Search Results (5,151)

Cloudberry (Rubus chamaemorus L.) is a dioecious, perennial plant that grows in the boreal climate zone. For the first time, intraspecific genetic variability of 174 individual cloudberry plants from 25 locations in Lithuania, Latvia, Estonia, and Belarus was examined. Genetic variation was assessed using microsatellite markers specific to the Rubus genus. Although high heterozygosity was observed across all sampling sites, allelic richness, the Shannon diversity index, and the number of unique genotypes revealed a geographic gradient in genetic diversity across the Eastern Baltic region, with the highest values in Estonia and the lowest in Belarus. Cluster analysis identified ten genetically distinct groups, revealing patterns of population differentiation. Principal coordinates analysis further demonstrated that some sampling sites were genetically distinct despite geographic proximity. PERMANOVA indicated that most genetic variation occurred among individuals within sampling sites rather than among sampling sites, despite the predominantly vegetative reproduction of this species. These findings improve our understanding of the intraspecific diversity and genetic structure of the cloudberry population at the southern edge of the distribution of the species, suggest factors shaping genetic structure, and provide valuable insights for conservation and management of this ecologically and economically important species. Full article

The strict requirement for a canonical TTTV protospacer adjacent motif (PAM) restricts target-site selection in clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 12a (CRISPR/Cas12a)-based diagnostics and limits the flexibility of assay design. Whether suboptimal PAMs can be effectively incorporated into one-pot detection systems for Clostridium perfringens has not been systematically examined. Here, we developed two one-pot recombinase polymerase amplification (RPA)–CRISPR/Cas12a assays targeting the plc and cpe toxin genes of C. perfringens and systematically evaluated 28 crRNAs spanning canonical (TTTV) and suboptimal (VTTV, TCTV) PAMs in both trans-cleavage and one-pot formats. Several suboptimal-PAM crRNAs, including crRNA 4 for plc (PAM: GTTG) and crRNA 7 for cpe (PAM: CTTA), maintained efficient detection in the one-pot system, whereas crRNA performance between the two formats was not predictable, underscoring the need for direct one-pot screening. The optimized assays achieved limits of detection of 50 copies (plc) and 10 copies (cpe), showed no cross-reactivity against four non-target bacterial species. The plc assay was successfully validated in pork, chicken, and beef samples spiked with C. perfringens, with results readable within 40 min using a simple isothermal device and naked-eye readout. The cpe assay was confirmed as a proof-of-concept at the genomic DNA level. These results demonstrate that suboptimal PAMs can serve as a deliberate design strategy to expand target accessibility in one-pot CRISPR/Cas12a diagnostics. Full article

Background: Fritillaria karelinii is an endangered medicinal herb mainly distributed in Central Asia, extending to northwestern China. Due to habitat fragmentation, overharvesting, and poor natural regeneration, this species has been designated as a Grade II national key protected species in China. Methods: To inform effective conservation strategies, we assessed the genetic diversity and population structure of F. karelinii using single nucleotide polymorphism (SNP) loci obtained via genotype-by-sequencing (GBS). A total of 87 individuals from 11 sampling sites across the Tacheng region in northern Xinjiang were genotyped, representing the species’ known extant distribution in China. Results: A relatively high level of genetic diversity (mean H_E = 0.1461) was detected in the species, and Bayesian assignment divided the sampled populations into two subtle but detectable genetic clusters. Conclusions: The relatively high diversity may be attributed to the edge-population effect and long-lived life-history traits, while the weak differentiation between the two groups may reflect restricted gene flow and genetic drift resulting from habitat isolation. Based on these findings, we propose conservation actions including immediate fencing of habitats to exclude livestock, ex situ germplasm collection separately from the two genetic groups as distinct management units, and cautious evaluation of potential germplasm introduction from Central Asia to broaden the genetic base while preserving local adaptation. Full article

