Search Results (10,615)

Bacillus safensis strains have emerged as versatile microbial platforms for bioproduction, combining the benefits of probiotic utility and biocontrol. In this study, we describe the isolation and in-depth characterization of a previously unreported B. safensis strain, LG01. The genome of this strain comprises a circular chromosome encoding 13 secondary metabolite biosynthetic gene clusters, 144 carbohydrate-active enzymes, 2 antibiotic resistance loci, and 1 prophage region, indicative of strong antimicrobial and metabolic capacity. Its protein secretion systems support nutrient acquisition, colonization, quorum sensing, and antibiotic synthesis. Our phenotypic assays confirmed the antifungal and antibacterial activity, proteolytic and cellulolytic functions, and robust biofilm formation of the strain. By performing a comparative genomic analysis, we identified 78 strain-specific genes enriched in the bacteriocin immunity and sporulation pathways. Signals of positive selection in the membrane and transcriptional regulator genes further reflect the adaptive evolution underlying the strain’s ecological fitness. Together, these findings advance our understanding of the genomic features of B. safensis LG01 and highlight its promise as a candidate for biocontrol and probiotic applications. Full article

Distant hybridization in fish serves to integrate the genetic material from two distinct, distantly related species. In this study, we successfully produced a new hybrid fish (BG) through the intergeneric hybridization of blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48, ♀) and green tip culter (Culter dabryi, GTC, 2n = 48, ♂). The objective of this research was to characterize the genetic, morphological, reproductive, and nutritional features of the hybrid compared with its parents. The DNA content and chromosomal number analysis revealed that BG was a diploid hybrid fish with 48 chromosomes. Integrated analysis of 5S rDNA, mitochondrial DNA, and Sox9 gene sequences revealed that BG predominantly inherited its genetic traits from BSB. Notably, certain gene fragments (376 bp segment of 5S rDNA class II and 718 bp segment of BG Sox9-II) originated from the paternal GTC, demonstrating biparental genomic integration. The growth performance analysis revealed that BG exhibited enhanced growth, achieving a body weight significantly greater than that of BSB and 1.81-fold that of GTC (both p < 0.05). The reproductive analysis indicated that BG possessed bisexual fertility, with testicular histology revealing accelerated spermatogenesis relative to BSB. Additionally, the nutritional analysis of BG muscle revealed elevated levels of crude protein (18.13%) and umami amino acids (5.45%) compared to those in its parents. BG showed higher growth, bisexual fertility, and improved muscle nutritional composition. This hybrid represents a promising resource for cyprinid breeding and aquaculture diversification. Full article

The Paraoxonase (PON) gene family consists of three paralogues (PON1, PON2 and PON3) that are tandemly located on chromosome 7. In this review paper, the structure and function of the encoded proteins is summarized. In addition, an overview is given on the generated animal models. Finally, their involvement in the pathogenesis of different diseases is discussed, starting from an extended screening of the literature using PUBMED and Web of Science. PON1 and PON3 are mainly expressed in the liver and released into the bloodstream, bound to high-density lipoprotein. PON2 is expressed in various tissues, including the liver, lungs, heart, placenta and testes, but remains intracellular. The name of the enzyme family reflects PON1′s ability to neutralize paraoxon, but they also exhibit lactonase and esterase activities. All three PON enzymes play a role in reducing lipid peroxides in High-Density Lipoproteïne (HDL) and low-density lipoprotein(LDL), giving them antioxidant properties. This links them to Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD), a metabolic liver condition marked by the excessive accumulation of triglycerides (TG) in liver cells. In addition to their association with MASLD, the PON genes are, due to their antioxidant properties, also associated with other conditions including cardiovascular diseases, chronic kidney disease, neurological and immunological conditions up to some forms of cancer. In the latter, the antioxidant properties can result in tumor progression by protecting malignant cells from oxidative damage thus supporting survival, proliferation and metastasis indicating them as potential drug targets for treatment of cancer. Therefore, further research on this protein family can provide novel insights into their function and their potential therapeutic applicability. Full article

