Search Results (472)

The study conducted a review of Listeria prevalence, virulence, and adaptations associated with leafy vegetables from small-scale farms and their journey to markets. PubMed, Taylor and Francis, Oxford, and Google Scholar databases were utilised to search for English-language journal articles published between January 1992 and 2025. Studies utilised multi-locus sequence typing (MLST), polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), multiplex PCR, pulsed-field gel electrophoresis (PFGE), and whole genome sequencing WGS, confocal scanning laser microscopy technique for the detection of Listeria species, followed by transcriptomic, phenotypic analyses, strand-specific RNA-sequencing, and membrane lipid profiling. ST₅, ST₁₂₁, and ST₃₂₁ are considered predominant and virulent and have been identified in two ready-to-eat commodities, while ST₁, ST₂, and ST₂₀₄ are considered hypervirulent strains in food processing environments. Immunocompromised groups can experience severe life-threatening infections, even death. Significant economic losses due to shutdowns for sanitary procedures can occur, impacting food security. Full article

The role of alternative nucleic acid structures (ANS) in biology is an area of increasing interest. These non-canonical structures include the Z-DNA and Z-RNA duplexes (ZNA), the three-stranded triplex, the four-stranded G-quadruplex (GQ), and i-motifs. Previously, the biological relevance of ANS was dismissed. Their formation in vitro often required non-physiological conditions, and there was no genetic evidence for their function. Further, structural studies confirmed that sequence-specific transcription factors (TFs) bound B-DNA. In contrast, ANS are formed dynamically by a subset of repeat sequences, called flipons. The flip requires energy, but not strand cleavage. Flipons are enriched in promoters where they modulate transcription. Here, computational modeling based on AlphaFold V3 (AF3), under optimized conditions, reveals that known B-DNA-binding TFs also dock to ANS, such as ZNA and GQ. The binding of HLH and bZIP homodimers to Z-DNA is promoted by methylarginine modifications. Heterodimers only bind preformed Z-DNA. The interactions of TFs with ANS likely enhance genome scanning to identify cognate B-DNA-binding sites in active genes. Docking of TF homodimers to Z-DNA potentially facilitates the assembly of heterodimers that dissociate and are stabilized by binding to a cognate B-DNA motif. The process enables rapid discovery of the optimal heterodimer combinations required to regulate a nearby promoter. Full article

Lignin is one of the primary biomass resources in nature; however, its highly stable structure makes it difficult to degrade and utilise. As efficient decomposers of lignocellulosic biomass, termites rely on their gut microbiota for digestion. Consequently, termite guts harbour abundant and specialized lignin-degrading microorganisms. In this study, we isolated a bacterium from the termite gut and identified it as Bacillus cereus BC-8. The laccase activity of B. cereus BC-8 reached the maximum of 87.8 U/L at 72 h, and the lignin degradation rate reached 33.66% within 7 days. Furthermore, we analyzed the structural changes in lignin after treatment with this bacterial strain. Field emission scanning electron microscopy observations revealed that the surface structural integrity of lignin was significantly disrupted after treatment. Fourier transform infrared spectroscopy analysis indicated that B. cereus BC-8 affected the side chains and aromatic skeleton structures of lignin. Thermogravimetric analysis further revealed that B. cereus BC-8 disrupted the primary inter-unit β-O-4 ether bonds of lignin. Whole-genome sequencing of B. cereus BC-8 revealed a genome length of 5,374,773 bp and a GC content of 35.34%. Functional gene annotation revealed that the B. cereus BC-8 genome contains genes encoding various lignin-degrading enzymes (laccase, cytochrome P450, and vanillin oxidase) and their auxiliary factors, along with the phenylalanine and benzoic acid metabolic pathways, which are associated with lignin degradation. In conclusion, B. cereus BC-8 can break down the side chains, aromatic skeletons, and β-O-4 ether bonds of lignin molecules, demonstrating excellent lignin degradation ability. At the molecular level, this study elucidates the key genes and metabolic pathways related to lignin degradation in the genome of B. cereus BC-8. Full article

