aureus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus, MRSA) and Gram-negative bacteria (e.g., Escherichia coli and Klebsiella aerogenes) using the agar well diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined. Among the extracts, D. elegans exhibited the most potent antibacterial activity, with inhibition zones ranging from six to 21 mm against gram-positive bacteria and low MIC/MBC values from 0.25 to three mg/ml. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis of D. elegans revealed the presence of bioactive compounds such as gallic acid, caffeic acid, bolinaquinone, dactyloquinone, and others, which are known for their antimicrobial properties. These findings suggest that D. elegans has promising antibacterial properties that could be valuable in combating antimicrobial resistance.},
}

Animals
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Porifera/chemistry/genetics
*Gram-Positive Bacteria/drug effects
*Haliclona/chemistry
*Gram-Negative Bacteria/drug effects
Tandem Mass Spectrometry

@article {pmid40755128,
year = {2025},
author = {Mat Jaafar, TNA and Seah, YG and Imamura, H and Motomura, H and Matsunuma, M},
title = {Rogadius azizahae, a new flathead (Perciformes: Platycephalidae) from the South China Sea.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70135},
pmid = {40755128},
issn = {1095-8649},
support = {20H03311//UMT/SRG/2023/55435; JSPS KAKENHI/ ; 21H03651//UMT/SRG/2023/55435; JSPS KAKENHI/ ; 23K20304//UMT/SRG/2023/55435; JSPS KAKENHI/ ; 24K02087//UMT/SRG/2023/55435; JSPS KAKENHI/ ; JPJSCCB20200009//JSPS Core-to-Core CREPSUM/ ; },
abstract = {A new flathead Rogadius azizahae (Platycephalidae) is described on the basis of five specimens [102.5-107.8 mm standard length (SL)] collected off the east coast of the Malay Peninsula, southern South China Sea. The new species is morphologically similar to Rogadius mcgroutheri Imamura, 2007, known from the Coral Sea off eastern Australia and New Caledonia, the two species sharing most diagnostic characters, including a minute, weakly developed antrorse spine on the preopercle [vs. a long, stout antrorse spine present in Rogadius asper (Cuvier in Cuvier & Valenciennes, 1829), Rogadius fehlmanni Knapp, 2012, and Rogadius pristiger (Cuvier in Cuvier & Valenciennes, 1829)]; usually a single preocular spine [vs. 2-4 in R. fehlmanni and 2-5 in Rogadius welanderi (Schultz in Schultz et al., 1966)]; no accessory spines along the preocular spine base [vs. present in R. fehlmanni and Rogadius serratus (Cuvier in Cuvier & Valenciennes, 1829)]; and no longitudinal black band on the caudal fin (vs. present in Rogadius patriciae Knapp, 1987). The new species can also be distinguished from R. mcgroutheri by having 11 dorsal-fin soft rays [vs. 11 or 12, modally 12 (25 of 30 specimens) in the latter]; 7 lower gill rakers [vs. 5-7, modally 6 (21 of 30)]; the caudal fin brown basally, broadly whitish (semitranslucent) anteriorly and almost entirely brown on the posterior half (vs. ca. 4 irregular variously sized vertical rows of black blotches); the pelvic fin with ca. 6-8 rows of narrow, wavy black bands or dotted lines (vs. largely brownish, with no defined bands or spots); a relatively large orbit, its diameter 12.4-12.8 (mean 12.6)% SL [vs. 11.4-12.3 (11.7)% SL in 100-110 mm SL specimens]; and relatively narrow interorbital region, its width 1.3-1.5 (mean 1.4)% SL [vs. 1.7-2.2 (1.9)% SL]. DNA barcoding also indicated distinct divergence (14.3-14.4% uncorrected p-distance) between the new species and R. mcgroutheri. A revised key to species of Rogadius is provided.},
}

@article {pmid40753185,
year = {2025},
author = {Li, L and Yang, W and Liu, Q and Jiang, X and Wu, K and Fang, L and Li, M and Zeng, S and Li, S},
title = {Comparative analysis of 18 chloroplast genomes reveals genomic diversity and evolutionary dynamics in subtribe Malaxidinae (Orchidaceae).},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1013},
pmid = {40753185},
issn = {1471-2229},
support = {32070224//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Chloroplast/genetics ; *Orchidaceae/genetics/classification ; Phylogeny ; *Genetic Variation ; *Evolution, Molecular ; },
abstract = {BACKGROUND: The subtribe Malaxidinae encompasses diverse species, many of which possess remarkable medicinal properties that have been employed in traditional Chinese medicine for centuries. Although recent advancements have improved our understanding of the backbone phylogeny of Malaxidinae, clarifying the complex intergeneric relationships remains challenging, largely owing to limited genomic data. To address this gap and further investigate the genetic diversity and evolutionary patterns within this subtribe, we sequenced and assembled complete chloroplast (cp.) genomes from sixteen Malaxidinae species. These newly acquired genomic resources, combined with two previously published cp. genomes from closely related species, were incorporated into a comprehensive comparative genomic and phylogenomic analysis.

RESULTS: The complete cp. genomes of all 18 Malaxidinae species were analyzed, revealing lengths ranging from 143,062 bp to 158,785 bp. Each genome contains 123-133 genes, including 74-86 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 1-8 pseudogenes. The chloroplast genomes of Malaxidinae species exhibit significant structural diversity, with particularly pronounced variations observed in the ndhF and ycf1 genes located at the IR/SSC boundary regions. In certain species, the SSC regions showed substantial size reduction, ranging from 10,224 to 15,582 bp. Notable variability in both gene loss and truncation patterns was observed in the ndh gene family across these species, accompanied by diverse modifications affecting the length, position, and pseudogenization of the ycf1 gene. Furthermore, our study identified genomic inversions and rearrangements occurring in both the LSC and SSC regions of specific species. The detection of abundant long dispersed repeats and SSRs provides valuable molecular markers for evaluating both intrageneric and interspecific polymorphism as well as genetic diversity patterns. Through codon usage bias analysis, we established that natural selection serves as the predominant evolutionary force shaping codon usage patterns in most Malaxidinae species. Detailed sequence alignment of the chloroplast genome revealed that structural variants are primarily concentrated within single-copy regions. Ten highly variable cpDNA markers were chosen as mutational hotspots, with the potential for development as DNA barcodes for Malaxidinae species. Our phylogenomic analysis clearly resolved the Malaxidinae into three well-supported major clades. Clade I comprises species of Liparis s.s., Malaxis, and Oberonioides. Clade II includes species of Crepidium, Dienia, Diteilis and Empusa. Clade III consists of species from the genera Blepharoglossum, Cestichis, Oberonia, Platystyliparis and Stichorkis.

CONCLUSION: This research provides valuable insights into the unique characteristics of the chloroplast genome in Malaxidinae orchids, significantly advancing our comprehension of their evolutionary mechanisms and phylogenetic architecture. The acquired genomic data establish a crucial foundation to advance medical resources and aid in species differentiation.},
}

*Genome, Chloroplast/genetics
*Orchidaceae/genetics/classification
Phylogeny
*Genetic Variation
*Evolution, Molecular

@article {pmid40747441,
year = {2025},
author = {Li, L and Lu, Z and Liu, Z and Liang, C and Wang, J and Wang, Y},
title = {Dataset of the complete mitogenomes of the mushroom corals Fungiidae.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111857},
pmid = {40747441},
issn = {2352-3409},
abstract = {Twenty-four mitogenomes of the mushroom corals (Fungiidae), representing 18 species from 12 genera, were sequenced and annotated. These mitogenomes exhibit high similarity, each containing the same 13 protein-coding genes (PCGs) and two rRNA genes as other scleractinian corals. Compared to the genes, the intergenic regions (IGRs) are more diverse. Interestingly, minisatellite sequences were identified in the IGRs between COX1 and trnM (IGR [COX1] [-] [trnM]) and between ND4 and rrnS (IGR [ND4] [-] [rrnS]) of most Fungiidae mitogenomes. Primarily due to the existence of minisatellites in IGR [COX1] [-] [trnM] , the length of Fungiidae mitogenomes varies from 16,292 to 17,399 bp. Similar to the phylogenetic tree based on partial COI sequences, Bayesian phylogenetic trees constructed using 13 PCGs, IGR [COX1] [-] [trnM] and IGR [ND4] [-] [rrnS] divide Fungiidae into four distinct clades. However, the latter three trees provide a higher resolution of genus- and species-level evolutionary relationships. This mitogenome dataset will be valuable for better understanding the phylogeny of Fungiidae. The diverse IGRs in these mitogenomes may serve as a useful resource for developing Fungiidae DNA barcodes, while the identified minisatellites can facilitate studies on the population biology of Fungiidae.},
}

@article {pmid40746709,
year = {2025},
author = {Crous, PW and Catcheside, DEA and Catcheside, PS and Alfenas, AC and Alfenas, RF and Barreto, RW and Lebel, T and Balashov, S and Broadbridge, J and Jurjević, Ž and De la Peña-Lastra, S and Hoffmann, R and Mateos, A and Riebesehl, J and Shivas, RG and Soliz Santander, FF and Tan, YP and Altés, A and Bandini, D and Carriconde, F and Cazabonne, J and Czachura, P and Gryta, H and Eyssartier, G and Larsson, E and Pereira, OL and Rigueiro-Rodríguez, A and Wingfield, MJ and Ahmad, W and Bibi, S and Denman, S and Esteve-Raventós, F and Hussain, S and Illescas, T and Luangsa-Ard, JJ and Möller, L and Mombert, A and Noisripoom, W and Olariaga, I and Pancorbo, F and Paz, A and Piątek, M and Polman-Short, C and Suárez, E and Afshan, NS and Ali, H and Arzanlou, M and Ayer, F and Barratt, J and Bellanger, JM and Bidaud, A and Bishop-Hurley, SL and Bohm, M and Bose, T and Campo, E and Chau, NB and Çolak, ÖF and Cordeiro, TRL and Cruz, MO and Custódio, FA and Couceiro, A and Darmostuk, V and Dearnaley, JDW and de Azevedo Santiago, ALCM and de Freitas, LWS and Yáñez-Morales, MJ and Domnauer, C and Dentinger, B and Dhileepan, K and De Souza, JT and Dovana, F and Eberhardt, U and Eisvand, P and Erhard, A and Fachada, V and García-Martín, A and Groenewald, M and Hammerbacher, A and Harms, K and Haroon, S and Haqnawaz, M and Henriques, S and Hernández, AJ and Jacobus, LM and Jaen-Contreras, D and Jangsantear, P and Kaygusuz, O and Knoppersen, R and Kumar, TKA and Lynch, MJ and Mahiques, R and Maraia, GL and Marbach, PAS and Mehrabi-Koushki, M and Miller, PR and Mongkolsamrit, S and Moreau, PA and Oberlies, NH and Oliveira, JA and Orlovich, D and Pérez-Méndez, AS and Pinto, A and Raja, HA and Ramírez, GH and Raphael, B and Rodrigues, A and Rodrigues, H and Ramos, DO and Safi, A and Sarwar, S and Saar, I and Sánchez, RM and Santana, JS and Scrace, J and Sales, LS and Silva, LNP and Stryjak-Bogacka, M and Tacconi, A and Thanh, VN and Thomas, A and Thuy, NT and Toome, M and Valdez-Carrazco, JM and van Vuuren, NI and Vasey, J and Vauras, J and Vila-Viçosa, C and Villarreal, M and Visagie, CM and Vizzini, A and Whiteside, EJ and Groenewald, JZ},
title = {Fungal Planet description sheets: 1781-1866.},
journal = {Persoonia},
volume = {54},
number = {},
pages = {327-587},
pmid = {40746709},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Septoria reinamora on leaf spots of Mutisia spinosa. Australia, Cortinarius albofolliculus on mossy soil, Cortinarius descensoriformis among leaf litter, Cortinarius kaki among leaf litter, Cortinarius lissosporus in leaf litter, Cortinarius malogranatus in leaf litter, Cortinarius meletlac on soil in mixed forest, Cortinarius sebosioides in long decayed wood litter, Helicogermslita australiensis as an endophyte from healthy leaves of Archontophoenix cunninghamiana, Puccinia clemensiorum on culms of Eleocharis ochrostachys, Puccinia geethae on leaves of Cyperus brevifolius, Puccinia marjaniae on leaves of Nymphoides indica, Puccinia scleriae-rugosae on leaves of Scleria rugosa. Brazil, Dactylaria calliandrae on living leaf of Calliandra tweediei, Mucor cerradoensis from soil, Musicillium palmae on living leaves of unidentified palm species, Neodendryphiella agapanthi from stalks of Agapanthus praecox, Parafusicladium riodejaneiroanum on living leaves of native bamboo, Parapenidiella melastomatis on living leaves of unidentified Melastomataceae, Pararamichloridium ouropretoense on living leaves of unidentified Poaceae, Pentagonomyces endophyticus (incl. Pentagonomyces gen. nov.) as endophytic from roots of Musa acuminata, Polyschema endophytica from healthy roots of coffee plant, Purimyces endophyticus as root endophyte of Cattleya locatellii, Ramularia rhododendri on living leaves of Rhododendron sp., Staphylotrichum soli from soil, Trichoderma sexdentis from leaves inside a nest of the leaf-cutting ant Atta sexdens rubropilosa, Wiesneriomyces soli from soil. France, Cosmospora nemaniae on dead or effete stromata of Nemania cf. colliculosa, Inocybe alnobetulae in subalpine green alder stands, Stylonectria hygrophila on dead twigs of Betula pubescens. Germany, Coniochaeta corticalis from bark humus, Coniochaeta fermentaria from fermentation residues from biogas plants, Coniochaeta fibricola from softwood fibres, Coniochaeta weberae from bark humus, Inocybe canicularis on calcareous to more acidic soil with conifers. Iceland, Inocybe islandica associated with Dryas octopetala. India, Vishniacozyma indica on dead twigs. Iran, Botryotrichum lycii on rotten leaf of Lycium depressum. Italy, Cuphophyllus dolomiticus among Salix retusa, Salix reticulata and Dryas octopetala, Inocybe subentolomospora on moss with the presence of Alnus incana, Populus nigra and Salix spp. Malaysia, Catenulostroma pellitae on leaf spots of Eucalyptus pellita. Mexico, Colletotrichum mexicanus from fruit of Persea americana cv. Hass. New Caledonia (France), Cortinarius caeloculus, Cortinarius luteigemellus and Cortinarius perpensus on soil under Nothofagus aequilateralis. New Zealand, Cytospora braithwaitei on branch of Malus domestica. Pakistan, Callistosporium khalidii on humus soil, Entoloma lilacinum on litter in conifer forest, Laccaria decolorans on litter in broad-leaved subtropical forest. Poland, Pseudoneoconiothyrium modrzynanum from resin of Larix decidua ssp. polonica, Tuberculiforma enigmatica isolated from sooty mould community on Quercus robur leaves. Portugal, Clavulus hemisphaericus (incl. Clavulus gen. nov.) on mossy slopes and under Laurus leaf litter, Entoloma daegae on sandy, granitic soil, Hygrocybe aurantiocitrina under laurel forest, Hygrocybe sanguineolutea gregarious in laurel forest, Hygrocybe vulcanica on mossy areas of laurel forest areas, Pachyphlodes algarvensis on sandy soil under Cistus salvifolius, Quercus suber and Pinus pinea. South Africa, Amycosphaerella podalyriae on leaf of Podalyria calyptrata, Erythrobasidium eucalypti from the gut of Gonipterus sp., Letendraea goniomae on leaves of Gonioma kamassi, Pezicula brabeji and Sphaerulina brabeji on twigs of Brabejum stellatifolium, Stachybotrys conicosiae on dead flower head of Conicosia elongata, Talaromyces ignescens from soil. Spain, Cortinarius phaeobrunneus on soil under Quercus ilex and Q. faginea, Inocybe pini-halepensis among grass and fallen leaves of Pinus halepensis, Inocybe subporcorum in sandy soils under Quercus ilex subsp. ballota and Pinus pinaster, Mycena morenoi on dead leaves of Betula pubescens and Salix atrocinerea, Pachyphlodes iberica on clayey and loamy soil under Quercus ilex and Quercus rotundifolia, Ramariopsis coronata in laurel forest. Switzerland, Inocybe minata in a bog on very wet acidic soil with Salix spp. and Betula spp. Thailand, Hypocrella khonsanitii on scale insects (Coccidae), Petchiella hymenopterorum on hymenopteran pupae in the nest (Hymenoptera). Trinidad and Tobago, Neodevriesia maravalensis from office swab. Türkiye, Russula anatolica under Quercus vulcanica. UK, Paracylindrosporium dactylorhizae (incl. Paracylindrosporium gen. nov.) on leaf spots of Dactylorhiza sp., Niesslia hepworthiae and Niesslia libertiae on living leaves of Libertia grandiflora. Ukraine, Lichenohendersonia cetrariae on thallus of terricolous Cetraria aculeata. USA, Atromagnispora indianensis (incl. Atromagnispora gen. nov.) on submerged wood in a freshwater stream, Cytospora michiganensis from utility room (settle plate), Exophiala aeris from air (settle plate), Hongoboletus americanus from mixed pine-hardwood forest, Lorrainsmithia pennsylvanica from bedroom, air, Superstratomyces massachusettsanus from lyse buffer. Vietnam, Aspergillus halopiscium on dry marine anchovy Stolephorus commersonnii. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Catcheside DEA, Catcheside PS, Alfenas AC, Alfenas RF, Barreto RW, Lebel T, Balashov S, Broadbridge J, Jurjević Ž, De la Peña-Lastra S, Hoffmann R, Mateos A, Riebesehl J, Shivas RG, Soliz Santander FF, Tan YP, Altés A, Bandini D, Carriconde F, Cazabonne J, Czachura P, Gryta H, Eyssartier G, Larsson E, Pereira OL, Rigueiro-Rodríguez A, Wingfield MJ, Ahmad W, Bibi S, Denman S, Esteve-Raventós F, Hussain S, Illescas T, Luangsa-ard JJ, Möller L, Mombert A, Noisripoom W, Olariaga I, Pancorbo F, Paz A, Piątek M, Polman-Short C, Suárez E, Afshan NS, Ali H, Arzanlou M, Ayer F, Barratt J, Bellanger J-M, Bidaud A, Bishop-Hurley SL, Bohm M, Bose T, Campo E, Chau NB, Çolak ÖF, Cordeiro TRL, Cruz MO, Custódio FA, Couceiro A, Darmostuk V, Dearnaley JDW, de Azevedo Santiago ALCM, de Freitas LWS, de J Yáñez-Morales M, Domnauer C, Dentinger B, Dhileepan K, De Souza JT, Dovana F, Eberhardt U, Eisvand P, Erhard A, Fachada V, García-Martín A, Groenewald M, Hammerbacher A, Harms K, Haroon S, Haqnawaz M, Henriques S, Hernández AJ, Jacobus LM, Jaen-Contreras D, Jangsantear P, Kaygusuz O, Knoppersen R, Kumar TKA, Lynch MJ, Mahiques R, Maraia GL, Marbach PAS, Mehrabi-Koushki M, Miller PR, Mongkolsamrit S, Moreau P-A, Oberlies NH, Oliveira JA, Orlovich D, Pérez-Méndez AS, Pinto A, Raja HA, Ramírez GH, Raphael B, Rodrigues A, Rodrigues H, Ramos DO, Safi A, Sarwar S, Saar I, Sánchez RM, Santana JS, Scrace J, Sales LS, Silva LNP, Stryjak-Bogacka M, Tacconi A, Thanh VN, Thomas A, Thuy NT, Toome M, Valdez-Carrazco JM, van Vuuren NI, Vasey J, Vauras J, Vila-Viçosa C, Villarreal M, Visagie CM, Vizzini A, Whiteside EJ, Groenewald JZ. (2025). Fungal Planet description sheets: 1781-1866. Persoonia 54: 327-587. doi: 10.3114/persoonia.2025.54.10.},
}

