Junken meat sheep undergo a developmental coat color transition from black fleece at birth to white body fleece by approximately 179 days of age, but the associated epitranscriptomic features remain unclear. Here, integrated MeRIP-seq and RNA-seq analyses were performed using skin samples from three newborn black-fleeced lambs and three 179-day-old white-fleeced lambs. m6A peaks were mainly enriched in CDS regions and near stop codons, with the canonical GGACU motif detected in both groups. Across three paired comparisons, 1,273–1,716 differential m6A peaks and 400–1,657 differentially expressed genes were identified. Functional enrichment analysis highlighted processes related to hair follicle development, epidermal morphogenesis, extracellular matrix remodeling, focal adhesion, and Wnt, TGF-β, PI3K-Akt, Notch, and melanogenesis-related pathways. Integrative analysis revealed comparison-dependent m6A–expression coupling patterns, including hyper-down in C11 vs. C1 and predominant hypo-up patterns in C22 vs. C2 and C33 vs. C3. Candidate m6A-associated genes, including FZD7, GAS1, COL4A1, PXDN, LAMC3, ARID1A, FA2H and RAPGEFL1, were prioritized, and qRT-PCR supported the RNA-seq expression trends of selected genes. Given the confounding between age and coat-color stage, these findings represent candidate molecular features associated with developmental coat color transition and provide a basis for future m6A-site validation and functional studies.
The root of Isatis indigotica (Radix Isatidis) is a valuable traditional Chinese medicine rich in bioactive flavonoids, yet the regulatory mechanism by which leaf cutting affects root flavonoid metabolism remains unclear. In this two‑year (2024 and 2025) field experiment, we investigated the dynamic responses of root flavonoids in I. indigotica cultivar “Yulan No. 1” at five time points (0, 4, 8, 12, 16 days) after leaf cutting. Total flavonoid content was lowest at day 0 and highest at day 16 after leaf cutting and measured in both years and showed a consistent trend. Using UPLC‑MS/MS‑based widely-targeted metabolomics on the second‑year samples, 148 flavonoid metabolites were identified, among which 64 were differentially accumulated. K‑means clustering revealed six distinct temporal patterns. Eleven candidate differential metabolites showed strong positive correlations with total flavonoid content, with tenuifone exhibiting the highest correlation. Transcriptome sequencing identified 69 differentially expressed genes involved in flavonoid‑related pathways, including phenylpropanoid and flavonoid biosynthesis. Integrated correlation analysis constructed a metabolite‑gene network, highlighting multiple 4CL and CYP81E genes as candidate genes potentially involved in the flavonoid response. Notably, different isoforms of the same gene family showed opposite correlation directions with the same metabolites, indicating isoform‑specific regulatory complexity. Our findings demonstrate that leaf cutting induces a biphasic, quantitative reprogramming of root flavonoid metabolism with a largely conserved qualitative metabolite profile. This study provides a correlative metabolomic and transcriptomic landscape of leaf-cutting-induced flavonoid accumulation in I. indigotica roots, offering a theoretical basis for quality-oriented cultivation and identifying candidate metabolites and genes for further functional validation.
Tenocytes are the principal effector cells responsible for tendon homeostasis and repair, whose functions are governed by precise transcription programs. However, the epigenetic basis underlying the establishment and maintenance of their cellular identity, particularly the genome-wide landscape of chromatin accessibility, histone modifications and chromatin states remains largely unexplored. We performed a multi-omics analysis of primary tenocytes, including ATAC-seq, CUT Tag profiling of six key histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K9me3 and H3K27me3), and RNA-seq. By utilizing ChromHMM algorithm, we defined a comprehensive chromatin state map for tenocytes. We established a high-resolution epigenetic atlas, segmenting the tenocyte genome into 10 distinct states with well-defined biological functions. Integrative analysis revealed that active promoter states, marked by H3K4me3, H3K27ac, and open chromatin, were tightly linked to the high expression of genes essential for tendon function, including extracellular matrix components and key transcription factors. Motif analysis revealed a putative regulatory network of these genes, which was centered on ETS and Zinc-finger family transcription factors. In contrast, repressed promoter states, enriched for the Polycomb-associated mark H3K27me3, were found at genes mainly involved in alternative developmental pathways (e.g., neural, epidermal) and hormone secretion functions, suggesting an active silencing mechanism that safeguards tenocyte lineage fidelity. This study provides an integrated epigenomic landscape of tenocytes, establishing a chromatin-level blueprint for understanding their cellular identity. This resource identifies key regulatory elements controlling tendon signature gene expression and offers a valuable dataset for future investigations into the epigenetic regulation of tendon homeostasis and regeneration.