Background/Objectives: Chronic lymphocytic leukemia (CLL) is a hematologic malignancy characterized by uncontrolled accumulation of B lymphocytes. A key feature of CLL is the presence of genetic aberrations, particularly alterations of chromosome 17, such as deletion of 17q and/or mutations in the TP53 gene. Since these abnormalities are highly relevant for therapeutic decision-making, assessment of TP53 mutational status is strongly recommended in routine diagnostics. This study aimed to evaluate the reliability of TP53 sequencing results depending on the type of DNA sample analyzed. Methods: DNA was isolated from two different sample types of the same patient: mononuclear cells (CLL1) and purified CD19+ cells (CLL2). The entire coding region of TP53 (exons 2–11), including splice sites (+/− 10 bp), was analyzed using capture-based next-generation sequencing (NGS). Reads were aligned to the GRCh37/hg19 reference genome, and variants were interpreted using DRAGEN Enrichment (Illumina) and Franklin (QIAGEN). Results: In sample CLL1, the NM_000546.6:c.626_627del mutation (Tier I) was identified with a variant allele frequency (VAF) of 57.06%. The same mutation was confirmed in CLL2, but with a higher VAF of 94.78%. Importantly, an additional Tier I mutation (NM_000546.6:c.825_826del) was detected exclusively in CLL2 at a VAF of 1.59%. Both findings met the required sequencing depth as well as coverage per sample, confirming their validity. Conclusions: The study demonstrates that inadequate starting material for DNA isolation may mask low-frequency TP53 mutations, resulting in false-negative results. Accurate detection requires ensuring sufficient CD19+ cell content, which is critical for reliable diagnostics and supports personalized treatment approaches in CLL. Full article

Background/Objectives: Large-scale (epi)genomic studies have substantially advanced our understanding of the molecular landscape of meningiomas, most recently embedded in the cIMPACT-NOW update 8. As a result, molecular data are increasingly integrated into risk-adapted treatment algorithms. However, it remains uncertain to what extent non-invasive MRI can capture underlying molecular variation and risk. Methods: We assembled a large, single-institution cohort of 225 newly diagnosed meningiomas (WHO grades 1–3) with available preoperative MRI, as well as comprehensive epigenome-wide methylation and copy-number profiling. Tumors were segmented into core and edema regions using a state-of-the-art automated pipeline from the BraTS challenge. Radiomic features were extracted and used to train Random Forest classifiers to predict WHO grade, molecular risk, and specific alterations such as 1p loss in a hold-out test set. Results: Our models achieved accuracy above 91% for integrated molecular risk classification, 87.5% for 1p chromosomal status, and 76.8% for WHO grade prediction, with corresponding AUCs of 0.91, 0.90, and 0.89, underscoring the robustness of radiomic features in capturing histopathological and, especially, molecular characteristics. Conclusions: Preoperative MRI effectively captures the underlying molecular biology of meningiomas and may enable rapid molecular assessment to inform decision-making and prioritization of confirmatory testing. However, it is not yet ready for clinical use, showing lower accuracy for current WHO grade classification. Full article

Amaranthus L. includes valuable and promising crops of multi-purpose use, having high morphological diversity and complicated taxonomy. Their karyotypes and genomic relationships remain insufficiently studied. For the first time, a comparative repeatome analysis of Amaranthus tricolor L., Amaranthus cruentus L., and Amaranthus hypochondriacus L. was performed based on the high-throughput sequencing data obtained via bioinformatic analyses using the RepeatExplorer2/TAREAN/DANTE_LTR pipelines. Interspecific variations in the abundance of Ty1 Copia and Ty3 Gypsy retroelements, DNA transposons, and ribosomal and satellite DNA (satDNA) were detected. Based on fluorescence in situ hybridization (FISH), chromosome mapping of 45S rDNA, 5S rDNA, and satDNAs AmC9 and AmC70, and unique karyograms of A. tricolor, A. cruentus, Amaranthus paniculatus L., and A. hypochondriacus were constructed. The analysis of the interspecies genome diversity/similarity in DNA repeat contents, sequences of the identified satDNAs, and chromosome distribution patterns of the studied molecular markers indicated that these species might also share a common evolutionary ancestor. However, the genomes of A. cruentus, A. paniculatus, and A. hypochondriacus were more similar compared to A. tricolor, which aligns with the previous phylogenetic data. Our results demonstrate that cytogenomic studies might provide important data on Amaranthus species relationships elucidating taxonomy and evolution of these valuable crops. Full article

