Search Results (15,412)

Background: Resistance to first-line anti-tuberculosis drugs in Mycobacterium tuberculosis represents a significant public health challenge, particularly in high-burden tuberculosis (TB) settings such as Pakistan, where multidrug-resistant (MDR) forms further complicate disease control efforts. Drug resistance is primarily associated with mutations in rpoB, inhA, katG, embA, embB, embC, and pncA. The emergence of novel, region-specific variants underscores the urgent need for integrating genomic surveillance into routine TB diagnostics and regional control programs. This study aimed to identify the spectrum of mutations contributing to first-line drug resistance in MDR-TB isolates from Khyber Pakhtunkhwa, Pakistan. Methods: Whole-genome sequencing was performed on 16 clinical isolates (12 MDR and 4 drug-susceptible) to identify resistance-associated mutations in rpoB, inhA, katG, embA, embB, embC, and pncA. Detected variants were interpreted using the World Health Organization (WHO) mutation catalogue to determine their association with drug resistance. Phylogenetic relationships were inferred using the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) platform. Results: A total of 16 M. tuberculosis isolates were analyzed to evaluate resistance to first-line anti-tuberculosis drugs. In rpoB, 76 distinct variants were identified, including canonical mutations such as Ser450Leu and His445Arg, as well as a potentially novel substitution, Ser431Phe, predicted to confer high-level rifampicin resistance. The katG and inhA genes harbored 24 and 27 mutations, respectively, including well-characterized substitutions such as Ser315Thr and Ala114Glu, which are strongly associated with isoniazid resistance. Mutations in embA and embB were linked to ethambutol resistance, with several variants localized within conserved transmembrane domains critical for drug interaction. Phylogenetic analysis revealed substantial genetic diversity and evidence of local transmission among MDR-TB isolates. Conclusions: This study suggests that the genetic landscape of drug resistance in M. tuberculosis is highly dynamic in endemic regions. The findings highlight the importance of integrating region-specific mutation profiles into molecular diagnostic frameworks to enhance early detection, guide individualized therapeutic interventions, and strengthen strategies aimed at controlling the transmission of MDR-TB. Full article

High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving four distinct sample preparation procedures (fresh (A), filtered (B), frozen (C) and cryogenic mycelium (D)) across mycelial cultures of eight Tunisian fungal strains representing Ascomycota and Basidiomycota to identify the optimal combination for genomic DNA extraction from mycelium. The eight phylogenetically diverse fungal species were analyzed using short-read (MiSeq and NextSeq550) and/or long-read (MinION Mk1C) sequencing technologies, giving a depth coverage between 3.7× and 83×. The generation and quality of the assemblies were assessed within the Galaxy platform, which revealed a gap percentage of 0–0.509%. Taxonomic characterization and phylogenetic inference were performed with SANGER technology using the Internal Transcribed Spacer (ITS) and D1/D2 region of the 26S rRNA gene, assigning the species to our eight different strains: Clitopilus baronii (BS6), Porostereum spadiceum (BS200), Trametes versicolor (BS22-9), Schizophyllum commune (BS23-13), Gloeophyllum abietinum (BS23-14), Irpex laceratus (BS100), Trichoderma asperellum (GC9) and Trichoderma harzianum (S3). The optimized DNeasy Plant Pro Kit protocol with cryogenic biomass treatment presents a safe and cost-effective method for fungal genome sequencing and taxonomic resolution. This integrated comparative evaluation of extraction for sequencing identifies an optimal Qiagen-based extraction strategy combined with cryogenic treatment for eight diverse Tunisian fungal species, guiding method selection based on specific cell wall characteristics rather than proposing a universal protocol limited by unequal replication and strain numbers. Full article