@article {pmid40746704,
year = {2025},
author = {Xie, ML and Dima, B and Wang, K and Phukhamsakda, C and Li, Y and Qi, LL and Li, GJ and Liu, TZ and Jia, PS and Wang, Q and Song, LR and Wei, TZ and Li, Y},
title = {Taxonomy and phylogeny of Cortinarius sect. Anomali in China.},
journal = {Persoonia},
volume = {54},
number = {},
pages = {225-263},
pmid = {40746704},
issn = {0031-5850},
abstract = {Cortinarius section Anomali is a species-rich group that occurs worldwide, particularly in Europe and North America. The overlapping morphological and microscopical characteristics of Anomali species pose significant challenges for species identification. Therefore, the focus of this study was to clarify the taxonomy and phylogeny of section Anomali in China. A total of 229 specimens of section Anomali were collected in China over the past two decades. The present study, based on a combination of extensive morphological investigations and molecular methods, reports 22 Anomali species. Eleven of them are recognized as new to science and formally described here as C. albocyaneoides, C. campanianomalus, C. microalbocyaneus, C. neocaninus, C. qilianensis, C. robustianomalus, C. rufolilacinus, C. subalbocyaneus, C. subanomalus, C. xizangensis, and C. vernalianomalus, respectively. Cortinarius albocyaneus, C. azureovelatus, C. caninus, C. kranabetteri, C. lepidopus, and C. perrotensis are reported in China for the first time. In addition, the occurrence of C. cinnamomeolilacinus, C. epsomiensis, C. subclackamasensis, C. tabularis, and C. tropicus in China is confirmed. Descriptions, accompanied by illustrations of morphological characters of the Chinese Anomali species, and comparisons with closely related taxa are provided. The present study reports Cortinarius section Anomali in China or Asia, clarifying taxonomy and conducting phylogeny analyses based on nrITS, nrLSU, rpb1 and rpb2 sequences. We compare the Anomali species from China with those in Europe and North America, enriching the species and sequences of sect. Anomali. In addition, the ornamentation of basidiospores was studied using scanning electron microscopy. Citation: Xie ML, Dima B, Wang K, Phukhamsakda C, Li Y, Qi LL, Li GJ, Liu TZ, Jia PS, Wang Q, Song LR, Wei TZ, Li Y (2025). Taxonomy and phylogeny of Cortinarius sect. Anomali in China. Persoonia 54: 225-263. doi: 10.3114/persoonia.2025.54.07.},
}

@article {pmid40744379,
year = {2025},
author = {Joseph, L and Murugesan, M and Jayarajan, J and Poojary, A and Ramasamy, J and Agarwal, V},
title = {Gap Assessment in Implementation of Biomedical Waste Management in Health Care Facilities: Nationwide Survey in India.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {100947},
doi = {10.1016/j.ijmmb.2025.100947},
pmid = {40744379},
issn = {1998-3646},
abstract = {BACKGROUND: Biomedical Waste (BMW) management presents significant challenges globally. Despite the establishment of BMW management rules in India and their subsequent amendments, compliance gaps persist. To address these, the Consortium of Accredited Health Care Organizations (CAHO) conducted a nationwide survey aimed to identify gaps in the implementation of the BMW rules in India.

METHODS: The survey was designed by CAHO in collaboration with experts across India. A validated tool with 144 questions captured information on BMW management practices across India. A purposive sampling technique was conducted via online survey tool from July to September 2023. Compliance among healthcare facilities (HCFs) was analyzed, and geographical maps were created.

RESULTS: A total of 267 HCFs responded to the survey with 178 (67%) were accredited. Among them, 51% of the HCFs directly discarded the needles in the sharps container and 49% cut the needles before disposal. In 50% of HCFs blue bins with blue covers were used. Around 115 (43%) only used dedicated tags to secure the BMW and 58% fully implemented barcoding. Autoclaving of laboratory waste was done in 211 HCFs (79%). Dedicated temporary storage areas were found in 245 (92%) HCFs. Mercury filled devices were still in use in 75 (28%) of the HCFs.

CONCLUSION: The survey provides valuable insights into the BMW management practices, gaps and areas of improvement in India. The most notable variations evidenced are sharps disposal practices, usage of blue bins, disposal of pharmaceutical waste and continued use of mercury devices.},
}

@article {pmid40743803,
year = {2025},
author = {Philpott, DE and Villacorta-Rath, C and DiBattista, JD and Rasheed, MA and Waltham, NJ and Smith, TM and York, PH},
title = {From nets to barcodes: Selecting suitable methods for assessing fish and prawn assemblages in seagrass meadows.},
journal = {Marine environmental research},
volume = {211},
number = {},
pages = {107395},
doi = {10.1016/j.marenvres.2025.107395},
pmid = {40743803},
issn = {1879-0291},
abstract = {Seagrass meadows are vital coastal ecosystems that support fish and prawn assemblages, providing essential resources such as food and refuge. They are especially important as nursery habitats for ecologically and economically important juvenile fish and prawns. However, seagrass ecosystems are declining globally due to their vulnerability to both natural disturbances and anthropogenic impacts. Effective monitoring and management strategies are therefore essential to ensure their conservation and ecological functionality. This review synthesises literature on methods for sampling fish and prawns in seagrass habitats, grouping them into three categories: capture, sensory, and molecular approaches. Capture methods, including beam trawls and seine nets, provide valuable biological data, but are extractive and can be destructive to the surrounding habitat. Sensory methods such as baited remote underwater video systems (BRUVs) and hydroacoustic techniques, offer a non-destructive alternative, but can be negatively influenced by environmental conditions such as turbidity and habitat complexity that are common in seagrass meadows. Molecular approaches, particularly environmental DNA (eDNA) metabarcoding, present a highly sensitive and non-invasive alternative approach, but challenges remain in quantifying species abundance and demographics. To guide method selection, we propose a structured framework of questions and visualisations to assist researchers in selecting the most appropriate sampling methods based on their specific research objectives. Given the biases and limitation of these methods individually, we suggest integrating multiple methods to enhance assessments of marine communities in seagrass habitats. Future research should focus on refining these methodologies to improve the accuracy of biodiversity monitoring in seagrass meadows, whilst minimising environmental impacts.},
}

@article {pmid40738429,
year = {2025},
author = {Chakraborty, R and Kannan, SP and Afrose, N and Narayanasamy, D},
title = {Tumor microenvironment expressed enzymes (Matrix metalloproteinases, cathepsins, urokinase-type plasminogen activator) triggered polymersomes for liquid biopsy and cancer diagnostics: A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {146375},
doi = {10.1016/j.ijbiomac.2025.146375},
pmid = {40738429},
issn = {1879-0003},
abstract = {Enzyme-triggered polymersomes have emerged as a transformative platform in liquid biopsy and cancer diagnostics, enabling high-accuracy biomarker detection through precise enzymatic responsiveness. This review comprehensively examines the rational design, synthesis, and functionalization strategies of enzyme-responsive polymersomes, which undergo programmed structural changes in the presence of tumor microenvironment-associated enzymes such as matrix metalloproteinases (MMPs), cathepsins, and urokinase-type plasminogen activator (uPA). Key advances in polymer chemistry, including block copolymer self-assembly, stimuli-responsive linker integration, and surface ligand conjugation, have been critical in tailoring polymer specificity, enzymatic sensitivity, and biocompatibility. These engineered nanocarriers exploit the overexpression of tumor-associated proteases and lipases to selectively release DNA stains, fluorescent probes, contrast agents, and molecular barcodes, facilitating ultrasensitive detection of circulating tumor cells (CTCs), extracellular vesicles (EVs), and cell-free nucleic acids (cfNAs) in liquid biopsies. Recent innovations in enzyme-triggered cargo release mechanisms, CRISPR-integrated biosensing, and machine learning-enhanced biomarker analysis have further amplified diagnostic precision. Additionally, multifunctional polymersomes bridge diagnostics and therapy, serving as potent theranostic agents. By integrating advanced material synthesis with enzymatic targeting, these systems offer minimally invasive, real-time monitoring and personalized cancer detection. This review highlights current breakthroughs and future directions in enzyme-responsive nanotechnology, underscoring its potential to revolutionize precision oncology.},
}

@article {pmid40737112,
year = {2025},
author = {Lancioni, GE and Alberti, G and Filippini, C and Abbinante, F and Singh, NN and O'Reilly, MF and Sigafoos, J},
title = {Technology and instructions to help people with blindness and intellectual disability manage indoor travel: a case series study.},
journal = {Disability and rehabilitation. Assistive technology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/17483107.2025.2541039},
pmid = {40737112},
issn = {1748-3115},
abstract = {PURPOSE: We evaluated a new technology system designed to help eight people with blindness and intellectual disability navigate indoor routes 70- to 140-meter long.

METHODS: The technology system entailed (a) a smartphone linked to two barcode readers that the participants wore, (b) barcodes printed on A-4 sheets of paper and displayed along the travel routes, and (c) a mini speaker. The technology system was set to provide verbal instructions at specific points of the travel routes to guide the participants to the destinations (to help them complete the scheduled traveling trials correctly). Each participant was exposed to an ABAB design in which A and B represented baseline phases (without system) and intervention phases (with system), respectively.

RESULTS: During the first baseline phase, the participants did not complete any traveling trial correctly (i.e., without research assistants' guidance). During the first intervention phase, the participants' percentage of traveling trials completed correctly increased to 83-97. The percentage declined during the second baseline phase and increased again (to 93-98) during the second intervention phase.

CONCLUSIONS: The findings suggest that the new system providing verbal instructions at specific points of the travel routes can help people with blindness and intellectual disability reach their scheduled destinations.},
}

@article {pmid40735452,
year = {2025},
author = {Feka-Homsy, P and L'Huillier, AG and Monod, L and Monin, E and Guinand, N and Schwob, JM},
title = {Cochliomyia hominivorax aural myiasis in a 7-year-old traveler.},
journal = {IDCases},
volume = {41},
number = {},
pages = {e02327},
pmid = {40735452},
issn = {2214-2509},
abstract = {•This is a very rare case of aural Cochliomyia hominivorax diagnosed in a pediatric-traveler outside endemic area.•Unlike common travelers' myiasis, Cochliomyia hominivorax can be invasive and destructive.•Cytochrome-C oxidase-I (COI) DNA-barcoding may be a useful tool for diagnosing rare parasitosis.},
}

@article {pmid40735391,
year = {2025},
author = {Loyola, DC and Placko, A and Fessl, B and McNew, SM},
title = {Novel microfilariae detected in Galápagos passerines.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {28},
number = {},
pages = {101115},
pmid = {40735391},
issn = {2213-2244},
abstract = {Emerging parasites pose a serious risk to the health and survival of wild animal populations, particularly on islands where species often lack prior exposure and evolved defenses. We present the first report of a novel microfilaria infection found in blood from six species of Galápagos passerines in the coastal zone of Santa Cruz Island. Across 13 months, spanning two wet seasons and one dry season, 294 individuals were sampled and evaluated for microfilarial presence through microscopy and/or polymerase chain reaction. We barcoded the mitochondrial Cytochrome c oxidase I (COI) gene to tentatively place this microfilaria in the genus Eufilaria. We found host species level variation in infection, with certain species, like the vegetarian finch (Platyspiza crassirostris) and the common cactus finch (G eospiza . scandens) having very high prevalence, while others, like the Galápagos mockingbird (Mimus parvulus) and small tree finch (Camarhynchus parvulus) showing significantly lower prevalence. We investigated leukocyte counts, H/L ratios and body condition to evaluate the potential effects of infection on birds and found no relationship between infection status and these health indices. We also tested to see if seasonality could predict the infection trends found in our data and found a relationship with monthly rainfall, where more rain predicts higher microfilarial prevalence. Although we cannot confirm exactly when this parasite established in the Galápagos, our study highlights the importance of continued disease surveillance in endemic systems and underscores the need for species-level COI barcodes to improve microfilaria identification and phylogenetics.},
}

@article {pmid40734901,
year = {2025},
author = {Liu, J and Zang, E and Tian, Y and Li, X and Xin, T and Zeng, L and Xu, L and Xiao, P},
title = {Applications and challenges of DNA barcoding in rapid radiation groups: Rhodiola (Crassulaceae) as a case study.},
journal = {Chinese herbal medicines},
volume = {17},
number = {3},
pages = {555-561},
pmid = {40734901},
issn = {2589-3610},
abstract = {OBJECTIVE: Rhodiolae Crenulatae Radix et Rhizoma (Hongjingtian in Chinese, RCRR), the roots and rhizomes of Rhodiola crenulata and its application in the medicinal market is very chaotic. In this study, DNA barcoding database and identification engine of Rhodiola species were established, decoction pieces from the medicinal market were identified, and the application and challenges of DNA barcoding in the rapid radiation of Rhodiola species were analyzed. This study provides reference for the protection, rational development, and utilization of endangered resources within Rhodiola species.

METHODS: A total of 50 original plant samples from 20 species of the genus Rhodiola from Hebei, Xinjiang, Tibet, Jilin, and other major production areas were collected. Theses samples cover the typical distribution area (Qinghai-Tibetan Platea) of Rhodiola species and other scattered alpine regions (Changbai Mountain, Taibai Mountain, Lushan Mountain, etc.), it encompasses all Rhodiola species with thick rhizomes in China. ITS2 and psbA-trnH barcode of Rhodiola database (BORD) were established and an identification engine named Rhodiola-IDE was developed. The stability and accuracy of the standard DNA barcoding database were evaluated using two datasets. Rhodiola-IDE identified 31 decoction pieces of RCRR from the medicinal material market.

RESULTS: The BORD containing 1 532 sequences of 88 Rhodiola species has been established, and the identification efficiency results showed good accuracy and stability. According to the Chinese Pharmacopoeia (2020 edition), 23 samples (74.2%) were identified as authentic R. crenulata, while the rest of the marketed varieties were R. kirilowii, R. dumulosa, and R. fastigiata. The product label "Larger flower, Hongjingtian" was identified as R. crenulata. Samples labeled as "Smaller flower, Hongjingtian" were identified as R. crenulata, R. kirilowii, and R. fastigiata.

CONCLUSION: ITS2 and psbA-trnH barcodes can identify monophyletic groups represented by R. crenulata. However, for non-monophyletic species, it is necessary to collect as many samples as possible and combine them with multiple markers for joint identification. This study discussed the application and challenges of DNA barcodes in Rhodiola under rapid radiation conditions, providing a scientific basis for the rational development and utilization of Rhodiola varieties.},
}

@article {pmid40733470,
year = {2025},
author = {Amin, A and Park, S},
title = {Chemotaxonomy, an Efficient Tool for Medicinal Plant Identification: Current Trends and Limitations.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40733470},
issn = {2223-7747},
abstract = {This review highlights the critical role of chemotaxonomy in the identification, authentication, and discovery of bioactive compounds in medicinal plants. By analyzing secondary metabolites using techniques like UV spectroscopy, FTIR, HPLC, GC-MS, NMR, LC-MS-Qtof, and MALDI-TOF MS, chemotaxonomy ensures accurate plant identification, supporting the safe and effective use of plants in herbal medicine. Key secondary metabolites used in chemotaxonomic identification include alkaloids, flavonoids, terpenoids, phenolics, tannins, and plant peptides. Chemotaxonomy also facilitates the discovery of novel compounds with therapeutic potential, contributing to drug development. The integration of chemotaxonomy with genomics and proteomics allows a deeper understanding of plant biosynthesis and the mechanisms behind bioactive compound production. However, challenges due to variability in metabolite profiles and the lack of standardized methods remain, and future research should focus on developing global databases, improving standardization, and incorporating artificial intelligence and machine learning to enhance plant identification and bioactive compound discovery. The integration of chemotaxonomy with personalized medicine offers the potential to tailor plant-based therapies to individual genetic profiles, advancing targeted treatments. This review underscores chemotaxonomy's importance in bridging traditional knowledge and modern science, offering sustainable solutions for medicinal plant use and drug development.},
}

@article {pmid40732093,
year = {2025},
author = {Frolova, MS and Kiselev, SS and Panyukov, VV and Ozoline, ON},
title = {Phylogroup Homeostasis of Escherichia coli in the Human Gut Reflects the Physiological State of the Host.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071584},
pmid = {40732093},
issn = {2076-2607},
support = {24-14-00433//Russian Science Foundation/ ; },
abstract = {The advent of alignment-free k-mer barcoding has revolutionized taxonomic analysis, enabling bacterial identification at phylogroup resolution within natural communities. We applied this approach to characterize Escherichia coli intraspecific diversity in human gut microbiomes using publicly available datasets representing diverse human physiological states. By estimating the relative abundance of eight E. coli phylogroups defined by their 18-mer markers in 558 fecal samples, we compared their distribution between gut microbiomes of healthy individuals, patients with chronic bowel diseases and volunteers subjected to various external interventions. Across all datasets, phylogroups exhibited bidirectional abundance shifts in response to host physiological changes, indicating an inherent bimodality in their adaptive strategies. Correlation analysis of phylogroup persistence revealed positive intraspecific connectivity networks and dependence of their patterns on both acute interventions like antibiotic or probiotic treatment and chronic bowel disorders. Along with predominantly negative correlations with Bacteroides, we observed a transition from positive to negative associations with Prevotella in Prevotella-rich microbiomes. Several interspecific correlations individually established by E. coli phylogroups with dominant taxa suggest their potential role in shaping intraspecific networks. Machine learning techniques statistically confirmed an ability of phylogroup patterns to discriminate the physiological state of the host and virtual diagnostic assays opened a way to optimize intraspecific phylotyping for medical applications.},
}

@article {pmid40730955,
year = {2025},
author = {Castellanos, NL and Gunawardana, DN and McCarthy, B and Sathish, P and George, S and Li, D},
title = {Mitochondrial genome of Bactrocera fruit flies (Tephritidae: Dacini): features, structure, and significance for diagnosis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {700},
pmid = {40730955},
issn = {1471-2164},
support = {406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; },
mesh = {Animals ; *Tephritidae/genetics/classification ; *Genome, Mitochondrial ; Phylogeny ; },
abstract = {BACKGROUND: True fruit flies (Diptera: Tephritidae) are among the most destructive pests of fruit and vegetables worldwide and are on the top of quarantine pest lists. To respond effectively to a fruit fly invasion, we need to identify the species rapidly and reliably to understand its biological features and guide response decisions. Molecular techniques have been used to improve the diagnostic ability circumventing many difficulties of morphological identification. However, the commonly used Cytochrome Oxidase I (COI) gene lacks sufficient variation to distinguish species within Bactrocera species complexes. Here we conducted mitochondrial genome sequencing to identify additional genetic markers that could aid diagnosis of Bactrocera fruit fly species.