Enterococcus spp. produce diverse bioactive molecules used for biotechnological purposes or as probiotic agents for livestock and human health. The main aim of this study was to decipher the genetic traits using whole-genome sequencing (WGS) of a bacteriocinogenic Enterococus faecium 1702 strain showing diverse probiotic traits. Genetic traits of the strain were determined by performing WGS using the NovaSeq6000 platform followed by consecutive sequence analysis using appropriate software. WGS showed that the genome of the E. faecium 1702 strain has a size of 2,621,416 bp, with a GC content of 38.03%. The strain belonged to the sequence type ST722 not known as a human clonal lineage. The strain was free of genes encoding clinically relevant antibiotic resistance; in addition, genes encoding sensu stricto virulence factors, plasmids, and prophages were not detected. Annotations through the Prokaryotic Genomes Automatic Annotation Pipeline (PGAP) tool revealed 2413 coding sequencing entries (CDC) out of 2521 predicted chromosomal genes. The functional annotation of the whole genome through the KEGG database using KofaScan revealed several genes related to several biological activities, including metabolic process, carbohydrate metabolism, amino acid metabolism, and nucleotide metabolism. The strain harbored three entero-bacteriocins (enterocins) encoded by entA, entB, and entX (enterocin X-alpha and X-beta) genes. Interestingly, the strain harbored the ansB, glsA, and arcA genes encoding L-asparaginase, L-glutaminase, and arginine deiminase, respectively, known for their anticancer activities. E. faecium 1702 harbored the gadB, gadC, and gadR genes implicated in gamma(γ)-aminobutyric acid (GABA) production, which is known for its analgesic, anti-anxiety, hypotensive, diuretic, and antidiabetic effects. The WGS findings and phenotypic traits of E. faecium 1702 revealed significant features that allow for its use as a probiotic or for biotechnological and pharmaceutical applications. Full article

MET exon 14 (METex14) skipping mutations differ from other non-small cell lung cancer (NSCLC) genomic biomarkers as they result in aberrantly spliced MET transcripts and increased MET-signaling. However, the most accurate method for their detection remains debated. We conducted a retrospective study of previously identified METex14 skipping NSCLC samples by using different, commercially available, diagnostic targeted DNA- /RNA-Next-Generation Sequencing (NGS) panels. We primarily used small DNA-NGS panels covering the 5′ splice site of METex14 and supplemented by targeted RNA sequencing for selected cases. Using this approach, we identified <0.2% patients with METex14 mutations. Due to this low frequency, we validated and introduced complementary NGS testing using combined DNA/RNA-panels. This resulted in an increased number of METex14-positive patients (3.5%) and allowed us to identify METex14 skipping transcripts. Collectively, data from our cohort (n = 34) demonstrated that optimal diagnostics of METex14 variants require a complementary DNA-NGS performed with targeted panels covering both METex14 splice sites, and RNA-NGS. Consequently, we propose a new workflow for interpretation of concordant and discordant findings in METex14 detection. Finally, the potential of DNA-identified METex14 variants to cause aberrant splicing was in silico assessed by the MaxEntScan tool, providing a quantitative approach to splicing disruption. Interestingly, we also identified two novel variants located inside METex14, which also produced the METex14 skipping transcript despite being located outside the canonical splice sites. The altered binding site resulting from these exonic mutations was in silico determined by SpliceTransformer. Full article