The phenotypic resistance of 56 Enterococcus faecalis isolates from Eurasian griffon vultures was subjected to surveillance testing with the microdilution method using a standardized panel of antimicrobials. Isolates were also characterized by MLST. Additionally, the genome of 19 isolates with phenotypic resistance to linezolid, ciprofloxacin, chloramphenicol and/or high-level resistance to gentamicin were sequenced to determine their antimicrobial resistance (ARGs) and virulence-associated genes and to identify mobile genetic elements (MGEs). Most isolates (82.1%) exhibited non-wild-type phenotypes to six antimicrobial agents, and multidrug resistance (MDR) was detected in 34% of the isolates. Most MDR isolates (53%) belonged to ST16, ST116 and ST35. ARGs were localized on the chromosome as well as on various MGEs previously reported in human, food and livestock isolates, suggesting that vultures may acquire antibiotic-resistant bacteria (ARBs) and/or ARGs as a consequence of anthropogenic pollution. Overall, 22 virulence-associated genes encoding cell surface and secreted factors were identified, some of which were located on MGEs that also carried ARGs. The significant proportion of E. faecalis isolates recovered from vultures that exhibited MDR phenotypes and harbored MGEs carrying ARGs and virulence-associated genes is cause for concern, since vultures may act as spreaders of these genes to the environment, domestic animals and humans. Full article

Background: Seed shattering enhances ecological adaptation in perennial grasses but severely limits harvestable seed yield in forage crops. Psathyrostachys juncea is an important perennial forage species in arid and cold regions, yet the genetic basis of its seed shattering remains largely unknown. Here we asked which genomic regions and biological pathways underlie natural variation in seed shattering in P. juncea, and whether cellulose synthase (CESA)-mediated cell-wall formation contributes to abscission-zone strength. Results: We evaluated seed shattering in a diverse association panel of P. juncea across four environment–-year combinations and performed a genome-wide association study (GWAS) using genotyping-by-sequencing single-nucleotide polymorphism (SNP) markers. The analysis identified 36 significant SNP loci distributed on multiple chromosomes, consistent with a highly polygenic and environment-responsive architecture. Candidate-gene annotation highlighted pathways related to cell-wall biosynthesis, hormone signaling and sugar transport. Notably, in the BT23SHT environment a cluster of association signals on chromosome 3D co-localized with several genes annotated as cellulose synthase (CESA). Abscission-zone transcriptome profiling and qRT-PCR at 7, 14, 21 and 28 days after heading revealed that CESA genes, including TraesCS3D02G010100.1 located near the lead SNP Chr3D_3539055, showed higher early expression in low-shattering lines and a decline toward baseline in high-shattering lines. Comparative analyses placed P. juncea CESA proteins within a broadly conserved but lineage-divergent framework among grasses. Conclusion: Together, these results define the genetic landscape of seed shattering in P. juncea and nominate cellulose-biosynthetic genes on chromosome 3D as promising targets for marker-assisted selection of low-shattering, high-seed-yield forage cultivars. Full article

Pecan is an important oilseed tree species valued for its nutrient-rich nuts. WRKY and VQ proteins play crucial roles in plant growth, development, and stress response. However, few WRKY and VQ genes in pecan have been functionally analyzed due to functional redundancy caused by gene duplication. In this study, 89 CiWRKYs and 47 CiVQs were identified in pecan genome, which were unevenly distributed across chromosomes. Gene structure and conserved motif analyses revealed high diversity among members. Duplication analysis indicated that segmental duplication was the major factor of family expansion of CiWRKY and CiVQ. Ka/Ks ratios revealed that most duplicated gene pairs underwent purifying selection. Promoter analysis identified numerous cis-acting elements associated with light response, hormone regulation, and abiotic stress, implying their potential regulatory roles in development and stress response. Expression data across six tissues demonstrated tissue-specific patterns, with several genes highly expressed in flowers and roots. Transcriptome analysis revealed that 63 CiWRKY and 27 CiVQ genes were significantly upregulated under drought stress. qRT-PCR validation confirmed that CiPaw.10G165200 and CiPaw.04G072500 were highly induced by salt treatment, with expression levels increasing over 100-fold at 8 d. Moreover, CiPaw.10G165200 was also highly expressed under ABA treatment, which indicated it might play a key role in the response to abiotic stresses. Our results provide valuable insights into the evolutionary patterns and functional roles of WRKY and VQ genes in pecan and lay a foundation for improving stress tolerance and molecular breeding in this economically important nut tree. Full article