RESULTS: We assembled 82 complete mitochondrial genomes from 16 Bactrocera species, including 13 species for which no mitochondrial genome data were previously available, as well as one species each from Dacus aneuvittatus, Dirioxa pornia and Zeugodacus gracilis. Phylogenetic analysis of the Tephritidae family confirmed the monophyly of the Bactrocera genus but could not properly resolve species within species complexes. Comparative mitochondrial genome analysis revealed that intergenic spacer and NADH dehydrogenase genes, specifically ND2 and ND6, harbour enough variations for new specific real-time PCR assays. Based on these findings, six TaqMan-based real-time PCR assays targeting ND2, COI, and CO3 genes were successfully designed and assessed for their specificity and sensitivity in detecting Bactrocera curvipennis, a member of the B. tryoni complex. Of these, one real-time PCR assay targeting the ND2 gene proved to be the most specific and sensitive. It detects B. curvipennis specifically at the level of 1 copy/µL of target DNA.

CONCLUSIONS: Mitochondrial sequence analysis and comparative studies indicate that mitochondrial genomes offer valuable genetic markers for accurate diagnosis of Bactrocera fruit flies. The successful development of the B. curvipennis real-time PCR assay highlights the importance of having additional genetic markers to advance the molecular diagnostics in economically important Bactrocera species.},
}

Animals
*Tephritidae/genetics/classification
*Genome, Mitochondrial
Phylogeny

@article {pmid40730843,
year = {2025},
author = {Li, N and Tang, TT and Gu, M and Fu, YQ and Qian, WW and Ma, NN and Shen, AR and Zhu, T and Huo, RB and Zhang, T and Xie, JF and Zhang, L and Liu, BC and Lv, LL},
title = {Single urinary extracellular vesicle proteomics identifies complement receptor CD35 as a biomarker for sepsis-associated acute kidney injury.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6960},
doi = {10.1038/s41467-025-62229-4},
pmid = {40730843},
issn = {2041-1723},
mesh = {Humans ; Biomarkers/urine ; *Extracellular Vesicles/metabolism ; *Acute Kidney Injury/urine/diagnosis/etiology ; Male ; Proteomics/methods ; Female ; Middle Aged ; *Sepsis/complications/urine ; *Receptors, Complement 3b/metabolism ; Aged ; Prospective Studies ; Podocytes/metabolism/pathology ; Adult ; ROC Curve ; },
abstract = {Sepsis-associated acute kidney injury (SA-AKI) portends severe health burden due to significant morbidity and mortality, while early diagnosis remains challenging. In this study, proximity-dependent barcoding assay (PBA) is established to profile the surface proteome of single urinary extracellular vesicle (uEV). Principle uEV clusters with unique function and origination are profiled in SA-AKI in a screening cohort. Complement receptor CD35 on single uEV (CD35-uEV) displays high diagnostic accuracy for SA-AKI (AUC-ROC 0.89 in validation cohort, n = 134). Besides, CD35-uEV enables identification of subclinical AKI (AUC-ROC 0.84 in prospective cohort, n = 72). Moreover, CD35-uEV correlates closely with AKI severity which also predicts persistent AKI (AUC-ROC 0.77), mortality risks (AUC-ROC 0.70) and progression to AKD (AUC-ROC 0.66). Multi-omics profiling reveals that CD35-uEV are predominantly released from injured podocytes exhibiting diminished CD35 expression. Overall, this study identifies a single uEV biomarker related to injured podocyte for early diagnosis and risk stratification of SA-AKI.},
}

Humans
Biomarkers/urine
*Extracellular Vesicles/metabolism
*Acute Kidney Injury/urine/diagnosis/etiology
Male
Proteomics/methods
Female
Middle Aged
*Sepsis/complications/urine
*Receptors, Complement 3b/metabolism
Aged
Prospective Studies
Podocytes/metabolism/pathology
Adult
ROC Curve

@article {pmid40728500,
year = {2025},
author = {Li, T and Gu, Z and Zhou, G},
title = {Next-Generation Barcoding for Single-Cell Omics.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c03587},
pmid = {40728500},
issn = {1520-6882},
abstract = {The ability to uniquely label and track individual cells at scale has become foundational to single-cell omics. Conventional barcoding strategies, ranging from plate-based combinatorial indexing to droplet microfluidics-based indexing, have enabled the rise of high-throughput single-cell profiling. However, these approaches each face trade-offs in throughput, cost, compatibility with complex biochemical workflows, or accessibility to nonspecialist laboratories. This perspective surveys the principles, benefits, and limitations of current barcoding methods and introduces emerging enzymatic and computational methods that may redefine how we uniquely index the cellular content, opening the door to simpler, more scalable, and more accessible single-cell analysis pipelines.},
}

@article {pmid40727006,
year = {2024},
author = {Abidin, DHZ and Nor, SAM and Seah, YG and Ali, MS and Jamaluddin, JAF and Rahim, MA and A, B and Zulkifly, NS and Tan, MP and Zain, KM and Jaafar, TNAM},
title = {An Odyssey of Integrative Taxonomy Unveils Marine Fish Diversity, New Records and Cryptic Species in Malaysian Waters.},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e30},
pmid = {40727006},
issn = {1810-522X},
abstract = {This study elucidates the species diversity of marine fishes in the Exclusive Economic Zone (EEZ) of Peninsular Malaysia (PM) using an integrative approach combining DNA barcoding and morphological identification. Our focus was on demersal surveys conducted on the east coast of PM in the South China Sea. We re-evaluated the diversity of 475 specimens across 93 putative species (92 barcoded morphospecies), from 16 orders and 41 families, including two IUCN vulnerable species. A total of two species - Saurida isarankurai and Oxyurichthys auchenolepis - are presented as new record, and three species - Nemipterus balinensoides, Gymnothorax reevesii and Synodus hoshinonis - as the first specimen-based records in Malaysian waters. Cytochrome c oxidase subunit I (COI) sequence analyses delineated 95 consensus Molecular Operational Taxonomic Units (MOTUs), exceeding morphological diversity. Interestingly, the barcode analysis revealed several MOTUs delimited within one morphologically identified fish species, with both intraspecific and interspecific genetic divergences exceeding 2%, indicating substantial intraspecific genetic divergence within species groups or the existence of morphologically cryptic species within our dataset. These findings highlight the complexity of species delimitation and the value of genetic methods. Our study provides valuable insights into marine fish diversity from the east coast of Peninsular Malaysia and enhances our understanding of genetic diversity, distribution, and conservation needs of ecosystems through DNA barcoding. By integrating DNA barcoding with morphology, we present a comprehensive framework for future research to develop conservation and management strategies for Malaysia's marine biodiversity. The expansion of the genetic barcode database generated in this study will facilitate future molecular taxonomy research.},
}

@article {pmid40725352,
year = {2025},
author = {Zhou, H and Yang, D and Li, X},
title = {Integrated Taxonomy Discovers Four New Species of Grypoctonus Speiser, 1928 (Diptera: Asilidae) from China.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725352},
issn = {2075-4450},
abstract = {The genus Grypoctonus Speiser, 1928 (Diptera: Asilidae) is a fuzzy-looking assassin fly, and adults have only been observed in autumn and winter. Currently containing four described species, this genus is readily distinguished from other Chinese asilids by the presence of two r-m crossveins. Through integrative taxonomic analysis of over 200 specimens from multiple Chinese provinces, we combined morphological assessment with DNA barcoding and four species delimitation methods (ABGD, ASAP, mPTP, and GMYC). Four species are newly described: G. aureussp. nov., G. sagittatussp. nov., G. solariussp. nov., and G. yongshanisp. nov. (the latter described solely from morphological examination of historical specimens). Genetic analyses revealed distinct barcoding gaps, with an interspecific distance of 1.38-7.07% versus an intraspecific distance of no more than 0.92%. We revised the generic diagnosis, provided a distribution map, and a revised key to all known species of Grypoctonus.},
}

@article {pmid40725306,
year = {2025},
author = {Xu, HF and Lv, MY and Zhao, Y and Zhang, ZC and Liu, Z and Lin, XL},
title = {Cryptic Diversity and Climatic Niche Divergence of Brillia Kieffer (Diptera: Chironomidae): Insights from a Global DNA Barcode Dataset.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725306},
issn = {2075-4450},
support = {12111300000018001-14//Innovative Research Project on the laboratory of Geo-Specimens Study and Testing at the Geological Museum of China/ ; 41502021//National Natural Science Foundation of China/ ; 31900344//National Natural Science Foundation of China/ ; 12110600000018003910//Ministry of Natural Resources' High-Level Scientific and Technological Innovation Talent Cultivation Program/ ; 2024HK157//Scientific Research Projects of the General Administration of Customs, China/ ; },
abstract = {Accurate species identification of small aquatic insects remains challenging due to their morphological similarities. This study addresses this issue by developing a DNA barcode reference library for the globally distributed Brillia (Diptera: Chironomidae). We analyzed cytochrome c oxidase subunit I (COI) sequences of 241 specimens belonging to 13 Brillia species from 18 countries, including 56 newly generated and 185 publicly available COI barcodes. Our integrated approach included genetic distance analysis, haplotype network construction, and ecological niche modeling. The results revealed remarkable cryptic diversity, with sequences clustering into 30 Barcode Index Numbers and 158 unique haplotypes, most being region-specific. Notably, East Asian and North American populations showed complete genetic distinctness, suggesting long-term isolation. Environmental factors, particularly temperature and precipitation gradients, were identified as key drivers of this diversification. The study also corrected several misidentifications in existing databases. These findings significantly advance our understanding of Brillia diversity and provide a reliable molecular tool for freshwater ecosystem monitoring, with important implications for biodiversity conservation and environmental assessment.},
}

@article {pmid40725296,
year = {2025},
author = {Jia, N and Ding, X and Xie, D and Chen, H and Chi, D and Yu, J},
title = {First Record of Dioryctria simplicella (Lepidoptera: Pyralidae) in China: Morphology, Molecular Identification, and Phylogenetic Position.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725296},
issn = {2075-4450},
support = {2022YFD140100//National Key R&D Program of China/ ; 2023ZX02B05//Key R&D Program of Heilongjiang Province/ ; },
abstract = {Dioryctria Zeller, 1846 (Lepidoptera: Pyralidae) is a significant genus whose species primarily infest coniferous trees and are predominantly distributed across the Northern Hemisphere. To date, 17 species within this genus have been recorded in China. This study reports the discovery of Dioryctria simplicella (Heinemann, 1863) in China. During field surveys in forests of Heilongjiang Province, D. simplicella was observed infesting the cones and trunks of Pinus sylvestris var. mongolica Litv. as larvae. Comprehensive morphological descriptions and diagnostic characteristics of the adult, larva, pupa, and egg stages of D. simplicella are provided herein to facilitate accurate species identification within the genus. Molecular phylogenetic analysis based on mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding sequences was conducted to assess the phylogenetic position of D. simplicella within Dioryctria. These results strongly support its species identity and clarify its phylogenetic relationships with congeners. This discovery not only expands the known diversity of Lepidoptera in China but also provides new data supporting taxonomic and phylogenetic studies of the genus Dioryctria.},
}

@article {pmid40725170,
year = {2025},
author = {Samarina, LS and Koninskaya, NG and Shkhalakhova, RM and Simonyan, TA and Tsaturyan, GA and Shurkina, ES and Kulyan, RV and Omarova, ZM and Tutberidze, TV and Ryndin, AV and Orlov, YL},
title = {The Potential of Universal Primers for Barcoding of Subtropical Crops: Actinidia, Feijoa, Citrus, and Tea.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40725170},
issn = {1422-0067},
mesh = {*Actinidia/genetics/classification ; *Citrus/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *Crops, Agricultural/genetics/classification ; *Tea/genetics ; Phylogeny ; },
abstract = {The molecular identification of valuable genotypes is an important problem of germplasm management. In this study, we evaluated the potential of 11 universal primer pairs for the DNA barcoding of locally derived cultivars of subtropical crops (actinidia, feijoa, citrus, and tea). A total of 47 accessions (elite cultivars, forms, and breeding lines) of these four genera were included in the study. The efficiency of the following universal primers was assessed using Sanger sequencing: ITS-p5/ITS-u4, ITS-p5/ITS-u2, ITS-p3/ITS-u4, 23S,4.5S&5S, 16S, petB/petD, rpl23/rpl2.l, rpl2 intron, rpoC1 intron, trnK intron, and trnE-UUC/trnT-GUU. Among these primers, trnE-UUC/trnT-GUU showed greater intraspecific polymorphisms, while rpl2 intron and 16S displayed the lowest polymorphism levels in all crops. In addition, the 23S,4.5S & 5S, and rpoC1 intron were efficient for intraspecific analysis of tea and actinidia species. Using five efficient chloroplast primers, a total of 22/6 SNPs/InDels were observed in tea accessions, 45/17 SNPs/InDels in actinidia, 23/3 SNPs/InDels in mandarins, and 5/4 SNPs/InDels in feijoa. These results will be useful for the further development of DNA barcodes of related accessions.},
}

*Actinidia/genetics/classification
*Citrus/genetics/classification
*DNA Barcoding, Taxonomic/methods
*DNA Primers/genetics
*Crops, Agricultural/genetics/classification
*Tea/genetics
Phylogeny

@article {pmid40725055,
year = {2025},
author = {Samarina, LS and Koninskaya, NG and Shkhalakhova, RM and Simonyan, TA and Kuzmina, DO},
title = {DNA-Barcoding for Cultivar Identification and Intraspecific Diversity Analysis of Agricultural Crops.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
doi = {10.3390/ijms26146808},
pmid = {40725055},
issn = {1422-0067},
mesh = {*Crops, Agricultural/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Genetic Variation ; DNA, Plant/genetics ; Computational Biology/methods ; },
abstract = {DNA barcoding of intraspecific diversity of agricultural crops is important to develop the genetic passports of valuable genotypes and cultivars. The advantage of DNA-barcoding as compared to traditional genotyping of cultivars is that the procedure can be unified and applied for the broad range of accessions. This not only makes it cost efficient, but also allows to develop open access genetic databases to accumulate information of the world's germplasm collections of different crops. In this regard, the aim of the review was to analyze the latest research in this field, including the selection of loci, universal primers, strategies of amplicons analysis, bioinformatic tools, and the development of databases. We reviewed the advantages and disadvantages of each strategy with the focus of cultivars identification. The data indicates that following chloroplast loci are the most prominent for the intraspecific diversity analysis: (trnE-UUC/trnT-GUU, rpl23/rpl2.l, psbA-trnH, trnL-trnF, trnK, rpoC1, ycf1-a, rpl32-trnL, trnH-psbA and matK). We suggest that the combination of three or four of these loci can be a sufficient DNA barcode for cultivar-level identification. This combination has to be selected for each crop. Advantages and disadvantages of different approaches of amplicons analysis are discussed. The bioinformatic tools and databases for the plant barcoding are reviewed. This review will be useful for selecting appropriate strategies for barcoding of intraspecific diversity of agricultural crops to develop genetic passports of valuable cultivars in germplasm collections worldwide.},
}

*Crops, Agricultural/genetics/classification
*DNA Barcoding, Taxonomic/methods
*Genetic Variation
DNA, Plant/genetics
Computational Biology/methods

@article {pmid40722035,
year = {2025},
author = {Andrianiaina, AF and Andry, S and Kettenburg, G and Ranaivoson, HC and Lacoste, V and Dussart, P and Heraud, JM and Laverty, TM and Guth, S and Young, KI and Andrianarimisa, A and Brook, CE},
title = {Diversity and seasonality of ectoparasite burden on two species of Madagascar fruit bat, Eidolon dupreanum and Rousettus madagascariensis.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {302},
pmid = {40722035},
issn = {1756-3305},
support = {EC-64015R-20//National Geographic Society/ ; 102825//National Geographic Society/ ; 1R01AI129822-01/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; },
mesh = {Animals ; *Chiroptera/parasitology/classification ; Madagascar/epidemiology ; *Ectoparasitic Infestations/veterinary/epidemiology/parasitology ; Seasons ; DNA Barcoding, Taxonomic ; *Diptera/classification/genetics/physiology ; Female ; Male ; Biodiversity ; Phylogeny ; Mites/genetics/classification ; },
abstract = {BACKGROUND: Bats are important reservoir hosts for a variety of pathogens, some of which are transmitted by ectoparasite vectors including mites, fleas, lice, ticks, and bat flies (families Nycteribiidae and Streblidae). All these ectoparasite taxa are known to parasitize two endemic fruit bats of Madagascar, Eidolon dupreanum and Rousettus madagascariensis. We aimed to describe the diversity of ectoparasite infestation for both bat species through morphological observation and DNA barcoding and elucidate ecological and climatic correlates of seasonal nycteribiid parasitism of these hosts.

