Search Results (4,525)

Rotavirus is a leading cause of severe, dehydrating diarrhea in infants and young animals, causing significant global morbidity and mortality. For decades, research was hindered by challenges in establishing reverse genetics systems due to the virus’s complex segmented genome and poor cell culture adaptation. The first helper virus-dependent system (2006) was limited by low efficiency. A 2017 breakthrough established the first fully plasmid-based system, which eliminated helper viruses and revolutionized the field. Subsequent optimizations, such as codon modification and CRISPR/Cas9 integration, have significantly enhanced efficiency, enabling viable systems for diverse human and animal strains. This narrative review summarizes the evolution and technological milestones of rotavirus reverse genetics. We discuss critical applications in analyzing viral gene function, developing novel vaccines, screening antiviral drugs, and investigating cross-species transmission. Finally, we provide an outlook on the future prospects of this transformative technology. Full article

The tire track eel (Mastacembelus favus) is a freshwater fish with high economic value and aquaculture potential. However, its sex determination mechanism remains unclear, which limits the development of monosex culture and sex-controlled breeding. To address this, preliminary female and male reference genomes were generated using second-generation sequencing, followed by whole-genome resequencing of four females and four males. Comparative analyses identified 69 male-specific sequences, with a total length of approximately 44.5 kb. Based on these sequences, two PCR-based sex-specific markers (W5 and W14) were developed. Both markers showed complete concordance with phenotypic sex in parental and offspring from controlled crosses populations, providing strong evidence for a male heterogametic (XY) sex determination system in M. favus. Although the markers were not transferable to the closely related species Mastacembelus armatus, the corresponding male-specific sequences exhibited high genomic conservation. In conclusion, this study provides reliable molecular tools for genetic sex identification in M. favus. These tools will support monosex aquaculture and sex-controlled breeding programs, while also offering insights into sex determination and sex chromosome evolution in the genus Mastacembelus. Full article

Background: Three-finger toxins (3FTxs) are a major axis of functional diversification in advanced snake venoms, with canonical paralytic activity mediated through muscle-type nicotinic acetylcholine receptors (nAChRs) and a broader set of non-nicotinic targets. This review integrates evidence bearing on coevolution between 3FTxs and target receptors, spanning toxin origin, diversification, receptor evolution, and ecological context. Methods: The synthesis draws on comparative genomic and transcriptomic studies of 3FTx gene-family evolution, codon-model analyses of selection, structural characterisation of toxin–receptor interfaces, and functional assays (including receptor-mimicking peptide binding) that link sequence variation to binding and toxicity. Results: Across lineages, 3FTx diversification is repeatedly structured by strong constraint on the disulphide-rich scaffold with accelerated change concentrated in solvent-exposed loops, alongside birth–death dynamics and exon/segment-level innovation that expand binding specificity. On the receptor side, resistance-associated variation is most intensively characterised for the nAChR α₁ orthosteric site and includes convergent, mechanistically distinct solutions such as electrostatic repulsion and glycosylation-mediated steric interference. Within the predominantly elapid systems currently examined, integrative datasets indicate that prey-selective binding and geographically variable susceptibility can arise from modest substitutions at toxin–receptor interfaces, but they also reveal substantial taxonomic and target-specific biases. Conclusions: Current evidence supports adaptive diversification in both toxins and receptors, while broader evolutionary interpretations are limited by uneven sampling and the frequent lack of matched toxin and receptor variants analysed within a common evolutionary framework. Development of predictive models will require joint pipelines linking genomics, structure-informed evolutionary inference, scalable functional assays, and explicit ecological network context. Full article

