Search Results (12,784)

Chemical agents have long been used to control plant diseases, but their effects on the environment and lack of alignment with sustainable development goals are making them gradually unsuitable. One trend in green agriculture is the use of Bacillus species for the biocontrol of plant diseases. Due to their vast metabolic and genetic diversity, Bacillus spp. can contribute significantly to the soil ecosystem, while also enhancing plant resilience to biotic and abiotic stresses. Bacillus spp. are widely used in the agrobiotech industry due to their multi-functional versatility and are well-known for protecting plants from numerous plant diseases. In this review, we discussed the diversity and functions of antimicrobial compounds (AMCs) produced by Bacillus spp., along with their roles in plant growth promotion (PGP), and immunity. Furthermore, we highlighted the potential of Bacillus spp. as biopesticides in host plants, ways to enhance their biocontrol efficacy, and also addressed their possibility to cause disease in host plants. Considering the beneficial impacts of Bacillus spp. on PGP and pathogen biocontrol and their disease-causing capability, we discussed the possible solutions for a safe development of Bacillus-based biocontrol agent (BCA). Collectively, these insights can guide the selection of Bacillus strains with broad-spectrum or target-specific activity against pathogens, ensuring minimal adverse effects on the host. Full article

Background/Objectives: Obesity remains a global health concern, and personalized prevention strategies that consider genetic predispositions can enhance existing strategies. Research suggests that variation in circadian rhythm-related genes, or clock genes, may influence obesity risk, in part through effects on dietary behaviour. However, associations between single-nucleotide polymorphisms (SNPs) in clock genes and dietary outcomes remain understudied, particularly in children. Therefore, we investigated cross-sectional associations between clock gene SNPs and dietary outcomes using baseline data from 226 adults (138 females, 88 males) aged 26–50 y and 168 children (90 females, 78 males) aged 2–6 y from the Guelph Family Health Study. Methods: DNA was extracted from saliva and genotyped using the Illumina Global Diversity Array, and dietary intake was assessed using the Automated Self-Administered 24 h Dietary Assessment Tool. Nine SNPs representing 8 clock genes were selected based on prior associations with dietary and obesity-related outcomes. Generalized Estimating Equations were used to test associations, adjusted for multiple comparisons with the Benjamini–Hochberg false discovery rate (FDR) procedure. Results: Ten nominal associations were identified (p < 0.05), and 2 remained significant after FDR correction (P_adj < 0.05); among children, rs2314339-T (NR1D1) was associated with a lower percentage of energy from protein (β = −2.4%, P_adj = 0.003) and rs11605924-A (CRY2) with higher energy intake (β = 118.0 kcal, P_adj = 0.044). Conclusions: Findings suggest that clock gene SNPs may influence dietary habits from early childhood. Future longitudinal and functional studies are needed to clarify whether these variants can inform precision nutrition strategies for obesity prevention. Full article

Type 1 Diabetes (T1D) is a complex autoimmune disorder characterized by immune-mediated destruction of pancreatic β cells, driven by genetic susceptibility and modulated by environmental factors, notably the gut microbiome. Dysbiosis, manifested as reduced microbial diversity, perturbations in the Firmicutes/Bacteroidetes ratio, and compromised short-chain fatty acid production, contributes to T1D pathogenesis through mechanisms involving immune system dysregulation and heightened intestinal permeability. Emerging evidence indicates a relationship between the gut and oral microbiomes, as well as the potential influence of the virome and mycobiome. This narrative review synthesizes the current literature on the intricate interplay between the gut microbial ecosystem, the host immune response, and the development of T1D, highlighting the potential for targeted microbiome-based interventions to ameliorate disease progression. A more nuanced understanding of these multi-kingdom interactions is essential for developing precise therapeutic strategies to prevent or delay T1D onset and to improve patient outcomes through restoration of immune tolerance and gut homeostasis. Full article

