Search Results (31)

Background: Cholesterol imbalances and elevated blood pressure (BP) are closely interrelated risk factors for cardiovascular disease (CVD) and are subject to genetic influences. We sought to identify novel associations between candidate genetic coding variants and CVD traits in our isolated study cohort and validate them in a general population cohort. Methods: We leveraged the population genetic features of the Norfolk Island Health Study (NIHS, n = 601), to identify candidate functional variants which were analysed for association with CVD and metabolic syndrome traits. We followed up suggestive variant-trait associations in the 2022 release of UK Biobank whole exome data (n = 200,625). Results: We identified a novel ten-base-pair in-frame missense multi-nucleotide variant (MNV), tagged by rs35724886, in the lipid metabolism gene ACOT4, which was associated with cholesterol levels and blood pressure. The MNV was associated with a lower incidence of ‘elevated BP’—systolic BP ≥ 130 mmHg or diastolic BP ≥ 80 mmHg—(OR: 0.70; 95% CI: 0.51, 0.97; p = 0.03), and higher total cholesterol levels (β = 0.08; p = 0.04) in the NIHS. Validation in the UK Biobank revealed consistent associations between the MNV (proxied by rs35725886) and lower incidence of ‘elevated BP’ (p = 0.0001), higher total cholesterol (p = 0.01), and reduced use of medication for managing blood pressure (p = 1.8 × 10⁻⁶) and cholesterol (p = 0.002). Structural modelling and in-silico predictions suggested that the MNV introduced destabilising changes in the ACOT4 protein, likely influencing peroxisomal lipid metabolism pathways critical to CVD risk. Conclusions: This study identified a coding MNV with potential implications for understanding the genetic regulation of lipid metabolism and its impact on cardiovascular health. Full article

Huanghuai sheep, a newly developed meat-specialized breed in China, are valued for their rapid growth and high meat quality, but the optimal slaughter age and the molecular basis of these traits remain poorly understood. Gaining insight into these mechanisms is vital for improving production efficiency and guiding molecular breeding in this economically important breed. Although previous studies have described the phenotypic characteristics of Huanghuai sheep, the genetic regulatory networks controlling muscle growth and meat quality at different developmental stages remain unclear. No thorough analysis of growth traits and transcriptomic variations across key age points has been conducted. Therefore, in this study, we aimed to evaluate how growth stage influences muscle development, carcass characteristics, and meat quality in Huanghuai sheep by integrating phenotypic characterization with transcriptomic profiling to identify key genes and molecular pathways underlying these economically important traits throughout development. Sixty Huanghuai sheep were assigned to three groups (twenty per group) representing key developmental stages (3, 9, and 18 months of age). Carcass traits and meat quality were evaluated. RNA sequencing of the longissimus dorsi muscle was performed to identify differentially expressed genes (DEGs), followed by bioinformatics analysis and experimental validation. The results indicated that the 9-month-old sheep presented a favorable balance of dressing percentage and intramuscular unsaturated fatty acid content, while those aged 18 months old exhibited the highest dressing percentage (61.23%). Transcriptome analysis identified 1395 DEGs (p < 0.05 and |log2FC| > 1) and enrichment analysis revealed key pathways involved in thyroid hormone synthesis, skeletal muscle satellite cell proliferation, and skeletal muscle tissue growth. Several candidate genes for muscle development (e.g., ACTC1, SIX2, HK2) and meat quality (e.g., TLR2, CHI3L1, ACOT7) were identified and validated. Their expression patterns showed significant correlations between critical growth performance and fatty acid composition metrics. These findings provide novel insights into the molecular networks regulating economically important traits in Huanghuai sheep, offering valuable targets for future molecular breeding programs aimed at enhancing productivity and meat quality. Full article

Ankylosing spondylitis (AS) displays wide inter-patient variability that is not accounted for by HLA-B27 alone, suggesting that additional immune and metabolic modifiers contribute to disease severity. Using a genetically matched design, we profiled peripheral blood mononuclear cells from two brother pairs discordant for AS severity and one healthy brother pair. Strand-specific RNA-seq was analyzed with a family-blocked DESeq2 model, while untargeted metabolites were quantified using gas chromatography–mass spectrometry (GC-MS) and liquid chromatography–mass spectrometry (LC-MS). Differential features were defined as follows: differentially expressed genes (DEGs) (|log₂FC| ≥ 1 and FDR < 0.05) and metabolites (VIP > 1, FC ≥ 1.2, and BH-adjusted p < 0.05). Pathway enrichment was performed with KEGG and Gene Ontology (GO). A total of 325 genes were differentially expressed. Type I interferon and neutrophil granule transcripts (e.g., IFI44L, ISG15, S100A8/A9) were markedly up-regulated, whereas mitochondrial β-oxidation genes (ACADM, CPT1A, ACOT12) were repressed. Metabolomics revealed 110 discriminant features, including 25 MS/MS-annotated metabolites. Primary bile acid intermediates were depleted, whereas oxidized fatty acid derivatives such as 12-Z-octadecadienal and palmitic amide accumulated. Spearman correlation identified two antagonistic modules (i) interferon/neutrophil genes linked to pro-oxidative lipids and (ii) lipid catabolism genes linked to bile acid species that persisted when severe and mild siblings were compared directly. Enrichment mapping associated these modules with viral defense, neutrophil degranulation, fatty acid β-oxidation, and bile acid biosynthesis pathways. This sibling-paired peripheral blood mononuclear cell (PBMC) dual-omics study delineates an interferon-driven lipid–bile acid axis that tracks AS severity, supporting composite PBMC-based biomarkers for future prospective validation and highlighting mitochondrial lipid clearance and bile acid homeostasis as potential therapeutic targets. Full article