Chemosensory proteins (CSPs) are found in the olfactory sensory organs (antennae and maxillary palps) and/or gustatory sensory organs (labellum and legs) and have long been accepted to function through the binding of odorants. However, the same CSPs are also expressed in many tissues other than olfactory and gustatory organs, such as the gut, brain, fat body, wing, epidermis, Corpora allata, salivary gland, pheromone gland, prothoracic gland, etc. In this report, we suggest renaming the “chemosensory protein (CSP)” the “4-Cysteine Soluble Protein (4CSP)”. This paradigm and nomenclature shift is based on molecular characteristics, genomic mining, tissue distribution, and functional roles beyond those related to olfaction. We examined prior studies on this protein gene family to bolster the renaming, highlighting the most recent findings that we ascribe to “pleiotropic properties” and evolutionary relevance rather than smell. The scope of the report, per se, is broad, and this is especially true given the volume of data that has been gathered on 4CSP expressed in ways that are not consistent with the olfactory paradigm. Statements outlining the many chemosensory properties of 4CSPs, particularly how they activate olfactory receptor neurons (ORNs), are currently scarce, if they exist at all. Many debates currently focus on 4CSPs’ non-chemosensory functions, which are backed by a multitude of evidence, from gene evolution to tissue distribution. Therefore, strong arguments in favor of renaming chemosensory proteins are becoming evident here, outweighing the drawbacks. Full article

Elsinoe fawcettii is a devastating citrus pathogen worldwide, yet high-quality genomic resources are lacking, limiting insights into its adaptive mechanisms. Seventeen strains collected from 13 host species across 5 Chinese provinces were confirmed as E. fawcettii by multi-loci (ITS, rpb2, tef1-α) phylogenetic and morphological analyses. A near-telomere-to-telomere (near-T2T) genome for representative strain FJ-Y-3 was constructed using integrated PacBio and Hi-C sequencing. The 24.40 Mb assembly was organized into 11 chromosomes with exceptional completeness (BUSCO: 97.1%) and continuity (scaffold N50: 2.18 Mb). Pan-genome analysis revealed a closed structure, with core genes representing 77.19% of the total, suggesting evolutionary adaptation through fine-regulation of conserved elements rather than extensive gene content variation. Accessory genes were significantly enriched in terpenoid/polyketide metabolism, cell surface remodeling, and xenobiotic degradation, underscoring metabolic plasticity. Whole-genome resequencing showed single-nucleotide polymorphisms as the dominant variant, with ~60% residing in regulatory regions, implicating cis-regulation as a key adaptive mechanism. This work provides a high-quality genome and multi-omics framework for E. fawcettii, establishing a crucial molecular foundation for understanding pathogen adaptation and developing sustainable disease management strategies. Full article

Hot springs represent unique geothermal ecosystems where extreme physicochemical conditions intersect with remarkable microbial diversity and metabolic innovation. These natural laboratories harbor specialized communities of thermophilic and hyperthermophilic microorganisms that have evolved exceptional adaptations to elevated temperatures, extreme pH, and high salinity. This review synthesizes current understanding of hot spring systems as multifunctional natural resources, examining their roles in fundamental microbiology, biotechnology, and sustainable development. We explore the ecological principles governing microbial community assembly, the taxonomic and functional diversity of prokaryotic and eukaryotic microorganisms, and the genomic mechanisms underlying thermophilic adaptation. Hot springs yield enzymes revolutionizing molecular biology and industrial catalysis, bioactive metabolites with pharmaceutical potential, and novel bioremediation capabilities including plastic degradation. Beyond biological significance, these systems contain valuable minerals and rare earth elements, supporting an emerging bioeconomy integrating wellness tourism, bioprospecting, and sustainable resource extraction. However, critical knowledge gaps remain regarding viral ecology, horizontal gene transfer, eukaryotic diversity, and climate change impacts. We emphasize that hot springs merit renewed interdisciplinary attention as model systems for understanding extremophile physiology, early life evolution, and the development of nature-based biotechnological solutions. Realizing their full potential requires balanced management strategies that preserve ecosystem integrity while enabling responsible utilization of these irreplaceable geobiological resources. Full article

