Ensuring superior quality is of paramount objective in modern rice (Oryza sativa L.) breeding program and investigating quality traits is crucial for developing superior rice varieties. The current study aimed for identifying single nucleotide polymorphisms (SNPs) and potential candidate genes for eleven quality traits, namely, hulling %, milling %, kernel length, kernel breadth, kernel length to breadth ratio, grain type, head rice recovery, chalkiness, amylose content, alkali spreading value, and gel consistency, using genome-wide association studies (GWASs) on diverse germplasm sourced from various rice-growing regions around the world. Phenotypic evaluation revealed significant genetic diversity among germplasm, with substantial natural variation observed across 10 quality-related traits. GWAS using 7K SNP chip identified 31 SNPs significantly linked to grain quality traits, of which 20 were novel and 11 had been previously reported, including two co-localized SNPs (GS3 and SNP-6.6652023) associated with multiple traits. In addition, 121 candidate genes related with these traits were identified and categorized into seven molecular functions, four cellular components, and nine biological processes. Notably, 17 putative grain quality-related genes were identified, viz., GS3 (Grain size regulator), Wx (granule-bound starch synthase), OsZIP7 (ZIP family protein), OsRING4 (RING-type E3 ubiquitin ligase), OsMKK3 (Mitogen-activated protein kinase), OsSSIV-2, OsSSIIa/SSII-3 (ALK; soluble starch synthase), and OsbZIP58 (bZIP transcription factor). The identified SNPs and potential candidate genes represent a valuable genomic resource for accelerating rice breeding programs focused on the enhancement of key quality traits.

Poly-γ-glutamic acid (γ-PGA) is a valuable biopolymer with diverse industrial applications, produced naturally by several Bacillus species. The dairy environment is an under-explored niche for identifying efficient, food-grade γ-PGA producers. In this study, four legacy dairy-derived Bacillus licheniformis strains: DPC3803, DPC6338, DPC6339, and DPC6340, producing high γ-PGA titres were examined using whole genome sequencing (WGS) and comparative genomic analysis to evaluate their suitability for future industrial applications. The genomes ranged from 4.19 to 4.29 Mb with an average GC content of 45.8–46.2%. Pangenome analysis of the four strains, together with 51 publicly available B. licheniformis genomes, identified 12,415 gene clusters, of which 18.9% and 81.1% were core and accessory genes respectively. Average nucleotide identity (ANI) analysis demonstrated >99% sequence identity among all 55 B. licheniformis genomes, despite their isolation from diverse environments, indicating strong genomic conservation within the species. Experimental validation confirmed γ-PGA production by all four strains, with maximum titres (g/L) of 43.27 ± 1.49, 59.54 ± 4.33, 27.93 ± 1.87, and 47.74 ± 0.19 for DPC3803, DPC6338, DPC6339, and DPC6340, respectively. Genomic screening revealed multiple γ-PGA metabolism and CAZyme-encoding genes, as well as unique secondary metabolite clusters with potential antimicrobial activity. Although no plasmids or virulence factors were detected, twenty-one prophages were identified, sharing no significant homology with known cultivated phages, and a single β-lactamase gene suggested intrinsic resistance to β-lactams. These findings highlight the genomic and functional potential of these dairy-derived B. licheniformis as efficient, food-grade candidates for industrial γ-PGA production.