Accurate bacterial quantification is critical in many biological fields, from clinical diagnostics to environmental microbiology. Here, we establish a robust workflow for absolute quantification of bacterial species within mixed communities using Crystal Digital PCR^TM. Using a synthetic consortium of Clostridium acetobutylicum and Nitratidesulfovibrio vulgaris, we optimized primer design for species-specific detection and demonstrated that Crystal Digital PCR^TM enables reliable quantification of low-abundance species, down to a 1:10,000 ratio. We further show that the presence of one species does not interfere with the quantification of another. Finally, we demonstrate that Crystal Digital PCR^TM can also be used to determine plasmid-to-chromosome copy number ratios in bacteria carrying megaplasmids. Full article

Gynogenesis is a reproductive mode where offspring inherit exclusively maternal chromosomes. Gynogenetic development in fish may be induced intentionally by activating eggs with the UV-irradiated, inactive spermatozoa. In the meiotic variant of gynogenesis, the resultant haploid gynogenetic zygote is then exposed to a physical shock to inhibit the release of the 2nd polar body and to reconstitute the diploid state of the embryo. Here, meiotic gynogenesis was induced in the rainbow trout eggs from different clutches to find any differences in terms of gene expression and antioxidant enzyme activity between eggs with high and low ability for gynogenetic development. The survival rates of the gynogenotes after hatching from the eggs originating from five females varied from 16.6 ± 4.3% to 53.8 ± 9.8%. Biochemical and molecular examination revealed that eggs with higher developmental potential for meiotic gynogenesis exhibited significantly greater glutathione peroxidase (GPx) activity than eggs with lower efficiency of gynogenesis. Moreover, eggs exhibiting the highest ability for gynogenetic development showed increased transcription of the keratin 8 gene and decreased abundance of keratin 18 and tubulin β mRNA transcripts. Since keratins protect oocytes from physical stress after ovulation, the high abundance of keratin 8 in the rainbow trout eggs may increase their resilience to the physical shock applied for the zygote diploidization during gynogenesis. On the other hand, a low level of tubulin-building microtubules may increase the efficiency of high hydrostatic pressure (HHP) shock used for diploidization of the gynogenetic zygotes. Full article

Extrachromosomal circular DNA (eccDNA) has been recognized as a key player in tumorigenesis and progression. However, eccDNA transcriptional regulatory mechanisms under DNA damage in cancer remain poorly characterized. Here, we used doxorubicin to induce DNA damage in the hepatocellular carcinoma cell line HepG2 and performed Circle-seq to profile eccDNAs before and after the damage. We observed a significant increase in the number, length, and chromosomal distribution density of eccDNAs following DNA damage. RNA-seq revealed that the expression of genes carried on eccDNA was positively correlated with eccDNA copy number under DNA damage. Further ATAC-seq profiling identified distinct chromatin characteristics at eccDNA breakpoint regions compared to other regions of eccDNA and linear genomic regions. Additionally, eccDNAs generated under DNA damage preferentially originated from linear genomic regions characterized by low GC content and hypomethylation. Finally, by integrating Hi-C and H3K27ac ChIP-seq, we uncovered that eccDNAs with mobile enhancer activity (ME-eccDNAs) display significantly enhanced chromatin interactions and H3K27ac enrichment after DNA damage. Overall, our findings systematically elucidate the DNA damage-driven mechanisms underlying eccDNA biogenesis, chromatin characteristics and transcriptional regulation in HCC HepG2 cells. Full article