The post-genomic era has transformed medical genetics, raising renewed debate over the role of medical cytogenetics in clinical practice. High-throughput sequencing and chromosomal microarray technologies now dominate cancer diagnostics, prenatal testing, and rare disease evaluation by enabling rapid detection of gene-level variation, often leading to the perception that cytogenetics is obsolete. However, this view overlooks the unique and complementary strengths of cytogenetic analysis. Although the relationship between cytogenetics and current NGS technologies can be compared to that between forests and trees versus leaves—both of which are necessary for clinical diagnosis—cytogenetic methods uniquely enable direct in situ visualization of chromosomes, allowing detection of large-scale structural and numerical genome alterations at the level of individual cells and cell populations. These system-level features that are frequently invisible or difficult to interpret using sequencing-based approaches alone yet are critical in disease contexts where genome architecture itself carries biological and clinical significance beyond individual genes. This article, therefore, advances a new perspective based on Genome Architecture Theory: that karyotype-level information organizes gene-level function and that many previous gene-centric genetic concepts require reexamination within a unified framework of clinical genomics. Rather than being replaced, cytogenetics is increasingly integrated with sequencing within a unified framework of clinical genomics that combines high-resolution molecular detail with system-level insight into genome organization. Reassessing the role of cytogenetics, therefore, has important implications for medical education, diagnostic strategy, and healthcare policy, as cytogenetics provides the appropriate platform for understanding system-level inheritance through karyotype coding and for advancing molecular medicine from a genome systems perspective. Full article

The silkworm (Bombyx mori) is essential to sericulture and is also becoming a key model organism in genomics and agriculture. For decades, genetic studies of the silkworm were limited by inefficient and inflexible genome tools. CRISPR genome editing allows precise and scalable alterations to genes regulating development, physiology, and industrial traits. This review summarizes silkworm genome-editing breakthroughs, highlighting CRISPR’s evolution from simple gene knockouts to large-scale genome-wide screening. We highlight how these advancements contribute to disease resistance, higher yields, and the development of new silk-based materials, as well as how they influence the development and growth rate of the sericulture. The creation of high-quality reference genomes, pangenomes, and genome-wide screening systems has made the silkworm a major model for integrating multiple biological datasets and approaches, such as genomic, transcriptomic, and proteomic. By considering the unique biological characteristics of the silkworm, this provides new insights for research on silk biology, piRNA synthetic biology, and hormonal signaling regulation. Finally, we examine new areas at the intersection of CRISPR, pangenomics, and artificial intelligence (AI) and suggest future paths for molecular breeding, pest control, and synthetic biology. Moreover, AI-assisted prediction of CRISPR outcomes is utilized to inform the design of targeted trait modifications, representing an approach to enhancing biomanufacturing efficiency and eco-friendly silk production. Together, these advances have made the silkworm a flexible genetic platform and an important part of sustainable agriculture and biomanufacturing. Full article

Background: Gastric biopsy remains central to diagnosing Helicobacter pylori infection, autoimmune gastritis, intestinal metaplasia, dysplasia, and gastric cancer. However, morphology-based assessment is limited by interobserver variability, sampling constraints, and an incomplete ability to capture molecular heterogeneity and predict progression. Objective: This mini review summarizes how multi-omics technologies and artificial intelligence (AI) are modernizing gastric biopsy diagnostics, enabling precision classification, risk stratification, and workflow improvement. Methods: A narrative synthesis was undertaken across key literature on gastric pathology, multi-omics (genomics, transcriptomics, epigenomics, proteomics, lipidomics, metabolomics, microbiomics, and spatial approaches), and AI in endoscopy and computational pathology. Results: Multi-omics profiling enhances mechanistic understanding and refines disease classification by capturing clonal evolution, pathway dysregulation, immune–microenvironment interactions, and metabolic remodeling, with potential for biomarker discovery and therapy prediction. AI applications demonstrate strong performance across the gastric diagnostic pathway, including improved lesion detection during endoscopy, reduced miss rates, lesion segmentation, classification of precancerous conditions, H. pylori recognition, and near-expert histopathology classification. Evidence from systematic reviews supports robust diagnostic accuracy, while prospective studies highlight real-time feasibility. Conclusions: Integrating AI with multi-omics is shifting gastric biopsy from descriptive histology toward data-driven precision gastroenterology. Key barriers include dataset quality, standardization, interpretability, cost, and regulatory and ethical governance; addressing these will be essential for routine clinical adoption. Full article