(1) Background: Backcross (BC) breeding is a key technology of crop improvement, yet its efficiency largely depends on the precise assessment of the genetic background recovery. Conventional molecular marker-assisted techniques suffer from inadequate genomic coverage or an inability to resolve true chromosomal structure. (2) Methods: To address major issues in maize BC breeding, we devised a G2H block-scanning strategy. This approach converts high-density point markers into haplotype blocks, enabling precise evaluation of the genetic background in backcross progenies. A key innovation is the CFDI, which quantifies the distribution of unrecovered fragments, allowing for visual tracking of chromosomal recombination and identification of ideal individuals with both a high genetic background recovery rate and few small fragments retention. (3) Results: We validated the accuracy and effectiveness of the G2H strategy across multiple backcross generations. Through enabling a precise “point-to-line-to-area” panoramic assessment of genetic background, G2H provides a powerful tool for developing ideal breeding materials with pure genetic background and minimized linkage drag. (4) Conclusions: Notably, this strategy significantly shortens the breeding cycle by 2–3 generations compared to conventional background assessment methods, thereby accelerating precision molecular design breeding in crops. Full article

Germplasm collections are a treasure trove of humanity. The accessions constituting those collections (wild crop relatives, landraces, cultivars, etc.) contain genes and allelic variants, which evolved prior to or post domestication, in the course of adaptation and selection, and can be used in breeding to address current and future needs. Precise characterisation of genetic diversity is essential for the efficient conservation of genetic resources and their effective utilisation in crop improvement. Detailed genetic profiles resulting from DNA genotyping constitute a basis for establishing the level of genetic diversity of a collection, analysing population structure, identifying redundancies, performing genome-wide association scans (given the availability of phenotypic information), detecting loci under selection, and many other applications. To obtain an accurate picture of genetic diversity (at the DNA sequence level), robust, high-density, high-throughput, and cost-effective methods are needed. With the advances in the next-generation sequencing, new genotyping approaches emerged (such as genotyping-by-sequencing, whole genome resequencing), which provide excellent genome coverage and low cost per datapoint (with tens of thousands to millions of loci analysed in a single assay). Crop-specific, custom, microarray-based genotyping solutions were also developed. The aim of this review is to provide a comparative description of the genome-wide, high-density genotyping technologies that are most frequently used nowadays, comprising their advantages and drawbacks, as well as factors that determine, which of the methods will best suit the particular germplasm characterisation project. Further, we characterise the current role of these methods in addressing the challenges related to the effective management and use of genetic resources and present recent examples of their application in selected crop plant groups. Finally, we briefly describe constraints to germplasm characterisation and future prospects. Full article

Aeromonas hydrophila is a typical pathogen that causes fish diseases and can easily infect different fish species. This study investigated the antibacterial activity, physicochemical properties and antibacterial mechanism of the BLIS UI-11 produced by Lactobacillus plantarum HYH-11, isolated from traditional kimchi in Hebei, China. It was found that BLIS UI-11 showed excellent inhibitory effect on the growth of A. hydrophila, and it also had a good antibacterial effect on various pathogens such as Vagococcus fluvialis, Listeria monocytogenes, Aeromonas dhakensis, Aeromonas salmonicida, Salmonella Typhimurium, Escherichia coli and Staphylococcus aureus. By measuring growth kinetics, it was found that the maximum antibacterial activity was reached after 30 h of culture, and both the optical density value at 600 nm (OD₆₀₀₎ and pH basically entered the stable phase after 20 h. Whole-genome analysis and gene cluster prediction identified a RiPP-like biosynthetic gene cluster, which comprises genes encoding precursor peptides, modification enzymes, and transport/immunity components. The molecular weight of the antimicrobial active substance was detected by dialysis and Tricine-SDS-PAGE, and it was shown to be an ultra-small molecular substance (<1 kDa). BLIS UI-11 was sensitive to protease K, but its antibacterial activity remained stable after treatment with acidic environment (pH 3.0–6.0), high-temperature treatment (121 °C for 30 min), and ultraviolet irradiation (4 h). After the sub-live cell assay (PI/SYTO9) and scanning electron microscopy (SEM), BLIS UI-11 inhibited the growth of bacteria by destroying the cell membrane of A. hydrophila to deform, collapse, and form holes that lead to accounting leakage. The hemolysis assay indicated that BLIS UI-11 exhibited incomplete hemolysis, suggesting its safety for application. The results showed that BLIS UI-11 produced by strain HYH-11 has great potential as an antimicrobial agent against A. hydrophila infection. Full article