The genus Tulipa L. is a common group of ornamental plants, characterized by high morphological variability and a complex taxonomy. Despite considerable interest in this group, assessments of its species composition remain inconclusive, as evidenced by discrepancies between contemporary taxonomic sources. The number of recognized taxa varies across major taxonomic databases, including Plants of the World Online, World Flora Online, and Euro+Med PlantBase, reflecting ongoing taxonomic revisions and differences in species concepts. In terms of distribution patterns, 7.6% are widely distributed taxa across transcontinental regions, 28.0% occur across multiple countries within a continent, and 66.9% are range-restricted taxa. The latter group includes 4.2% transnational endemics, 44.1% single-country endemics, 8.5% single-region endemics, and 10.2% single-site endemics. Recent taxonomic and evolutionary studies of Tulipa increasingly rely on molecular approaches, particularly DNA barcoding and chloroplast genome analyses, which have improved phylogenetic resolution and species delimitation in several cases. However, truly comprehensive studies combining morphological, cytogenetic, and molecular datasets remain limited and are typically restricted to individual taxa or species complexes rather than the genus as a whole. Modern molecular genetic studies demonstrate the high informativeness of both nuclear and plastid markers for studying the phylogeny, systematics, and genetic diversity of Tulipa species. Natural populations of Tulipa are under pressure from anthropogenic factors and climate change, resulting in reduced range and habitat degradation. According to the International Union for Conservation of Nature Red List of Threatened Species, among 118 taxa of the genus Tulipa, T. sprengeri Baker is classified as Extinct in the Wild, 5.9% as Critically Endangered, 5.9% as Endangered, 8.5% as Vulnerable, 11.9% as Near Threatened, and 11.0% as Least Concern. The use of exclusively national assessments to determine species extinction risk may be insufficiently objective, whereas global assessments provide a more informative and reliable approach for evaluating conservation status. In this review, we combine investigations of the morphology, taxonomy, and geographic diversity; population genetic structure and molecular diversity; and molecular phylogenetics and plastome-based genomics of the genus Tulipa. Furthermore, the review examines current challenges and future research prospects, emphasizing that studies of the genus Tulipa should integrate morphological, genomic, and ecological approaches to refine taxonomy and conserve genetic resources. Full article

Introduction: Stenotrophomonas maltophilia (S. maltophilia) has emerged as an important opportunistic pathogen. It is resistant to most available antibiotics due to its intrinsic resistance, leaving only some antibacterial agents as possible therapeutic options, which is further complicated by acquired mechanisms of antimicrobial resistance. This study aimed to provide a comprehensive genomic characterization of clinical S. maltophilia complex (Smc) isolates, focusing on molecular characterization of its resistance and virulence, since studies tackling this are scarce in Oman. Methods: This study is a prospective cross-sectional study, in which a total of 21 clinical isolates of Smc were collected from different clinical samples and further characterized using Whole Genome Sequencing. Results: Besides S. maltophilia, the isolates included S. hibiscicola, S. pavanii, and S. muris for the first time in Oman. All isolates were found to be susceptible to cefiderocol, levofloxacin, and minocycline. Sequence types (STs) were diverse among the isolates, with more than half of the isolates showing new STs with novel alleles. Additionally, blaOXA-2, sul1, and the recently described aac(6′)-Iap and aph(9)-Ic were detected among the isolates. Moreover, virulence-associated genes (smf-1, pilT, pilQ, gpmA, rmlA, spgM, stmPr1, plcN, clpP, and katE) were highly conserved across all isolates. Mobile genetic elements were detected in most of the isolates (76.20%). Conclusions: The collected isolates showed high ST diversity and showed no specific pattern in terms of antibiotic susceptibility and resistance genes. More studies are needed to establish relationships between the different members of the Smc and the different molecular resistome and virulome. Full article

