Search Results (1,223)

The artificially cultivated edible mushroom Stropharia rugosoannulata is widely promoted and cultivated in China because of its ability to efficiently decompose agricultural and forestry waste. However, methods for CRISPR/Cas9 genome editing have not yet been established for S. rugosoannulata. In this study, we identified three SrU6 promoters in S. rugosoannulata and constructed the CRISPR/Cas9 expression vector GPiE-SrU6. Moreover, we found that mutant strains were obtained only when the expression of the single guide RNA (sgRNA) was driven by the SrU6-3 promoter. We subsequently employed a tandemly repeated SrU6-tRNA-sgRNA module to knock out two sites within the ura3 gene. The expression vector was introduced into the mycelium via Agrobacterium-mediated transformation (ATMT). Following dual selection with 60 μg/mL hygromycin (Hyg) and 0.2 mg/mL 5-fluoroorotic acid (5-FOA), stable transformants were obtained and subcultured. The mutation efficiency at the targeted ura3 locus was subsequently assessed. The CRISPR/Cas9 system successfully disrupted the target marker gene (ura3), achieving an editing efficiency of 14.9%. In summary, this study reports the first successful establishment of a CRISPR/Cas9 genome editing system in S. rugosoannulata. This study not only meets a future need for genetic manipulation tools for S. rugosoannulata but also provides a robust platform for engineering superior strains for eco-circular agriculture. Full article

The liver’s anatomic position and immune specialization make it both a major target and a major filter for systemically delivered therapeutics. Because portal venous inflow exposes the liver early to gut-derived molecules and exogenous compounds, many intravenously administered agents, including gene-based medicines and their viral and non-viral delivery systems, preferentially enter and accumulate in hepatic tissue. This review synthesizes how core liver physiology and immunobiology influence the performance, safety, and clinical translation of genomic medicines in hepatology, and outlines near-term practice and research shifts likely to define a genomics-driven future in liver disease care. We review the hepatic microarchitecture relevant to therapeutic trafficking, including sinusoidal transit, the space of Disse, hepatocyte uptake, and hepatobiliary elimination, and highlight the gatekeeping roles of liver sinusoidal endothelial cells and Kupffer cells in clearing particulate material and shaping inflammatory signaling. We then discuss how these same features create both opportunities, such as efficient hepatic targeting, and constraints, including innate immune activation, vector clearance, and variable intrahepatic distribution, for DNA- and RNA-based platforms. Finally, we propose five actionable developments poised to move genomics from a niche tool to a routine component of hepatology practice: earlier genomic testing in unexplained liver disease, multidisciplinary hepatology genome rounds, a centralized liver-specific gene resource, genetics-aware clinical trial design, and expansion of genetic therapies. Integrating liver biology with genomic medicine is essential to improve diagnostic yield, personalize therapy, and accelerate translation of gene-based treatments while mitigating immunologic and delivery-related barriers. Full article

Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework. Full article

Parasitoid wasps play a fundamental role in the biological control of pests. However, their morphological identification may be limited due to their small size and the high morphological similarity between species. Our objective was to identify specific genomic variants of the target species Palmistichus elaeisis Delvare & LaSalle, 1993, Tetrastichus howardi (Olliff, 1893), Trichospilus diatraeae Cherian & Margabandhu, 1942, and Trichogramma pretiosum Riley, 1879, (Hymenoptera: Chalcidoidea) by whole-genomic sequencing. Parasitoids were collected from their hosts and established in the laboratory after adult emergence. A sample of each parasitoid was sent to the Departamento de Ciências Biológicas at Universidade Federal do Espírito Santo (UFES) and “Oscar Monte” Entomophagous Insect Collection for morphological identification. Subsequently, samples composed of 20 individuals were preserved in absolute ethanol for DNA extraction. The DNA was extracted, quantified and sequenced on the Illumina Novaseq 6000 platform. Bioinformatic tools were used for quality control, detection of specific genomic variants, principal component analysis (PCA), and support vector machine (SVM). Genomic sequencing generated high-quality data for the analyzed parasitoids, allowing the identification of four specific variants for P. elaeisis, two for Te. howardi, four for Ts. diatraeae and five for Tg. pretiosum. These results provide a precise molecular tool for distinguishing parasitoids used in biological control programs. Full article