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) and multidrug-resistant (MDR) P. aeruginosa limit therapeutic options but have been sparsely documented in Ghana. From November 2023 to December 2024, we conducted a prospective cross-sectional study of P. aeruginosa isolates from acute-care hospitals in Greater Accra, Ghana. Isolates were identified by matrix-assisted laser desorption ionization-time of flight, and antimicrobial susceptibility was assessed by disk diffusion as per Clinical Laboratory Standard Institute guidelines. Meropenem-resistant isolates with positive carbapenemase phenotype were subjected to whole-genome sequencing. Multivariable logistic regression models identified risk factors for infections caused by MDR and carbapenemase-producing Pseudomonas aeruginosa (CRPA). P. aeruginosa accounted for 0.32% (n = 267/83,589) of all bacterial infections identified from submitted clinical specimens and 2.82% (n = 267/12,236) of culture-positive infections. Of the 267 P. aeruginosa isolates, 20.2% (n = 54/267) were MDR and 13.5% (n = 36/267) were CRPA. Amikacin retained the highest activity against P. aeruginosa. The mean multiple antibiotic resistance index among MDR isolates (0.51 ± 0.26) was significantly higher than that among non-MDR P.aeruginosa isolates(0.02 ± 0.07; p < 0.001), with a large between-group difference (Hedges' g = 3.70). Only one isolate (2.7%) harbored a single carbapenemase gene, blaNDM-1. The remaining 35 carried a blaOXA-50-type backbone that co-occurred with either class A carbapenemases (blaKPC [n = 7], blaSME-1 [n = 4], blaGES-5 [n = 1]) or class B metallo-β-lactamases (blaNDM-1 [n = 19], blaVIM-5 [n = 3], blaIMP-15 [n = 1]). blaNDM-1 was the most dominant carbapenemase gene (n = 20/36) . Wound infection was the strongest predictor of MDR infections (adjusted odds ratio [aOR] = 3.01; 95% confidence interval (CI) = 1.43-4.47; p = 0.001], whereas inpatient status was the strongest predictor of CRPA infection (aOR = 3.32; 95% CI = 0.98-4.09; p = 0.001). MDR P. aeruginosa and carbapenem Resistant P.aeruginosa (CRPA), mostly blaNDM-1 producers, are major causes of infection in our setting. Restricting carbapenem use through stewardship and strengthening infection control is essential to limit CRPA spread.

Enhancing environmental stress tolerance of Saccharomyces cerevisiae by deletion of NTH1 and FKS3: Implications for beer brewing.

Fusarium graminearum is a major pathogen of wheat and barley, causing fusarium head blight (FHB) and contaminating grain with harmful mycotoxins. Azole fungicides (demethylation inhibitors) are among the key tools available for managing F. graminearum infections. In an attempt to characterize how resistance to azole fungicides arises, we performed an experimental evolution study that imposed selection by exposing F. graminearum to increasing concentrations of prothioconazole (PTZ), tebuconazole (TBF), a combination of both fungicides (CMB), or a no-drug control. All evolved lineages exceeded the ancestral minimum inhibitory concentration before strain extinction, retained normal in vitro colony growth in the absence of drugs, and were able to successfully infect a fusarium head blight-susceptible wheat cultivar. However, most lineages lost their apparent resistance improvements after being revived from preservation at -80°C. One lineage (TBF1), however, showed stable enhanced resistance to tebuconazole, which was accompanied by a phenotype of precocious germination of macroconidia. Genomic analyses indicated no change in the cyp51 genes in any lineage but identified a single base insertion resulting in a premature stop codon in the aos1 gene (involved in SUMOylation) in the TBF1 genome. We created aos1 gene deletion strains, which phenocopied TBF1 for both tebuconazole resistance and altered macroconidial germination. This work suggests that adjustments to spore germination processes may influence sensitivity toward fungicides and also highlights the role of SUMOylation in spore dormancy.IMPORTANCEFusarium graminearum is a major crop pathogen that can acquire mutations over time to common fungicides. Historically, studies have focused their attention on a single gene, cyp51, as the primary cause of resistance. However, there may be other pathways to enhanced resistance. For example, changes in macroconidium germination rates and transitions between cell types offer a route to fungicide resistance that has not been adequately appreciated to date. This study highlights a novel pathway to azole resistance, providing new insights into how F. graminearum may circumvent chemical controls. Through laboratory evolution, a single base insertion arose within the aos1 gene, which caused phenotypes of altered macroconidium dormancy and reduced fungicide sensitivity. This research highlights the importance of experimental approaches that remain open to surprising evolutionary innovations and unexpected resistance mechanisms.