Background/Objectives: Flea beetles (Coleoptera, Chrysomelidae: Alticinae) show extensive karyotypic diversity, yet cytogenetic and genomic data remain scarce for many taxa. Species of the genus Podagrica are characterized by unusually high chromosome numbers compared with the modal condition in Alticinae, suggesting a history of chromosomal fissions. This study aimed to characterize the karyotype and repetitive DNA composition of Podagrica fuscicornis, with special emphasis on the satellitome and its contribution to chromosome organization. Methods: Male specimens of P. fuscicornis collected in southern Spain were analyzed using conventional cytogenetic techniques, including Giemsa staining, DAPI staining, and C-banding. Fluorescence in situ hybridization was employed to map nucleolar organizer regions (NORs), telomeric repeats, and major satellite DNA (satDNA) families. The satellitome was characterized using Illumina short-read sequencing and analyzed with the RepeatExplorer2/TAREAN pipeline to identify satDNA families and estimate their genomic abundance and divergence. Results: The male karyotype of P. fuscicornis was 2n = 40 (38 + XY), with an Xy_p sex chromosome system. Constitutive heterochromatin was mainly pericentromeric, and the Y chromosome was largely heterochromatic. NORs were located on a single autosomal pair, and the ancestral insect telomeric motif (TTAGG)_n was detected at chromosome ends. The satellitome comprised at least 70 different satDNA families, representing 9.51% of the genome, some of them related to transposable elements. Ten of these 70 satDNAs are shared in other Alticinae species. The most abundant families were primarily localized in pericentromeric regions and showed differential distribution between autosomes and sex chromosomes. Conclusions: These results indicate that extensive chromosomal fissions and high satDNA dynamics could drive the high chromosome number and heterogeneous genome organization in P. fuscicornis, highlighting the role of repetitive DNA in karyotype evolution within Chrysomelidae. Full article

Pseudomonas syringae pv. syringae (Pss) is an economically significant bacterial pathogen that causes canker in sweet cherry trees. In Chile, sweet cherry (Prunus avium L.) is a key crop whose exponential production growth has increased phytosanitary pressure. However, the genetic diversity and adaptive mechanisms of local Pss populations have remained poorly understood. This study characterized 41 Pss isolates from major Chilean production regions. Their genomes were sequenced and compared with 152 public genomes from the PG2 phylogenetic group. The analysis revealed a predominance of the PG2d subgroup among the Chilean isolates, with a population structure defined by at least 18 genomic clusters, some of which are exclusive to Chile. A characteristic feature of this entire PG2d subgroup is the presence of indole-3-acetic acid (IAA) synthesis genes (iaaM and iaaH). Furthermore, this subgroup displayed a marked increase in ancestral gene gain and loss events, indicating extensive remodeling of the shell genome and supporting a model of lineage-specific adaptive evolution. We also identified lineage-specific orthogroups, structural variants of the T-PAI pathogenicity island, and a differential distribution of Hop-type effector proteins. Furthermore, an extended copper resistance operon (cop and cus systems) was detected in a subset of strains, and a dominant lineage was found to have a dual i1-type of T6SS system. These findings highlight the local diversification of Pss in Chile, likely driven by agro-environmental pressures. This study provides crucial insights into the evolution, adaptation, and pathogenic potential of this important pathogen in a crop of high strategic value. Full article

The post-genomic era, defined by large-scale sequencing initiatives, has generated an unprecedented catalogue of human genetic variation. Yet, the vast majority of genetic variants remain classified as variants of uncertain significance or are located within poorly characterized non-coding regions, thereby hindering the effective translation of genomic data into meaningful biological understanding and clinical application. Bridging this genotype-to-phenotype gap requires precise, high-throughput functional genomics. Early CRISPR–Cas9 knockout and CRISPR interference/activation (CRISPRi/a) screens mapped gene-level functions but could not assess single nucleotide variants (SNVs). Bridging this genotype-to-phenotype gap demands precise, high-throughput functional genomics. Multiplexed assays of variant effect (MAVEs), like saturation genome editing, systematically test all possible mutations using CRISPR–Cas9 and donor libraries. Base editors allow targeted single-base changes without double-strand breaks but are limited in scope, while prime editing can introduce any small substitution, insertion, or deletion without double-strand breaks (DSBs) or donor templates. This review traces the evolution of functional screens from gene-level knockouts to saturation genomic editing (SGE), and highlights how prime editing is driving a new paradigm for the systematic functional characterization of thousands of variants across disease-relevant genes. We also detail the architecture, mechanism, and progressive optimization of PE systems and their delivery methods. Collectively, prime editing stands as a transformative platform poised to accelerate precision functional genomics and advance the diagnosis and treatment of genetic diseases. Full article