Background/Objectives: Certain strains of Lactobacillus acidophilus are widely used as probiotics. However, their functional potential for female reproductive tract health remains insufficiently characterized. While most studies have focused on individual strains, the distribution of putative probiotic-associated genes across the species remains unclear. This study aimed to evaluate the vaginal probiotic potential of Lb. acidophilus using population genomic analysis and comparative phenotypic characterization. Methods: Pan-genomic analysis was performed on 109 Lb. acidophilus genomes (107 public genomes and 2 vaginal isolates). Putative probiotic-associated gene clusters were identified by functional annotation, categorized into functional modules, and compared among ecological-origin groups. Two vaginal isolates (strains A2 and A3) were characterized in vitro for growth under different pH conditions, cell surface hydrophobicity, lactic acid and hydrogen peroxide production, antimicrobial activity, hemolysis, and antimicrobial susceptibility. Results: The Lb. acidophilus pan-genome was closed, with 1782 of 1902 gene clusters (93.69%) classified as core. Thirty-six putative probiotic-associated gene clusters were identified and grouped into four modules: environmental tolerance, adhesion/colonization, exopolysaccharide/biofilm synthesis, and nutrient metabolism/microbial competition. Thirty-four of the 36 gene clusters were present in all 109 genomes, and no general ecological origin-specific distribution pattern was observed. Three bacteriocin-related gene clusters were conserved across all genomes. A2 and A3 exhibited similar lactic acid production and growth patterns at pH 4–6. Both produced relatively low amounts of hydrogen peroxide compared with the reference strains. A3 showed higher cell surface hydrophobicity and moderate inhibition against Gardnerella vaginalis, while A2 showed no inhibition of this organism. Both isolates were non-hemolytic, and were susceptible to vancomycin and linezolid, resistant to clindamycin, and non-susceptible to daptomycin. No acquired antibiotic resistance genes were detected. Conclusions: Most putative probiotic-associated gene clusters were conserved across the Lb. acidophilus population, whereas A2 and A3 showed strain-dependent phenotypic differences. These findings support combining population genomic analysis with strain-level phenotypic testing when selecting Lb. acidophilus candidates for bacterial vaginal infections. Full article

Background: Cunninghamia lanceolata (Lamb.) Hook. (C. lanceolata) is an important timber tree species in southern China. However, the molecular regulatory mechanisms underlying adventitious root formation during cutting propagation remain largely unclear. The lack of genetic resources has hindered molecular breeding efforts in this species. Methods: In this study, transcriptome analysis was performed on the root systems of scions from elite C. lanceolata clones at 7, 30, and 60 d after cutting. Results: Approximately 69.30 Gb of clean data were obtained. De novo assembly and gene prediction yielded 43,433 protein-coding genes, of which 32,886 (75.7%) were functionally annotated. Temporal clustering and comparative functional enrichment analyses revealed a distinct temporal functional shift during adventitious root development in C. lanceolata. Early stages were dominated by metabolic processes such as pyrimidine metabolism and carbohydrate biosynthesis, whereas later stages were governed by phytohormone signal transduction. Key components of the auxin pathway, including AUX1, AFB, IAA, and SAUR, exhibited dynamic and differential expression, which may be associated with adventitious root growth. Based on the transcriptome data, we identified nine members of the PIN gene family. Both transcriptomic expression profiles and qRT-PCR validation demonstrated that these PIN genes showed divergent expression trends across developmental stages, suggesting that they may participate in rooting by regulating polar auxin transport. Conclusions: This study systematically elucidates the molecular network underlying adventitious root formation in C. lanceolata cuttings. It enriches the omics resources for conifers and provides a theoretical foundation and omics basis for molecular breeding and efficient propagation of elite C. lanceolata clones. Full article

Nemacheilus subfusca is an endemic fish species in the lower Yarlung Zangbo River. Its habitats are potentially threatened by geological disturbances and anthropogenic activities, but information on population status remains limited. However, existing research has been largely confined to basic biology, with limited information on its population genetic structure and connectivity. Consequently, targeted investigations are urgently needed to provide a scientific basis for the conservation of this species. In this study, genetic diversity and population structure were analyzed in 50 individuals from two geographic populations (Motuo (MT) and Chayu (CY)) in the lower Yarlung Zangbo River, using mitochondrial cytb and D-loop markers. The populations exhibited high haplotype diversity but relatively low nucleotide diversity (cytb: H_d = 0.870, P_i = 0.00281; D-loop: H_d = 0.931, P_i = 0.01655). Notably, the MT population exhibited lower diversity levels compared to the CY population (cytb: H_d = 0.757, P_i = 0.00205; D-loop: H_d = 0.633, P_i = 0.00153). Substantial genetic differentiation was observed between the two populations (cytb: F_ST = 0.322; D-loop: F_ST = 0.733); The observed mitochondrial divergence did not provide clear evidence of species-level differentiation (cytb = 0.00331; D-loop = 0.02492). The ML phylogenetic tree and haplotype network revealed geographically associated clustering of the two populations, indicating geographic structuring of mitochondrial haplotypes. Furthermore, demographic analyses were consistent with a possible historical population expansion. In conclusion, The mitochondrial data revealed high haplotype diversity but relatively low nucleotide diversity, together with substantial genetic differentiation between the two sampled populations, forming geographically associated clusters. This study elucidates the genetic background of this species’ germplasm resources, providing baseline genetic information for future conservation and management of this species. Full article