Background/Objectives: Popcorn (Zea mays L. var. everta) is an important specialty maize type; however, the genetic variation underlying popping-related quality traits remains insufficiently characterized in breeding. Methods: In this study, 18 popcorn inbred lines were analyzed using 25 simple sequence repeat (SSR) markers distributed across all 10 maize chromosomes, and 16 lines were further evaluated for popping performance and image-based flake morphology. Results: Substantial phenotypic variation was observed among the tested lines, with expansion volume ranging from 173.33 to 343.33 mL and expandability ranging from 16.79- to 32.46-fold. Image-based analysis of 957 popped kernels revealed continuous variation in flake circularity, indicating that flake morphology represents a quantitative trait rather than a strictly discrete classification. SSR analysis detected 2 to 11 alleles per locus, with polymorphism information content values ranging from 0.05 to 0.85, indicating moderate-to-high genetic diversity among the tested lines. Principal component analysis (PCA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and population structure analysis revealed clear genetic differentiation and heterogeneous genetic backgrounds within the germplasm collection. Marker–trait association analysis identified several putative SSR loci associated with expansion efficiency, flake morphology, pericarp retention, and popping dynamics. Notably, marker M18 was putatively associated with both expansion volume and expandability. Conclusions: Based on these results, a conceptual framework was proposed in which popping-related traits were organized into partially independent but interconnected functional modules. Overall, this study provides SSR-based genetic information for popcorn germplasm characterization and offers preliminary marker resources for quality-oriented popcorn breeding. Full article

Herein we reply to the commentary of Cowman et al. on our Review of Coral Taxonomy, Evolution, and Diversity. We demonstrate that many of their central criticisms are mischaracterisations, contain factual errors, or extend beyond the evidentiary scope of available molecular datasets. Our Review did not dismiss the legitimacy or importance of molecular approaches, nor the value of integrative taxonomy. Rather, it emphasised the evidentiary thresholds required for formal species-level revision in morphologically variable and geographically widespread coral taxa. Genetic differentiation should not, without comprehensive sampling and contextualisation, be treated as sufficient grounds for immediate species-level restructuring. We reiterate that the concept of reticulate evolution in corals is supported by a growing body of molecular and other evidence. Furthermore, the “biological entities” discussed in our Review are not subjective impressions or non-reproducible opinions but are empirically documented, repeatedly recognisable, and diagnosable, characterised by coherent suites of morphological, ecological and geographic traits. These constitute structured, testable species hypotheses within an integrative framework. Our Reply addresses issues of field variability, type specimens, sampling design, molecular and morphological incongruence, and the taxonomic and conservation implications of premature rank assignment. Where multiple, independent lines of evidence converge, taxonomic revision is warranted; where sampling remains limited, geographically restricted, or analytically unstable, and where different lines of evidence conflict, nomenclatural stability and biological coherence are better served by restraint. Full article

Forensic biotechnology is a rapidly evolving interdisciplinary field integrating molecular biology, genomics, and data science to address complex investigative challenges. Its applications span diverse domains, including criminalistics, food authentication, environmental monitoring, and bioterrorism preparedness. Advanced technologies such as Next-Generation Sequencing (NGS), CRISPR-Cas biosensors, and Artificial Intelligence (AI) play pivotal roles in modern diagnostics. NGS and eDNA revolutionize genetic profiling and ecological tracking, while microbiome analysis provides crucial insights into post-mortem intervals, cause of death, and geolocation. Simultaneously, CRISPR-based methods enable ultra-rapid pathogen detection, nanobiotechnology facilitates portable Lab-on-a-Chip (LOC) DNA analysis, and AI-driven algorithms optimize the interpretation of complex genomic mixtures and epigenetic age estimation. Despite these breakthroughs, significant challenges persist, including the strict legal admissibility of novel methodologies, the “black-box” dilemma in AI, ethical concerns regarding genetic privacy, and the critical need for global standardization. This review critically examines current biotechnological progress and future prospects, emphasizing the necessity of interdisciplinary collaboration to ensure reliable, accurate, and ethically sound forensic practices. Full article

Background: Homologous recombination deficiency (HRD) is emerging as a clinically relevant biomarker across diverse tumor types, in addition to ovarian cancer. In this study, we evaluated the genomic instability score (GIS) across multiple tumor types using the TruSight Oncology 500 HRD assay, which incorporates the Myriad Genetics GIS algorithm, a widely used reference standard for HRD assessment. Methods: A total of 162 tumor samples (17 ovarian cancers and 145 non-ovarian tumors) underwent next-generation sequencing using the TruSight Oncology 500 HRD assay. Results: A total of 14 tumors were classified as GIS-High, defined as a GIS score ≥42, representing 8.6% of all cases. Among ovarian cancers, 7 out of 17 cases (41.2%) met the GIS-High threshold. Among non-ovarian tumors, seven GIS-High tumors were identified, accounting for 4.8% of cases (7/145). GIS-High cases occurred in breast (n = 4), lung (n = 2), and hepatobiliary tract (n = 1) cancers. GIS scores showed significant associations with BRCA1/2 and TP53 mutational status. In contrast, alterations in HRD-related genes other than BRCA1/2 did not show significant associations with GIS score. Conclusions: GIS-High tumors were identified in a small subset of non-ovarian cancers. These findings support further investigation of GIS as an exploratory biomarker of HRD-like genomic scarring beyond ovarian cancer, but its predictive and therapeutic relevance in non-ovarian tumors requires additional validation. Full article