The first influenza A(H5N1) human case associated with the A(H5N1) dairy cattle outbreak in the United States was identified in April 2024. The U.S. CDC response to this outbreak was activated days later and remained active until July 2025. During this time, 70 human cases of influenza A(H5N1) were detected with a range of epidemiological links to sources of exposure. Next-generation sequencing (NGS) of human samples was an effectual mechanism for tracking and analyzing the outbreak evolution throughout the response. Due to the specimens’ importance and their variable physical quality, an assortment of laboratory methods was utilized including influenza segment-specific amplification, enrichment capture, short-read, and long-read sequencing. Combining these methods allowed for high-quality genomic data production with rapid turnaround times—typically 2 days from sample receipt to public database submission. By leveraging replicate sequencing, enrichment capture, and sequencing of diagnostic amplicons, valuable genomic data could be produced directly from human clinical specimens that would have normally been considered too weak for routine virologic surveillance sequencing. The resulting assemblies were characterized and analyzed by CDC and shared with local and state public health authorities to facilitate case investigations and risk assessment. These data were further used for phylogenetic analyses of viruses from human cases to investigate likely animal-to-human transmission events and identify clusters within the outbreak that might indicate trends in the types of exposures. Through the adaptable laboratory workflow and the rapid release of viral genomic data, the public health risk mitigation strategies could be evaluated and adjusted in real time. Full article

Avian reovirus (ARV) causes viral arthritis and leads to considerable economic losses in the poultry industry. In this study, six ARV strains of distinct genotypes (FJNP01–FJNP06) were isolated from commercial broiler farms. Through gene sequencing and pathogenicity assessment, we analyzed the genetic evolution and pathogenic characteristics of the σC, P10, σB, μB, and λC genes. Pathogenicity tests revealed that inoculation with FJNP01–FJNP06 by footpad or oral gavage induced symptoms in specific-pathogen-free (SPF) chickens, including mortality and growth retardation. Among the isolates, FJNP04 (genotype IV) showed the highest pathogenicity, causing increased mortality, weight loss, and severe lesions in the footpads and bursa of Fabricius, followed by FJNP05 and FJNP02. The pathogenicity of FJNP06 varied by inoculation route, with enhanced pathogenicity observed following oral gavage. In contrast, FJNP01 and FJNP03 demonstrated relatively low pathogenicity. Identity analysis indicated that σC and P10 were highly variable, σB was relatively conserved, while μB and λC displayed considerable divergence. Phylogenetic analysis placed FJNP01–FJNP06 into genotypes I to Ⅵ, respectively, forming six distinct branches on the σC and P10 phylogenetic trees, yet clustering more closely on the σB, μB, and λC trees. The pathogenicity of different genotypes of ARV varies, among which FJNP04 (genotype IV) exhibits the strongest pathogenicity. Genetic sequence analysis revealed that σC and P10 are highly variable, σB is relatively conserved, while μB and λC display a wide range of variation. This study provides insights into the genetic variation and pathogenic characteristics of ARV and serves as a reference for future research. Full article

Haptophytes are ubiquitous single-celled eukaryotic plankton in coastal and open oceans that play a key role in marine biogeochemical cycling. Understanding the size structure and community composition of active haptophytes is crucial for elucidating their diversity and ecological functions. This study investigated the diversity and community structure of pico- (0.2–3 μm) and nano-sized (3–20 μm) haptophytes in the surface waters of the western Pacific Ocean using high-throughput sequencing targeting the hypervariable V4 region of the 18S rRNA. The pico-sized community exhibited significantly higher diversity than the nano-sized community. Community composition varied significantly between size fractions, driven primarily by the genera Chrysochromulina and Syracosphaera. Furthermore, the nano-sized community was more strongly influenced by environmental variables than the pico-sized community, although neither size fraction displayed a clear coastal-to-open-ocean distribution pattern. Null and neutral community model analyses indicated that both size-fractionated communities were primarily regulated by stochastic processes, while deterministic processes exerted a greater influence on the nano-sized community. Co-occurrence network analysis revealed stronger interconnections and a higher number of keystone species within the nano-sized community. In both networks, intermediate taxa (relative abundances of 0.01% to 0.1%) exhibited the highest diversity and abundance among keystone species, highlighting their pivotal role in shaping the network structure and stability. Additionally, phylogenetic analyses revealed that while the majority of ZOTUs clustered with known taxa, multiple deep-branching, uncultured lineages were identified across both size fractions, indicating substantial uncharacterized genetic diversity. This study underscores the variability and hidden diversity of size-fractionated haptophyte community structures in oligotrophic open oceans, providing valuable insights into their functional significance in global biogeochemical cycles. Full article