METHODS: Eidolon dupreanum and R. madagascariensis fruit bats were live-captured in northern and central-eastern Madagascar periodically from 2013 to 2020. Ectoparasites on all captured bats were counted and identified in the field and then collected into ethanol. Field identification of a subset of samples was confirmed via microscopy and DNA barcoding of the cytochrome C oxidase subunit 1 (COI) and 18S genes. The seasonal abundance of nycteribiid bat flies on both host bats was analyzed using generalized additive models, and the role of climate in driving this seasonality was assessed via cross-correlation analysis combined with generalized linear models. Phylogenetic trees were generated to compare COI and 18S sequences of Madagascar nycteribiid and streblid bat flies with available reference sequences from GenBank.

RESULTS: Ectoparasites corresponding to four broad taxa (mites, ticks, fleas, and bat flies) were recovered from 628 of 873 E. dupreanum (71.9%) and 831 of 862 R. madagascariensis (96.4%). Eidolon dupreanum were most commonly parasitized by Cyclopodia dubia nycteribiids and R. madagascariensis by Eucampsipoda madagascariensis nycteribiids and Megastrebla wenzeli streblids. We observed significant seasonality in nycteribiid abundance on both bat hosts, which varied by bat sex and was positively correlated with lagged temperature, precipitation, and humidity variables. Barcoding sequences recovered for all three bat fly species grouped with previously reported sequences, confirming morphological species identification. Our study contributes the first DNA barcodes of any kind reported for M. wenzeli and the first 18S barcodes for C. dubia.

CONCLUSIONS: This study explores the diversity and abundance of ectoparasite burdens in two Malagasy fruit bat species, highlighting the importance of seasonal ecology and the influence of climate variables on parasitism, which correlates with resource availability.},
}

Animals
*Chiroptera/parasitology/classification
Madagascar/epidemiology
*Ectoparasitic Infestations/veterinary/epidemiology/parasitology
Seasons
DNA Barcoding, Taxonomic
*Diptera/classification/genetics/physiology
Female
Male
Biodiversity
Phylogeny
Mites/genetics/classification

@article {pmid40722002,
year = {2025},
author = {Jordan, S and Pothier, JF and de Maayer, P and Broders, K and Kvitko, BH and Coutinho, TA and Smits, THM},
title = {Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {456},
doi = {10.1186/s12866-025-04175-1},
pmid = {40722002},
issn = {1471-2180},
support = {310030L_204333//Swiss National Science Foundation (SNSF)- South-African National Research Foundation (NRF) Lead Agency project/ ; 2019-51181-30013//USDA NIFA SCRI/ ; },
mesh = {*Enterobacter/genetics/classification/isolation & purification ; *Polymerase Chain Reaction/methods ; *DNA Primers/genetics ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.

RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.

CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.},
}

*Enterobacter/genetics/classification/isolation & purification
*Polymerase Chain Reaction/methods
*DNA Primers/genetics
DNA, Bacterial/genetics
Phylogeny

@article {pmid40720603,
year = {2025},
author = {Tran, HL and Zheng, W and Issadore, DA and Im, H and Cho, YK and Zhang, Y and Liu, D and Liu, Y and Li, B and Liu, F and Wong, DTW and Sun, J and Qian, K and He, M and Wan, M and Zeng, Y and Cheng, K and Huang, TJ and Chiu, DT and Lee, LP and Zheng, L and Godwin, AK and Kalluri, R and Soper, SA and Hu, TY},
title = {Extracellular Vesicles for Clinical Diagnostics: From Bulk Measurements to Single-Vesicle Analysis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c00706},
pmid = {40720603},
issn = {1936-086X},
abstract = {Extracellular vesicles (EVs) play a crucial role in intercellular communication, signaling pathways, and disease pathogenesis by transporting biomolecules such as DNA, RNA, proteins, and lipids derived from their cells of origin, and they have demonstrated substantial potential in clinical applications. Their clinical significance underscores the need for sensitive methods to fully harness their diagnostic potential. In this comprehensive review, we explore EV heterogeneity related to biogenesis, structure, content, origin, sample type, and function roles; the use of EVs as disease biomarkers; and the evolving landscape of EV measurement for clinical diagnostics, highlighting the progression from bulk measurement to single vesicle analysis. This review covers emerging technologies such as single-particle tracking microscopy, single-vesicle RNA sequencing, and various nanopore-, nanoplasmonic-, immuno-digital droplet-, microfluidic-, and nanomaterial-based techniques. Unlike traditional bulk analysis methods, these methods contribute uniquely to EV characterization. Techniques like droplet-based single EV-counting enzyme-linked immunosorbent assays (ELISA), proximity-dependent barcoding assays, and surface-enhanced Raman spectroscopy further enhance our ability to precisely identify biomarkers, detect diseases earlier, and significantly improve clinical outcomes. These innovations provide access to intricate molecular details that expand our understanding of EV composition, with profound diagnostic implications. This review also examines key research challenges in the field, including the complexities of sample analysis, technique sensitivity and specificity, the level of detail provided by analytical methods, and practical applications, and we identify directions for future research. This review underscores the value of advanced EV analysis methods, which contribute to deep insights into EV-mediated pathological diversity and enhanced clinical diagnostics.},
}

@article {pmid40720372,
year = {2025},
author = {Delocado, ED and Banzon, VRH and Sanchez, EGS},
title = {A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {221},
pages = {},
doi = {10.3791/68323},
pmid = {40720372},
issn = {1940-087X},
mesh = {*Coleoptera/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; Philippines ; },
abstract = {Biodiversity decline is transpiring at rates unimaginable, yet biodiversity monitoring is hampered by a plethora of factors, including the incomplete inventory of baseline diversity and the dwindling population of skilled taxonomists. Bridging this impediment in species inventory of "dark taxa", or hyperdiverse groups often understudied in taxonomy, is particularly crucial in the tropics facing insurmountable environmental pressures. While morphology-based alpha-taxonomy remains the gold standard in species identification, DNA-based methods have been showing tremendous potential in accelerating species delineation and discovery. Here, we describe a concoction pipeline for generating molecular operational taxonomic units (MOTUs) involving six molecular species delimitation approaches implemented on two highly inconspicuous beetle genera, namely Byrrhinus Motschulsky, 1858 of family Limnichidae and Anacaena Thomson, 1859 of family Hydrophilidae, from the Philippines. As this protocol focuses on processing DNA barcodes and given that these genetic data can be obtained either by sequencing or by downloading from online databases, the starting point for the protocol described here are the DNA sequences. Given the COI barcodes, the pipeline utilizes a combination of three threshold-based molecular species delimitation approaches, namely TaxonDNA, K2P, and ASAP, which use sequence alignment as input data. Additionally, the pipeline proceeds with three coalescent-based approaches, namely PTP-ML, PTP-BI, and mPTP, which require a tree file as input data. Some approaches entail the use of web servers, while others utilize local software. With the selection of algorithmic methods presented, MOTUs can be identified, whether by consensus or by majority. Remarkably, this pipeline delineated almost conspicuous beetle species from the Philippines, even those documented from the same or adjacent localities.},
}

*Coleoptera/genetics/classification
Animals
*DNA Barcoding, Taxonomic/methods
Philippines

@article {pmid40717983,
year = {2025},
author = {Li, X and Zhang, Y and Song, M and Xu, N and Qu, L and Li, H and Wang, Y and Duan, B and Zhang, Z},
title = {Molecular identification and phylogenetic analysis of confusing Tetrastigma species based on DNA barcoding and chloroplast genome.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1607947},
pmid = {40717983},
issn = {1663-9812},
abstract = {BACKGROUND: Tetrastigma plants are widely utilized in traditional medicine (such as Tetrastigma. obtectum and Tetrastigma. serrulatum, two important commonly medicinal plants), primarily for their properties in promoting blood circulation, strengthening bones and tendons, and so on. However, the high diversity of species differentiation poses a challenge in accurately identifying the various Tetrastigma species without specialized taxonomic knowledge.

MATERIALS AND METHODS: To screen the candidate barcode sequences of Tetrastigma species, we first report the complete chloroplasts (CP) genomes of T. obtectum and T. serrulatum obtained via high throughput Illumina sequencing and compare them with fourteen previously sequenced species. Furthermore, we collected fresh leaf samples from T. obtectum and T. serrulatum (totally 37 samples) and evaluated the discriminatory efficacy of the nuclear DNA Internal Transcribed Spacer 2 (ITS2) fragment through comparative analysis of sequence variations and secondary structures. Finally, to analyze the phylogenetic position of Tetrastigma species, we constructed a Maximum Likelihood (ML) phylogenetic tree using CP genome sequences of 46 species from seven genera within the Vitaceae family.

RESULTS AND DISCUSSION: The CP genomes of Tetrastigma exhibited a typical circular tetramerous structure, including a large single-copy region (LSC) (87,381-88,979 bp), a small single-copy region (SSC) (18,649-19,339 bp), and a pair of inverted repeats (IRa and IRb) (26,288-26,934 bp). The guanine-cytosine content of the CP genomes is 37.35%-37.62%. The codon usage shows a significant preference for end with A/T. Then, the results of nucleotide diversity analysis showed that ten polymorphic hotspots (psbM-trnD-GUC, ndhF-rpl32, trnS-GCU-trnG-UCC, ycf1, rpl32-trnL-UAG, trnS-UGA-psbZ, psbE-petL, matK-rps16, rpl16, and rpl22) could be the candidate DNA marker suitable for Tetrastigma species. Furthermore, our results demonstrate that the ITS2 sequence could effectively discriminate T. obtectum and T. serrulatum, whereas the secondary structure cannot, proving that ITS2 can be used as an efficient barcode fragment to accurately identify the two species. The aim of this study was not only to determine the identification efficiency of the CP genome and ITS2 for T. obtectum and T. serrulatum but also to clarify the phylogenetic relationship and screen the candidate DNA marker suitable for Tetrastigma species, provide valuable data support for further accurate identification of the Tetrastigma genus.},
}

@article {pmid40709241,
year = {2024},
author = {Cheng, SJ and Hsu, YC},
title = {Use of DNA Barcode Sequences for Distinguishing the Three Species in the Arctic Warbler (Phylloscopus borealis) Species Complex.},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e33},
pmid = {40709241},
issn = {1810-522X},
abstract = {he Arctic warbler (Phylloscopus borealis) species complex is commonly present in the Palearctic region. By 2014, the three bird subspecies were split into three species, Arctic warbler (P. borealis), Japanese leaf warbler (P. xanthodryas), and Kamchatka leaf warbler (P. examinandus), based on different breeding areas and distinct vocalizations. However, their similar coloration and body size make it difficult to distinguish these species in the nonbreeding season. Taiwan is located in the potential migration routes of the Arctic warbler species complex; however, no confirmed record of P. xanthodryas and P. examinandus exists. In this study, we compared the mitochondrial cytochrome c oxidase subunit 1 (CO1) sequences of samples from breeding sites during the breeding season and confirmed that the three species could be distinguished based on CO1 gene sequences. We also examined the species of the Arctic warbler species complex samples collected from eastern Taiwan. For the first time, we confirmed that all three species visited Taiwan during migration season. In the Taiwanese samples, no clear distinction could be made between species based on plumage coloration and size, indicating that these traits are not reliable for species identification. Reassessment of the CO1 gene sequences of the three species deposited in the Barcode of Life Data System revealed that the taxonomic status needs to be updated for 31.8% of the samples.},
}

@article {pmid40708897,
year = {2025},
author = {Taberer, TR},
title = {On the identity of the type species of Parasa (Lepidoptera: Limacodidae): investigations into the Nearctic Parasa chloris and related taxa.},
journal = {Annals of the Entomological Society of America},
volume = {118},
number = {4},
pages = {276-289},
pmid = {40708897},
issn = {0013-8746},
abstract = {The pantropical Limacodid genus Parasa Moore [1860] comprises a charismatic group of moths, whose adults display green banding on the forewing while the larvae are often brightly colored, possessing stinging hairs. Three previously unidentified syntypes of the type species Parasa chloris (Herrich-Schäffer [1854]) were identified in the National Museum of Natural History, Smithsonian Institution, USA, having passed through several collections over the past ca. 180 years. Described from specimens with a vague provenance, the true type locality was unveiled utilizing COI barcoding of the lectotype designated herein, together with other barcoded specimens from North and Central America, morphological observations in adults and male genitalia, as well as distribution records from museum specimens and the citizen science database iNaturalist. Results suggest the type locality of P. chloris as north-eastern USA, likely from the southern states. In addition, the nomenclatural history of P. chloris is here discussed in detail, and its synonyms are clarified with regard the morphologically-similar, sympatric species Parasa indetermina (Griffith and Pidgeon, 1832 nec Boisduval), and Limacodes viridus Reakirt (1864) syn. rev. is here revived as a synonym of the latter. Taxonomic remarks are also made regarding species closely related to P. chloris (Parasa minima (Schaus, 1892), Parasa huachuca Dyar (1905) stat. nov., Parasa cuernavaca Dyar (1907) stat. rev., and Parasa maysi Schaus (1920)), resulting from COI barcoding, and morphological examinations of all primary type and additional material. This research represents the first step in delimiting Parasa in preparation for future taxonomic work testing the monophyly of this widespread genus.},
}

@article {pmid40708374,
year = {2025},
author = {Lozano-Sardaneta, YN and Huerta, H and Benítez-Guzmán, A and Cervantes-Torres, JB and Contreras-Ramos, A},
title = {Appearance may be deceiving: Mexican sand flies (Diptera: Psychodidae: Phlebotominae) embrace a high diversity of cryptic species.},
journal = {Journal of insect science (Online)},
volume = {25},
number = {4},
pages = {},
pmid = {40708374},
issn = {1536-2442},
support = {//Biodiversidad de Diptera y Neuropteroidea de la Reserva de la Biósfera Tehuacán-Cuicatlán con herramientas novedosas/ ; },
mesh = {Animals ; *Psychodidae/classification/genetics ; Mexico ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {Phlebotomine sand flies stand out for their role in vector-borne diseases, having taxonomic priority in aspects of public health. Traditional identification based on morphology involves some limitations that have been corrected with the implementation of complementary methodologies such as cytochrome c oxidase subunit I barcoding and recently mass spectrometry. In Mexico, nearly 38% of sand fly species count with a molecular characterization, but additional information is still necessary for improving sand fly species delimitation. We carried out a molecular species delimitation study of sand flies distributed in the Mexican Transition Zone, between the Nearctic and Neotropical regions, with newly generated cytochrome c oxidase subunit I barcodes, and the first protein profiles created. Compelling evidence showed putative new taxa emerge from Micropygomyia aff. durani (Vargas & Diaz-Nájera) and Pintomyia Series serrana Barretto, and several cryptic species be contained within the genera Micropygomyia and Psathyromyia, which could be of biological and epidemiological interest. However, for some taxa an exhaustive taxonomic revision at the morphological and molecular levels is recommended, especially for sand flies of wide distribution in the New World.},
}

Animals
*Psychodidae/classification/genetics
Mexico
Electron Transport Complex IV/genetics
DNA Barcoding, Taxonomic
Phylogeny

@article {pmid40708054,
year = {2025},
author = {Bunchom, N and Saijuntha, W and Tantrawatpan, C and Maleewong, W and Valencia, J and Agatsuma, T and Bounavong, V and Buchy, P and Iwagami, M},
title = {Micro-scale genetic structure and genetic variation of Neotricula aperta (Gastropoda: Pomatiopsidae), the intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae) in Champasak Province, Laos.},
journal = {Tropical medicine and health},
volume = {53},
number = {1},
pages = {97},
pmid = {40708054},
issn = {1348-8945},
support = {No. N42A670561//National Research Council of Thailand (NRCT) through the High-Potential Research Team Grant Program/ ; No. JP24jm0110028; 2022-2028//Japan International Cooperation Agency (JICA) and the Japan Agency for Medical Research and Development (AMED) through the SATREPS project, titled "Project for Malaria and Neglected Parasitic Diseases Control and Elimination using Advanced Research Technique, Communication Tools, and Eco-Health Education"/ ; },
abstract = {BACKGROUND: Neotricula aperta, a freshwater snail found in the Mekong River, serves as the intermediate host of the blood fluke Schistosoma mekongi, the causative agent of schistosomiasis mekongi in Cambodia and Laos. Understanding the genetic diversity, population structure of this snail in relation to its geographical distribution is crucial for a comprehensive understanding of disease transmission. In this study, we investigated the genetic diversity, and genetic structure of N. aperta in Champasak Province, Laos.

METHODS: A total of 80 N. aperta snails were collected from 13 various localities across five villages in Khong and Mounlapamok districts in Champasak Province, Laos in May 2024. Species of snails were initially identified based on morphology and subsequently confirmed by DNA barcoding. Molecular analyses were conducted using specific primers to amplify two mitochondrial DNA genes, namely cytochrome c oxidase subunit 1 (cox1) and 16S ribosomal RNA (16S rRNA), in order to assess the genetic diversity of N. aperta populations.

RESULTS: Based on cox1 sequences, the overall haplotype diversity was 0.996, while the overall nucleotide diversity was 0.049. For the 16S rRNA marker, the overall haplotype diversity was 0.911, and the overall nucleotide diversity was 0.015. Analysis of molecular variance (AMOVA) confirmed significant genetic differentiation (P-value < 0.05) among populations at different spatial scales, including villages, catchments, and countries. This genetic structure likely reflects limited gene flow among snail populations, potentially due to geographical barriers. Although local environmental factors may also contribute to differentiation, the current genetic data are insufficient to distinguish between geographic isolation and adaptive divergence. Further ecological and functional investigations will be needed to determine whether adaptive processes are influencing population structure.