Runs of homozygosity (ROH) provide a genome-wide measure of autozygosity and are useful for evaluating the genomic consequences of selection and inbreeding in commercial pig populations. This study investigated ROH architecture and associations between ROH-based genomic inbreeding coefficients ( F_ROH ) and production-related traits in American Duroc (DD), American Landrace (LL), and American Yorkshire (YY) pigs. After quality control, 5,859 genotyped pigs were analysed. Using a 1 Mb ROH definition restricted to SSC1-18, we detected 416,225 ROH segments and observed the highest individual-level ROH in DD. Mixed models incorporating a genomic relationship matrix (GRM) identified 19 nominally significant F_ROH –trait associations (P < 0.05) among 51 population–trait tests, of which 13 remained significant after Benjamini–Hochberg FDR correction, with the broadest pattern in LL, fewer associations in DD, and nominal associations in YY restricted to BL and BH, with only BH surviving FDR correction. Sex-specific analyses detected F_ROH × Sex interactions that were nominally significant in DD, none of which remained significant after FDR correction across 45 estimable interaction tests. Segmented models further showed 25 nominally significant threshold responses (P < 0.05), none of which survived FDR correction (minimum q = 0.118); these exploratory patterns suggested that nominal candidate F_ROH breakpoints differed by population, trait, and ROH length class. These results indicate that the effects of genomic autozygosity on production traits vary across commercial pig populations with trait-dependent associations supported by FDR correction and sex- and ROH-length-class-related patterns remaining exploratory. The population-specific F_ROH associations and threshold responses observed in this study provide insight into how different sources of inbreeding may influence production performance. These findings provide a basis for population-specific evaluation of inbreeding load and for improving genomic management strategies in commercial pig breeding.
Cardiac regeneration has been characterized in individual species of fish and amphibians, vertebrates whose hearts are comparatively simple in structure, and function at low pressure. Here, we use quantitative proteomics to characterize the cellular response in the heart of the gecko (Eublepharis macularius) following injury. Gecko hearts are more complex, and function at higher pressure, than those of fish and amphibians. Hearts were damaged using a cryoprobe and wound sites were sampled at 3-, 14-, 30- and 100-days post injury (dpi). Samples were also taken from sham operated geckos. Overall, 579 proteins were differentially expressed across at least two time points. Importantly, we found increased expression of agrin at 14-dpi, a protein that facilitates cardiomyocyte dedifferentiation. This is the first time that an increase in agrin expression following cardiac injury, has been reported. Gene Ontology (GO) analysis indicates that by 14-dpi there is a decrease in oxidative and glycolytic capacity as well as in sarcomere organization and mitochondrial content. However, by 100-dpi these were all recovered. There were also no GO terms between sham and 100-dpi hearts, suggesting that the cardiac proteome is returning to the pre-injury state. This work indicates that heart regeneration in geckos involves reorganization of cellular pathways associated with mitosis, energy production and contractile function.
Hoxc13 is a critical transcription factor that regulates the expression of hair keratin genes. Our previous study showed that during mammalian evolution, the Hoxc13 protein acquired a characteristic polyglycine repeat (polyG) insertion. This insertion distinguishes Hoxc13 from its non-mammalian homologs and may contribute to hair production. To investigate the effect of the polyG fragment on the DNA-binding profile of Hoxc13, the normal Hoxc13-W protein and a polyG-deleted Hoxc13-S protein from cashmere goats were synthesized using an in vitro expression system. Their genomic binding profiles were compared using DNA affinity purification sequencing (DAP-seq), genome alignment, pathway enrichment, motif analysis, and molecular docking. Hoxc13-W and Hoxc13-S exhibited markedly different genome-wide DNA-binding capacities. Hoxc13-W identified 12,679 binding peaks, whereas Hoxc13-S identified only 3,634, with only 243 peaks shared between the two proteins. Functional enrichment analysis showed that Hoxc13-W specifically bound genes involved in key pathways regulating hair follicle morphogenesis and cycling. In contrast, Hoxc13-S targets were enriched primarily in the axon guidance pathway. Within the Wnt signaling pathway, Hoxc13-W bound 30 genes, whereas Hoxc13-S bound only 5. Motif analysis further demonstrated that the polyG fragment substantially influenced cis-regulatory motifs beyond the core Hoxc13-binding motif (5′-ATAAA-3′). Molecular docking analysis indicated that the polyG fragment altered the N-terminal structure of Hoxc13, thereby affecting its protein-protein interaction capacity. Collectively, these findings suggest that the polyG fragment enhances the Hoxc13-mediated gene regulatory network during the evolutionary transition from non-mammalian to mammalian vertebrates and may have contributed to the evolution of mammalian hair-related phenotypic traits.