Drought stress significantly impacts potato (Solanum tuberosum) yield and quality, necessitating the identification of molecular regulators involved in stress response. This study presents a systems-level, integrative in silico strategy to characterize StABCG25 transporter homologs, key players in abscisic acid (ABA) export in Arabidopsis, to evaluate their potential role in drought adaptation. We performed a genome-wide scan of the potato genome and identified four StABCG25 isoforms. A comprehensive computational framework was applied, including transcriptomic profiling, Weighted Gene Co-expression Network Analysis (WGCNA), AlphaFold2-based 3D modeling, docking, and long-timescale Molecular Dynamics (MD) simulations. Expression analyses revealed the coordinated upregulation of StABCG25-2 and -4 in the drought-tolerant FB clone, contrasted by suppression or instability in sensitive cultivars. WGCNA placed StABCG25-2 as a hub gene in ABA-enriched stress response modules, while StABCG25-4 was associated with plastid-related pathways, suggesting functional divergence. Structurally, StABCG25-2 and -6 exhibited high conformational stability in MD simulations, supported by consistent RMSD/RMSF profiles and MM/PBSA-based binding energy estimates. In contrast, StABCG25-5B, despite favorable docking scores, demonstrated poor dynamic stability and unreliable binding affinity. Overall, this study highlights the critical role of transcriptional coordination and structural robustness in the functional specialization of StABCG25 isoforms under drought stress. Our findings underscore the value of combining WGCNA and molecular dynamics simulations to identify structurally and functionally relevant ABA transporters for future crop improvement strategies. Full article

Serratia species are opportunistic human pathogens found in diverse environmental habitats. Here, we report the first isolation of Serratia nevei from food samples in Nigeria. During a two-month epidemiological surveillance at a local food market in Dutsin-Ma, Katsina State, Nigeria, a total of 180 food samples were collected, and isolation and species identification were performed using chromogenic agar and MicroScan autoSCAN-4, respectively. Antimicrobial susceptibility and minimum inhibitory concentrations (MICs) were determined using the MicroScan autoSCAN-4 system. Strain F129B, recovered from a fresh, unprocessed beef sample, was initially identified as Klebsiella pneumoniae by chromogenic agar and MicroScan autoSCAN-4, and subsequently as Serratia marcescens by MALDI-TOF MS. Only Whole Genome Sequencing (WGS) and bioinformatics analyses confirmed its identity as S. nevei. The strain was then selected for further characterization by Whole Genome Sequencing (WGS) and bioinformatics analyses to confirm its identity. The strain was phenotypically resistant to amoxicillin/clavulanic acid and colistin, with elevated MICs for aztreonam (4 mg/L) and cefuroxime (16 mg/L). In silico analyses of its genome confirmed the isolate as S. nevei, harboring genes conferring resistance to β-lactams (blaSTR-2), aminoglycosides (aac (6′)-Ic), fosfomycin (fosA), streptomycin (satA), and tetracycline (tet (41)). Its virulence repertoire comprises genes associated with adhesion (yidE, yidR, yidQ), colicin tolerance (creA and creD), and heavy metal resistance (czcD, chrBACF operon). These findings underscore the need for genomic characterization for accurate species identification within the Serratia genus. Our findings revealed the emergence of S. nevei in the food supply chain and highlighted its potential for zoonotic transmission. Robust surveillance of the local food supply chain is urgently needed in north-western Nigeria. Full article