CONCLUSIONS: The genetic divergence of N. aperta observed in this study indicates a high level of genetic differentiation both among and within populations. This pattern suggests that N. aperta is possibly undergoing localized adaptation or that barriers to gene flow, such as physical, ecological, or behavioral factors, are promoting the accumulation of genetic differences. Micro-scale genetic structuring within populations may be driven by microhabitats or small-scale ecological gradients, while limited dispersal, localized mating preferences, or other behavioral traits may contribute to differentiation among populations.},
}

@article {pmid40707727,
year = {2025},
author = {Lim, H and Jun, S and Kim, T and Lee, JH and Bang, D},
title = {Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1098},
pmid = {40707727},
issn = {2399-3642},
support = {2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; 2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; 2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; 2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; 2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; },
mesh = {*Polymerase Chain Reaction/methods ; Humans ; *Alleles ; *Gene Library ; Mutation ; *Circulating Tumor DNA/genetics ; },
abstract = {Molecular barcoding methods enable high-sensitivity detection of circulating tumor DNA that is rarely present in liquid biopsy samples. Many methods involve ligation of molecular barcodes to DNA prior to hybridization capture, enabling recovery of starting molecules. Development of polymerase chain reaction (PCR)-based methods could facilitate more cost- and labor- effective detection; however, tracking molecular identity can be difficult, as new barcodes overwrite old barcodes in each cycle. Here, we present a sensitive genotyping method based on a peer-to-peer network-derived identifier for error reduction in amplicon sequencing (SPIDER-seq) and enable molecular identity tracking with PCR-derived libraries using overwritten barcodes. SPIDER-seq detected mutations at frequences as low as 0.125% after only two consecutive general PCR cycles and systematically analyzed the error pattern in the peer-to-peer network. Our method could facilitate the rapid detection of mutations associated with various cancers.},
}

*Polymerase Chain Reaction/methods
Humans
*Alleles
*Gene Library
Mutation
*Circulating Tumor DNA/genetics

@article {pmid40705799,
year = {2025},
author = {Wacira, TN and Makonde, HM and Kamau, JN and Aura, CM and Kibiti, CM},
title = {Characterization and bioactivity potential of marine sponges (Biemna fistulosa, Callyspongia diffusa, and Haliclona fascigera) from Kenyan coastal waters.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325642},
doi = {10.1371/journal.pone.0325642},
pmid = {40705799},
issn = {1932-6203},
mesh = {Animals ; *Porifera/chemistry/genetics ; Microbial Sensitivity Tests ; Kenya ; *Haliclona/chemistry/genetics ; Anti-Bacterial Agents/pharmacology ; Pseudomonas aeruginosa/drug effects ; Escherichia coli/drug effects ; Candida albicans/drug effects ; Gas Chromatography-Mass Spectrometry ; Staphylococcus aureus/drug effects ; *Anti-Infective Agents/pharmacology ; Humans ; },
abstract = {Sponges have been reported as a rich source of bioactive compounds, which could potentially be developed into lead compounds for pharmaceutical use. The present study aimed to identify sponges and assess the biological activity of their extracts against human disease-causing organisms, including Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans. Morphological characterization and DNA barcoding of the cytochrome c oxidase subunit I (COI) gene characterized three sponge species (Biemna fistulosa, Callyspongia diffusa and Haliclona fascigera). The Kirby-Bauer test assessed the antimicrobial activity of the extracts, and the inhibition zone diameters (IZD) were measured. The extracts were further subjected to minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) tests to determine the antibiotic susceptibility. The Gas Chromatography-Mass Spectrometry (GC-MS) was used to identify and quantify the organic compounds in the sponges' extracts. The methanolic extract of B. fistulosa (28.00 ± 3.5 mm) and H. fascigera. (28.33 ± 3.8 mm) exhibited a broad spectrum of antibacterial activity against E. coli, surpassing the positive control (27.67 ± 0.9 mm). The inhibitory activity of ethyl acetate extract of the C. diffusa (29.33 ± 2.4 mm) against P. aeruginosa was observed to be higher compared to the standard antibiotic streptomycin (26.67 ± 0.7 mm). The methanolic extract of H. fascigera demonstrated the lowest MIC (0.53 ± 0.0 mg mL-1) compared to the streptomycin drug (1.36 ± 0.0 mg mL-1), and showed an MBC of 1.25 mg mL-1 against E. coli. The GC-MS chromatogram data analysis identified 114 distinct compounds categorized into 39 classes across three sponge extracts: 11.4% of these compounds demonstrated documented antimicrobial activity against human pathogens. This study corroborates sponges as a promising source of bioactive compounds, which are valuable leads for drug discovery and development. Future research must explore their mechanisms, molecular-level toxicity, and lead optimization to enhance drug development.},
}

Animals
*Porifera/chemistry/genetics
Microbial Sensitivity Tests
Kenya
*Haliclona/chemistry/genetics
Anti-Bacterial Agents/pharmacology
Pseudomonas aeruginosa/drug effects
Escherichia coli/drug effects
Candida albicans/drug effects
Gas Chromatography-Mass Spectrometry
Staphylococcus aureus/drug effects
*Anti-Infective Agents/pharmacology
Humans

@article {pmid40703786,
year = {2025},
author = {Kim, S and Sohn, J and Kim, H},
title = {Three new species and a new record of the genus Lipolexis (Hymenoptera, Braconidae, Aphidiinae) from South Korea.},
journal = {ZooKeys},
volume = {1245},
number = {},
pages = {323-342},
pmid = {40703786},
issn = {1313-2989},
abstract = {The genus Lipolexis Förster, 1863 consists of 11 species worldwide, with two species previously recorded in South Korea. In this study, three new species: L.depressiceps S. Kim & H. Kim, sp. nov., L.sulcata S. Kim & H. Kim, sp. nov., and L.longipetiolata S. Kim & H. Kim, sp. nov. with an unrecorded species, L.peregrina, Tomanović & Kocić, 2020, are described and reported with photographs, mitochondrial cytochrome c oxidase subunit I (COI) data (barcode region), and a gene tree.},
}

@article {pmid40703784,
year = {2025},
author = {Wägele, H and Raubold, LM and Papu, A and Undap, N and Yonow, N},
title = {On two new Phyllidia species (Gastropoda, Nudibranchia, Doridina) and some histology from the Coral Triangle.},
journal = {ZooKeys},
volume = {1245},
number = {},
pages = {1-18},
pmid = {40703784},
issn = {1313-2989},
abstract = {Two new species of Phyllidia from North Sulawesi, Indonesia, Phyllidiafontjei sp. nov. and Phyllidiaovata sp. nov., are described based on morphology and molecular barcoding of CO1 and/or 16S. Both species are rare and distinctive and can be easily recognised by their colouration. Additionally, histological sections were made of the holotype of Phyllidiafontjei sp. nov. and a similarly sized Phyllidiaocellata and these morphologies are compared with the only other detailed histological examination of the Mediterranean Phyllidiaflava.},
}

@article {pmid40702707,
year = {2025},
author = {Fu, Y and Youness, M and Virzì, A and Song, X and Tubeeckx, MRL and De Keulenaer, GW and Heidbuchel, H and Segers, VFM and Sipido, KR and Thienpont, B and Roderick, HL},
title = {Benchmarking of computational demultiplexing methods for single-nucleus RNA sequencing data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf371},
pmid = {40702707},
issn = {1477-4054},
support = {20-VLIR-iBOF-027//BOF/ ; C14/21/093//KU Leuven/ ; //China Scholarship Council/ ; G0C7319N//FWO, Research Foundation - Flanders/ ; },
mesh = {Humans ; *Software ; Benchmarking ; *Sequence Analysis, RNA/methods ; *Computational Biology/methods ; Polymorphism, Single Nucleotide ; *Cell Nucleus/genetics ; *Single-Cell Analysis/methods ; },
abstract = {Single-nucleus RNA sequencing (snRNA-Seq) has transformed our understanding of complex tissues, providing insights into cellular composition and heterogeneity in gene expression between cells, and their alterations in development and disease. High costs however constrain the number of samples analysed. Sample pooling and their demultiplexing following sequencing based on prior labelling with antibodies or lipid anchors conjugated to DNA barcodes (cell hashing and MULTI-seq), or using genetic differences between samples, provides a solution. However, there remains no comprehensive evaluation of these demultiplexing tools to guide selection between them. Here, we benchmark the leading software (Vireo, Souporcell, Freemuxlet, scSplit) used for sample demultiplexing using genetic variants. We further compared obtaining genetic variants from SNP array analysis of gDNA and from sample-matched bulk-RNA-Seq data, identified using three different variant calling tools (BCFtools, cellSNP, FreeBayes). Demultiplexing performance was evaluated on simulated multiplexed datasets comprising two, four, and six samples with doublet percentages between 0% and 30%, and validated against demultiplexing using sex-linked genes. Software implementation and execution were evaluated by run speed, robustness, scalability, and usability. Our results show that all tools excluding scSplit provide high recall and precision with an accuracy of 80%-85%. Vireo achieved the best accuracy. Demultiplexing tools were differentially affected by the variant calling tool with which it was paired. For all tools, accuracy decreased with the increasing percentage of doublets. Deployment of demultiplexing during analysis of pooled real-world 10x RNA-Seq data from the human heart and from different species is shown, as are advantages for doublet detection and removal.},
}

Humans
*Software
Benchmarking
*Sequence Analysis, RNA/methods
*Computational Biology/methods
Polymorphism, Single Nucleotide
*Cell Nucleus/genetics
*Single-Cell Analysis/methods

@article {pmid40702435,
year = {2025},
author = {Dong, LN and Liu, ZF and Xu, WB and Yang, JB and Kidner, CA and Hughes, M and Yan, HF and Wang, H and Li, DZ},
title = {Identification of herbal medicine species of Lysimachia L. (Primulaceae) in Southern China using genome skimming.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {953},
pmid = {40702435},
issn = {1471-2229},
support = {2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; },
mesh = {China ; *DNA Barcoding, Taxonomic/methods ; *Primulaceae/genetics/classification ; *Plants, Medicinal/genetics/classification ; *Genome, Plant ; Phylogeny ; DNA, Plant/genetics ; Herbal Medicine ; Sequence Analysis, DNA ; Lysimachia ; },
abstract = {BACKGROUND: The accurate identification of herbal medicine is a prerequisite for safe and effective use. DNA barcoding has been widely used for the identification of herbal medicine. However, choosing and refining a suitable barcode is complex in plants. The genus Lysimachia includes over 180 species and is widely used as herbal medicine in China and elsewhere. Species identification within this genus based on morphological, microscopic, or chemical characters is often challenging. In this study, 44 accessions representing 17 putative species of Lysimachia from southern China were sequenced using genome skimming. Whole plastome and nrDNA sequences were successfully recovered from these data. Combining 13 published plastomes of Lysimachia, the discrimination power of standard barcodes, along with plastome and hypervariable sequences from the plastome were compared across 57 plastomes from 22 putative species.

RESULTS: Standard barcodes have limitation in providing accurate species level identification; however, they can facilitate the rapid classification of unknown samples at the generic level. The plastomes exhibit a highly degree of conservation in the structure and gene content, yet they successfully identify all studied taxa. Five highly variable loci from plastomes were identified: petN-psbM, ycf1, rpl22, trnK-rps16, and ndhC-trnV. While these regions improved the discrimination power compared to standard barcodes, they still could not yield accurate identification of all taxa studied. However, when combined with ITS, ycf1 provides 100% successful species identification.

CONCLUSIONS: We recommend that the use of whole plastome and the combination of ycf1 + ITS as accurate and effective barcodes for species identification in Lysimachia. This study also highlights the potential for effective use of genome skimming data.},
}

China
*DNA Barcoding, Taxonomic/methods
*Primulaceae/genetics/classification
*Plants, Medicinal/genetics/classification
*Genome, Plant
Phylogeny
DNA, Plant/genetics
Herbal Medicine
Sequence Analysis, DNA
Lysimachia

@article {pmid40700316,
year = {2025},
author = {Stoeva, D and Gencheva, D and Radoslavov, G and Hristov, P and Yordanova, R and Beev, G},
title = {Novel DNA Barcoding and Multiplex PCR Strategy for the Molecular Identification and Mycotoxin Gene Detection of Fusarium spp. in Maize from Bulgaria.},
journal = {Methods and protocols},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/mps8040078},
pmid = {40700316},
issn = {2409-9279},
support = {AF3/24//Trakia University/ ; },
abstract = {Fusarium spp. represent a critical threat to maize production and food safety due to their mycotoxin production. This study introduces a refined molecular identification protocol integrating four genomic regions-ITS1, IGS, TEF-1α, and β-TUB-for robust species differentiation of Fusarium spp. isolates from post-harvest maize in Bulgaria. The protocol enhances species resolution, especially for closely related taxa within the Fusarium fujikuroi species complex (FFSC). A newly optimized multiplex PCR strategy was developed using three primer sets, each designed to co-amplify a specific pair of toxigenic genes: fum6/fum8, tri5/tri6, and tri5/zea2. Although all five genes were analyzed, they were detected through separate two-target reactions, not in a single multiplex tube. Among 17 identified isolates, F. proliferatum (52.9%) dominated, followed by F. verticillioides, F. oxysporum, F. fujikuroi, and F. subglutinans. All isolates harbored at least one toxin biosynthesis gene, with 18% co-harboring genes for both fumonisins and zearalenone. This dual-protocol approach enhances diagnostic precision and supports targeted mycotoxin risk management strategies.},
}

@article {pmid40699425,
year = {2025},
author = {Al Hayek, S and Praité, A and Lambert, JM and Bender, S and Delpy, L},
title = {5'RACE Method for RNA-Based Sequencing of the Mouse Immunoglobulin Repertoire.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2962},
number = {},
pages = {103-119},
pmid = {40699425},
issn = {1940-6029},
mesh = {Animals ; Mice ; *High-Throughput Nucleotide Sequencing/methods ; B-Lymphocytes/immunology/metabolism ; *Immunoglobulins/genetics ; Immunoglobulin Heavy Chains/genetics ; *Sequence Analysis, RNA/methods ; DNA, Complementary/genetics ; *RNA/genetics/isolation & purification ; Spleen/cytology ; },
abstract = {This chapter outlines a detailed methodology for high-throughput sequencing of the immunoglobulin (Ig) repertoire from mouse RNA samples. We describe RNA extraction from splenic B cells, followed by the conversion into cDNA using the 5'RACE (Rapid Amplification of cDNA Ends) technique and PCR amplification of the Ig heavy and light chain repertoire. The amplified products are prepared using specific primers for Illumina next-generation sequencing (NGS) and unique molecular identifiers (UMI) as molecular barcodes. The protocol includes stringent quality control steps to ensure the integrity of RNA and the accuracy of amplification. We describe the amplification of Ighm and all Ighg subclasses, for Ig heavy chains and for the predominant Igκ light chain isotype. RNA-based 5'RACE-RepSeq proves very useful to analyze the diversity and clonality of Ig repertoire, as well as somatic hypermutations, providing insights into the adaptive immune response. This method enables the high-throughput characterization of the mouse Ig repertoire in immunological contexts.},
}

Animals
Mice
*High-Throughput Nucleotide Sequencing/methods
B-Lymphocytes/immunology/metabolism
*Immunoglobulins/genetics
Immunoglobulin Heavy Chains/genetics
*Sequence Analysis, RNA/methods
DNA, Complementary/genetics
*RNA/genetics/isolation & purification
Spleen/cytology

@article {pmid40698406,
year = {2025},
author = {Alpsoy, L and Tieu, S and Dehestanizad, S and Brandstetter, T and Rühe, J},
title = {Hydrogel beads for enhanced nucleic acid analysis in complex fluid matrices.},
journal = {Lab on a chip},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5lc00447k},
pmid = {40698406},
issn = {1473-0189},
abstract = {We present a functionalized hydrogel bead platform designed to capture cell-free DNA (cfDNA), which is released from tumor cells into the bloodstream, and the use of this cfDNA as a biomarker for cancer detection. Hydrogel beads with covalently incorporated probes (HBP) are generated via photo-cross-linking in a two-phase microfluidic system. The precursor solutions from which the beads are generated are comprised of a photoreactive copolymer, magnetic nanoparticles, Cy3-labelled oligonucleotides serving as a barcode for bead identification, and a specific probe designed to bind the target DNA. From these solutions, droplets are generated in the microfluidic system and photocross-linked through C, H-insertion cross-linking (CHic). As a demonstration case, the hydrogel beads are used to detect a mutation (c.1633G>A) in MCF-7 cells, which is known to promote breast cancer progression by activating oncogenic signalling pathways. The HBPs were successfully employed to detect a fluorescently labelled mutation sequence (92 bp) in phosphate-buffered saline (PBS), serum, and whole blood using a fluorescent reader, followed by amplification through polymerase chain reaction (PCR). The sensitivity of the cfDNA detection method described here demonstrates a detection limit as low as 0.36 ng mL[-1], which is lower than any other detection limit in the literature so far. The sensitivity of the hydrogel bead platform can be further significantly increased. This is because beads containing the captured DNA can be subjected directly to PCR for the amplification of the target sequence, eliminating the need for any additional purification steps. The simplicity of production, modification, and functionalization of the hydrogel beads, coupled with their high sensitivity in detecting cfDNA, makes this platform a promising approach for diagnosing a range of diseases.},
}

@article {pmid40698045,
year = {2025},
author = {Kamani, J and Irene, S and Yakubu, AR and Bwala, FH and Nahum-Biala, Y and Nnabuife, EH and Budaye, J and Harrus, S and Schaer, J},
title = {Vector Abundance and Genetic Diversity of Anopheles Mosquitoes Collected in a Laboratory-Office Complex in Vom, Nigeria: Implications for Vector Control.},
journal = {Public health challenges},
volume = {4},
number = {3},
pages = {e70079},
pmid = {40698045},
issn = {2769-2450},
abstract = {Malaria remains a significant threat in high-burden high-impact (HBHI) countries despite substantial investments in disease control. This highlights the need for more comprehensive and inclusive strategies to meet national and international targets. Although agricultural and poorly maintained environments are known for mosquito breeding, workplaces are rarely considered in conventional malaria control measures. In this pilot investigation, we assessed the presence of Anopheles spp. in a laboratory-office complex in Vom, Nigeria, to assess workplace malaria risk and its implications for control strategies. We conducted molecular barcoding on 74 Anopheles specimens targeting the mitochondrial cytochrome oxidase I gene (cox1). Our analyses identified Anopheles funestus (n = 29; 54.6%), Anopheles gambiae sensu lato (n = 17; 32.1%), and Anopheles rufipes (n = 6; 11.3%). Haplotype network analyses revealed 12, 8, and 6 distinct haplotypes for A. funestus, A. gambiae, and A. rufipes, respectively. Genetic divergence estimates for cox1 sequences were ≤0.011% for A. funestus, ≤0.007% for A. gambiae, and ≤0.018% for A. rufipes. The detection of genetically diverse Anopheles vector species in an office setting underscores the potential risk of workplace malaria transmission. This pilot study provides initial evidence that workplace environments can harbor genetically diverse malaria vectors and should be considered in future surveillance and control strategies. We recommend subnational tailoring (SNT) of intervention strategies to incorporate workplace environments and public places into malaria control efforts.},
}