Galeruca daurica (Joannis) (Coleoptera: Chrysomelidae) is an oligophagous pest in which both adults and larvae prefer to feed on Allium forage grasses of the Liliaceae family. In this study, we identified gustatory receptor (GR) genes based on the transcriptome data of G. daurica; analyzed the expression profiles of these GR genes across different larval instars and various tissues of male and female adults using quantitative real-time PCR (qRT-PCR); detected the electrophysiological responses of the mouthparts of male and female G. daurica adults to flavonoids and carbohydrates using single sensillum recording (SSR); and recorded the changes in food consumption of G. daurica adults after feeding on six host plant-derived metabolites. A total of 26 GR genes were identified from the transcriptome data of adult and larval of G. daurica. Phylogenetic analysis was performed to screen candidate functional gustatory receptor genes, including four sugar receptors (GdauGR7, GdauGR10, GdauGR14 and GdauGR28), seven bitter receptors (GdauGR11, GdauGR16~17, GdauGR22, GdauGR25~26 and GdauGR30), and two CO₂ receptors (GdauGR15 and GdauGR20). Larval expression profiling of GdauGRs in G. daurica revealed that the relative expression levels of 17 genes exhibited dynamic changes during larval growth and development. GdauGRs were expressed to varying degrees in the antennae, mouthparts, brain, gut, and forelegs of adult G. daurica, with sex-specific differences. Notably, the expression levels of GdauGR4, GdauGR9 and GdauGR16 in the gut were extremely significantly higher than those in other tissues. In the SSR test, the six tested flavonoids and one carbohydrate were able to induce robust electrophysiological responses in the gustatory sensilla on the antennae and mouthparts of adult G. daurica at specific concentrations. In addition, the supplementation of several host-derived metabolites altered the food consumption of adult G. daurica. These findings lay a solid foundation for elucidating the molecular mechanisms underlying gustatory recognition and host adaptation in G. daurica. Full article

Bovine rotavirus (BRV) poses a major threat to the global cattle industry, driving significant morbidity and mortality in young calves. In Yunnan Province, China, BRV is the primary cause of neonatal calf diarrhea (NCD), yet the molecular epidemiology of circulating strains remains poorly understood. This study aimed to investigate the molecular characteristics of bovine rotavirus strains associated with a severe outbreak of the NCD on a local farm. Fecal samples were collected from 396 calves and screened for BRV by RT-PCR targeting the VP6 gene. Positive samples were subjected to virus isolation in MA104 cells, followed by whole-genome sequencing, phylogenetic analysis, and pathogenicity assessment in suckling mice. Of 396 samples, 85 tested positive for BRV, corresponding to an animal-level prevalence of 21.5% (95% CI: 17.5–25.8%), with four fatalities recorded. A strain designated as BRV-YN1-2021 was successfully isolated, exhibiting characteristic cytopathic effects, specific immunofluorescence, and typical rotavirus morphology by electron microscopy. Genomic analysis revealed the constellation G8-P[¹]-I2-R2-C2-M2-A3-N2-T6-E2-H3, identified as genotype G8P[¹]. BLAST analysis showed that four genomic segments shared the highest identity with deer rotavirus strains, five with human rotavirus strains, and two with bovine rotavirus strains. Phylogenetic analysis demonstrated close relationships with US deer strains, Japanese bovine strains, and human strains circulating in China. Experimental infection in suckling mice induced diarrhea and significant intestinal histopathology, degeneration of villous epithelial cells, goblet cell hyperplasia, and inflammatory infiltration. This study reports the first isolation of a G8P[¹] bovine rotavirus from a diarrhea outbreak in Chinese cattle. The multi-host genetic composition provides evidence of interspecies reassortment events, highlighting the zoonotic potential of BRV and emphasizing the need for continuous molecular surveillance to inform effective control strategies. Full article