Molecular chaperones including the heat-shock protein 70-kilodalton (HSP70) family and the J-domain containing protein (JDP) co-chaperones maintain homeostatic balance in eukaryotic cells through regulation of the proteome. The expansive JDP family helps direct specific HSP70 functions, yet loss of single JDP-encoding genes is widely tolerated by mammalian cells, suggesting a high degree of redundancy. By contrast, essential JDPs might carry out HSP70-independent functions or fill cell-context dependent, highly specialized roles within the proteostasis network. Using a genetic screen of JDPs in human cancer cell lines, we found the RNA recognition motif (RRM) containing DNAJC17 to be pan-essential and investigated the contribution of its structural domains to biochemical and cellular function. We found that the RRM exerts an auto-inhibitory effect on the ability of DNAJC17 to allosterically activate ATP hydrolysis by HSP70. The J-domain, but neither the RRM nor a distal C-terminal alpha helix are required to rescue cell viability after loss of endogenous DNAJC17. Knockdown of DNAJC17 leads to relatively few conserved changes in the abundance of individual mRNAs, but instead deranges gene expression through exon skipping, primarily of genes involved in cell cycle progression. Concordant with cell viability experiments, the C-terminal portions of DNAJC17 are dispensable for restoring splicing and G2-M progression. Overall, our findings identify essential cellular JDPs and suggest that diversification in JDP structure extends the HSP70-JDP system to control divergent processes such as RNA splicing. Future investigations into the structural basis for auto-inhibition of the DNAJC17 J-domain and the molecular regulation of splicing by these components may provide insights on how conserved biochemical mechanisms can be programmed to fill unique, non-redundant cellular roles and broaden the scope of the proteostasis network.

Alternative splicing (AS) represents a pivotal post-transcriptional regulatory mechanism, profoundly expanding proteomic diversity and functional complexity by enabling single genes to generate multiple mRNA isoforms. In plants, AS serves as a survival toolkit, dynamically modulating stress-responsive signaling pathways, transcriptional networks, and protein functional specialization to optimize environmental fitness. Recent advances in high-throughput sequencing technologies and computational tools have significantly deepened our understanding of AS regulation in plants. Notably, breakthroughs such as long-read transcriptome sequencing and single-cell RNA analysis have revolutionized the resolution at which we can characterize AS landscapes. These developments have collectively illuminated the critical role of AS in mediating plant responses to diverse abiotic stresses, including drought, salinity, and extreme temperatures. The resulting discoveries have opened transformative avenues for crop improvement through precise manipulation of splicing patterns. Innovative strategies such as CRISPR-Cas9-based splice editing and engineered splicing factors now provide powerful platforms for developing climate-resilient, high-yielding crop varieties with enhanced stress tolerance and nutritional quality. Here, we systematically examine the molecular mechanisms underlying AS-mediated plant stress responses, and cutting-edge applications of AS engineering in precision agriculture. By synthesizing fundamental insights with biotechnological innovations, we highlight the transformative potential of AS manipulation in addressing the pressing global agricultural challenges.

Japanese cedar (Cryptomeria japonica D. Don) is a major plantation species in Japan, but its abundant pollen production is a primary cause of seasonal allergic rhinitis (pollinosis). To mitigate this public health issue, the use of male-sterile cultivars has been promoted. Five types of recessive male-sterile mutations (ms1-ms5) have been identified, and the causal genes and mutations for MS1 and MS4 have been elucidated. However, the gene responsible for MS2-type male sterility remains unknown. We aimed to identify the candidate gene responsible for MS2-type male sterility using a map-based cloning strategy. High-resolution linkage mapping localized the MS2 locus to a 1.56cM interval on linkage group 5, corresponding to an 8.64Mb region of the reference genome. Ninety-one genes in this region were subjected to functional annotation, gene expression analysis, and mutation screening. Among these, a single gene, SUGI_0493010, encoding a GDSL-type esterase/lipase protein (GELP), fulfilled all three criteria: it showed homology to pollen development genes in Arabidopsis thaliana, was specifically expressed in male strobili, and carried a deleterious amino acid substitution (S40F) within the predicted catalytic domain in ms2 mutant. The same mutation was also detected in a heterozygous individual (Ms2/ms2) from a separate breeding population, whose genotype was confirmed through progeny testing. Structural annotation revealed that the affected serine residue lies within the conserved GDSL motif, suggesting a functional disruption of enzymatic activity. Our results strongly suggest that SUGI_0493010 (GELP) is the candidate gene for MS2-type male sterility in C. japonica. This finding enhances our understanding of male sterility mechanisms in conifers and provides a valuable genetic resource for breeding pollen-free trees. The study also demonstrates the effectiveness of combining genetic mapping with transcriptomic and mutational data in forest tree genomics.

Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related B4galnt2 gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal B4galnt2 expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce the adverse effects of microbiome-targeted therapies.

Replicated repurposing of an ancestral transcriptional complex in land plants.

Epigenome regulators imbue a single eukaryotic promoter with diverse gene expression dynamics.

Nasopharyngeal colonization by Streptococcus pneumoniae is characterized by bacterial adherence to epithelial cells, microinvasion, and innate immune activation. Previously, we have shown that two serotype 6B S pneumoniae mutant strains affecting bacterial metabolism (ΔproABC/pia and Δfhs/pia) colonize humans and mice, but in a murine disease model do not cause invasive infection. Using an experimental human pneumococcal challenge model, ex vivo airway cells, and in vitro nasopharyngeal epithelium, we explore whether microinvasion and innate immune responses persist despite disease attenuation. We show that under serum stress, these biosynthesis gene mutations had a broad but different impact on pneumococcal virulence gene expression, oxidative stress regulation, and purine and carbohydrate metabolism genes. However, although these mutations did not attenuate microinvasion in human challenge and epithelial models, there was less transmigration of Detroit 562 nasopharyngeal epithelial cells by the mutants compared to wild-type. Cellular reorganization of primary human airway epithelium varied considerably between strains. Compared to wild-type, infection of Detroit 562 epithelial cells by the Δfhs/piaA strain, but not the ΔproABC/piaA strain, was less proinflammatory, induced less caspase 8 production, and was associated with increased pneumococcal hydrogen peroxide and reduced pneumolysin secretion. These findings suggest that differences in microinvasion and epithelial responses were driven by the differential expression of multiple bacterial virulence and metabolic pathways. These data highlight the complex impact of single gene mutations on bacterial virulence and suggest that the virulence determinants of pneumococcal epithelial colonization, microinvasion, and innate immunity are not necessarily directly linked to disease.

Mink self-biting behaviour causes skin damage, reducing fur quality and restricting the development of the mink farming industry. The aim of this study was to investigate the genetic mechanisms underlying self-biting behaviour in minks from a genomic perspective. Using weighted gene coexpression network analysis (WGCNA), we identified functional gene modules and then explored their associations with phenotype, thereby identifying key genes influencing this behaviour. The daily behaviours of minks were analysed through behavioural observation. Gene expression profiles of hippocampi from self-biting and healthy minks (8 males and 10 females in each group) were constructed using transcriptome sequencing. The results revealed significant differences in self-biting, feeding, playing, and lying behaviour between self-biting and healthy minks (P < 0.01). Notably, grooming was significantly correlated with self-biting behaviour (P < 0.05), and slow pace, lying, playing, shaking, and feeding behaviours were strongly correlated with self-biting behaviour (P < 0.01). Differentially expressed genes between self-biting and healthy minks were identified and analysed via WGCNA; then, the correlation coefficient method was used to identify 50 and 20 single genes that may affect mink self-biting in females and males, respectively. Database annotation identified a single gene in the female group, corresponding to Hspa2. This gene is associated with neurological disorders. The Hspa2 gene showed functionally enriched expression under cold and heat stress. Therefore, we speculate that such stress induces abnormal changes in the Hspa2 gene in mink hippocampal tissue, leading to nerve stimulation and neurological disorders, including self-biting behaviour, in mink.