@article {pmid40697875,
year = {2025},
author = {Xiang, R and Hu, J and Chuluunbat, J and Wu, F and Qin, B and Zhang, X and Jiang, R},
title = {Comparative chloroplast genomes and phylogenetic analysis of the Phlegmariurus (Lycopodiaceae) from China and neighboring regions.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1543431},
pmid = {40697875},
issn = {1664-462X},
abstract = {The lycophyte genus Phlegmariurus (Herter) Holub (Huperzioideae, Lycopodiaceae) is ecologically and pharmaceutically significant, notably as a natural source of Huperzine A-a promising therapeutic candidate for Alzheimer's disease. Despite its medicinal potential, taxonomic ambiguities on species delimitation and infrageneric classification have impeded conservation and sustainable utilization efforts. Here, we assembled 40 Phlegmariurus complete chloroplast genomes, including all taxa from China, most of which were reported for the first time. Our results revealed the conserved quadripartite architectures and little variation in genome size and GC content in the genus. Comparative analyses on genome sequences identified seven hypervariable loci as prospective DNA barcodes for species discrimination. The phylogenetic toopologies reconstructed from nuclear ribosomal DNA and chloroplast genome data consistently resolved four monophyletic clades, further validated by SNP-based discriminant analysis of principal components. They are well corresponding to the four sections' classification on Chinese taxa (sect. Squarrosurus, sect. Phlegmariurus, sect. Fargesiani, sect. Hamiltoniani). Notably, nuclear and chloroplast data congruently yielded a sister relationship between sect. Squarrosurus and sect. Phlegmariurus. However, the phylogenetic positions of sect. Fargesiani and sect. Hamiltoniani conflicted across different datasets. The diversification of the Chinese Phlegmariurus was traced back to the Oligocene (ca. 26.04 Ma). The comprehensive genetic resources generated herein provide a foundation for future research on species identification, population genomics and genetic diversity preservation in this medicinally significant vital genus.},
}

@article {pmid40694563,
year = {2025},
author = {Kar, O and Mukherjee, A and Mukherjee, K and Pramanik, D and Naskar, A and Banerjee, D},
title = {Molecular identification and genetic variations of forensically significant blow flies (Diptera: Calliphoridae) from Eastern India using DNA barcoding.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327039},
doi = {10.1371/journal.pone.0327039},
pmid = {40694563},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Calliphoridae/genetics/classification ; India ; Electron Transport Complex IV/genetics ; *Genetic Variation ; *Forensic Entomology/methods ; Phylogeny ; *Diptera/genetics/classification ; Species Specificity ; },
abstract = {Flies, especially those from the Calliphoridae family, play a crucial role in decomposition and are the first to colonize a cadaver. Firstly, accurate species identification is a prerequisite for entomological evidence-based calculation of postmortem interval (PMI). While morphological criteria for identifying the species of adult blow flies exist, there are either absent or inadequate keys for younger stages. In all phases of blow fly development, molecular identification offers a quick and accurate procedure. It is widely known that mitochondrial cytochrome oxidase subunit I has the capacity for molecular identification but is ineffective in certain species. This study was conducted to assess the effectiveness of the cytochrome oxidase 1 gene in the identification of seventeen different species of calliphorid flies involving four genera, Calliphora, Chrysomya, Lucilia, and Hemipyrellia. In West Bengal, 2,977 blow fly specimens were gathered from four distinct geo-climatic zones. COI barcodes were able to confirm morphological identification through low K2P intraspecific genetic divergences (0% to 1%) and moderate to high K2P interspecific genetic divergences (0.39% to 12.29%). The Neighbour-Joining (NJ) analysis demonstrated well-supported reciprocal monophyly among the species. The species grouping was in agreement with morphological and molecular identifications. The four delimitation methods, BIN, ASAP, PTP, and GMYC, used for species identification produced similar results and facilitated the proper identification of species. Therefore, it can be concluded that COI barcodes are a highly successful alternative for the molecular identification of blow flies, facilitating forensic cases and biodiversity research in India.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Calliphoridae/genetics/classification
India
Electron Transport Complex IV/genetics
*Genetic Variation
*Forensic Entomology/methods
Phylogeny
*Diptera/genetics/classification
Species Specificity

@article {pmid40694500,
year = {2025},
author = {Zhong, S and Wang, R and Gao, X and Guo, Q and Lin, R and Luo, M},
title = {Modular DNA barcoding of nanobodies enables multiplexed in situ protein imaging and high-throughput biomolecule detection.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.105225},
pmid = {40694500},
issn = {2050-084X},
support = {32322032//National Natural Science Foundation of China/ ; 2022ZD0206700//China Brain Initiative/ ; 20230484303//Beijing Nova Program/ ; 2021ZD0202803//China Brain Initiative/ ; Research Unit of Medical Neurobiology 2019RU003//Chinese Academy of Medical Sciences/ ; },
mesh = {Animals ; *Single-Domain Antibodies/genetics ; Mice ; *SARS-CoV-2/immunology/isolation & purification ; *DNA Barcoding, Taxonomic/methods ; Humans ; COVID-19/diagnosis ; Brain ; Immunoglobulin G ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays/methods ; },
abstract = {Current immunodetection methods using antibody-DNA conjugates enable multiplexed target detection through orthogonal DNA barcodes, but existing conjugation approaches are labor-intensive and often compromise antibody function. Here, we present a modular, site-specific, and cost-efficient DNA tagging strategy - multiplexed and modular barcoding of antibodies (MaMBA). Utilizing nanobodies as modular adaptors, MaMBA enables direct site-specific labeling of off-the-shelf IgG antibodies with a one-component design. We first applied MaMBA to develop the MaMBA-assisted immunosignal hybridization chain reaction (misHCR) method for highly multiplexed in situ protein imaging via orthogonal HCR. Its cleavable variant, misHCR[n], achieves simultaneous visualization of 12 different targets within the same mouse brain sections through iterative probe use. We further extended the cleavable MaMBA to develop the barcode-linked immunosorbent assay (BLISA) for multiplexed and high-throughput biomolecule detections. By combining BLISA with next-generation sequencing, we successfully measured SARS-CoV-2 IgG and hepatitis B virus (HBV)-associated antigens in a large number of human serum samples. Additionally, we demonstrated a small-scale drug screen by using BLISA to simultaneously detect eight protein targets. In conclusion, MaMBA offers a highly modular and easily adaptable approach for antibody DNA barcoding, which can be broadly applied in basic research and clinical diagnostics.},
}

Animals
*Single-Domain Antibodies/genetics
Mice
*SARS-CoV-2/immunology/isolation & purification
*DNA Barcoding, Taxonomic/methods
Humans
COVID-19/diagnosis
Brain
Immunoglobulin G
High-Throughput Nucleotide Sequencing
High-Throughput Screening Assays/methods

@article {pmid40693379,
year = {2025},
author = {Choi, W and Moestopo, WP and Gu, S and Lee, T and Yoo, JH and Xia, X and Armstrong, MR},
title = {Helical Photonic Metamaterials for Encrypted Chiral Holograms.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e07931},
doi = {10.1002/advs.202507931},
pmid = {40693379},
issn = {2198-3844},
support = {DE-AC52-07NA27344//Lawrence Livermore National Laboratory/ ; 22-ERD-056//LLNL Laboratory Directed Research and Development/ ; 24-LW-035//LLNL Laboratory Directed Research and Development/ ; },
abstract = {Helical structures are among the most quintessential three-dimensional (3D) forms that exhibit mirror asymmetry, a hallmark of chirality. Various structural parameters of helices directly linked to chiroptical properties highlight their importance as essential optical metamaterials for polarization-resolved sensors, imaging, and spectroscopies. However, such function-defining properties remain incompletely understood due to fabrication challenges and the lack of a relationship between structure and optical properties. Here, helical structures are analyzed parametrically, and correlations are established that are applicable to the design of chiral helical optical metamaterials. By systematically varying independent parameters-such as from single-turn to five-turn helices and from small major radii to larger ones optimized to fit the unit cell-the underlying relationships with ellipticty are revealed. In addition to theoretical modeling, the findings are experimentally validated using 3D printing and terahertz spectroscopy. The results demonstrate that optimized helical structures are mechanically tunable and exhibit unprecedented optical properties, including broadband and high-magnitude ellipticity spectra. Being embedded in soft elastomers, helical arrays can serve as soft, stretchable optical-mechanical sensors and holograms containing encoded information, such as barcodes and quick response (QR) codes. Chiral QR codes are realized using pixelated single helices with different handedness, demonstrating their potential as advanced encryption/decryption systems for security applications and chiral metaholograms.},
}

@article {pmid40692849,
year = {2025},
author = {Rowe, CE and Ahyong, ST and Figueira, WF and Burghardt, I and Keable, SJ},
title = {Identification of Cassiopea sp. in Lake Macquarie, Australia and revision of the taxonomic status of Cassiopea maremetens Gershwin, Zeidler & Davie, 2010 (Cnidaria: Scyphozoa: Cassiopeidae).},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19669},
pmid = {40692849},
issn = {2167-8359},
mesh = {Animals ; *Scyphozoa/genetics/classification/anatomy & histology ; Lakes ; Phylogeny ; Australia ; Queensland ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {Scyphozoans of the genus Cassiopea are notable for their unusual benthic habit of lying upside-down with their exumbrella resting on the substrate and oral arms facing upwards resulting in their common name "upside-down jellyfish". Cassiopea includes species that have been historically confused because of taxonomic ambiguity. Additionally, some species are considered to be invasive, which can have significant economic and environmental consequences by impacting fisheries, tourism, and trophic structures. In temperate southeastern Australia, Cassiopea medusae were first reported in temperate Wallis Lake and Lake Illawarra in 2016, and then Lake Macquarie in 2017, though historically these jellyfish have a more northern tropical distribution in Queensland, eastern Australia. Owing to the invasive potential of Cassiopea, correct species identification is crucial for future management. To address this knowledge gap, this study used genetic comparison through the cytochrome c oxidase subunit I (COI) barcoding gene and morphometric analysis, together with revision of type and topotype material of Cassiopea maremetens Gershwin, Zeidler & Davie, 2010, an incompletely known nominal species from Queensland, to investigate the identity of Cassiopea occurring in Lake Macquarie. The morphometric analysis was also used to identify key features that distinguish the Lake Macquarie species from a second species, designated Cassiopea sp.3, that is also expanding its range southwards in eastern Australia, and which may be sympatric in some areas. The results of this study show the species occurring in Lake Macquarie is Cassiopea xamachana Bigelow, 1892, originally described from Jamaica and subsequently widely reported from the Western Atlantic and the Indo-West Pacific. Additionally, we demonstrate that Cassiopea maremetens, is a junior synonym of C. xamachana. Morphological characters that can be most readily used to distinguish mature specimens of C. xamachana from C. sp.3, which has an overlapping distribution on the Australian east coast, are: (1) the number of large appendages on the oral disc, which is much higher in Cassiopea sp.3 (at least 1 but up to 14) vs. a maximum of two in C. xamachana; (2) the oral arm branching pattern, which is usually alternating for C. xamachana, but a combination of alternating, bifurcating and pinnate for Cassiopea sp.3; (3) the length of the large appendage on the oral arm, which is proportionally longer relative to the bell diameter in C. xamachana.},
}

Animals
*Scyphozoa/genetics/classification/anatomy & histology
Lakes
Phylogeny
Australia
Queensland
Electron Transport Complex IV/genetics
DNA Barcoding, Taxonomic

@article {pmid40692202,
year = {2025},
author = {Ansai, E and Sekine, H and Munakata, K and Sase, T and Sasaki, M and Nitta, M and Suzuki, S and Abe, T and Takano, T and Fukumori, H and Nakatsubata, Y and Suzuki, M and Waki, T},
title = {Life cycles of trematodes infecting six species of intertidal gastropods in Japan.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e83},
doi = {10.1017/S0022149X25100485},
pmid = {40692202},
issn = {1475-2697},
mesh = {Animals ; Japan ; *Trematoda/classification/genetics/isolation & purification/growth & development/anatomy & histology ; *Gastropoda/parasitology ; *Life Cycle Stages ; Phylogeny ; *Snails/parasitology ; DNA, Helminth/genetics/chemistry ; Metacercariae ; },
abstract = {A variety of larvae and parthenitae of trematodes have been detected in gastropods in the intertidal zone in Japan. However, because of the difficulty associated with the morphological identification of these stages, they have rarely been identified to the species or higher taxonomic levels. In this study, trematodes of these stages were sampled from intertidal gastropods in the Japanese coastal regions and were identified to the species, genus, or family levels morphologically and molecularly to elucidate or predict their life cycles. Investigation of 17 gastropod species (682 individuals in total) from 14 localities led to the detection of trematodes in 47 individuals belonging to six snail species. The infected gastropods were morphologically identified as Nipponacmea fuscoviridis, Monodonta confusa, Trochus sacellum, Batillaria attramentaria, Littorina brevicula, and Purpuradusta gracilis. Our molecular analyses revealed that sporocysts, rediae, and metacercariae from the gastropods were divided into 14 species belonging to nine families: Philophthalmidae, Fellodistomidae, Gymnophallidae, Lepocreadiidae, Heterophyidae, Opisthorchiidae, Notocotylidae, Microphallidae, and Opecoelidae. These trematodes were thought to use fishes, octopuses, seabirds, and marine mammals as their definitive hosts. Marine organisms such as jellyfishes, crustaceans, and fishes are also thought to act as the second intermediate and paratenic hosts of few present trematode species. As for the other trematode species, DNA barcodes of trematodes from various marine organisms will also illuminate the life cycles in future.},
}

Animals
Japan
*Trematoda/classification/genetics/isolation & purification/growth & development/anatomy & histology
*Gastropoda/parasitology
*Life Cycle Stages
Phylogeny
*Snails/parasitology
DNA, Helminth/genetics/chemistry
Metacercariae

@article {pmid40689223,
year = {2025},
author = {Adamčíková, K and Kiran, M and Caboň, M and Matheny, BP and Sánchez-García, M and Arnolds, E and Caboňová, M and Corriol, G and Dima, B and Friebes, G and Griffith, GW and Grootmyers, D and Harries, D and Karich, A and Mešić, A and Mihaljevič, M and Moreau, PA and Pošta, A and Shapkin, V and Tkalčec, Z and Vizzini, A and Vondrovicová, L and Adamčík, S and Jančovičová, S},
title = {A phylogenetic and morphological study of the genus Dermoloma (Agaricales, Tricholomataceae) in Europe and North America exposes inefficiency of opportunistic species descriptions.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e157337},
pmid = {40689223},
issn = {2210-6340},
abstract = {Dermoloma is traditionally known as a small genus of agarics classified in the family Tricholomataceae. This study implemented a multilocus phylogeny of six DNA regions to recognize phylogenetic species within the genus. The species concept is reinforced by observations of well-defined morphological characters enhanced by long term sampling effort in Europe and North America. Thirty European Dermoloma species are described, including 16 new species from Europe and three from North American. These species are classified into two subgenera morphologically distinguished by spores with positive or negative amyloid reaction. A new genus Neodermoloma is introduced for the Dermoloma-like species N.campestre. Localized or continental-scale species endemicity was confirmed based on studied material, but more inclusive phylogenetic clustering supported a mixture of North American species among the European clades. Of the 22 names validly published from Europe prior to this study, 11 could be assigned to well-defined Dermoloma species recognized here. Of the remaining 11 names, two were considered representing Dermoloma species not recorded since their description, and nine were established as later synonyms of other species. Morphological studies of Dermoloma are challenging due to the relatively low number of characters suitable for identification of species. The majority of morphological characters showed continuous variation with high overlap throughout the genus. For this reason, species identification requires an awareness of morphological variability within species, and multiple distinguishing characters need to be combined, and furthermore, often a barcode sequence is needed for a certain identification. Stable isotope analysis in Dermoloma of δ[13]C and δ[15]N revealed an ecological signature similar to known CHEGD fungi, i.e. Clavariaceae and Hygrocybe s.l. This indicates that Dermoloma species are biotrophic but neither ectomycorrhizal nor saprotrophic and may form mutualistic root endophytic associations with vascular plants.},
}

@article {pmid40689039,
year = {2025},
author = {Platzgummer, K and Kniha, E and Dvorak, V and Halada, P and Walochnik, J and Vomackova Kykalova, B and Hanusniakova, I and Farkas, R and Volf, P and Trájer, AJ},
title = {Updating the distribution of sand flies in Hungary with implications on their biology and ecology.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {8},
number = {},
pages = {100293},
pmid = {40689039},
issn = {2667-114X},
abstract = {In Europe, sand flies (Diptera: Psychodidae: Phlebotominae) are characteristic Mediterranean fauna, though some species expand their range further north. However, the sand fly fauna of Central Europe remains underreported, particularly in Hungary where recent data is lacking due to limited and outdated entomological surveys. To address this gap, a series of sand fly surveys were conducted in Hungary, with significant findings from two trapping efforts in 2017 and 2024. In 2017, only a single female Phlebotomus papatasi was trapped in northern Hungary, which marks one of the northernmost records of the species. In 2024, a more extensive and geographically wider survey recorded 264 sand flies at 34 sites, including three species: Ph. mascittii, Ph. neglectus, and Ph. papatasi. Sand flies were found across diverse environmental settings, including urban, agricultural, and natural habitats. Particularly, the previously rare presence of Ph. mascittii at rural sites (natural rock formations) was reported. Analysis of historical and current data revealed the presence of four sand fly species in Central and South Transdanubia, with evidence suggesting potential range expansion. Blood meal analysis of engorged females identified a variety of domestic and wild host species, but no Leishmania or Phlebovirus infections were detected. Habitat modelling and linear discriminant analysis indicated substantial climate suitability across Southeast Europe, with most positive sand fly observations observed in discontinuous urban fabric CORINE Land Cover classes. This study offers important insights into the ecology, distribution, and climatic preferences of sand flies in Hungary and provides crucial baseline data to monitor potential future spread.},
}