Hu sheep are a well-known Chinese dual-purpose breed valued for meat production, early sexual maturity, high prolificacy, and adaptability to hot, humid environments. In this study, we combined whole-genome sequencing, GWAS, and eQTL analyses to investigate the genetic basis of growth and slaughter traits in 420 eight-month-old Hu sheep. Using a discovery cohort (N = 112) and a validation cohort (N = 308), we integrated high-throughput SNP genotyping and RNA sequencing, identifying 559,996 high-quality SNPs and multiple significant loci associated with traits such as live weight and carcass weight. Among the 2,368 cis-eQTLs detected, the most significant was linked to ZNF280B expression in the longissimus lumborum muscle. Functional validation showed that ZNF280B downregulation significantly inhibited skeletal muscle satellite cell proliferation and induced apoptosis, highlighting its critical role in muscle development and fat metabolism. The novelty of this study lies in its large sample size, comprehensive multi-trait analysis, and the integration of functional validation, providing reliable genetic markers for marker-assisted selection in Hu sheep. These findings deepen our understanding of the genetic mechanisms underlying growth and slaughter performance and offer valuable insights for improving production efficiency and promoting sustainable livestock development.
Long non-coding RNAs (lncRNAs) are important regulators of developmental gene expression, but their roles during key windows of embryonic hair follicle morphogenesis in cashmere goats remain unclear. This study aimed to identify temporally specific lncRNAs associated with early hair follicle development and to evaluate a candidate cytoplasmic lncRNA and its potential regulatory relationship in an in vitro dermal fibroblast model. Temporal screening identified 32 candidate lncRNAs with transient, stage-specific expression changes at embryonic day 55, suggesting that this stage may represent an important window of transcriptional regulation associated with embryonic hair follicle morphogenesis. Enrichment analysis showed positive enrichment of Wnt-related gene sets in the day 55 vs. day 45 and day 65 vs. day 55 comparisons; however, this finding does not constitute a direct measurement of Wnt pathway activity. Among the prioritized candidates, MSTRG.18075.2 showed relatively high expression at day 55 and was predominantly localized to the cytoplasm. In a heterologous 293T-cell reporter system, chi-miR-145-5p reduced the activity of wild-type reporters containing the predicted MSTRG.18075.2 or WNT16 3’ UTR site, whereas the corresponding mutant reporters did not show the same changes, supporting sequence-specific reporter responses mediated by these predicted sites. In cashmere goat dermal fibroblasts, MSTRG.18075.2 knockdown was associated with reduced apoptosis, slower cell-cycle progression, impaired proliferation and migration, and increased intracellular reactive oxygen species (ROS). Combined knockdown of chi-miR-145-5p partially reversed some phenotypes induced by MSTRG.18075.2 or WNT16 knockdown. These results are consistent with a candidate MSTRG.18075.2/chi-miR-145-5p/WNT16 regulatory model. This study provides supporting evidence for a relationship between MSTRG.18075.2 and the candidate chi-miR-145-5p/WNT16 regulatory axis at the levels of temporal expression, cytoplasmic localization, sequence-specific reporter responses, and in vitro cellular phenotypes. Because endogenous RNA complexes, downstream Wnt activity, and effects on hair follicle morphogenesis in vivo were not examined, the current findings do not directly establish an endogenous ceRNA mechanism or a causal relationship in vivo.
