Search Results (524)

In this study, we conducted a whole-genome analysis of the Lacticaseibacillus paracasei subsp. paracasei 2LB isolated from Kazakh traditional fermented milk (koumiss) to identify genes associated with the safety and probiotic potential of the strain. A comparative genomic analysis of the core and pan-genome of L. paracasei 2LB was performed. Functional annotation revealed the presence of genes putatively involved in metabolism, genetic information processing, and cellular processes. In terms of safety parameters, the stability of its genetic material, the absence of the ability to synthesize virulence factors, and genes responsible for antibiotic resistance were characterized. Also, in vitro studies of the L. paracasei 2LB strain showed resistance to stress factors and antimicrobial activity, and the presence of coding sequences encoding adhesion factors, bacteriocins, bile salts, pH, cold and heat shock, and osmotic stress was observed through genomic analysis. These results indicate that the L. paracasei 2LB strain is a potential probiotic candidate and demonstrate that whole-genome analysis is a useful method for assessing the quality and safety of probiotics. Full article

The methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an opportunity to decipher the interplay between differences in the primary DNA sequence and epigenetic variation. Here, we performed high-coverage long-read whole-genome direct DNA sequencing of one individual using Oxford Nanopore technology. We also used Illumina whole-genome sequencing of the parental genomes in order to identify allele-specific methylation sites with a trio-binning approach. We have compared the results of the haplotype-specific methylation detection and revealed that trio binning outperformed other approaches that do not take into account parental information. Also, we analysed the cis-regulatory effects of the genomic variations for influence on CpG methylation. To this end, we have used available Deep Learning models trained on the primary DNA sequence to score the cis-regulatory potential of the genomic loci. We evaluated the functional role of the allele-specific epigenetic changes with respect to gene expression using long-read Nanopore RNA sequencing. Our analysis revealed that the frequency of SNVs near allele-specific methylation positions is approximately four times higher compared to the biallelic methylation positions. In addition, we identified that allele-specific methylation sites are more conserved and enriched at the chromatin states corresponding to bivalent promoters and enhancers. Together, these findings suggest that significant impact on methylation can be encoded in the DNA sequence context. In order to elucidate the effect of the SNVs around sites of allele-specific methylation, we applied the Deep Learning model for detection of the cis-regulatory modules and estimated the impact that a genomic variant brings with respect to changes to the regulatory activity of a DNA loci. We revealed higher cis-regulatory impact variants near differentially methylated sites that we further coupled with transcriptomic long-read sequencing results. Our investigation also highlights technical aspects of allele methylation analysis and the impact of sequencing coverage on the accuracy of genomic phasing. In particular, increasing coverage above 30X does not lead to a significant improvement in allele-specific methylation discovery, and only the addition of trio binning information significantly improves phasing. We investigated genomic variation in a single human individual and coupled computational discovery of cis-regulatory modules with allele-specific methylation (ASM) profiling. In this proof-of-concept analysis, we observed that SNPs located near methylated CpG sites on the same haplotype were enriched for sequence features suggestive of high-impact regulatory potential. This finding—derived from one deeply sequenced genome—illustrates how phased genetic and epigenetic data analyses can jointly put forward a hypotheses about the involvement of regulatory protein machinery in shaping allele-specific epigenetic states. Our investigation provides a methodological framework and candidate loci for future studies of genomic imprinting and cis-mediated epigenetic regulation in humans. Full article

Introduction: Genes in the endolysosome and autophagy pathways are major contributors to hereditary spastic paraplegia (HSP). A pathogenetic link between HSP and Alzheimer disease (AD) involving macroautophagy is well established. Sortilin-related receptor 1 (SORL1), an endosomal trafficking protein, plays a key role in glutamatergic neuron homeostasis and white matter tract integrity. Until now, SORL1 has only been associated with dominant AD and cerebral amyloid angiopathy. Methods: A case of HSP with cerebroretinal vasculopathy (CRV) negative on exome sequencing was further investigated using whole-genome sequencing. RNA-seq, Western blot, and immunofluorescence imaging were performed to explore a potential loss-of-function mechanism. Results: Sequencing revealed a biallelic SORL1 splice donor variant (c.1211 + 1G > A). Transcriptomics confirmed nonsense-mediated decay and aberrant splicing, predicting a disrupted reading frame. Reduced SORLA protein levels and significant enlargement of endolysosomes in patient-derived fibroblasts further cemented the pathogenicity of the variant. Conclusions: The probability that SORL1 acts as a recessive disease-causing gene gathers support from the following data: SORL1 genomic constraint score pRec = 1, high meiotic recombination rates on the locus, phenotype of Sorl1^−/− mice reminiscent of HSP with CRV, and endolysosomal enlargement in SORL1^−/− glutamatergic neurons in vitro. Taken together, SORL1 is probably a new candidate for a recessive form of complicated HSP. Full article