Sparassis latifolia is an edible and medicinal mushroom with significant economic value, now commercially cultivated on a large scale in China. However, current cultivars face challenges, including an extended mycelial growth period and unstable fruiting body yields. Advances in molecular breeding and functional genomics for this species are hindered by the absence of a reliable genetic transformation system. In this study, we first determined that S. latifolia is highly sensitive to carboxin and hygromycin, two selective agents commonly used in fungal genetics. We subsequently constructed a novel binary vector, pCbxHyg, harboring a carboxin resistance cassette driven by its native Pleurotus eryngii promoter and a hygromycin resistance cassette under the control of the P. eryngii Glycerol 3-phosphate dehydrogenase (GPD) gene promoter. Initial transformation attempts using Agrobacterium-mediated transformation of liquid-cultured mycelial pellets were unsuccessful. During microscopic examination, we discovered that S. latifolia mycelia produce abundant asexual chlamydospores. Using these chlamydospores as recipient material, we efficiently and reproducibly obtained transformants with the pCbxHyg vector under both carboxin and hygromycin selection. This method highlights the advantage of using asexual spores of Basidiomycetes as recipients for genetic transformation. PCR analysis confirmed the stable integration of the exogenous resistance genes into the fungal genome. The functionality of the system was further validated by transforming chlamydospores with a vector carrying a β-glucuronidase (GUS) reporter gene, whose expression was confirmed via histochemical staining of the resulting transformant mycelia. This work establishes the first successful Agrobacterium-mediated genetic transformation system for S. latifolia, providing a foundational platform for future gene function studies and molecular breeding efforts. Full article

West Nile virus (WNV) is a mosquito-borne flavivirus of growing importance for both human and equine health in Europe. Horses are highly susceptible to neurological disease and, because they share ecological exposure with humans, they represent valuable sentinels for detecting local viral circulation within a One Health framework. However, diagnosis of WNV infection in equines is complicated by the short and low-level viraemia, which limits the sensitivity of molecular assays, and by serological cross-reactivity with related flaviviruses and the confounding effects of vaccination. In this narrative review, we summarise the current diagnostic tools for WNV in horses, including direct detection methods (RT-qPCR, virus isolation, antigen detection) and indirect serological approaches (IgM and IgG ELISA, virus neutralisation tests), and discuss their practical performance and constraints in clinical and surveillance settings. We further examine equine surveillance systems, passive clinical reporting, active serosurveys and sentinel cohorts, and their integration with vector, avian and environmental monitoring. Key challenges include methodological heterogeneity, limited access to confirmatory testing and variable cross-sector data sharing. Finally, we outline future directions, highlighting the need for harmonised laboratory protocols, innovative field-deployable diagnostics, genomic surveillance and integrated, multi-source monitoring systems to strengthen early warning capacity and improve preparedness for WNV outbreaks in equine populations. Full article

Autophagy-mitophagy pathways are essential for regulating immune homeostasis. However, their contribution to population-level chronic low-grade systemic inflammation (SI) remains unclear. The objective was to investigate the association between variation in the genes related to the autophagy-mitophagy pathways and SI, and to examine whether lifestyle factors modify this relationship. We conducted genome-wide association studies and gene-set enrichment analyses using data from the Korean Genome and Epidemiology Study (KoGES, n = 28,102) and UK Biobank (UKBB, n = 343,892). SI was defined as an elevated white blood cell count or high-sensitivity C-reactive protein. Using Core Longevity State Vectors (CLSVs)—gene sets representing immune-longevity pathways derived from comparative transcriptomic analysis—we tested six pathways and constructed a weighted genetic risk score (GRS) from significant variants. Gene–lifestyle interactions were examined with respect to major dietary and lifestyle factors. Among six CLSVs, only CLSV-2 (mitophagy and autophagy) showed a significant association with SI (β = 0.425, p = 0.008). Six single nucleotide polymorphisms (SNPs) in autophagy-mitophagy genes (INPP5D, ATG16L1, ATG7, AP3S1, OPTN, and VPS33A) were associated with SI in KoGES (p < 5 × 10⁻⁵), and ten SNPs (genes selected in KoGES plus RAB7A, ATG12, VPS33A, BECN1) reached genome-wide significance in UKBB (p < 5 × 10⁻⁸). A higher GRS was associated with increased SI in both cohorts and was strongly associated with metabolic syndrome (MetS, OR = 1.91 in KoGES; OR = 1.62 in UKBB). SI was characterized by neutrophilia with relative lymphopenia. In UKBB, significant gene–lifestyle interactions were observed for diet, physical activity, smoking, and alcohol (p < 0.01). Favorable lifestyle factors reduced SI most effectively in individuals with protective genotypes. Among individuals with a high vegetable/fruit intake, SI prevalence was 35%, 36%, and 38% in the negative-, zero-, and positive-GRS groups, respectively, compared with 36%, 45%, and 48% in the low-intake groups. In conclusion, genetic variations in autophagy-mitophagy pathways specifically influence SI. Genetic predisposition substantially modifies the benefits of lifestyle, underscoring the importance of integrating genetic and lifestyle factors in understanding SI susceptibility. Full article