Rumen flukes, particularly the trematode Calicophoron daubneyi, are emerging parasites of livestock in Europe, yet transcriptomic insights into their environmental and intermediate host stages remain limited. Here, we present a comprehensive transcriptomic analysis of eggs at three distinct developmental stages (freshly excreted, early developmental and eye-spot stages), as well as rediae and cercariae, of C. daubneyi. High-quality RNA-sequencing (RNA-seq) datasets revealed both shared and stage-specific transcriptional profiles with each developmental stage exhibiting its own distinct expression pattern. Subsequent GO-Term enrichment analyses revealed that fully embryonated eggs in eye-spot-stage especially upregulated genes related to cilia assembly, movement and motility, reflecting preparation for miracidial hatching and host-seeking behavior. Rediae showed enhanced transcription of genes involved in diverse metabolic and biosynthetic processes, supporting rapid asexual proliferation within the snail intermediate host. Cercariae exhibited predominant upregulation of genes associated with signal transduction and energy metabolism, indicating the adaptation to its changing environmental conditions. These findings provide the first transcriptomic insights into the biology of C. daubneyi outside the definitive host, reveal molecular mechanisms underlying development, transmission and adaptation to a changing environment and identify stage-specific genes as potential targets for interventions aimed at disrupting the parasites life cycle and controlling rumen flukes in the future.
Hemiptera exhibits repeated and independent transitions among distinct feeding strategies, including phytophagy, carnivory, omnivory and hematophagy, a trait that offers an ideal model system to dissect the genomic basis of dietary adaptation. To comprehensively explore the dynamic genomic changes accompanying dietary adaptation, we performed comparative genomic analyses on 27 hemipteran species, which collectively represent four distinct feeding habits. Our analyses uncovered extensive genomic changes associated with dietary adaptation, including the expansion, contraction, and loss of gene families. We observed functional-level convergence in enriched biological processes across independent lineages undergoing parallel dietary shifts, despite limited overlap at the specific gene family level, as well as recurrent changes in specific gene families during reverse transitions. Moreover, comparative transcriptomic analysis of salivary glands across these species identified numerous species-specific genes and gene families may be associated with feeding biology, generating candidate hypotheses for future functional validation. Together, our results provide insights into the dynamic genomic architecture underlying dietary diversification in hemipterans and highlight candidate genes and pathways for future experimental investigation of dietary adaptation mechanisms.
Deciphering how enhancers encode regulatory information in DNA remains a central genomics challenge, as sequencing outpaces functional annotation. A key question is whether enhancers possess recurring, sequence-based enhancer-associated features—here termed “enhancerness”—that distinguish them from other genomic regions across species, cell types, and experimental assays.Confirming its existence and learnability is both biologically fundamental and essential for scalable genome annotation. We introduce EnhancerDetector, a convolutional neural network-based framework for cross-species enhancer prediction that combines high accuracy with biological interpretability. Trained on human data, EnhancerDetector achieves strong performance across human, mouse, and fly datasets, consistently outperforming existing methods in precision and F1. It generalizes to datasets generated using diverse experimental assays. Unlike chromatin feature-based predictors requiring complex post hoc thresholding, EnhancerDetector directly outputs enhancer probability scores from short sequence windows, simplifying enhancer discovery workflows. An ensemble strategy further improves prediction reliability by reducing false positives. EnhancerDetector supports fine-tuning on new species and retains strong performance even when adapted with as few as 20,000 enhancer sequences, making it ideal for newly sequenced genomes with limited experimental data. For interpretability and visualization, we apply class activation maps to identify sequence regions predictive of enhancer activity. Experimental validation in transgenic flies confirms the predictive power of EnhancerDetector: five of six tested candidates drove reporter expression, and four exhibited expression patterns supported by prior literature. These analyses identify distinct sequence and contextual features associated with enhancer activity, collectively referred to here as “enhancerness,” suggesting that enhancers share learnable sequence characteristics. EnhancerDetector provides a sequence-based and interpretable framework for enhancer discovery across species and experimental contexts. Our results support the presence of recurring enhancer-associated sequence features that can be learned from DNA sequence and transferred across genomes. By combining cross-species prediction, fine-tuning, model interpretation, and experimental validation, EnhancerDetector offers a practical approach for prioritizing candidate enhancers in well-studied genomes. These features position EnhancerDetector as a useful first-stage annotation tool for identifying putative enhancers in newly sequenced genomes with limited experimental data.