Nanoplastics and microplastics have become an increasing ecological and health concern due to their widespread presence in the environment and food chain. In this study, Caco-2 cells were used as an in vitro model of the human intestinal epithelium to investigate the cytotoxic effects of polystyrene nanoparticles and microparticles of varying sizes, concentrations, and surface modification. Oxidative stress and apoptosis were evaluated following particle exposure. Raman spectroscopy, combined with machine learning analysis, was employed to detect and characterize biochemical alterations in the cells. Several peak ratios were selected to cluster data depending on size. A correlation between apoptosis and both concentration and Raman score was established highlighting its potential as a non-invasive tool to monitor nanoparticle-induced cellular damage. Resveratrol pretreatment reduced some of these harmful effects of amine-modified nanoplastics, reducing reactive oxygen species generation. This study demonstrates the potential of combining Raman spectroscopy and machine learning to assess the cytotoxic effects of micro- and nanoplastics and identifies protective strategies such as antioxidant pretreatment. Full article

Cacao swollen shoot disease (CSSD) remains a major viral threat to cacao production in West Africa and is associated with a genetically diverse complex of badnaviruses. We combined alignment-free whole-genome distances with circular sliding-window mosaic barcodes to characterize global divergence and local compositional modularity across 48 full-length CSSD-associated badnavirus genomes, hereafter termed the cacao swollen shoot virus (CSSV) complex. Whole-genome tetranucleotide cosine distance clusters matched published species assignments exactly (adjusted Rand index = 1.00; normalized mutual information = 1.00; silhouette = 0.703) and were strongly concordant with an alignment-based distance derived from open reading frame 3 (ORF3) proteins (Spearman ρ ≈ 0.951; permutation p ≈ 0.0002). A three-component mosaic-complexity score summarized low dominant-label purity, barcode entropy normalized by log₂(K), and circular switch rate; ORF–mosaic agreement was retained as a separate diagnostic and did not contribute to the ranking. Threshold sensitivity showed that barcode switchpoints were enriched within ±100 and ±200 bp of predicted ORF boundaries, but not within ±400 bp. The ten highest-scoring genomes showed slightly higher mean local nucleotide entropy but lower entropy variance and dispersion than the remaining genomes, indicating more uniformly distributed compositional complexity rather than isolated local spikes. These analyses provide a transparent framework for post-sequencing classification, comparison, and prioritization of complete viral genomes. The barcode and score outputs are exploratory summaries and are not direct field diagnostic assays or nucleotide-resolution recombination tests. Full article

Lithium-oxygen (Li-O₂) batteries are a compelling next-generation energy storage candidate owing to their ultrahigh theoretical specific energy, but their practical deployment is critically limited by sluggish cathodic oxygen reduction/evolution kinetics, severe polarization, and poor cyclability. Here, we design a composite catalyst consisting of ultrasmall iron clusters uniformly anchored on a three-dimensional nitrogen-doped carbon aerogel (Fe@NC). The material is synthesized via bidirectional freeze-drying followed by high-temperature reduction carbonization using chitosan, cellulose nanocrystals, and zinc acetate; sublimation of zinc during pyrolysis effectively suppresses iron aggregation, yielding highly dispersed Fe0 clusters of ~10 nm while preserving the aerogel’s hierarchical porous architecture rich in pyridinic and pyrrolic N species. Electrochemical tests show that Fe@NC delivers a deep-discharge specific capacity of 18,000 mAh/g, substantially outperforming pristine carbon aerogel and commercial Ketjen black, and maintains stable cycling over 280 cycles at 500 mAh/g. Microscopic and spectroscopic analyses confirm that Fe@NC promotes uniform, fine-particle Li₂O₂ deposition without pore blockage and enables its complete reversible decomposition upon charging, effectively mitigating electrode passivation. This work demonstrates that the synergistic combination of carbon aerogel mass-transport benefits and iron cluster catalytic activity provides a viable, scalable route to high-performance Li-O₂ battery cathodes. Full article