@article {pmid40688177,
year = {2025},
author = {Piasecki, W and Boxshall, GA and Panicz, R and Eljasik, P},
title = {New identification traits of Tracheliastes maculatus (Copepoda: Lernaeopodidae), a parasite of bream, Abramis brama (Cyprinidae).},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {27},
number = {},
pages = {101108},
pmid = {40688177},
issn = {2213-2244},
abstract = {The parasitic copepod Tracheliastes maculatus Kollar, 1835, infects the freshwater bream, Abramis brama, a key species in European freshwater ecosystems. Despite its widespread occurrence and potential to cause skin hemorrhages, scale erosion and perforation, and fish mortality, species-level identification within the genus Tracheliastes has been problematic due to insufficient diagnostic traits. This study refines identification criteria by integrating morphological and genetic approaches. We present the first DNA barcode (COI gene sequence) for Tracheliastes maculaus, providing a molecular basis for taxonomic clarification. Additionally, scanning electron microscopy (SEM) reveals novel morphological details, including the number and distribution pattern of secondary denticles on endopodal Claw 1 of the antenna and structural differences in endopodal and exopodal side denticles of the antenna, both of which, may serve as new diagnostic features within the genus. Furthermore, we regard Tracheliastes mourkii as a nomen nudum because it was not morphologically diagnosed, and no museum specimen is extant. These findings improve species discrimination and set a benchmark for future taxonomic revisions of Tracheliastes, facilitating more precise ecological and parasitological assessments. A mini-review of the genus is also provided.},
}

@article {pmid40687770,
year = {2025},
author = {Mwesige, R and Maosa, J and Couvreur, M and Bert, W},
title = {Morphological and Molecular Characterization of Hoplolaimus tuberosus n. sp. (Nematoda: Hoplolaimidae) Associated with Potato in Uganda.},
journal = {Journal of nematology},
volume = {57},
number = {1},
pages = {20250025},
pmid = {40687770},
issn = {0022-300X},
abstract = {The new nematode species Hoplolaimus tuberosus n. sp., isolated from potato rhizosphere in Budwale sub-county, Mbale district, Eastern Uganda, is characterized based on light and scanning electron microscopy alongside four molecular markers. Females of H. tuberosus n. sp. are moderately large (1.2-1.6 mm) and exhibit distinctive morphological features, including an offset lip region with 4-5 lip annuli, a basal lip annule divided into 10-12 irregular blocks, a robust stylet (45-50 μm), a variable lateral field, characterized by one incisure (zigzag longitudinal line formed by anastomoses) anteriorly and posteriorly, and 2-3 irregular, incomplete striae at mid-body, a secretory-excretory pore positioned anterior to the hemizonid, 6 gland nuclei, and a hemispherical to bluntly rounded tail with 8-10 annuli. Males are slightly smaller at 1.0-1.3 mm, have a basal lip annule divided into 2-4 blocks and relatively long spicules (46-58 μm). Phylogenetic analyses of COI mtDNA, ITS-rRNA, 18S-rRNA and D2D3 of 28S-rRNA demonstrated a close relation of the new species with morphologically similar species (Hoplolaimus columbus, Hoplolaimus indicus, Hoplolaimus seinhorsti, Hoplolaimus dubius and Hoplolaimus pararobustus) yet H. tuberosus n. sp. had in all analyses a distinct phylogenetic position. The population density of 50-75 H. tuberosus n. sp. per 100 ml of soil, combined with the polyphagous nature of related Hoplolaimus species, suggests that this new species could pose a significant pest threat to potato crops, warranting further pathogenicity studies.},
}

@article {pmid40687555,
year = {2025},
author = {Naji, SS and Mahmood, MA and Hussein, HM and Mahmood, AA and Baker, HS},
title = {The Effect of Quercus robur Bark on Oral Candidiasis Caused by Candida albicans and Candida glabrata Isolated from a Pediatric Oral Infection as Comparison to Azole Antifungal.},
journal = {Clinical, cosmetic and investigational dentistry},
volume = {17},
number = {},
pages = {285-292},
pmid = {40687555},
issn = {1179-1357},
abstract = {BACKGROUND: The original diversity of Quercus rubra L. (oak) is in eastern America and then distributed to European districts. Oral candidiasis is the most common fungal infection among humans. Azole antifungal drugs can be used to treat Candida infection. Candida albicans and Candida glabrata have emerged as the most common pathogenic yeasts in cases of oral candidiasis.

AIM OF THE STUDY: This study aimed to explore the genotype Candida spp. and evaluate the antifungal activity of hot water extract of oak bark against C. albicans and C. glabrata as an alternative pharmacotherapy compared to azole antifungal agents.

MATERIALS AND METHODS: The sample was isolated from an 8-year-old child with aggressive oral candidiasis and identified by culturing on sabouraud dextrose agar (SDA) CHROMagar. Genotyping of Candida spp. was performed using the internal transcribed spacer (ITS) region. Standard discs of the antifungal's fluconazole, itraconazole, ketoconazole 10 mg/L for each, amphotericin 100, nystatin 50 mg/L, and hot water oak bark extract were administered to C. albicans and C. glabrata in vitro.

RESULTS: Genotyping of Candida spp. showed that 98% of oral candidiasis cases were C. glabrata which had an 870 bp genotype, while 2% were C. albicans which had a 550 bp genotype based on ITS barcoding region size. The findings that the oak bark extract had high antifungal activity against C. glabrata showed an inhibition zone diameter of 3.067 mm compared to high resistance to antifungals.

CONCLUSION: Oak extract is considered a successful alternative for the treatment of oral candidiasis infections by antifungals such as azole and nystatin in children.},
}

@article {pmid40687156,
year = {2025},
author = {Zhang, J and Du, Q and Dai, Y and Yu, H},
title = {Re-description of Clubionahuaban (Araneae, Clubionidae), with the first description of the female.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e157384},
pmid = {40687156},
issn = {1314-2828},
abstract = {BACKGROUND: Clubionahuaban Xin, Zhang, Li, Zeng & Yu, 2020, one of the members of the Clubionatrivialis group, was described, based on two male types from Xiangzhigou Scenic Spot, Guyang City, Guizhou Province, China.

NEW INFORMATION: Recently, new material of sac spiders has been collected from southwest China, including the type locality. The males were identified as C.huaban, based on comparison with the holotype. On the basis of the morphological characters and DNA barcoding, we credibly matched the females and males together as C.huaban. Therefore, C.huaban is re-described, based on new material and the female is described and illustrated for the first time.},
}

@article {pmid40685845,
year = {2025},
author = {Araujo, GS and Sampaio, CLS and Rocha, LA and Leite, CEF},
title = {Integrative taxonomy reveals a new species of the soapfish genus Rypticus (Teleostei: Grammistidae) from the eastern Atlantic Ocean.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70132},
pmid = {40685845},
issn = {1095-8649},
support = {#2023/12231-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; PROTAX #443302/2020//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; #4-22-0314//Lakeside Foundation/ ; //Hope for Reefs/ ; //Fundação de Amparo à Pesquisa do Estado de Alagoas/ ; //Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; #7937-05//National Geographic Society/ ; },
abstract = {A new species of the soapfish genus Rypticus is described based on 14 specimens from the eastern Atlantic Ocean. The new species was previously misidentified as the greater soapfish, R. saponaceus, due to their similar appearance. However, it differs from R. saponaceus in several key characteristics, including a comparatively shorter head, snout and upper jaw, and a deeper body. Molecular data, obtained from the mitochondrial cytochrome oxidase I gene, strongly suggest the monophyly of the new species and support its description as new.},
}

@article {pmid40685410,
year = {2025},
author = {Pikalo, J and Sychra, O and Peña-Espinoza, M and Galat, M and Unterköfler, MS and Heddergott, M and Glawischnig, W and Fuehrer, HP},
title = {Chewing lice (Phthiraptera) on a wild Golden eagle (Aquila chrysaetos) and a zoo-kept Eurasian griffon vulture (Gyps fulvus) in Tyrol, Austria.},
journal = {Parasitology research},
volume = {124},
number = {7},
pages = {85},
pmid = {40685410},
issn = {1432-1955},
mesh = {Animals ; Austria ; *Lice Infestations/veterinary/parasitology ; *Bird Diseases/parasitology ; *Eagles/parasitology ; *Falconiformes/parasitology ; Animals, Zoo/parasitology ; *Phthiraptera/classification/anatomy & histology ; Male ; DNA Barcoding, Taxonomic ; },
abstract = {Chewing lice (Phthiraptera) are obligate and permanent ectoparasites commonly found on birds. The life cycle of these insects is completed on the body of the host and therefore many are host specific. This is the first report of chewing lice on a wild Golden eagle (Aquila chrysaetos) and a zoo-kept Eurasian griffon vulture (Gyps fulvus) in Tyrol, Austria. Three different species of chewing lice were identified: Craspedorrhynchus aquilinus was found on Aquila chrysaetos and Colpocephalum turbinatum and Falcolipeurus quadripustulatus were found on Gyps fulvus. The lice were identified morphologically and by barcoding. Chewing lice (Phthiraptera) of eagles, vultures, and other Accipitriformes are understudied, and further research is needed.},
}

Animals
Austria
*Lice Infestations/veterinary/parasitology
*Bird Diseases/parasitology
*Eagles/parasitology
*Falconiformes/parasitology
Animals, Zoo/parasitology
*Phthiraptera/classification/anatomy & histology
Male
DNA Barcoding, Taxonomic

@article {pmid40685354,
year = {2025},
author = {Kapustová, A and Kulich Fialová, M and Svobodová, M and Brzoňová, J},
title = {Combining blood meal analysis and parasite detection yields a more comprehensive understanding of insect host feeding patterns.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {288},
pmid = {40685354},
issn = {1756-3305},
support = {598120//Grant Agency of Charles University/ ; CA22108//WIMANET-COST Action/ ; UNCE/24/SCI/011//Charles University Research Centre program/ ; },
mesh = {Animals ; *Feeding Behavior ; Czech Republic ; *Ceratopogonidae/parasitology/physiology ; Host-Parasite Interactions ; Haemosporida/isolation & purification/genetics ; Female ; *Mosquito Vectors/parasitology/physiology ; *Culicidae/parasitology/physiology ; Trypanosoma/isolation & purification/genetics ; *Insect Vectors/parasitology/physiology ; Polymerase Chain Reaction ; *Blood/parasitology ; },
abstract = {BACKGROUND: Traditionally, blood meal analysis has been the primary method used to assess feeding patterns of insects. In contrast, parasite detection is commonly applied to monitor parasite circulation and prevalence in vectors, but rarely to study host feeding patterns. Our study aimed to test whether broad-target screening for haemosporidian and trypanosome parasites could complement blood barcoding by revealing additional host associations. We hypothesised that combining both methods would provide a more comprehensive understanding of vector feeding behaviour than either method alone. In addition to evaluating the two methods, we also analysed the vector species composition and their abundance, providing important faunistic and prevalence data that contribute to the broader understanding of local vector-parasite dynamics.

METHODS: Mosquitoes and biting midges were trapped over a 5-year period at three localities in Czechia. Blood-fed individuals underwent blood meal barcoding analysis. In parallel, parasite detection was conducted using nested polymerase chain reaction (PCR) and gut dissection techniques.

RESULTS: A total of 10,152 mosquitoes were collected, with Culex pipiens (66%) and Aedes vexans (18%) being the predominant species. In addition, 1701 biting midges, primarily Culicoides pictipennis (61%) and C. festivipennis (12%), were captured. Among the collected samples, 281 mosquitoes (3%) and 52 biting midges (3%) were blood-fed. Parasites were detected in 468 mosquito pools (5%, 341 trypanosomes, 127 haemosporidians) and 21 midge pools (1%, 8 trypanosomes, 13 haemosporidians). Blood meal barcoding of engorged Aedes, Anopheles, Culiseta, and Mansonia samples revealed only mammalian hosts; however, parasite detection indicated previous feeding on birds. Culex displayed stronger ornithophily according to parasite detection, although blood meal analysis showed a more opportunistic behaviour, with the detection of avian, mammalian and even amphibian blood. Avian parasites were detected in five Culicoides species (Culicoides alazanicus, C. festivipennis, C. kibunensis, C. nubeculosus and C. pictipennis) while human blood was detected only in C. pictipennis. Overall, four Haemoproteus lineages and 15 Plasmodium lineages were identified, 11 of which were new records for Czechia and 4 were newly described.

CONCLUSIONS: Integrating blood meal analysis with parasite detection provides a more comprehensive understanding of insect feeding patterns and vector-host dynamics. Blood meal analysis remains the gold standard for identifying recent host interactions, offering direct and often species-level evidence of feeding events. In addition, parasite detection extends the window of detectability beyond the digestion of host blood and can reveal additional or otherwise-overlooked host associations. Together, these complementary approaches increase the likelihood of detecting interactions with a broader range of hosts, including humans, who might be missed by parasite screening alone.},
}

Animals
*Feeding Behavior
Czech Republic
*Ceratopogonidae/parasitology/physiology
Host-Parasite Interactions
Haemosporida/isolation & purification/genetics
Female
*Mosquito Vectors/parasitology/physiology
*Culicidae/parasitology/physiology
Trypanosoma/isolation & purification/genetics
*Insect Vectors/parasitology/physiology
Polymerase Chain Reaction
*Blood/parasitology

@article {pmid40683866,
year = {2025},
author = {Fu, Y and Kim, H and Roy, S and Huang, S and Adams, JI and Grimes, SM and Lau, BT and Sathe, A and Ji, HP and Zhang, NR},
title = {Single cell and spatial alternative splicing analysis with Nanopore long read sequencing.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6654},
pmid = {40683866},
issn = {2041-1723},
support = {R33CA247700//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35HG011292-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U01CA217875//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Alternative Splicing/genetics ; *Single-Cell Analysis/methods ; Humans ; *Nanopore Sequencing/methods ; *Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Protein Isoforms/genetics ; },
abstract = {Long-read sequencing boosts alternative splicing analysis but faces technical and computational barriers in single-cell and spatial settings. High Nanopore error rates compromise cell barcode and UMI recovery, while read truncation and misalignment undermine isoform quantification. Downstream, a statistical framework to assess splicing variation within and between cells or spatial spots is lacking. We introduce Longcell, a statistical and computational pipeline for isoform quantification from single-cell and spatially barcoded Nanopore long reads. Longcell efficiently recovers cell barcodes and UMIs, corrects sequencing errors, and models splicing diversity within and between cells or spots. Applied across multiple datasets, Longcell allows accurate identification of spatial isoform switching. Longcell also reveals widespread high intra-cell isoform heterogeneity for highly expressed genes. Finally, on a perturbation experiment for 9 splicing factors, Longcell identifies regulatory targets that are validated by targeted sequencing.},
}

*Alternative Splicing/genetics
*Single-Cell Analysis/methods
Humans
*Nanopore Sequencing/methods
*Nanopores
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods
Sequence Analysis, RNA/methods
Protein Isoforms/genetics

@article {pmid40682185,
year = {2025},
author = {Barazandeh, M and Gaikani, HK and Pattanshetti, R and Ogbede, JU and Sinha, S and Moore, R and Carr, CE and Giaever, G and Nislow, C},
title = {Bar-seq: A robust, platform-agnostic method for massively parallel cell-based screens.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf166},
pmid = {40682185},
issn = {2160-1836},
abstract = {Bar-seq (barcode sequencing) is a high-throughput method originally developed for systematically identifying gene-drug interactions and genetic dependencies in yeast using pooled deletion mutant libraries. This approach enables high-resolution profiling of large mutant libraries over time, across diverse experimental conditions, providing relative fitness values for each individual within the population. As the technology for enumerating barcodes has evolved, we have continued to incorporate improvements to the method. Here, we present an optimized Bar-seq workflow adaptable to multiple sequencing platforms, including instruments from Illumina, MGI, Element, and Oxford Nanopore. We highlight the advantages and limitations of each approach to aid in experimental design decisions. We introduce refinements in barcode amplification, sequencing strategies, and data analysis to enhance accuracy and scalability while making adoption as straightforward as possible.},
}

@article {pmid40681695,
year = {2025},
author = {Ali, MA and Gowda, NR and Allam, MA and Fayed, SA},
title = {Conservation of Verbascum sinaiticum Benth using innovative tissue culture technique and DNA barcoding.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26075},
pmid = {40681695},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Verbascum/genetics/growth & development ; *Tissue Culture Techniques/methods ; Plant Shoots/growth & development/genetics ; Culture Media ; Plants, Medicinal/genetics/growth & development ; *Conservation of Natural Resources/methods ; },
abstract = {Egypt has diverse medicinal plants, many of which are endangered because of environmental and human pressures. Verbascum sinaiticum Benth (V. sinaiticum) is a medicinal plant from the Scrophulariaceae family and a locally rare species endemic to Sinai. This study introduces an innovative in vitro regeneration protocol for V. sinaiticum, developed for the first time using optimized tissue culture techniques. Additionally, the incorporation of molecular identification by DNA barcoding and biochemical profiling (via HPLC and SDS-PAGE) presents a complete strategy to conservation and genetic documentation, to support future biotechnological applications. An efficient in vitro regeneration system for V. sinaiticum was established using tissue culture techniques. The study investigated the effects of three different shoot induction media on growth, The first medium was BA medium, a combination of 0.5 mg L[- 1] benzyl adenine (BA), 5 mg L[- 1] thiamine HCl, 0.5 mg L[- 1] nicotinic acid, and 0.5 mg L[- 1] pyridoxine was added to the initial medium. The second medium was MD medium supplemented with 3 mg L[- 1] BA, 0.2 mg L[- 1] naphthaleneacetic acid (NAA), 10 mg L[- 1] thiamine HCl, 1 mg L[- 1] nicotinic acid, and 1 mg L[- 1] pyridoxine. The third medium was AB medium formulated with 1 mg L[- 1] Adenine sulfate, 1 mg L[- 1] benzyl adenine, 10 mg L[- 1] thiamine HCl, 1 mg L[- 1] nicotinic acid, and 1 mg L[- 1] pyridoxine, and three media for rooting, The first medium was IB medium supplemented with 0.4 mg L[- 1] indol butyric acid, 5 mg L[- 1] thiamine HCl, 0.5 mg L[- 1] nicotinic acid, and 0.5 mg L[- 1] pyridoxine. The second medium was IA medium containing 5 mg L[- 1] thiamine HCl, 0.5 mg L[- 1] nicotinic acid, and 0.5 mg L[- 1] pyridoxine. The third medium was NA media formulated with 0.4 mg L[- 1] naphthaleneacetic acid, 5 mg L[- 1] thiamine HCl, 0.5 mg L[- 1] nicotinic acid, and 0.5 mg L[- 1] pyridoxine. All media were prepared using Murashige and Skoog (MS) basal salts 4.4 g L[- 1] supplemented with 30 g L[- 1] sucrose, and solidified with 2.8 g L[- 1] gelrite. Various propagation protocols were tested based on the availability of plant materials. We have devised flexible methods for large-scale micropropagation that offer a sustainable and quick production strategy, even in the face of resource constraints. The surface sterilization technique was refined, resulting in up to 75% contamination-free cultures. The highest germination rate was observed with 20% Clorox for 15-20 min, but extended exposure (25-30 min) resulted in decreased germination.HPLC analysis revealed that the ethanolic extract had the highest quantities of rutin (19.07 µg/mL) and vanillin (6.29 µg/mL), while the aqueous extract had the highest levels of gallic acid (7.02 µg/mL) and chlorogenic acid (6.02 µg/mL). SDS-PAGE examination revealed five protein bands ranging in molecular weight from 240 kDa to 28 kDa. This study introduces an innovation and preservation strategy for V. sinaiticum, a locally rare species in Egypt. DNA barcoding was used for molecular authentication, and the acquired sequence was matched to GenBank database sequences using the BLAST tool.},
}