The greater wax moth Galleria mellonella (Lepidoptera: Galleriinae) represents a ubiquitous apicultural pest that poses significant threats to global beekeeping industries. The larvae damage honeybee colonies by consuming wax combs and tunneling through brood frames, consequently destroying critical hive infrastructure including brood-rearing areas, honey storage cells, and pollen reserves. Larval feeding behavior is critically dependent on chemosensory input for host recognition and food selection. In this study, we conducted a transcriptome analysis of larval heads and bodies in G. mellonella. We identified a total of 25 chemosensory genes: 9 odorant binding proteins (OBPs), 1 chemosensory protein (CSP), 5 odorant receptors (ORs), 4 gustatory receptors (GRs), 4 ionotropic receptors (IRs) and 2 sensory neuron membrane proteins (SNMPs). TPM normalization was employed to assess differential expression patterns of chemosensory genes between heads and bodies. Nine putative chemosensory genes were detected as differentially expressed, suggesting their potential functional roles. Subsequently, we quantified expression dynamics via reverse transcription quantitative PCR in major chemosensory tissues (larval heads, adult male and female antennae), revealing adult antennal-biased expression for most chemosensory genes in G. mellonella. Notably, two novel candidates (GmelOBP22 and GmelSNMP3) exhibited particularly high expression in larval heads, suggesting their crucial functional roles in larval development and survival. These findings enhance our understanding of the chemosensory mechanisms in G. mellonella larvae and establish a critical foundation for future functional investigations into its olfactory mechanisms. Full article

Vascular calcification (V) is an independent risk factor for all-cause and cardiovascular mortality. Vascular smooth muscle cells (VSMCs) play a major role in VC as they can acquire mineralizing properties when exposed to osteogenic conditions. Despite its clinical impact, there are still no dedicated therapeutic strategies targeting VC. To address this issue, we used human calcified and non-calcified atherosclerotic arteries (ECLAGEN Biocollection) to screen and identify microRNA (miR) associated with VC. We combined non-biased miRNomic (microfluidic arrays) and transcriptomic analysis to select miR candidates and their putative target genes with expression associated with VC and ossification. We further validated miR functional regulation and function in relation to cell mineralization using primary human VSMCs. Our study identified 12 miRs associated with VC in carotid and femoral arteries. Among those, we showed that miR136, miR155, and miR183 expression were regulated during VSMC mineralization and that overexpression of these miRs promoted VSMC mineralization. Cross-analysis of this miRNomic and a transcriptomic analysis led to the identification of CD73 and Smad3 pathways as putative target genes responsible for mediating the miR155 pro-mineralizing function. These results highlight the potential benefit of miR155 inhibition in limiting VC development in peripheral atherosclerotic arteries. Full article

The RNA-directed DNA methylation (RdDM) pathway is a crucial epigenetic mechanism governing plant responses to environmental stress. While the RdDM pathway has been extensively studied in Arabidopsis thaliana, the comprehensive understanding of its components in cucumber (Cucumis sativus L.) remains lacking. In this study, we performed a genome-wide identification and characterization of RdDM pathway genes in cucumber, followed by an analysis of their expression patterns across various tissues and under multiple abiotic stress conditions. A total of 67 putative CsRdDM genes were identified, which are unevenly distributed across the cucumber’s chromosomes. Phylogenetic and gene structure analyses revealed considerable evolutionary divergence, particularly within the key Argonaute gene family (CsAGO). Crucially, the promoter regions of CsRdDM genes were found to contain cis-regulatory elements associated with abiotic stress, light signaling, and development, suggesting their potential involvement in complex regulatory networks. RT-qPCR assays confirmed that CsRdDM genes exhibit distinct and stress-specific transcriptional patterns. Notably, several genes such as CsAGO4 and CsIDN2 showed antagonistic expression between roots and leaves under drought (PEG-6000) stress, implying a sophisticated, tissue-specific defense mechanism. Among them, CsAGO4 emerged as a candidate gene responsive to abiotic stress. Those findings provide new insights into the regulatory roles of CsRdDM genes under abiotic stress and highlight candidate genes for the genetic improvement of stress tolerance in cucumber. Full article

Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent organic pollutants composed of two or more fused benzene rings, posing serious threats to ecological environments and human health. Biodegradation is an efficient, economical, and sustainable approach for remediating PAHs pollution. In our previous work, we isolated and characterized a PAH-degrading bacterium, Burkholderia sp. FM-2. FM-2 demonstrated strong tolerance and efficient degradation capacity toward various PAHs, achieving 81.98% degradation of 2 mM phenanthrene within 3 days, and over 58% degradation of 2 mM fluorene, dibenzofuran, and dibenzothiophene under the same conditions. Through combined genomic and transcriptomic analyses, a putative PAH degradation gene cluster was identified in the FM-2 genome. Phylogenetic and domain architecture analyses were conducted on seven oxygenase genes within the cluster. Using AlphaFold 3, we predicted the three-dimensional structure of the downstream transport protein OmpW and proposed a potential transmembrane channel for PAHs uptake. To eliminate the phenanthrene degradation intermediate 1-hydroxy-2-naphthoic acid, a genetically engineered strain FM-2::nahG was constructed by heterologous expression of the salicylate hydroxylase gene (nahG). The modified strain completely abolished the accumulation of 1-hydroxy-2-naphthoic acid and achieved complete mineralization of phenanthrene. This study not only reveals the molecular basis of PAHs degradation in Burkholderia sp. FM-2 but also demonstrates the potential of metabolic engineering to enhance biodegradation ability, providing a promising microbial candidate for the bioremediation of PAH-polluted environments. Full article

Social interaction between the domesticated animal and the domesticator is one of the key features of the “domestication syndrome”. Recent research has identified genes in the WBSCR (Williams–Beuren syndrome control region) locus as significant contributors to social behavior in dogs. Large chromosomal deletions and duplications in the human WBSCR locus lead to the development of WBS (Williams–Beuren syndrome) and WBSCR duplication syndrome, respectively. Hypersociability is one of the key symptoms of WBS, while the duplication syndrome is manifested as an autism spectrum disorder (ASD). The data from both humans and dogs highlight the WBSCR locus as one of the key genetic determinants of social behavior in mammals. Several genes in the WBSCR are candidates for the regulation of social behavior in mammals including GTF2I, GTF2IRD, AUTS2 and GALNT17. Here, we discuss the role of WBSCR locus in the regulation of social behavior in mammals including the recent data that highlight the importance of 3D genome alterations in this genomic region for both domestication of animals and development of neurobehavioral disorders in humans. In addition, we bring attention to the role of the poorly characterized GALNT17 gene as a putative player in the development of ASD symptoms and in the regulation of social behavior in animals. We provide a brief summary of its known functions and propose the future research directions aimed at the elucidation of Galnt17 involvement in the regulation of central nervous system (CNS) functions. Full article

Sex determination is a fundamental biological process governing animal reproduction. Although substantial progress has been made in elucidating its genetic basis, the genetic architecture underlying complex sex determination systems remains poorly understood. In this study, we identify sex-associated insertion–deletion (indel) variants, screen candidate genes, and compare sex-associated variation across populations with different genetic backgrounds in the Fujian oyster (Magallana angulata). Based on whole-genome resequencing data of a culture strain (designated FL), a total of 299,774 high-quality indels were identified. By integrating genome-wide association analysis (GWAS), fixation index (F_ST) analysis, and sex-biased genotype frequency comparisons, 77 overlapping sex-associated indels were identified, predominantly clustered within a 1.8 Mb (8.3–10.1 Mb) region on chromosome 9. Principal component analysis (PCA) based on the sex-associated markers and their subsets consistently separated male and female individuals in the FL strain. For two representative sex-associated indels, PCR-based genotyping methods were developed and validated. Functional annotation identified putative candidate genes for sex determination, including PKD1L1, 5-HTRL, SCP, and CCKRa. Comparative analysis of variants within PKD1L1 across wild, farmed, and selectively bred populations revealed a progressive enrichment of male-linked alleles in domesticated and selectively bred groups, particularly in male individuals. This study provides direct evidence that sex in the Fujian oyster is genetically determined and reveals that domestication and artificial selection may drive the emergence of major sex-determining loci, offering important insights into the genetic basis of sex determination in the Fujian oyster, and establishing a theoretical and practical foundation for molecular marker-assisted breeding of monosex lines for this species. Full article