Background: Liquid biopsy, particularly through the analysis of circulating tumor DNA (ctDNA), represents a significant advancement in oncology. Unlike traditional tissue biopsies, ctDNA offers a minimally invasive, real-time approach to cancer management. It has demonstrated considerable potential in early cancer detection, monitoring of therapeutic responses, and assessing minimal residual disease (MRD) to predict recurrence. By enabling comprehensive molecular profiling through a simple blood test, ctDNA supports the core principles of precision oncology, facilitating more personalized and adaptive treatment strategies. Methods: In the following article we describe the recent developments focused on refining ctDNA detection assays to improve sensitivity and specificity. Advanced technologies, including next-generation sequencing (NGS) and digital PCR, are commonly employed. The integration of artificial intelligence (AI) and multi-omics approaches—such as combining genomic, epigenomic, and transcriptomic data—has further enhanced the analytical power of ctDNA assays. Results: Emerging evidence shows that ctDNA-based liquid biopsy enables dynamic, real-time tracking of tumor evolution and therapeutic resistance. Clinical studies have demonstrated its efficacy in detecting early-stage cancers, guiding treatment selection, and predicting relapse with higher accuracy than some conventional methods. Moreover, AI-enhanced algorithms have improved signal detection, allowing for more precise and earlier identification of actionable mutations and MRD. Conclusions: ctDNA analysis via liquid biopsy is poised to revolutionize cancer care by offering a non-invasive, precise, and adaptive tool for tumor characterization and monitoring. Although obstacles remain—particularly regarding assay sensitivity, standardization, and economic feasibility—ongoing technological innovations and multi-omics integration are rapidly advancing its clinical viability. With continued progress, ctDNA-based liquid biopsy is likely to become a cornerstone of routine oncology practice. Full article

The biosynthesis of melanin in plants remains an enduring biochemical enigma. Unlike the well-characterized pathways of animals and fungi that produce the canonical “true melanins”, the enzymatic origins and physiological functions of melanin-like pigments in plants are poorly described. Recent advances in Juglans regia (walnut) have begun to illuminate this “dark metabolism,” revealing a dual polyphenol oxidase (PPO) system, constitutive JrPPO1 and stress-inducible JrPPO2, that orchestrates the oxidation of phenolics into amorphous, heterogeneous polymeric pigments. Functional studies demonstrate that JrPPO1 maintains tyrosine and redox homeostasis, while silencing triggers a lesion-mimic phenotype, highlighting the enzyme’s role in detoxifying reactive intermediates. In contrast, JrPPO2 responds to redox and pathogen stress, driving pigment formation as part of the defense response. The integration of biological evidence, encompassing genomics, genetics, and phenotyping, reveals that walnut pigmentation represents a genetically encoded, developmentally regulated adaptation balancing metabolic cost and oxidative protection. Decoding this system reframes melanin biosynthesis in plants as a strategic redox resilience mechanism, one that transforms potentially toxic phenolic oxidation into protective polymerization, bridging primary metabolism, defense, and evolution. Full article

Genetic variation underlies the capacity of populations to adapt, yet what drives how this variation is generated and maintained in natural populations remains poorly understood. Fundamental processes such as mutation, ploidy, and recombination are known to shape genetic variation and adaptive potential but are typically studied in isolation and under controlled laboratory conditions. How these processes act together under varying environmental conditions to structure genetic variation across complex natural populations remains unresolved. In yeasts, these processes are dependent on reproductive mode, ploidy shifts, and environmental stressors, which jointly shape genomic stability and adaptive potential. Here, we review our current knowledge on the roles of mutation, ploidy, and recombination in adaptation in the model yeasts Saccharomyces cerevisiae and the human pathogenic Cryptococcus. We highlight heterogeneity in mutation rates, recombination, and ploidy states across strains, environments, and populations, challenging the assumption that these parameters are uniform. We argue that fluctuating environments, increasingly driven by climate change, are likely to intensify interactions among these processes to impact evolution in ways that remain difficult to predict. Integrating population genomics with ecologically realistic frameworks will be essential for understanding natural evolutionary dynamics and anticipating fungal adaptation and disease emergence. Full article