Yeast infections are becoming an increasing public health concern, mainly due to the spread of opportunistic species and the emergence of strains resistant to commonly used antifungal drugs. Marine resources are a promising source of bioactive compounds, including polysaccharides and other biopolymers with potential antifungal applications. In this study, a sulphated polysaccharide-rich extract was obtained from the red alga Jania pedunculata var. adhaerens and chemically characterized. Its antifungal activity was compared with that of a commercial chitosan formulation against clinically relevant yeasts, including species of Candida, Cryptococcus, Clavispora, Naganishia and Trichosporon. Growth kinetics were monitored in liquid medium over 24 h, and antifungal activity was evaluated through growth rate analysis, growth inhibition at 20 h and susceptibility clustering. The sulphated polysaccharide-rich extract showed moderate but consistent growth inhibition, with the strongest effects observed at 5 mg mL⁻¹. Maximum growth inhibition reached 60.9% in Cryptococcus deuterogattii and 59.8% in Candida albicans, although no complete inhibition was observed within the tested concentration range. Chitosan showed a stronger antifungal effect, with minimal inhibitory concentration (MIC) values between 10 and 20 µg mL⁻¹ in several species and maximum inhibition values above 80% in the most susceptible yeasts. However, C. albicans showed marked resistance to chitosan, with inhibition below 12%. K-means clustering confirmed distinct susceptibility profiles between treatments, supporting a species-dependent response. Overall, these results highlight marine-derived biopolymers as promising antifungal candidates and show that chitosan and algal sulphated polysaccharides produce distinct, species-dependent antifungal profiles. Full article

Rabies remains one of the most significant zoonotic infections, characterized by high mortality. In Kazakhstan, the virus circulates among both domestic and wild animals, necessitating ongoing molecular genetic monitoring and improved laboratory diagnostic methods. The aim of this study was to investigate the genetic characteristics of the rabies virus circulating among animals in Kazakhstan using nucleoprotein (N) gene analysis and to develop a regionally adapted real-time RT-PCR method for its detection. Kazakhstani rabies virus isolates deposited in GenBank revealed that all belong to a cosmopolitan lineage and form a single phylogenetic cluster, regardless of host species. Isolates from neighboring countries, including China and Russia, were also included in this cluster, demonstrating the regional relationship of circulating virus variants. The obtained data were used to develop a real-time PCR method based on the genetic characteristics of the rabies virus circulating in Kazakhstan. The diagnostic performance of the method was evaluated using 144 samples of various origins obtained from domestic and wild animals, including bats. The developed assay demonstrated a sensitivity of 86.4%, a specificity of 98.4%, and a diagnostic efficiency of 96.5%. The proposed method ensures reliable detection of rabies virus variants circulating in Kazakhstan and can be used for laboratory diagnostics and epidemiological monitoring. Full article

Background: Lycium ruthenicum, commonly known as Black goji berry, is a shrub species native to western China and is rich in bioactive compounds that contribute to its nutritional and health-promoting effects. However, the transcriptional dynamics associated with fruit development and quality formation in black goji berry remain incompletely understood. This study aimed to investigate transcriptional dynamics during fruit development and identify candidate genes associated with sugar accumulation and fruit enlargement. Methods: Fruits were sampled at five developmental stages (S1–S5), and RNA-seq was performed to investigate the alterations in gene expression. Differential expression analysis, temporal expression-pattern analysis, functional enrichment analysis, and weighted gene co-expression network analysis (WGCNA) were performed, followed by the integration of differential expression, temporal expression patterns, co-expression relationships, and functional annotation. Results: Fruit diameter, fresh weight, and total soluble sugar content increased markedly during the later developmental stages. Differential expression analysis revealed extensive transcriptional changes across successive developmental transitions, while temporal expression-pattern analysis identified distinct increasing and decreasing gene clusters. Functional enrichment analysis showed that the DEGs were mainly associated with carbohydrate metabolism, sugar transport, hormone-related processes, photosynthesis, and cell-wall modification. WGCNA identified 13 co-expression modules, among which MEyellow and MEbrown showed strong but opposite associations with developmental stage, total soluble sugar content, fruit diameter, and fruit fresh weight. The integrated analysis highlighted several candidate genes associated with sugar metabolism and transport during late fruit development. Conclusions: These findings provide a transcriptomic perspective on the coordinated changes in sugar accumulation and fruit enlargement during L. ruthenicum fruit development. Full article