The adoption of next-generation sequencing (NGS) into research and clinical routine has deeply transformed precision medicine. However, it has also introduced significant challenges in sample tracking and authentication across increasingly complex analytical workflows. While the frequency of sample misidentification may be low, potential negative outcomes are worrying. Existing SNP-based quality control solutions rely on non-coding genetic markers or require advanced technologies. There is a gap for small, robust panels that are portable across technologies, compatible with diagnostic panels, applicable across diverse populations and that have straightforward wet-lab implementation. We applied a stringent filtering pipeline to identify a set of highly discriminant, cross-platform compatible genetic markers supported by predesigned TaqMan assays, prioritizing broad applicability across world populations. We prioritized SNPs present in clinical sequencing panels. The panel was validated using whole-genome sequencing (WGS) data from 150 neuropathology samples in the NAGENDATA cohort and cross-validated with qPCR genotyping. We identified and validated a TaqMan-compatible 44-SNP panel for cross-platform sample authentication. The full panel demonstrates exceptional discriminatory power, with theoretical cumulative random match probabilities (CRMPs) ranging from 2.43 × 10⁻¹⁹ (European) to 9.37 × 10⁻¹⁸ (East Asian). We validated the panel in the NAGENDATA cohort using both NGS and qPCR-based methods. Cross-platform comparison revealed 99
Strategies to improve survival of wildlife impacted by emerging infectious disease are needed for species of conservation concern. We investigated how prior infection by the skin fungal pathogen, Batrachochytrium dendrobatidis (Bd), affected subsequent disease outcomes in a highly susceptible and critically endangered toad, Atelopus glyphus. Our experimental design consisted of: (1) Bd infection followed by itraconazole clearance and Bd re-infection (Bd-Bd n = 20), (2) mock infection followed by itraconazole treatment and Bd infection (mock-Bd n = 20), (3) Bd infection followed by itraconazole clearance and mock infection (Bd-mock n = 10), (4) mock infection followed by itraconazole treatment and mock infection (mock-mock n = 10), (5) untreated animals (untreated n = 10). Prior infection shifted the skin bacterial and fungal communities to a new state enriched in putatively anti-Bd bacteria. However, prior infection worsened disease outcomes, accelerating Bd infection and mortality in prior infected animals compared to naïve animals. Prior infection animals not re-infected (Bd-mock) showed immune gene downregulation compared to re-infected Bd-Bd animals suggesting that even after Bd clearance, Bd caused sustained immunosuppression in genes that respond to Bd; this likely led to lowered immune efficacies when re-infected. Upon re-infection, as Bd load increased, Bd became the primary driver of both immune expression and bacterial composition changes regardless of infection history. Observed bacterial community differences were closely tied to host immune gene expression. The fungal community did not shift in response to re-infection, suggesting that the initial shift was due to itraconazole treatment. Prior infected Bd-Bd animals did not show any novel shifts in immune gene expression, rather they had similar expression patterns that were just more pronounced compared to naïve mock-Bd animal. This suggests that the infection-clearance-infection treatment was ineffective in improving animal survival because there was limited long-lasting effects on immune genes once the pathogen was re-encountered. Unlike previous studies demonstrating protective effects following Bd clearance in other species, this highly susceptible amphibian showed no evidence of acquired resistance. Our results underscore the species-specific nature of disease outcomes and the value of integrative approaches for examining strategies to reduce pathogen susceptibility in endangered wildlife.
Animal gut microbiota play important roles in host immunity, nutrient metabolism and energy acquisition. Captivity significantly affects the abundance and community structure of gut microbiota. In this study, controlled feeding experiments were performed, and 16 S rRNA sequencing and metabolomics were applied to investigate the gut microbiota, metabolite profiles and physiology of wild and captive T. roborowskii. Our results demonstrated that the dominant microbial components among the groups consisted of Firmicutes, Bacteroidetes, and Proteobacteria while there were also Verrucomicrobia enriched in wild lizards and Fusobacteria increased in individuals fed mealworms. Furthermore, compared with the wild group, gut microbiota diversity of T. roborowskii was reduced by captivity. Higher metabolic activity was found in wild T. roborowskii, with significant enrichment of amino acid and linoleic acid metabolism pathways. In contrast, altered lysine degradation was observed in individuals fed mealworms and cockroaches in a 1:1 ratio. Wild lizards showed higher α-amylase and cellulase activities, while captive lizards with a high-protein diet exhibited elevated trypsin activity. Moreover, captive lizards showed higher leukocyte counts, whereas a higher antioxidant capacity was found in wild lizards. Captivity significantly affected the Chao1 index, but no significant differences were observed in other alpha-diversity indices. Notably, captivity altered community structure in T. roborowskii, leading to changes in metabolism and digestive enzyme activities, along with trends in immune status, whereas wild individuals exhibited enhanced metabolic adaptability and antioxidant capacity. Our study offers valuable insights into the gut microbiota of desert lizards, and a theoretical basis for host health management under captive conditions.