*DNA Barcoding, Taxonomic/methods
*Verbascum/genetics/growth & development
*Tissue Culture Techniques/methods
Plant Shoots/growth & development/genetics
Culture Media
Plants, Medicinal/genetics/growth & development
*Conservation of Natural Resources/methods

@article {pmid40679848,
year = {2025},
author = {Vereecke, N and Yoon, TB and Luo, TL and Corey, BW and Lebreton, F and Mc Gann, PT and Dekker, JP},
title = {An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0066425},
doi = {10.1128/jcm.00664-25},
pmid = {40679848},
issn = {1098-660X},
abstract = {UNLABELLED: In this work, we present an optimized nanopore long-read only sequencing workflow for epidemiologic analysis of clonal outbreaks built with open-source tools. A set of unrelated clinical Pseudomonas aeruginosa isolates (n = 10) was chosen for workflow optimization, and sequencing libraries were prepared using a modified rapid barcoding strategy that incorporates temperature ramps to improve performance for high-GC content genomes. Sequencing data were used to benchmark the performance of the dorado suite (v0.9.1), including its basecaller, pre-assembly read error correction, and post-assembly polishing algorithms. All long-read assemblies and core genome multilocus sequence typing (cgMLST) were performed with Flye and pyMLST, respectively. Results were compared with a standard reference Illumina short-read approach, and discordant positions were determined at the core and whole-genome levels. Optimal performance was found with dorado sup@v5.0.0 basecalling with the inclusion of dorado error correction and dorado polish with its bacterial model. This workflow was then validated with four retrospective hospital outbreak isolate sets, including Klebsiella pneumoniae (n = 12), P. aeruginosa (n = 11), Enterococcus faecium (n = 10), and Staphylococcus aureus (n = 10). The nanopore-only assemblies obtained from the optimized pipeline demonstrated fully concordant cgMLST-based minimum spanning trees compared to the Illumina short-read reference. At the whole-genome level, high concordance was also observed, with as few as two discordant positions per genome compared to short-read assemblies. This optimized library preparation and open-source computational workflow enables nanopore-only clonality and outbreak analysis with performance comparable to that of Illumina short-read sequencing and will contribute critically to hospital infection control.

IMPORTANCE: For the past decade, bacterial whole-genome sequencing has been performed using high-accuracy short-read sequencing. More recently, long-read sequencing with Oxford Nanopore Technologies (ONT) instruments has emerged as a potential alternative based on multiple advantages, including lower costs, portability, and speed. However, this platform has suffered from basecall error rates that were too high for many applications in clinical microbiology, including outbreak tracing. With the release of new flow cell chemistries and basecall algorithms, the accuracy has improved dramatically, making this approach feasible for outbreak investigations. In this work, we optimize a streamlined nanopore-only workflow for epidemiologic analysis of bacterial pathogens. The workflow was validated with isolates from four previously identified clinical outbreaks with varying GC content and demonstrated fully concordant cgMLST clustering as compared to short-read references. This workflow will facilitate the broader implementation of ONT-only genomes and cgMLST analysis to assist in hospital outbreaks worldwide.},
}

@article {pmid40679398,
year = {2025},
author = {Goldstein, I and Hale, JJ and Ehrenreich, IM},
title = {Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyaf136},
pmid = {40679398},
issn = {1943-2631},
abstract = {Global epistasis is a phenomenon in which the effects of genetic perturbations depend on the fitness of the individuals in which they occur. In populations with natural genetic variation, global epistasis arises from interactions between perturbations and polymorphic loci that are mediated by fitness. To investigate the prevalence and characteristics of loci involved in these interactions in the budding yeast Saccharomyces cerevisiae, we used combinatorial DNA barcode sequencing to measure the fitness of 169 cross progeny (segregants) subjected to 8,126 CRISPRi perturbations across two environments. Global epistasis was evident in these data, with more fit segregants within each environment exhibiting greater sensitivity to genetic perturbations than less fit segregants. We dissected the genetic basis of this global epistasis by scanning the genome for loci whose effects covary with CRISPRi-induced reductions in population fitness. This approach identified 58 loci that interact with fitness, most of which exhibited larger effects in the absence of genetic perturbations. In aggregate, these loci explained the observed global epistasis in each environment and demonstrated that the loci contributing to global epistasis largely overlap with those influencing fitness in unperturbed conditions.},
}

@article {pmid40677748,
year = {2025},
author = {Bae, S},
title = {Validation of improved cytochrome c oxidase I (COI) primers for comprehensive biodiversity assessment of ascidians.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19671},
pmid = {40677748},
issn = {2167-8359},
mesh = {Animals ; *Urochordata/genetics/classification/enzymology ; *Biodiversity ; *Electron Transport Complex IV/genetics ; *DNA Primers/genetics ; Polymerase Chain Reaction ; *DNA Barcoding, Taxonomic/methods ; },
abstract = {Reliable molecular tools are needed for effective biodiversity assessment of marine organisms. These tools can be used in ascidians species, which are one of the most invasive taxa worldwide and morphologically difficult to identify. This study aimed to redesign and improve ascidian-specific primers and validate the new primer pair (AscCOI2) for comprehensive biodiversity assessment. To design an optimized primer, 3,948 COI sequences from 273 ascidian species were used as a dataset. The AscCOI2 pair was developed through strategic modifications to the binding site and validated using in silico and in vitro approaches. Analysis of penalty scores showed the improved efficiency of the redesigned AscCOI2 pair, with ascidians scoring less than 150 points for both forward and reverse primers and the non-target groups maintaining a score above 480. Primer-binding analysis results showed a significant improvement in amplification success rate from 47.99% to 82.42% at the species level. In vitro validation using conventional polymerase chain reaction (PCR) confirmed the successful amplification of six ascidian species and failure for a non- ascidian taxon. Barcoding gap analysis showed a clear gap of 0.015 between intraspecific and interspecific genetic distances. The species detection capability of the redesigned AscCOI2 pair greatly improved, and the high taxonomic specificity of ascidians is maintained. Overall, this study demonstrates that the AscCOI2 pair is an effective tool for both metabarcoding and mini-barcode applications in biodiversity assessment and molecular systematics research of ascidians.},
}

Animals
*Urochordata/genetics/classification/enzymology
*Biodiversity
*Electron Transport Complex IV/genetics
*DNA Primers/genetics
Polymerase Chain Reaction
*DNA Barcoding, Taxonomic/methods

@article {pmid40678274,
year = {2024},
author = {Liao, J and Yang, L},
title = {Multimode Sensing by Optical Whispering-gallery-mode Barcodes: A New Route to Expand Dynamic Range for High-resolution Measurement.},
journal = {IEEE transactions on instrumentation and measurement},
volume = {73},
number = {},
pages = {},
pmid = {40678274},
issn = {0018-9456},
support = {R21 EB030845/EB/NIBIB NIH HHS/United States ; },
abstract = {Sensors play a vital role in detecting and quantifying various parameters relevant to the physical and biochemical aspects of the world. In the field of optical sensing, Whispering-Gallery-Mode (WGM) microresonators have emerged as promising candidates, offering the advantages of high sensitivity, high resolution, and small footprint. However, conventional sensing methods, which rely on tracking changes in a single mode, have a limited dynamic range of measurement. In this study, we develop a theoretical framework that offers comprehensive analytical insights for multimode-sensing techniques. We demonstrate an optical WGM barcode technique that enables simultaneous monitoring of the patterns of multiple modes that can provide over-FSR (Free spectral range) tracking with high resolution. By analyzing the Cramer-Rao bound (CRB) for resonance shift estimation, we assess the theoretical limits of measurement resolution and dynamic range, independent of specific sensing system and estimation algorithm. Comparative analysis of the CRBs for single-mode sensing and multimode sensing confirms the improvement in resolution and dynamic range achievable through the barcode technique based on the multimode spectrum. This work lays the foundation for developing a high-resolution sensor with superior sensitivity across a drastically expanded dynamic range.},
}

@article {pmid40677746,
year = {2025},
author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D},
title = {Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19674},
pmid = {40677746},
issn = {2167-8359},
mesh = {*DNA Barcoding, Taxonomic/methods/standards ; Pacific Ocean ; Animals ; *Aquatic Organisms/genetics/classification ; Biodiversity ; Electron Transport Complex IV/genetics ; *Databases, Nucleic Acid/standards ; *Databases, Genetic ; },
abstract = {DNA barcoding is a widely used tool for species identification, with its reliability heavily dependent on reference databases. While the quality of these databases has long been debated, a critical knowledge gap remains in their comprehensive evaluation and comparison at regional scales. Marine metazoan species in the western and central Pacific Ocean (WCPO), a region characterized by high biodiversity and limited sequencing efforts, are an example of this gap. This study developed a systematic workflow to assess mitochondrial cytochrome c oxidase subunit I (COI) barcode coverage and sequence quality in two commonly used reference databases for DNA barcoding: the nucleotide reference database from the National Center for Biotechnology Information (NCBI); and from the Barcode of Life Data System (BOLD). Comparative analyses across marine phyla and WCPO regions identified significant barcode gaps and quality problems, providing insights to guide future barcoding efforts. NCBI exhibited higher barcode coverage, but lower sequence quality compared to BOLD. Quality issues, including over- or under-represented species, short sequences, ambiguous nucleotides, incomplete taxonomic information, conflict records, high intraspecific distances, and low inter-specific distances were identified in both databases, likely resulting from contamination, cryptic species, sequencing errors, or inconsistent taxonomic assignment. The barcode identification number (BIN) system in BOLD demonstrated potential for identifying and addressing problematic records, highlighting the benefits of curated databases. Significant barcode deficiencies and quality issues were observed in the south temperate region of WCPO and phyla such as Porifera, Bryozoa, and Platyhelminthes. Additionally, the COI barcode showed limited species-level resolution for certain taxa, including Scombridae and Lutjanidae. Addressing barcode coverage gaps, improving taxonomic representation, and enhancing sequence quality will be essential for strengthening future barcoding initiatives and advancing biodiversity monitoring and conservation in the WCPO and beyond. This study highlights the need for standardized database curation and sequencing practices to improve the global reliability and applicability of DNA barcoding.},
}

*DNA Barcoding, Taxonomic/methods/standards
Pacific Ocean
Animals
*Aquatic Organisms/genetics/classification
Biodiversity
Electron Transport Complex IV/genetics
*Databases, Nucleic Acid/standards
*Databases, Genetic

@article {pmid40677014,
year = {2025},
author = {Li, H and Cai, Y and Zhang, L and Hu, E and Yang, J and Guo, H and Cui, Y and Chen, B and Qian, G},
title = {Anisotropic Excitation-Modulated Multi-Color Three-photon Excited Luminescence in Ln-MOF Heterostructure.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e09590},
doi = {10.1002/adma.202509590},
pmid = {40677014},
issn = {1521-4095},
support = {52402206//National Natural Science Foundation of China/ ; 52302200//National Natural Science Foundation of China/ ; 52025131//National Natural Science Foundation of China/ ; LQN25E020013//Natural Science Foundation of Zhejiang Province/ ; LQ23E020004//Natural Science Foundation of Zhejiang Province/ ; 2024-3-029//Key Projects of Jinhua Science and Technology Bureau/ ; },
abstract = {Multi-photon excited luminescence (MPEL) modulation is of great application value for optoelectronics, especially MPEL with the characteristics of multi-color emission and optical anisotropy. However, it still suffers from the obstacles in highly-integrating and orientedly-assembly of various MPEL units. Herein, a hierarchical assembly-in situ doping strategy is proposed to establish a novel lanthanide-graded metal-organic framework based heterostructure. Well-designed ligand and Ln[3+] ions are respectively selected as the MPEL energy donor and acceptor units (MEDU and MEAU). Through utilizing the effective energy transfer between them, the as-obtained triblock heterostructure displays multi-dimensional three-photon excited luminescence (3PEL) modulation, where the emission band and intensity can be switched by manipulating excited regions and excitation polarization based on a single pump source. This is attributed to the precise integration and orientation of photonic units. As a result, the heterostructure exhibits multi-color 3PEL with a record-high MPEL color gamut (>30% of sRGB area) in MOFs and high degree of linear polarization values (max ≈88.6%). Such anisotropic 3PEL modulation shows promising potential in nonlinear optical switches, programmable logic gates, and multi-level optical barcodes. These findings open up an intriguing way to develop up-conversion luminescent materials with functions on demand toward photonic modulation.},
}

@article {pmid40676502,
year = {2025},
author = {Univaso, L and Peña, F and Román-Figueroa, C and Paneque, M},
title = {The rps15-rpl32 intergenic locus is a phylogeographic marker for Latin American Zea mays landrace varieties and subspecies.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {672},
pmid = {40676502},
issn = {1471-2164},
support = {40035912-0/2022//FIC ÑUBLE/ ; },
mesh = {*Zea mays/genetics/classification ; Phylogeography ; Genetic Markers ; Latin America ; Phylogeny ; *Ribosomal Proteins/genetics ; *DNA, Intergenic/genetics ; *Plant Proteins/genetics ; Genetic Loci ; },
abstract = {BACKGROUND: Maize (Zea mays L.) has a deep cultural significance in Latin America, with traditional and native varieties cultivated for millennia. Approximately 220 maize races have been identified in the region. These races have adapted to the diverse environmental conditions, resulting in a considerable diversity of varieties. Although DNA barcoding is widely used for species identification, distinguishing between varieties within a species remains challenging in plants, owing to the conserved nature of standard barcoding loci. Intragenic marker combinations are often used to address this limitation. However, they remain insufficient for variety-level resolution. Therefore, we developed a pipeline to identify robust markers that can distinguish maize varieties based on their phylogeographic origins.

RESULTS: In this study, the small single-copy (SSC) region of the chloroplast genome exhibited the highest mutation rate per nucleotide. Furthermore, the intergenic regions rps15-rpl32 and ndhD-ndhF exhibited the highest mutation rates in the SSC. Comparatively, the coding genes in this region were more conserved. The rps15-rpl32 locus demonstrated improved resolution for phylogeographic analysis when concatenated with a short genetic anchor sequence. This marker accurately identified the geographic origin of maize samples. Overall, it was the most informative marker despite its relatively low SNP and InDel frequency and moderate divergence levels. Contrastingly, the ndhF-ndhD locus exhibited higher mutation rates but failed to effectively resolve phylogenetic relationships.

CONCLUSIONS: Our findings demonstrate that concatenated loci can accurately identify the geographic origin of Zea mays varieties and subspecies and elucidate their relationships. Moreover, the superior performance of rps15-rpl32 in the delineation of phylogenetic relationships among regional genomes shows its potential application as a marker for distinguishing closely related varieties and subspecies. This locus can facilitate the streamlined validation of Zea mays varieties for regional authenticity.},
}

*Zea mays/genetics/classification
Phylogeography
Genetic Markers
Latin America
Phylogeny
*Ribosomal Proteins/genetics
*DNA, Intergenic/genetics
*Plant Proteins/genetics
Genetic Loci

@article {pmid40675575,
year = {2025},
author = {Ortega-Morales, AI and Rodríguez-Rojas, JJ and Fernández-Santos, NA and Medrano-Santillana, M and Ayala-Sulca, YO and Arque-Chunga, W and Colos-Galindo, P and Ortega-Morales, NB and López-Hernández, I and Rodríguez-Pérez, MA},
title = {THE PRESENCE OF AEDES HENDERSONI IN MEXICO.},
journal = {Journal of the American Mosquito Control Association},
volume = {},
number = {},
pages = {},
doi = {10.2987/25-7223},
pmid = {40675575},
issn = {1943-6270},
abstract = {The mosquito species commonly named Henderson American pointy mosquito, Aedes hendersoni, was found during a routine mosquito vector surveillance from 2020 to 2023 in diverse collection sites with conserved forested vegetation at the Eco-Parks Rincón de la Silla and El Salto in Nuevo León, northeastern Mexico. Collected specimens were labeled, mounted, and identified using taxonomic keys. Further confirmation of Ae. hendersoni was performed by deoxyribonucleic acid (DNA) barcoding and cytochrome oxidase-I (COI) sequences served to confirm the identity of Ae. hendersoni by comparison with other sequences of species with Triseriatus group and Protomacleaya subgenus of Aedes. Voucher specimens were curated and are available in 2 Mexican collection repositories and COI sequences were deposited in the NCBI GenBank with accession number MG242473.1. Hence, the presence of Ae. hendersoni in México is documented for the first time. Now, geographic occurrence of this species is from Canada throughout United States to northeastern México. With this new record, there are the 4 mosquito species in the Triseriatus group [Aedes: (Protomacleaya)] and 252 species in México.},
}