The family of uterine mesenchymal neoplasms is diverse in etiology and clinical impact. While histomorphology remains central to diagnostic classification, numerous biomarkers have been developed to aid in refining diagnoses and informing optimal treatment strategies. Indeed, a growing number of neoplasms are being primarily classified on the basis of key pathognomonic genetic events, and this number is expected to continue expanding as access to next-generation sequencing rapidly democratizes. Moreover, several quantitative biomarker tests have been developed to aid in the prognostic stratification of tumours with ambiguous morphologic features, providing critical insights to clinicians seeking optimal oncologic management while minimizing unnecessary treatment morbidity. In this review, we discuss key advances in the utilization of biomarkers for diagnostic classification, prognostication, and the prediction of response to targeted therapeutics in uterine mesenchymal neoplasms, with the aim of highlighting the most clinically impactful biomarkers used by pathologists to enhance the clinical care of patients. Full article

Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are conserved microbial proteins that contain immunogenic patterns capable of activating plant pattern-triggered immunity (PTI). NLP patterns from Sclerotinia sclerotiorum (SsNLPs), a destructive necrotrophic fungal pathogen with a broad host range, have been identified, and their roles in PTI have been revealed. Nevertheless, the molecular mechanisms by which SsNLPs stimulate plant immunity remain largely unknown. In this study, we phylogenetically characterized SsNLPs and demonstrated the involvement of the phytocytokine receptor-like kinases PEPRs in SsNLP1-triggered immunity. SsNLPs contained the NPP1 domain and GHRHDWE motif and were phylogenetically closely associated with Botrytis cinerea NLPs. SsNLP1 treatment strongly induced the expression of PEPR genes. Further genetic analyses using Arabidopsis wild-type, pepr1 pepr2 double mutant, and PEPR1 overexpression lines showed that SsNLP1 elicited diverse immune responses, including reactive oxygen species (ROS) accumulation and defense gene activation, and induced plant resistance to S. sclerotiorum. Notably, the induced plant resistance and immune responses were strengthened in PEPR1 overexpression lines and significantly reduced in the pepr1 pepr2 mutant, indicating a positive role of PEPR signaling in SsNLP1-triggered immunity. Overall, our results revealed that phytocytokine PEPR1 signaling amplifies PAMP SsNLP1-triggered immunity, thereby enhancing resistance against S. sclerotiorum. Our findings provide an example of the coordination between PAMP- and phytocytokine-triggered immunity for robust resistance to a necrotrophic pathogen. Full article

Egg production in Gallus gallus domesticus represents a complex, economically critical trait shaped by multiple interrelated phenotypes, including age at first egg, total egg number, egg weight, and clutch characteristics. These traits are governed by polygenic inheritance and modulated by environmental factors, making the dissection of their genetic architecture essential for improving breeding efficiency, particularly under the emerging “long-life layers” production model. This systematic review aimed to integrate current knowledge on the genetic and molecular basis of egg production traits through analysis of genome-wide association studies and related genomic approaches. A structured literature search identified 27 eligible studies, which were evaluated following PRISMA guidelines. Data extraction and meta-analysis were conducted using standardized genome annotations and computational pipelines. The synthesis of available evidence demonstrates moderate to high heritability for key reproductive traits and highlights consistent genomic signals across multiple chromosomes. Importantly, the findings reveal a shift toward a systems-level understanding of egg production, involving conserved biological pathways related to neuroendocrine regulation, folliculogenesis, and energy metabolism. The integration of diverse genomic approaches enables the development of more precise, breed-specific selection strategies. Overall, these advances support a transition from traditional selection toward molecularly informed breeding frameworks, with significant implications for productivity, sustainability, and global food security. Full article