Acetolactate synthase (AHAS) mutations conferring imidazolinone herbicide resistance typically occur at conserved amino acid positions (Ala122, Ser653) in wheat. This study employed ethyl methanesulfonate (EMS) mutagenesis using two complementary approaches: in vivo seed treatment (50,000 M₁ seeds) and in vitro callus-based mutagenesis (126,000 calli) to generate novel AHAS-resistant wheat lines. Multi-stage selection across M₂–M₄ generations using germination-stage and foliar herbicide applications identified four stable mutant lines: ML-1, ML-2, ML-3 (seed-derived), and InVitML-1 (in vitro-derived). Sanger sequencing of the 1,123 bp AHAS fragment identified five distinct SNPs: G→A at position 502, T→C at position 1075, T→A at position 11, A→T at position 386, and a rare adjacent dual substitution (T→C, C→T) at positions 1119–1120. Notably, all five mutations were located outside canonical hotspots (Ala122, Pro197, Ala205, Trp574, Ser653), suggesting the involvement of alternative structural mechanisms for AHAS tolerance. Bradford assay showed mutant lines maintained AHAS protein concentrations of 4.60–4.93 µg/mL under imazamox stress, compared with 1.97 µg/mL in susceptible controls, consistent with target-site resistance. The mutation spectrum predominantly exhibited G: C→A: T transitions, as expected from EMS mutagenesis, confirming the chemical mutagen’s signature. These results provide strong initial evidence that non-canonical AHAS mutations can confer herbicide tolerance in polyploid wheat, extend the known genetic basis of imidazolinone resistance, and demonstrate the effectiveness of dual mutagenesis strategies for generating novel allelic resources for non-transgenic crop improvement programs.
Acinetobacter baumannii is a major cause of healthcare-associated infections, and carbapenem-resistant strains pose a critical public health threat owing to limited treatment options and the dissemination of AMR determinants. However, genomic data on carbapenem-resistant A baumannii(CRAB) in Ethiopia are limited. This study characterized 30 A. baumannii isolates from the National Clinical Bacteriology Reference Laboratory (NRL) using phenotypic and whole-genome sequencing (WGS). All 30 A. baumannii isolates exhibited multidrug-resistant (MDR) phenotypes, and 29/30 (96.7
Phosphate-solubilizing bacteria are soil-dwelling probiotics that promote plant growth and convert unavailable phosphorus into absorbable forms for plants. A phosphate-solubilizing strain, YNK-FB0058, which potentially represents a novel species within the genus Phyllobacterium, was isolated from the rhizosphere of safflower in a tobacco–safflower rotation field. Whole-genome sequencing and in vitro verification tests were conducted to explore its genetic basis and functional traits. Phylogenetic analysis based on the 16 S rRNA gene, together with comprehensive ANIm and dDDH comparisons against the available Phyllobacterium type-strain genomes and genome-scale taxonomic analysis using TYGS, suggested that strain YNK-FB0058 may represent a novel species within the genus Phyllobacterium. Its draft genome assembly size is 4,694,147 bp with a GC content of 61.14
The metabolic interplay between Trichinella spiralis (Ts) and its host remains a critical but underexplored aspect of trichinosis pathogenesis. Understanding how the parasite manipulates host metabolism is key to developing new diagnostic and therapeutic strategies. We employed targeted metabolomics using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) to investigate alterations in central carbon metabolism. Targeted metabolomic profiling of 23 central carbon metabolism–related metabolites were performed in serum and intestinal contents collected from Ts-infected and control C57BL/6J mice (n = 6 per group) at 14 days post-infection. Serum (representing systemic changes) and intestinal contents (representing the local microenvironment). The infection induced distinct, spatially-specific metabolic reprogramming. In serum, we observed significant increases in sedoheptulose 7-phosphate and dihydroxyacetone phosphate, alongside a notable decrease in lactic acid. This profile suggests a systemic shift towards the pentose phosphate pathway and altered glycolysis, indicative of a host-wide immune and stress response. Conversely, the intestinal contents of infected mice showed significantly elevated levels of lactic acid and pyruvic acid, pointing to a localized inflammatory environment and intense nutrient competition. Notably, receiver operating characteristic (ROC) curve analysis identified serum lactic acid and intestinal pyruvic acid as potential biomarkers of infection. Ts infection fundamentally reprograms host central carbon metabolism in a tissue-specific manner, disrupting systemic energy balance while creating a metabolically distinct niche within the intestine. These findings provide novel insights into the metabolic pathogenesis of trichinosis and highlight key metabolites as potential targets for future diagnostic and therapeutic interventions.