The obligate biotrophic fungus Phakopsora pachyrhizi Syd. & P. Syd., the causal agent of soybean rust, is among the most formidable pathogens of soybean (Glycine max [L.] Merr.). The pathogen is now established in all major soybean-growing areas of the world and presents a significant impediment to global soybean production. Most soybean germplasm is susceptible, enabling the fungus to penetrate and colonize the leaf tissue, causing tan-colored necrotic lesions to form at the site of infection. Severe infection reduces photosynthesis and causes premature defoliation, which ultimately decreases crop yield and seed quality. Eight genetic loci, Rpp1/Rpp1b to Rpp7 and Rpp6907, that confer race-specific resistance to P. pachyrhizi (Rpp) have been identified. Rpp2 was identified and characterized in the soybean accession PI 230970 and fine-mapped to a 188.1-kb interval on chromosome 16, a region predicted to contain several toll/interleukin-1 receptor nucleotide-binding leucine-rich repeat (TIR-NLR) genes. To identify Rpp2, we constructed a bacterial artificial chromosome (BAC) library from the resistant soybean accession PI 230970. Sequencing BACs that span the Rpp2 locus identified 14 candidate genes with homology to the TIR-NLR family of resistance genes. Of these, seven are predicted to encode full-length R proteins. Co-silencing the Rpp2 candidate genes compromised resistance in soybean accession PI 230970. Gene expression analysis suggests that a single gene, Rpp2C7_PI, which shares the greatest homology to Rpp2C6_Wms82 (Glyma.16G136600) in the Williams 82 reference genome, is responsible for Rpp2-mediated resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.

ProteinNetworkSight (https://proteinnetworksight.jce.ac) addresses a pervasive bottleneck in modern systems biology: the inability to simultaneously analyze multiple feature vectors generated by quantitative techniques-such as machine learning, deep learning, or statistical modeling-that provide series of patterns in a dataset. Modern computational pipelines, ranging from PCA to deep autoencoders, rarely identify a single gene list; instead, they extract a series of distinct patterns representing diverse patient subgroups or independent components. Current web servers are ill-equipped for this high-dimensional reality, forcing researchers to analyze vectors one-by-one or merge them into a static consensus, obliterating unique topological signatures. ProteinNetworkSight introduces a novel web server architecture for simultaneous multi-pattern analysis. Unlike standard tools, our server accepts multi-column tables and transforms every input vector into a discrete, interactive protein-protein interaction network in a single run. This batch vector architecture allows side-by-side visualization of distinct topologies, preserving disease heterogeneity. Furthermore, the server enables prescriptive intervention by calculating a composite perturbation score to identify key protein nodes specific to each pattern. By mapping FDA-approved anti-cancer drugs to these targets, it facilitates the rapid design of personalized combinatorial therapies.

Genetic and epigenetic predictors of antidepressant response.

With the continuous advancement of research on life systems and disease mechanisms, analytical technologies are now moving toward the resolution of single molecules and individual genes. Among them, surface-enhanced Raman scattering (SERS) has garnered widespread interest because of its ultrahigh sensitivity, allowing even single-molecule detection. When integrated with microfluidics, SERS-based platforms combine the strengths of both techniques, offering complementary and synergistic effects. This integration enables rapid, non-invasive, ultrasensitive, and high-throughput analysis of biological samples, which is highly valuable for biomedical research and potential clinical applications. Consequently, this interdisciplinary approach has emerged as a major focus of current investigations. In this review, we outline recent developments and applications of microfluidic SERS systems in bioanalysis. The discussion first introduces the basic concepts and classifications of SERS-microfluidic strategies, such as continuous-flow, microarray, droplet-based, lateral flow assay (LFA), and digital formats. We then highlight their applications in biomolecular detection, cellular analysis, and disease diagnostics. Overall, the evidence suggests that microfluidic SERS platforms represent a powerful and promising tool for advancing bioanalytical science.