Massive Open Online Courses (MOOCs) have expanded access to education, but many courses continue to face problems such as learner dropout and uneven engagement. One reason is that course updates are not always guided by learner feedback. This study examines how learner feedback can support systematic MOOC updates. An optimisation framework is proposed to help instructors decide which course elements to revise under limited time and effort. The framework considers three aspects: learner value, instructor effort, and diversity of updates. Survey responses were collected from 437 learners enrolled in the July 2025 offering of the Introduction to Cyber Security MOOC on SWAYAM. Based on this feedback, 26 candidate updates were identified and described using learner value, effort, and category. The Non-Dominated Sorting Genetic Algorithm II (NSGA-II) was applied under five effort budgets (8–16 units) to generate alternative update plans. The results show that learner value increases rapidly at lower effort levels but slows beyond 12 effort units. Diversity also improves initially and then stabilises. Comparison with a greedy method and an instructor-designed plan shows that the optimisation approach produces more balanced update decisions. The study shows that structured optimisation can support clear and evidence-based MOOC revision. Full article

Phytoplasmas are a group of wall-less, unculturable prokaryotic pathogenic bacteria that colonize the phloem of plants and are transmitted by piercing–sucking insects. As a typical tropical island province in China, Hainan Island has abundant biodiversity due to its unique geographical location and climatic conditions, which provide a favorable ecological environment for the survival and propagation of phytoplasmas, which infect different hosts, cause different symptoms, or belong to different subgroups. Based on host species, disease symptoms and 16Sr subgroups, 69 representative phytoplasma records from four 16Sr groups have been identified on Hainan Island, showing rich diversity in host range and pathogen species. The diversity of plant hosts and the evolutionary relationship of phytoplasmas not only affect the occurrence and prevalence of phytoplasma-related diseases but also bring great challenges to the epidemic monitoring, detection, diagnosis and prevention management of these diseases. This review summarizes current research progress on host diversity, phylogenetic evolution, mixed infection, diversity of transmission vectors, and geographical isolation differentiation, as well as adaptive evolution of phytoplasmas on Hainan Island. Furthermore, the challenges brought by plant host diversity and phylogenetic evolution to disease monitoring, diagnosis and prevention management are discussed. This review aims to provide a comprehensive theoretical basis for the in-depth study of phytoplasma-related diseases on Hainan Island, and to offer practical guidance for scientific monitoring, early warning and comprehensive prevention and control of these diseases. Full article

The systematics of white-tailed deer (Odocoileus virginianus) has been controversial. Some mammalogists consider the white-tailed deer to be a single species, whereas others consider it to consist of multiple species. To help resolve the controversy, we sequenced mitochondrial cytochrome B (mtCyt-b) in samples collected from 83 Neotropical white-tailed deer. Furthermore, we analyzed mitogenomes of samples collected from 19 white-tailed deer. There were five main results, as follows: (1) Phylogenetic analyses with the mtCyt-b dataset showed the existence of eight groups of O. virginianus, three in North and Central America and five in South America. It was hypothesized from different analyses that a Central American O. virginianus population generated the white-tailed deer populations in South America. (2) The haplotype temporal diversification within O. virginianus occurred during the Pleistocene. With the mitogenome dataset, it was dated to have occurred approximately 2.2 mya, using both Bayesian inference and haplotype networks. (3) All of these O. virginianus groups showed elevated levels of mitochondrial genetic diversity for the mtCyt-b dataset, with the exception of the Ecuadorian population (4) Some groups of O. virginianus yielded significant evidence of female population expansions with the mtCyt-b dataset. (5) Although the genetic heterogeneity among these O. virginianus groups was significant, the genetic distances were relatively small. Provisionally, the karyotypic differences between North American and Colombian specimens were very small; therefore, until further karyotypic studies demonstrate otherwise, we consider the existence of a single species of O. virginianus. Because mtDNA genomes have only one quarter of the effective number of autosomal nuclear genes, this generates relatively rapid coalescence times, which can inflate estimates of divergence among populations. Therefore, it is very important to soon sequence the nuclear genes for the different geographic assemblages of O. virginianus found. Full article