The objectives of this paper were to assess the genetic diversity, population structure, genetic differentiation, and phylogenetic relationships among seven duck populations using 14 microsatellite (MS) markers. This paper included 176 individuals representing seven duck populations of Bangladesh: indigenous duck (BLD), Nageswari (NAG), Rupali (RUP), Jinding (JIN), Pekin (PEK), BAU Black and White (BWC), and BAU White (WHC). A total of 133 alleles were observed with a mean of 9.50 alleles per locus. Genetic diversity was evaluated using measures such as allele frequency, observed and expected heterozygosity, and Shannon’s information index with average values of 5.44 ± 0.31, 0.59 ± 0.02, 0.64 ± 0.02, and 1.28 ± 0.05, respectively. Population differentiation and inbreeding analysis (F-statistics) indicated moderate genetic diversity and a slight degree of inbreeding across populations. Analysis of molecular variance indicated that 75% of the total genetic diversity was attributable to the within-population variation, whereas 9% and 16% were attributed to the variation among individuals and population differentiation, respectively. Indigenous duck populations (BLD, NAG, and RUP) had a close genetic relationship with JIN ducks and an intermediate relationship with two crossbreds (BWC and WHC), and the highest genetic distance was observed with PEK ducks. Neighbor-joining phylogenetic analysis revealed that the Bangladeshi indigenous duck populations formed a single cluster, while the two crossbreds (BWC and WHC) and PEK exhibited their distinct genetic identities in separate clusters. Furthermore, structure analysis at K = 2 to 5 confirmed the distinct genetic architecture (ΔK = 4.00) of the studied duck populations. This paper provides important insights into genetic diversity measures and population differentiation that will be helpful in future genetic improvement, conservation initiatives, and the design of appropriate breeding programs. Full article

Solitary living is an evolutionarily widespread yet comparatively under-theorized social system, despite its occurrence across diverse animal taxa. Shrikes (family Laniidae) are small predatory passerines that combine raptorial behavior, strong territoriality, and predominantly solitary space use, making them a powerful model for examining the ecology and evolution of solitary living. Here, I synthesize published work on shrike behavioral ecology and explicitly link these traits to the costs and benefits of a solitary lifestyle. I argue that shrikes exemplify how solitary species can offset the absence of social buffering through cognitive innovation, finetuned habitat selection, and flexible yet tightly bounded sociality. I then compare shrike ecology to solitary mammals and reptiles, highlighting convergent patterns in resource dispersion, spatial memory, risk management, and juvenile dispersal. I further examine how anthropogenic pressures, such as habitat fragmentation, climatic instability, and urbanization, interact with solitary life histories and review evidence from management interventions in both European farmland and North American systems that demographic recovery is achievable but remains contingent on addressing broader land-use conflicts and sources of adult mortality. Finally, I outline five interconnected research priorities—spanning cognitive ecology, trophic interactions, movement ecology, genomics, and formal comparative analyses—that would move shrike research from its current observational foundation toward a more experimental, mechanistic, and phylogenetically informed programme. By reframing shrikes as a model taxon for solitary living, this review aims to integrate avian behavioral ecology into broader comparative frameworks of social organization, cognition, and resilience under global change. Full article