Mugil cephalus is a cosmopolitan marine fish highly relevant from ecological and economic perspectives. Previous studies identified sex-associated variants in the follicle-stimulating hormone receptor (fshr) gene following an XX/XY sex determination (SD) system. However, these variants could not be fully associated with sex in all samples. This suggests other genes and/or environmental factors may be involved in the SD of this species, denoting intraspecific variation. In this study, we constructed a new high-quality genome assembly of M. cephalus. We then re-sequenced the whole genome in males and females from two divergent Mediterranean populations to ascertain whether other genetic variants could also be involved in SD. fshr gene variants showed to only partially explain SD, while a new intronic variant in the sestd1 gene appeared to be associated with SD following a ZZ/ZW system. The presence of other putative candidate SD variants showing significant differences between the two populations suggested a regional pattern of variation in SD in the Mediterranean Sea. The incomplete association of all the identified variants also pointed to a potential role for environmental factors. Full article

Conidiobolus coronatus (Entomophthorales), a fungal pathogen with a broad insect host range, is a promising candidate for biocontrol applications. We sequenced a C. coronatus strain isolated from a Rhopalomyia sp. cadaver using PacBio long-read sequencing to elucidate the molecular basis of its wide host adaptability. The newly assembled 44.21 Mb genome exhibits high completeness (BUSCO score: 93.45%) and encodes 11,128 protein-coding genes, with 23.1% predicted to mediate pathogen–host interactions. Comparative genomics with the aphid-obligate pathogen C. obscurus revealed significant expansions in gene families associated with host adaptation mechanisms, including host recognition, transcriptional regulation, degradation of host components, detoxification, and immune evasion. Functional annotation highlighted enrichment in cellular component organization and energy metabolism. Pfam annotation identified one hundred twenty-five seven-transmembrane receptors (putative GPCRs), sixty-seven fungus-specific transcription factors, three hundred sixty-one peptidases (one hundred ninety-eight serine proteases and one hundred three metalloproteases), one hundred twenty-seven cytochrome P450 monooxygenases (P450s), thirty-five cysteine-rich secretory proteins, and fifty-five tyrosinases. Additionally, four hundred thirty carbohydrate-active enzymes (CAZymes) across six major modules were characterized. Untargeted metabolomics detected 22 highly expressed terpenoids, consistent with terpenoid biosynthesis gene clusters in the genome. Collectively, these expansions underpin the broad host range of C. coronatus by enabling cross-host signal decoding and gene expression reprogramming, breaching diverse host physicochemical barriers, and expanding its chemical ecological niche. This study provides genomic insights into broad host adaptability in entomopathogenic fungi, facilitating further understanding of pathogen–host interactions. Full article

Background/Objectives: Disruption of AMPAR trafficking at excitatory synapses contributes to impaired synaptic plasticity and memory formation in several neurological and psychiatric disorders. Arc, an immediate early gene product, has been shown to interact with the AMPAR auxiliary subunit TARPγ2, affecting receptor mobility and synaptic stabilization. Methods: To investigate the in vivo functional effects and protein interactions of the Arc-TARPγ2 interfering peptide RIPSYR, we performed in vivo electrophysiology and spatial memory assessments in male rats. as well as proteomic analyses of peptide-protein interactions in synaptosome lysates. We then used in silico docking to evaluate candidate binding partners. Results: In the present study, in vivo electrophysiological measurements revealed that RIPSYR administration altered early-phase long-term potentiation at CA3 synapses of male rats. Subsequent behavioral testing that assessed spatial memory performance revealed depleted memory retrieval after 24 h, indicating that the peptide has a systemic effect on experience-dependent plasticity. Then, we examined the molecular interactome of RIPSYR using magnetic bead-based immunoprecipitation and subsequent LC-MS identification on synaptosome lysates, and identified additional candidate binding partners, suggesting that the peptide may have broader modulatory effects. RIPSYR binding to the other putative binding partners are investigated by in silico methods. Conclusion: Our results raise the question of how the molecular interactions of RIPSYR contribute to its sum effects on electrophysiology and behavior. Full article