Background/Objectives: Antimicrobial agents have revolutionized disease management in humans and animals; however, their misuse and overuse have accelerated the emergence and spread of antimicrobial resistance (AMR) and antimicrobial resistance genes (ARGs). Dairy farms are recognized as potential hotspots for ARG dissemination, particularly through Escherichia coli, which acts as a reservoir and vector of ARGs, enabling their horizontal transfer via plasmids and other mobile genetic elements. This study aimed to characterize the genomic diversity, ARG profiles, plasmid content, and phylogenetic relationships of E. coli isolated from dairy farm environments and milk using whole-genome sequencing. Methods: A total of 31 E. coli isolates recovered from soil, effluent, cow dung, and milk samples underwent deoxyribonucleic acid extraction, library preparation, and sequencing on the Illumina MiSeq platform, followed by comprehensive bioinformatic analysis. Results: The E. coli isolates exhibited 20 distinct sequence types, including one novel sequence type. Plasmids were detected in 71% of the isolates, with the IncF plasmid family being the most predominant. Furthermore, 12 ARG groups were identified, with β-lactam resistance genes detected in 67.7% of isolates. Notably, blaCTX-M genes were identified in all phenotypically confirmed extended-spectrum β-lactamase-producing isolates. Additional ARGs, including those conferring resistance to tetracyclines (tet(A), tetX4), quinolones (qnrS1), aminoglycosides (aph, aad, ant), and folate pathway inhibitors (dfr and sul), were widely distributed throughout the samples. Phylogenetic analysis revealed clustering of isolates from different sample types, particularly among ST58 isolates, suggesting cross-environmental transmission. Conclusions: This study demonstrates that E. coli from dairy farm environments harbor diverse ARGs and plasmids, confirming their role as reservoirs of AMR. These findings underscore the importance of prudent antimicrobial use, routine genomic surveillance, and enhanced biosecurity measures to limit cross-environmental transmission. Full article

Dirofilaria immitis constitutes a significant global veterinary burden and an emerging zoonotic risk. Despite decades of study, the structural evolution of its scientific landscape remains unexplored. This study provides a comprehensive longitudinal analysis of global research on D. immitis to evaluate its trajectory, intellectual structure, and conceptual shifts over the last eight decades. A systematic bibliometric analysis was conducted following PRISMA guidelines adapted for bibliometrics. Data were retrieved from Web of Science Core Collection and Scopus, covering the period from 1945 to 2025. After deduplication and manual screening, a final corpus of 3589 documents was analyzed using performance indicators and science mapping techniques to assess growth patterns, geographic leadership, collaboration networks, and thematic evolution. The field exhibits a mature profile with a sustained mean annual growth rate of 2.39%. Production is geographically polarized, with the United States and Italy acting as the primary research hubs, though international collaboration networks are increasingly integrating endemic regions in the Global South. Thematic analysis reveals a profound paradigm shift: while early research (1945–1980) focused on parasite morphology and clinical description, the 21st century is characterized by a multidisciplinary approach dominated by molecular biology, the study of the endosymbiont Wolbachia, and the genetic mechanisms of macrocyclic lactone resistance. The intellectual structure is currently organized into distinct but interconnected clusters, linking established clinical pathology with emerging genomic and environmental control strategies. Research on D. immitis has evolved from a classical parasitology discipline into a complex biomedical ecosystem aligned with the One Health framework. The persistence of the disease, driven by drug resistance and climate-mediated vector expansion, has catalyzed a transition toward integrative research models. Future control strategies must transcend geographic borders, combining advanced genomic surveillance with ecological modeling to mitigate the impact of this transboundary disease on both animal and human health. Full article