Fengjing pigs are a Chinese native breed known for their high reproductive ability. Runs of homozygosity (ROHs) have emerged as an effective tool for evaluating inbreeding levels and identifying relevant genes in selection. However, the declining population of Fengjing pigs in recent years has raised concerns about inbreeding. Therefore, this study aimed to investigate the ROH patterns, estimate genomic inbreeding levels, and identify candidate genes associated with economic traits using whole-genome resequencing data from 105 Fengjing pigs. A total of 2448 ROHs were identified, with an average of 23.31 ROHs per individual and an average length of 9.50 Mb. The inbreeding coefficient, based on ROHs, was 0.098. Additionally, three genomic regions with a high frequency of ROHs were identified. These regions contained 64 unique genes, including 14 genes associated with important economic traits. Moreover, six overlapping quantitative trait loci (QTLs) and four candidate genes (HSPG2, CDC42, EPHB2, and GRHL3) were identified on Sus scrofa chromosome (SSC) 6. These QTLs are associated with birth traits (health and reproductive efficiency) and meat development traits (meat quality and growth). This study identified many candidate genes and QTLs that overlapped with ROHs and are associated with economically significant traits. These findings can be used in future breeding, conservation, and utilization of specific Chinese native pig breeds. Full article

Conventional plant breeding relies on the occurrence of chromosomal crossover and spontaneous or non-targeted mutations in the genome induced by physical or chemical stressors. However, constraints exist concerning the number and variation of genotypes that can be achieved in this way, as the occurrence and combination of mutations are not equally distributed across the genome. The underlying mechanisms and causes of reproductive constraints can be considered the result of evolution to maintain the genomic stability of a species while at the same time allowing necessary adaptations. A continuous horizon scan was carried out to identify plants derived from new genomic techniques (NGTs), which show that CRISPR/Cas is able to circumvent at least some of these mechanisms and constraints. The reason for this is the specific mode of action: While physico-chemical mutagens such as radiation or chemicals merely cause a break in DNA, recombinant enzymatic mutagens (REMs), such as CRISPR/Cas, additionally interfere with cellular repair mechanisms. More recently developed REMs even expand the capabilities of NGTs to introduce new genetic variations within the target sequences. Thus, NGTs introduce genetic changes and combinations that are unknown in the current breeding pool and that are also unlikely to occur as a result of any previously used breeding methods. The resulting genotypes may need to be considered as ‘new to the environment’. The technical potential of NGTs should also be taken into account in regulatory provisions. Previously unknown genotypes and phenotypes may negatively impact plant health, ecosystems, biodiversity, and plant breeding. It must further be acknowledged that the different outcomes of NGTs and conventional breeding are not always evident at first sight. As a starting point, within a process-oriented approval process, molecular characterization can inform the following steps in risk assessment and guide requests for further data. Full article

Background: TCF20-associated neurodevelopmental disorder (TCF20-NDD) is a heterogeneous clinical condition resulting from defects in gene-encoding Transcription Factor 20, which plays a key role in neuronal development and synaptic function. Here, we present a novel case involving an 11-year-old boy who was referred to us for a neuro-developmental disorder characterized by attention deficit hyperactivity disorder (ADHD), tremor in the upper limbs, tilted head posture, motor delay, impaired executive functioning, and oculomotor dyspraxia. Methods: Genetic tests were performed, including CGH array, molecular analysis of the FMR1 gene, molecular analysis using a next-generation sequencing gene panel targeted for spinocerebellar diseases, and finally, WES including mitochondrial genome analysis. A neuroimaging study of brain and spine was performed using MRI. Results: Trio Whole Exome Sequencing revealed a de novo pathogenic frameshift variant NM_001378418.1:c.5009dup, p.(Thr1671Aspfs*5) in the TCF20 gene. The MRI scan of the brain, cervical, dorsal, and lumbosacral spine revealed Chiari type I malformation. Regarding the pathogenic mechanism underlying Chiari I malformation, it could be found in the homology between TCF20 and the RAI1 gene, the latter being associated with alterations in the posterior cranial fossa. Conclusions: We emphasize the use of exome sequencing in patients with unclear clinical presentations, with awareness of TCF20-associated neurodevelopmental disorder; paying attention to brain MRI findings would be useful to further expand the phenotype of TCF20-NDD. Full article