This study highlights a new avenue to improve polyhydroxybutyrate (PHB) productivity by optimizing genes related to arginine catabolism, which influences nitrogen metabolism in cyanobacteria based on the carbon/nitrogen metabolism balance. In the Synechocystis sp. PCC 6803 wild type (WT) and its adc1 mutant (Δadc1), the native putA gene, responsible for the oxidation of proline to glutamate, was overexpressed to create the OXPutA and OXPutA/Δadc1 strains, respectively. PHB accumulation was considerably higher in OXPutA and OXPutA/Δadc1 under the nitrogen-deprived condition than in strains that overexpressed the proC gene, involved in proline synthesis. The increased transcript level of glgX, associated with glycogen degradation, confirmed that glycogen served as the primary carbon source for PHB synthesis under nitrogen stress without any carbon source addition. Furthermore, proline and glutamate level changes helped cells deal with nitrogen stress and considerably improve intracellular carbon/nitrogen metabolism. As indicated by elevated levels of proA and argD transcripts as well as chlorophyll a accumulation, this impact was most noticeable in strains that overexpressed putA, which was crucial for the synthesis of glutamate, a precursor for important metabolic pathways that respond to nitrogen stress. Therefore, our metabolic model presents PHB-producing strains as promising candidates for biomaterial biotechnology applications in medical and agricultural fields. Full article

Leaf phenology of trees responds to temperature and photoperiod cues, mediated by underlying genes and plasticity. However, uncertainties remain regarding how smaller-scale phenological variation in cold-limited regions has been affected by modified selection pressures from herbivores, pathogens, and climate conditions, and whether this leaves genetic signatures allowing for projections of future responses. We investigated environmental correlates and genetic variation putatively associated with spring and autumn leaf phenology in northern range margin oak (Quercus robur L.) populations in Sweden (55.6° N–60.8° N). Results suggested that budburst occurred later at higher latitudes and in locations with colder spring (April) temperatures, whereas leaf senescence occurred earlier at higher latitudes. Several candidate loci associated with phenology were identified (n = 40 for budburst and 47 for leaf senescence), and significant associations between these loci and latitude were detected. Functions associated with some of the candidate loci, as identified in previous studies, included host defence and heat stress tolerance. The proportion of polymorphic candidate loci associated with budburst decreased with increasing latitude, towards the range margin. Overall, the Swedish oak population seems to comprise genetic diversity in phenology-related traits that may provide resilience to a rapidly changing climate. Full article

Verticillium longisporum, a soil-borne fungus responsible for Verticillium wilt, primarily colonizes members of the Brassicaceae family. Using Arabidopsis thaliana roots as an experimental host, we systematically identify V. longisporum-responsive genes and pathways through comprehensive transcriptomic analysis, alongside screening of potential hub genes and evaluation of infection-associated regulatory mechanisms. The GSE62537 dataset was retrieved from the Gene Expression Omnibus database. After performing GEO2R analysis and filtering out low-quality data, 222 differentially expressed genes (DEGs) were identified, of which 184 were upregulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed on these DEGs. A protein–protein interaction network was constructed using the STRING database. CytoHubba and CytoNCA plugins in Cytoscape v3.10.3 were used to analyze and evaluate this network; six hub genes and four functional gene modules were identified. The GeneMANIA database was used to construct a co-expression network for hub genes. Systematic screening of transcription factors within the 14 DEGs revealed the inclusion of the hub gene NAC042. Integrative bioinformatics analysis centered on NAC042 enabled prediction of a pathogen-responsive regulatory network architecture. We report V. longisporum-responsive components in Arabidopsis, providing insights for disease resistance studies in Brassicaceae crops. Full article