Vascular Plant One-Zinc finger (VOZ) transcription factors are pivotal regulators of plant growth and stress adaptation, yet their functional roles in Gossypium hirsutum, a key fiber crop, remain poorly characterized. In this study, we systematically identified six VOZ genes in G. hirsutum and conducted a comprehensive analysis of their phylogenetic relationships, genomic distribution, promoter architecture, and expression profiles. Phylogenetic classification placed the GhVOZ proteins into three distinct clades, and chromosomal localization revealed that family expansion was likely driven by segmental duplication events. Promoter analysis uncovered an abundance of stress-related cis-regulatory elements, suggesting a potential role in abiotic stress signaling. Consistent with this, expression profiling demonstrated that GhVOZ1/3, GhVOZ2/4/5, and GhVOZ6 were specifically induced under drought, salt, and cold stress, respectively, with qRT-PCR further confirming their tissue-specific dynamic regulation under salt treatment. Furthermore, the GhVOZ family exhibited stage-specific expression patterns during somatic embryogenesis. GhVOZ1, GhVOZ3, and GhVOZ4 were upregulated at the early induction phase, implicating them in the initiation of cell reprogramming. In contrast, GhVOZ2 and GhVOZ4 showed sustained expression in embryogenic callus at later stages, suggesting a role in maintaining embryogenic competence, whereas GhVOZ5—preferentially expressed in non-embryogenic callus—may act as a repressor of embryogenesis. Synteny analysis further highlighted evolutionary conservation and subgenomic divergence of VOZ genes in G. hirsutum. Collectively, these findings establish GhVOZs as key regulators integrating abiotic stress response and somatic embryogenesis, providing a genetic framework for future functional studies and crop improvement. Full article

Importin α (IMPα) proteins are key mediators of nucleocytoplasmic transport and play crucial roles in plant development and stress adaptation. Here, we performed a genome-wide identification of the IMPα gene family in Glycine max, followed by gene structure and conserved motif analyses, chromosomal distribution and duplication inference, synteny and selection (Ka/Ks) analyses, and expression profiling across tissues and stress conditions using public RNA-seq datasets and expression browsers. The GmIMPα genes exhibited diverse gene structures and conserved motifs, suggesting functional diversification within the family. Segmental duplication was identified as the main contributor to family expansion, and most duplicated gene pairs underwent purifying selection. Promoter analysis revealed numerous stress- and hormone-responsive cis-elements, implying complex transcriptional regulation. Expression profiling demonstrated that GmIMPα5 and GmIMPα7 were strongly induced under drought, heat, and salt stresses, indicating potential roles in abiotic stress tolerance. Collectively, our results provide a comprehensive framework for the evolution and functional divergence of the GmIMPα family in soybean and offer candidates for improving stress resilience. Full article

The normal metabolism of transient starch in leaves plays a vital role in determining photosynthesis and final crop yield. However, the molecular mechanisms linking abnormal transient starch metabolism to premature leaf senescence remain unclear. Here, we isolate a rice mutant, lses1, with leaf yellowing and premature senescence, as well as excessive accumulation of starch granules in chloroplasts. Genetic analysis revealed that this trait is controlled by a single recessive nuclear gene. Through BSA-seq preliminary gene mapping, map-based cloning, and sequencing alignment, the candidate gene was pinpointed to LOC_Os02g40860 on chromosome 2, which encodes OsCKI1, a casein kinase I family member. The identity of LSES1 was confirmed functionally: genetic complementation with the native genomic sequence rescued the wild-type phenotype, while CRISPR/Cas9 knockout of the gene in wild-type plants recapitulated the premature senescence. This confirmed that LSES1/OsCKI1 is involved in the regulation of leaf senescence. Notably, one improved knockout line, KO-2, displayed significant agronomic improvements in grain length, grain width, number of productive ears, and number of filled grains per panicle, along with a significant increase in grain yield per plant, highlighting its potential breeding value. Subcellular localization and tissue-specific expression analysis showed that LSES1 is primarily nuclear-localized and constitutively expressed. Full article