Komagataella phaffii (K. phaffii) is used to manufacture biologic medicines, food proteins, reagents, and materials. Despite its increasing prevalence, further improvements to its productivity would enhance its economic and operational benefits. Genomic engineering represents one approach to increase its cell-specific productivity. We hypothesized that combining the metrics for the relative essentiality of genes with biological inference for relevance to protein secretion could identify genes that, when disrupted, would improve specific productivity in the resulting strains. The essentiality of genes in K. phaffii (NRRL Y-11430) were predicted through a genome-wide knockout screen using CRISPR-Cas9. Based on the results from this screen, we selected and subsequently disrupted the least essential genes from two gene groups heavily associated with secretion, namely those relating to the cell wall and vacuolar transport. Strains of K. phaffii with single gene disruptions from these gene sets showed significantly improved production of a monoclonal antibody (mAb). These strains exhibited no discernible differences in growth or apparent profiles of host cell proteins when compared to the parental strain. The best-performing strains consistently showed 2-3x enhancements in specific productivity and titers across scales (3-150 mL), culture formats (plates, flasks, bioreactors), and processing operations (batch and fed-batch). This study demonstrates how combining data on gene essentiality and prior knowledge of biological pathways related to a phenotypic trait of interest (here protein secretion) can inform strain engineering to enhance the trait. This study expands the catalog of genetically engineered strains of K. phaffii with improved productivity. These strains support the long-term goal of achieving low-cost, high-volume production of recombinant proteins using this host. Further engineering of these strains and optimization of fermentation processes could enable volumetric productivities comparable to those of other established hosts used to produce mAbs and other complex recombinant proteins.

Aphids are among the most damaging pests in agriculture. Under environmental stress, aphids can transition from a wingless to a winged morph. Wingless aphids maximize local reproduction, while winged aphids facilitate rapid, long-distance dispersal, increase plant virus transmission, and promote the spread of insecticide resistance genes within populations. However, the mechanisms regulating wing polyphenism in Rhopalosiphum padi, one of the most destructive cereal pests worldwide, remain poorly understood. Crowding stress induced by high-density conditions can trigger the transition of R. padi from wingless to winged. Twenty-six ABCG genes were identified and classified into five subfamilies. Under high-density conditions, a single ABCG transporter gene, ABCG23-4, was upregulated. RNA interference (RNAi)-mediated knockdown of this crowding-responsive target effectively disrupted the wing polyphenism decision. RNAi-mediated knockdown of ABCG23-4, accomplished through either direct application of dsRNA or the use of nanomaterial-based carriers, significantly decreased the proportion of winged offspring during the first 2 days following crowding. Hormone assays further demonstrated that the knockdown of ABCG23-4 led to reductions in both insulin and 20-hydroxyecdysone titers. These results identify ABCG23-4 as a critical regulator of density-induced wing polyphenism and a promising RNAi target for limiting dispersal and population growth of R. padi, thereby offering new opportunities for integrating molecular tools into sustainable aphid management strategies. © 2026 Society of Chemical Industry.

Cold stress at the booting stage severely disrupts pollen development and drastically reduces grain yield in rice. Uncovering the genetic basis of cold tolerance is essential for breeding resilient varieties. Here, we identified a cold‑sensitive mutant, csb1, from an EMS‑mutagenized population of the cold‑tolerant japonica variety MK1, which exhibits significantly impaired seed‑setting under cold stress. Genetic analysis indicated that the phenotype is controlled by a single recessive nuclear gene. Using MutMap, we mapped the causal locus to a 26.3-27.0Mb interval on chromosome 8. Among candidate genes, OsPPR7, encoding a PLS‑class pentatricopeptide repeat (PPR) protein, showed strong cold‑induced expression in anthers. A promoter mutation in OsPPR7 was linked to the csb1 phenotype, as confirmed by genetic complementation. CRISPR/Cas9 knockout lines displayed increased cold sensitivity and severe pollen sterility, whereas overexpression enhanced tolerance. Cytological observations revealed that loss of OsPPR7 leads to defective anther development, abnormal pollen nuclei, and failed germination under cold stress. Mechanistically, OsPPR7, localized to mitochondria, regulates cold tolerance by fine‑tuning abscisic acid (ABA) biosynthesis and reactive oxygen species (ROS) homeostasis in young panicles. Haplotype analysis across diverse germplasm identified natural variation in OsPPR7, with the superior cold‑tolerant haplotype Hap_I showing strong selective sweep signals in temperate japonica rice, indicating its role in adaptation to high‑latitude environments. Our study identifies OsPPR7 as a novel positive regulator of reproductive stage cold tolerance and provides a valuable genetic target for improving rice climate resilience.