Horse fat is a valuable lipid source for traditional meat products, but its flavor quality is remains unclear during processing conditions. To investigate the effect of dry fractionation on the volatile profile of refined horse fat, samples obtained at different temperature were analyzed using an E-nose, HS/GC-IMS, and SPME/GC-MS. The E-nose results showed that the volatile profiles of the samples differed markedly, with the solid fractions obtained at 25 and 15 °C (S25 and S15) exhibiting stronger sensor responses and clustering together, whereas the liquid fraction at 5 °C (L5) showed the weakest overall signals. HS/GC-IMS identified total 55 volatile compounds, mainly aldehydes, alkenes, esters, alcohols, ketones, and nitrogen-containing compounds. Compared with refined horse fat, S25 and S15 were enriched in ketones, sulfur-containing compounds, and nitrogen-containing compounds, while L5 was dominated by alcohols and aldehydes. SPME/GC-MS identified 53 volatile compounds, with aldehydes as the main class in all samples. S5 showed the highest number of volatile species and the richest aroma profile, whereas S25 and S15 showed the lowest complexity. The total volatile content ranked as refined horse fat > S5 > L5 > S15 > S25, and ester content followed the order S5 > L5 > refined horse fat > S25 > S15. Overall, dry fractionation temperature significantly regulated the distribution of volatile compounds in horse fat. These findings may provide a theoretical basis for the potential application of horse fat in food processing and product development. Full article

Upland cotton (Gossypium hirsutum, AD1) is the most important fiber crop for the world’s textile industry. The genetic base of Upland cotton is narrow, and the introgression of germplasm from other species into Upland cotton can broaden its genetic diversity, including the introduction of new qualitative traits. The objectives of this study were to determine the inheritance, allelism, and linkage relationships of the red anther trait introduced into Upland from the red anther donor G. armourianum (D2-1) through crosses involving a synthetic tetraploid A1D2-1. After two generations of backcrossing to Upland cotton, followed by inbreeding, homozygous red-anthered plants (RA) were selected and used for crosses with two Upland lines, the Upland standard TM-1, the multiple recessive marker line T582, and the multiple dominant marker line T586. All Upland cotton parents, except the RA parents and T586 (possessing yellow anthers), had cream anthers. The anther color of the F₁ plants was red, indicating that the red anther trait is dominant. In nine of ten F₂ populations and four of five testcross populations, the segregation of anther color followed a 3:1 and 1:1 ratio, respectively, as expected under a one-gene model. In three F₂ populations with a total of 885 plants between RA with green leaf and T586 with red leaf (R₁ on chromosome D07), no double recessive genotype (yellow/cream anther and green leaf) was observed, indicating the allelic relationship between R₁ and red anther allele, designated R₁^a. The recombination frequency between R₁^a and cluster-1 (cl₁) on D07 was estimated to be 0.112 in 256 F₂ plants of a cross between RA and T582 based on the maximum likelihood estimation. This new red anther trait and its associated new gene allele provide an important genetic source for understanding the biosynthesis of anthocyanins and may have utility for improving resistance to anther-feeding insects in cotton. Full article

The genus Sigara Fabricius, 1775 (Hemiptera: Corixidae) is an important freshwater bioindicator, but its conservative morphology complicates traditional species identification. This study combines DNA barcoding, traditional taxonomy, and climatic factors within an integrative framework to provide new insights into species delimitation. We analyzed cytochrome c oxidase subunit I (COI) sequences from 501 Sigara specimens collected from 15 countries, including 95 newly generated COI barcodes. Our integrated approach included phylogenetic analyses, genetic distance assessments, and ecological niche modeling. The results revealed remarkable diversity, with sequences clustering into 46 Barcode Index Numbers (BINs). COI genetic distances showed a pronounced bimodal pattern, with most intraspecific divergences below 1% and interspecific divergences mainly ranging from 8–16%, while the few intermediate divergences (4–8%) suggested potential cryptic diversity or recent species divergence. Most morphologically defined species corresponded to distinct molecular lineages, supporting traditional taxonomy, whereas some morphospecies exhibited genetic discordance potentially associated with species divergence. Integrative analyses revealed that climatic factors, particularly isothermality and seasonal temperature and precipitation, are major drivers of Sigara MOTU distributions, highlighting the important role of climate in shaping their geographic patterns. These findings indicate that although COI barcodes are not sufficient to define the species boundaries of Sigara alone, they provide a key entry point for the accurate division of species, which in turn promotes the development of molecular tools for freshwater ecological monitoring and conservation. Full article