CCCH zinc-finger proteins constitute a unique class of transcription factors that play vital roles in mediating plant tolerance to biotic and abiotic stresses and regulating various physiological and developmental processes. This study systematically identified and characterized the apple (Malus domestica) CCCH (MdC3H) gene family, aiming to elucidate its evolutionary patterns, functional characteristics, and regulatory mechanisms under drought stress. Genome-wide analysis revealed 85 MdC3H genes, which were unevenly distributed across chromosomes and exhibited significant differences in physiochemical properties, suggesting functional divergence. Phylogenetic analysis classified these genes into 9 subfamilies with distinct conservation. Collinearity analysis indicated a close evolutionary relationship between apple and Malus sieversii, with 150 collinear gene pairs identified, highlighting the conservation of the C3H gene family during speciation. Cis-acting element prediction in promoter regions uncovered abundant stress-responsive elements (e.g., ABRE, DRE, MYB), implying the potential of MdC3H genes in coordinating environmental signals. Functional verification demonstrated that MdC3H49, a key member of the family, is localized in the nucleus and possesses transcriptional activation activity. Overexpression of MdC3H49 in Arabidopsis and apple calli significantly enhanced drought tolerance, characterized by reduced malondialdehyde (MDA) content, relative electrical conductivity, and increased proline accumulation. Mechanistic studies revealed that MdC3H49 directly regulates the expression of MdP5CS, a core gene in proline biosynthesis, thereby strengthening the cellular antioxidant capacity and mitigating drought-induced damage. Collectively, this study establishes MdC3H49 as a critical regulator in apple drought stress response, providing valuable insights into the molecular mechanisms underlying abiotic stress tolerance in perennial plants and laying a foundation for genetic improvement of drought resistance in apple breeding. Full article

The genus Siccibacter consists primarily of environmental bacteria, with strains of Siccibacter colletis previously isolated only from plant materials and related environments. This study aims to characterize the first clinical isolate of S. colletis and explore its genomic evolution and clinical relevance. Strain S25242 was isolated from the urine of a 64-year-old male with a severe urinary tract infection. The genome of S25242 is 4.19 Mb, containing 4012 coding sequences, 73 tRNAs, 10 rRNAs, and 38 snRNAs. Phylogenetic and phylogenomic analyses indicated that strain S25242 is closely related to S. colletis type strain 1383^T. The strain shared >70% of digital DNA-DNA hybridization (dDDH) values and >96% of average nucleotide identity (ANI) values with the type strain of S. colletis 1383^T, thereby confirming its taxonomic status. The isolate was susceptible to all 11 tested antimicrobials. Comparative genomics identified 1942 S. colletis-specific genes (including multidrug efflux systems) and 13 unique genes in S25242 related to transposition and DNA integration. This study reports the first clinical isolate of S. colletis, providing evidence that genomic plasticity facilitates its transition from an environmental inhabitant to an opportunistic pathogen. The findings highlight the need for enhanced clinical surveillance of the Siccibacter genus and offer insights into its genomic evolution and clinical adaptation. Full article

Background: Differentiating plant species is complex, complicated by morphological similarities that confound species’ delineation. For hundreds of years, researchers have used herbarium specimens to study plant morphology, and over the last forty years, these samples have also served as material for molecular phylogenetic research. Taxonomists have alternately split and combined morphotypes of Pediomelum tenuiflorum for two centuries. With samples of P. tenuiflorum from across its distribution, this research aimed to (1) infer a robust phylogeny using molecular data, i.e., gene sequences from chloroplast and nuclear genomes; (2) assess genetic diversity using molecular markers, specifically Inter Simple Sequence Repeats (ISSRs); (3) provide evidence to support the taxonomic placement and possible splitting of P. tenuiflorum; and (4) identify consistent morphological characteristics using a correlation matrix to distinguish among the morphotypes. Results: Striking morphological differences among the individuals of P. tenuiflorum from across the species’ distribution resulted in more than two morphotypes. Phylogenetic data suggest hybridization is occurring among genetically and morphologically distinct members of P. tenuiflorum and with other species in the genus Pediomelum, whereas ISSR results indicate detectable genetic variation but do not resolve discrete clusters. This study reports the first ISSR markers used to assess genetic diversity in Pediomelum species. Conclusions: Morphological and genetic variation exist across individuals of P. tenuiflorum but not in monophyletic groups that support splitting the morphotypes into multiple species. Future investigations into chromosome numbers might reveal polyploidization in the lineage, and phylogenies estimated from low-copy nuclear genes could elucidate hybridization pathways. Full article