Epilepsy affects more than 50 million individuals worldwide, and approximately one-third of patients remain refractory to existing antiseizure medications. Advances in gene therapy and genome editing have opened new possibilities for disease-modifying interventions that directly target the molecular and circuit-level mechanisms underlying epileptogenesis. Recent progress in central nervous system tropic viral vectors, non-viral delivery systems, and programmable genome-editing technologies has enabled precise manipulation of neuronal and glial function in preclinical epilepsy models. Strategies range from restoration of haploinsufficient genes implicated in monogenic epilepsies, such as SCN1A in Dravet syndrome, to modulation of neuronal excitability through engineered ion channels, neuropeptides, and astrocyte-based approaches. In parallel, CRISPR-derived platforms, including transcriptional activation and repression systems, base editing, and prime editing, offer new avenues for regulating gene expression in post-mitotic neurons without introducing double-strand DNA breaks. Despite these advances, significant translational challenges remain, including efficient and cell-type-specific delivery, long-term safety, and the risk of network-level side effects in the epileptic brain. This review critically examines recent gene therapy and genome-editing approaches for epilepsy, highlights key technological and biological barriers to clinical translation, and discusses emerging strategies that may enable durable and targeted treatments for drug-resistant epilepsies. Full article

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9, a genome-editing technology pioneered in 2012, enables the precise correction of deleterious mutations or disruption of disease-causing genes through targeted double-strand breaks (DSBs), offering potential for treating genetic diseases. However, CRISPR/Cas9 can cause off-target cleavage at non-specific DNA sites, leading to unintended insertions or deletions (indels), which limit its safety and applicability despite ongoing improvements in specificity. Recently, prime editing (PE), an advanced CRISPR-derived technology, has been employed with a Cas9 nickase (Cas9n) fused with a reverse transcriptase and a prime editing guide RNA (pegRNA) to enable precise insertions, deletions, and transversions without inducing DSBs, thus reducing risks of indels and chromosomal aberrations. Furthermore, ongoing optimizations, such as improved pegRNA design and enhanced editing efficiency, have expanded the applications of PE in medical therapeutics, agriculture, and fundamental research. This review summarizes recent advancements in the PE system, including optimized pegRNA designs and enzyme engineering for enhanced efficiency and specificity, alongside novel delivery methods. It also evaluates cutting-edge delivery strategies, such as adeno-associated virus (AAV) vectors, lipid nanoparticles (LNPs) and novel extracellular vesicle (EV)-based systems, and explores PE applications in vitro and in vivo, including disease modeling and therapeutic gene correction. Full article

The escalation of bacterial resistance to existing antibiotics represents a growing global health challenge, exacerbated by the widespread misuse of antimicrobial agents. As a result, alternative antibacterial strategies are increasingly being explored, including phage-derived lytic proteins. In this study, we report a preliminary characterisation of a novel phage-derived lytic protein identified through computational screening of bacteriophage genome sequences. A putative open reading frame, designated SM07 (1383 bp), was selected from bacteriophage sequences contributed by the University of KwaZulu-Natal to a global phage repository. The gene was synthesised, sub-cloned into the pET-30b(+) vector with an N-terminal histidine tag, and recombinantly expressed in Escherichia coli BL-21(AI) cells. The protein was purified using affinity and ion-exchange chromatography. Purified SM07 exhibited in vitro antimicrobial activity against Pseudomonas aeruginosa, with a minimum inhibitory concentration of 4 µg/mL, while no significant cytotoxic effects were observed in Vero kidney cells at concentrations substantially above the effective dose. Together, these findings provide initial evidence supporting the antimicrobial potential of SM07 and highlight phage-derived lytic proteins as candidates for further investigation as alternative agents against P. aeruginosa-associated infections. Full article