Aquatic hypoxia frequently occurs as a recurring environmental stressor, exerting detrimental effects on the growth and survival of fish. As a typical endemic fish species inhabiting the Qinghai-Tibetan Plateau, Gymnocypris eckloni displays outstanding resilience to hypoxia, however, limited knowledge exists regarding the dynamic changes of immune system in G. eckloni to hypoxic environments with varying DO levels. G. eckloni liver and blood biochemical parameters and transcriptomes were investigated in response to severe hypoxia for 12 h and moderate hypoxia for different durations (24, 96 and 168 h) to highlight the differences in immune responses, and the expression patterns of key immune-related genes in the gills and spleen following hypoxia stress were also analyzed. Integrating biochemical parameters and mRNA expression profiles, we found that severe short-term hypoxia exacerbated oxidative damage and significantly altered the expression of genes related to apoptosis and autophagy compared with moderate prolonged hypoxia. Phagosome, lysosome, TLR and NLR signaling pathways were significantly enriched under severe short-term hypoxia, whereas no comparable enrichment was observed under moderate prolonged hypoxia. Through STEM and WGCNA, several key immune-related genes were identified, including nod1, irf3, ifnα, pi3k, akt, p38, il-12, jak1, stat1, nlrp3, bax, bcl2, bcl-xl, atg5 and lc3, and most of them showed a similar expression trend in the hypoxia-challenged gills. Besides, the expression of nod1, irf3, akt, pi3k, jnk and cyld in the spleen was remarkably induced by severe short-term hypoxia. The results elucidated the immunoregulatory strategies of G. eckloni in response to hypoxia stress, and provided valuable information for breeding hypoxia-tolerant fish.
Genomic prediction based on medium-density SNP chips is widely used in dairy cattle breeding; however, causal variants may be missing or insufficiently tagged, potentially limiting prediction accuracy. The increasing availability of imputed whole-genome sequence (WGS) -level variants provide an opportunity to prioritize informative variants, yet the optimal strategy for integrating GWAS-selected variants into routine chip-based prediction remains unclear. Based on 100K SNP chip data, whole-genome sequence-level variants were obtained through imputation, and significant SNPs were filtered using the mixed linear model (MLM) and Fixed and random model Circulating Probability Unification (FarmCPU) at different feature selection thresholds. These SNPs were then merged with the chip data to construct models under different genetic architectures for comparison. The results suggested that genomic prediction accuracy was significantly superior to that of pedigree-based best linear unbiased prediction (PBLUP), and the Bayesian four-distribution mixture model generally outperformed genomic best linear unbiased prediction (GBLUP). Although FarmCPU detected a greater number of SNPs than MLM, the SNPs selected by MLM provided more stable improvements in prediction performance. Under feature selection thresholds (0.001 and 0.0001), incorporating MLM-selected SNPs significantly enhanced the prediction accuracy for milk fat rate (MFR) and milk fat yield (MFY) (p < 0.05). Furthermore, the two-component GBLUP architecture better utilized the selected SNPs to improve prediction performance, while the single-component Bayesian model already showed strong adaptability. Stringent SNP selection via MLM, combined with either a two-component GBLUP or a single-component Bayesian model, can effectively enhance genomic prediction accuracy, offering a feasible strategy for optimizing genomic prediction in Chinese Holstein cattle. The selection of informative variants from imputed WGS-level data based on genome-wide association studies (GWAS) represents an efficient strategy to utilize genomic information not captured by conventional SNP arrays. The optimal methodology involves employing the MLM for SNP screening under feature selection thresholds (e.g., 0.001 and 0.0001), in combination with either a two-component GBLUP framework or a single-component Bayesian mixture model. This integrated approach consistently enables superior predictive performance.