Background: INDETERMINATE DOMAIN proteins (IDDs) are a plant-specific transcription factor family, and members of this family play crucial roles in regulating growth and development as well as environmental adaptation. However, a comprehensive analysis of the IDD family in soybean [Glycine max (L.) Merrill] is limited. Methods and Results: A total of 27 GmIDD genes were identified in the soybean genome, unevenly distributed across 14 chromosomes, and their encoded proteins all harbor a conserved INDETERMINATE (ID) domain with two Cys2His2 (C2H2) and two Cys2HisCys (C2HC) zinc finger motifs. Phylogenetic analysis classified these GmIDD genes into three subgroups. Soybean GmIDD genes exhibit high homology with their Arabidopsis thaliana IDD counterparts. Cis-acting element analysis indicated that the promoters of GmIDD genes are enriched in light-responsive elements (such as Box4), hormone-responsive elements (such as ABRE and AuxRR-core), and abiotic stress-responsive elements (such as MBS and LTR). The qRT-PCR results showed that GmIDD3/5/14/22/26 were upregulated under salt stress, while GmIDD8/9/10/12/16/17/19/20/23/24/25/27 were obviously downregulated during treatment. Under drought stress, the expression levels of GmIDD4/6/7/10/14/16/19/22/24/25/26/27 were upregulated during the treatment. The expression levels of GmIDD1/2/3/4/12/14/15/16/17/18/22/23/25/26 were induced by short-day conditions, whereas GmIDD9/13/19/21 were induced by long-day conditions in soybean leaves. Conclusions: This study provides a theoretical basis for further understanding the functions of the soybean IDD gene family in abiotic stress tolerance and photoperiod adaptability. Full article

Background/Objectives: Sepsis is a leading cause of hospital mortality and represents a time-sensitive medical emergency. Current diagnostic strategies rely on clinical assessment, severity scores, biomarkers, and blood cultures. However, blood cultures require 24–72 h for pathogen identification and demonstrate limited sensitivity, while biomarkers such as procalcitonin and C-reactive protein lack optimal specificity. These limitations support the widespread empirical use of broad-spectrum antibiotics and highlight the need for rapid, sensitive, and culture-independent diagnostic tools. Methods: A narrative literature review was conducted using PubMed and Google Scholar, including 28 studies published over the past 10 years, encompassing observational and preclinical investigations. Current evidence on the application of Raman spectroscopy in sepsis was summarized, with a dual focus on pathogen identification and the assessment of the host response. Results: Raman spectroscopy has demonstrated the ability to detect early molecular alterations in circulating immune cells and mitochondrial redox status, potentially preceding conventional biomarkers. For pathogen identification, Raman techniques have achieved diagnostic accuracies comparable to automated systems, but with significantly shorter turnaround times. Integration with microfluidics, optical tweezers, and deep learning algorithms has further enhanced performance, although these applications remain largely experimental. Conclusions: Despite these promising results, the lack of methodological standardization, spectral overlap among phylogenetically related species, limited large-scale validation, and challenges in interpreting certain spectral signatures remain unresolved. Most available evidence originates from preclinical, single-center, and controlled studies, underscoring the need for prospective multicenter trials and harmonized protocols. Full article

The genus Acanthosaura is characterized by a high level of cryptic species diversity and is subdivided into several species complexes. The phylogenetic relationships within the A. coronata complex remain unresolved due to the presence of cryptic lineages and limited molecular data for several species. In this study, these relationships are clarified using a molecular genetic analysis that integrates newly collected field samples and historical museum specimens with previously uncertain identification. Three mitochondrial genes (cyt b, COI, and ND2) from samples, including fresh collections of A. murphyi from Phu Yen Province (Vietnam) and museum specimens from Vietnam and Myanmar, were analyzed. In addition, morphological characters of the examined specimens with diagnostic traits of known species were compared. Phylogenetic analyses confirmed the distinct species status of A. murphyi and enabled the taxonomic reassignment of previously undetermined museum specimens to this species. Specimens from Vietnam and Myanmar formed a single, well-supported clade, suggesting a broader distribution for A. murphyi than previously recognized. It is demonstrated for the first time that A. murphyi belongs to the A. coronata complex, together with A. coronata and A. cuongi, a result consistently supported by both genetic distances and phylogenetic tree topology. Full article