Background: The integration of multi-omics data, such as genomics and transcriptomics, into artificial intelligence models has advanced precision medicine. However, their clinical applicability remains limited due to model complexity. We integrated DNA mutation, RNA expression, and A>I(G) RNA editing data to develop a predictive model for drug response in breast cancer. Methods: We analyzed 104 patients from the Breast Cancer Genome-Guided Therapy Study (ClinicalTrials.gov: NCT02022202). Clinical variables, gene expression, tumor and germline DNA variants, and RNA editing features were integrated into machine learning models to predict therapy response. Generalized linear models (GLM), random forest (RF), and support vector machines (SVM) were trained and evaluated across multiple random 70/30 train-test splits. Feature selection was performed exclusively within the training set using LASSO regularization. Model performance was assessed using the F1-score on independent test sets. The additive effect of RNA editing was evaluated using paired comparisons across identical train/test splits. Results: We characterized the cohort using clinical, mutational, transcriptomic, and RNA editing profiles in 69 non-responders and 35 responders. Across repeated splits, adding RNA editing frequently maintained or modestly improved predictive performance, particularly in expression-based models, with paired analyses showing a statistically significant increase in F1-score. Conclusions: RNA editing represents a complementary molecular layer that can enhance multi-omic models for therapy response prediction in breast cancer, supporting further investigation of epitranscriptomic features in precision oncology. Full article

Background/Objectives: The large size of commonly used regulatory elements such as the cytomegalovirus (CMV) immediate-early promoter imposes a significant burden on the already restricted payload capacity of first-generation adenoviral vectors, potentially hindering the development of multi-antigen vaccine candidates. To address this limitation, we have engineered a panel of novel, small, semi-synthetic promoters designed to leverage the changes in transcriptomic milieu following adenoviral vector entry. Methods: Eight synthetic enhancer modules (SE1–SE8) were designed in silico, each composed of transcription factor binding sites (TFBSs) previously found in host genes that are upregulated during early adenoviral infection. These synthetic enhancers were coupled with a minimal CMV core promoter to generate a panel of compact semi-synthetic promoters (cSE1–cSE8), and their activity was evaluated in the context of ChAdOx1 viral vectors expressing GFP or a modified Plasmodium falciparum circumsporozoite (CSN) antigen. Promoter performance was characterised in vitro via flow cytometry, RT-qPCR, and Western blotting, and in vivo by quantifying antigen-specific T-cell (IFN-γ ELISpot) and IgG antibody (ELISA) responses in BALB/c mice. Results: In vitro characterisation revealed a wide range of promoter activity across the panel, with cSE3 and cSE5 driving transgene expression levels comparable to the benchmark CMV promoters despite their markedly reduced genomic footprint. In vivo, ChAdOx1 vectors incorporating cSE3 and cSE5 elicited potent antigen-specific T-cell and IgG responses that were comparable to those induced by the larger CMV control promoters. Conclusions: We have successfully developed semi-synthetic promoters that match the potency of the much larger, frequently used CMV promoters whilst simultaneously reducing genomic footprint. These novel regulatory elements will facilitate the design of next-generation vaccines, particularly those requiring large antigens or multi-antigen cassettes. Full article

Theileria haneyi, a recently discovered tick-borne hemoparasite infecting equids globally, has significant implications for equine health. Although it is closely related to T. equi (sharing 23% genomic divergence), it establishes an asymptomatic carrier state in persistently infected horses, creating a silent transmission reservoir. Its discovery and unique genetics justify its classification as a new taxon. A critical diagnostic challenge is that the lack of the ema-1 gene in T. haneyi prevents its detection by the standard T. equi cELISA, emphasizing the need for species-specific tools. Although species-specific PCR assays, including PCR and qPCR targeting genes like chr1sco or ema-11, respectively, and an indirect ELISA targeting the EMA-11 recombinant protein, have been developed, global genetic variations may limit their serological utility. Therapeutically, T. haneyi exhibits resistance to the key antiparasitic drug, imidocarb dipropionate (ID), and interferes with the clearance of co-infecting T. equi. Major knowledge gaps persist, particularly regarding the identification of its competent vector. The current work presents an overview of T. haneyi virulence, transmission, diagnostics, and therapeutic gaps while pinpointing the deficits in current information necessary for advancing our understanding of the parasite’s biology. Finally, the review discusses and recommends further studies to develop effective control and surveillance strategies for T. haneyi infection. Full article