Objectives: To develop two different radiomic models based on preoperative contrast-enhanced computed tomography (PP CT) to predict microsatellite instability (MSI) in patients with colorectal cancer (CRC) before surgery. Methods: PP CT scans of 115 CC patients were segmented using 3DSlicer (v5.6.1). Model I included images from three different scanners (GE, Siemens, Philips), while Model II used only one scanner (GE). For Model I, 80 patients were used for training and 35 for internal validation; for Model II, 46 and 24 patients were used, respectively. Data on sex, age, tumour location, and MSI genomic status were collected. A total of 107 radiomic features (RFs) were extracted, and 30 and 35 RFs were identified as relevant for Models I and II, respectively, using the t-test or Mann–Whitney test (p < 0.05). The most robust RFs were selected using the LASSO regression method. Both models were internally validated. Results: Model I, based on 2 RFs and 1 clinical feature (LOCATION) achieved an AUC of 0.76 (95% CI: 0.65–0.87) in the training cohort and 0.74 (95% CI: 0.56–0.92) in the validation cohort. Model II, based on 3 RFs, achieved an AUC of 0.85 (95% CI: 0.73–0.96) in the training cohort and 0.72 (95% CI: 0.50–0.94) in the validation cohort. Conclusions: Both radiomic models showed good performance in distinguishing between MSI and non-MSI tumours, potentially reducing the need for invasive histological testing and improving treatment timing. Despite achieving a higher AUC, Model II showed signs of overfitting when compared to Model I, which incorporated two RFs and one clinical feature (LOCATION). Radiomics may function as a non-invasive preoperative screening tool to inform decisions regarding MSI testing and treatment. Building radiomic models on larger, more diverse datasets is preferable to enhance generalizability and reduce overfitting. Full article

Background: Efflux-mediated macrolide resistance represents an emerging threat in Streptococcus infections globally. However, molecular epidemiological data from the Gulf region, particularly the United Arab Emirates (UAE), remain limited. This study addresses this knowledge gap by investigating efflux pump resistance mechanisms in clinical Streptococcus isolates. Methods: A cross-sectional study analyzed 100 clinical isolates (99 Streptococcus and 1 Enterococcus) from Thumbay Hospital, Ajman, UAE (October–December 2024). Antimicrobial susceptibility testing for minimum inhibitory concentration (MIC) determination was performed using the DxM 1096 MicroScan WalkAway system (Beckman Coulter Inc., Brea, CA, USA; LabProv4.42). PCR detected mef(A/E), msr(D), and tet(K) resistance genes with sequencing confirmation. Comparative genomic analysis was performed using a total of 30 publicly available Streptococcus genomes: 15 from India and 15 from Saudi Arabia. Statistical analysis employed chi-square tests, Fisher’s exact tests, and multivariate logistic regression with Bonferroni correction (α = 0.05). Results: Among the isolates, erythromycin resistance occurred in 39 isolates (39%, 95% CI: 29.4–49.2%) and clindamycin resistance in 31 isolates (31%, 95% CI: 22.1–40.9%). The mef(A/E) gene was detected in 31 isolates (31%, 95% CI: 22.1–40.9%), and msr(D) in 3 isolates (3%, 95% CI: 0.6–8.5%), with co-occurrence in 3 isolates (3%). No isolates harbored tet(K). Multivariate analysis identified mef(A/E) as the strongest predictor of macrolide resistance (OR = 18.7, 95% CI: 7.9–44.2, p < 0.001). Regional comparison revealed significant differences: mef(A/E) prevalence was 31% (UAE), 87% (India), and 0% (Saudi Arabia) (p < 0.001). Conclusions: This study provides the first molecular characterization of efflux-mediated macrolide resistance in UAE Streptococcus isolates. The predominance of mef(A/E)-mediated resistance with confirmed efflux activity highlights the clinical significance of active surveillance and targeted antimicrobial stewardship in the region. Full article