Adipose tissue exhibits dynamic metabolic and structural changes in response to environmental stimuli, including temperature fluctuations. While continuous cold exposure has been extensively studied, the molecular effects of prolonged intermittent cold exposure (ICE) remain poorly characterized. Here, we present a proteomic analysis of inguinal white adipose tissue (IWAT) from mice subjected to a 16-week regimen of short-term daily ICE (6 °C for 6 h, 5 days per week) without compensatory caloric intake. Mass spectrometry identified 1108 proteins, with 140 differentially expressed between experimental and control groups. ICE significantly upregulated mitochondrial proteins associated with lipid and carbohydrate catabolism, the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, and lipogenesis, including LETM1, AIFM1, PHB, PHB2, ACOT2, NDUA9, and ATP5J. These changes reflect enhanced metabolic activity and mitochondrial remodeling. In contrast, proteins linked to oxidative stress, insulin resistance, inflammation, and extracellular matrix remodeling were downregulated, such as HMGB1, FETUA, SERPH1, RPN1, and AOC3. Notably, gamma-synuclein (SYUG), which inhibits lipolysis, was undetectable in ICE-treated samples. Our findings support the hypothesis that ICE promotes thermogenic reprogramming and metabolic rejuvenation in subcutaneous fat through activation of futile cycles and mitochondrial restructuring. This study offers molecular insights into adaptive thermogenesis and presents intermittent cold exposure as a potential strategy to mitigate adipose tissue aging. Full article

β-hydroxybutyrate (BHB) serves as an alternative cellular fuel during states of low glucose availability, such as fasting or carbohydrate restriction, when the body shifts to using fats and ketone bodies for energy. While BHB has shown potential metabolic benefits, its mechanisms of action in the context of obesity are not fully understood. In this study, we examined the effects of BHB supplementation on subcutaneous adipose tissue (SAT) metabolism in a diet-induced obesity (DIO) mouse model. Adult male mice were first fed a high-fat diet for six weeks, followed by a standard diet with or without BHB supplementation for an additional six weeks. BHB supplementation led to significant body weight loss independent of food intake. This weight reduction was associated with decreased adipocyte differentiation, reflected by reduced peroxisome proliferator-activated receptor gamma (PPARγ) protein levels and lower uncoupling protein 1 (UCP1) expression, indicating altered SAT function. Transcriptomic analysis of SAT revealed upregulation of genes involved in fatty acid activation and transport (e.g., Slc27a2, Plin5, Acot4, Acsm3, Rik). Functional enrichment highlighted the activation of the PPAR signaling pathway and enrichment of peroxisomal components in the BHB group. Together, these results suggest that BHB promotes lipid remodeling in SAT, enhancing fatty acid metabolism while suppressing thermogenic pathways, and thus may represent a novel mechanism contributing to adiposity reduction and metabolic improvement. Full article

Background/Objectives: CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats)-associated protein 9 is now widely used in agriculture and medicine. Off-target effects can lead to unexpected results that may be harmful, and these effects are a common concern in both research and therapeutic applications. Methods: In this study, using pineapple as the gene-editing material, eighteen target sequences with varying numbers of PAM (Protospacer-Adjacent Motif) sites were used to construct gRNA vectors. Fifty mutant lines were generated for each target sequence, and the off-target rates were counted. Results: Selecting sequences with multiple flanking PAM sites as editing targets resulted in a lower off-target rate compared to those with a single PAM site. Target sequences with two 5′-NGG (“N” represents any nucleobase, followed by two guanine “G”) PAM sites at the 3′ end exhibited greater specificity and a higher probability of binding with the Cas9 protein than those only with one 5′-NGG PAM site at the 3′ end. Conversely, although the target sequence with a 5′-NAG PAM site (where “N” is any nucleobase, followed by adenine “A” and guanine “G”) adjacent and upstream of an NGG PAM site had a lower off-target rate compared to sequences with only an NGG PAM site, their off-target rates were still higher than those of sequences with two adjacent 5′-NAG PAM sites. Among the target sequences of pineapple mutant lines (AcACS1, AcOT5, AcCSPE6, AcPKG11A), more deletions than insertions were found. Conclusions: We found that target sequences with multiple flanking PAM sites are more likely to bind with the Cas9 protein and induce mutations. Selecting sequences with multiple flanking PAM sites as editing targets can reduce the off-target effects of the Cas9 enzyme in pineapple. These findings provide a foundation for improving off-target prediction and engineering CRISPR-Cas9 complexes for gene editing. Full article

Background/Objectives: Climate change-induced temperature elevations pose significant challenges to livestock reproduction, particularly affecting testicular function in small ruminants. This study investigates the acute heat-stress response in goat Sertoli cells (SCs), aiming to elucidate the molecular mechanisms underlying heat-induced damage to male reproductive tissues. Methods: SCs were isolated from testes of 4-month-old black goats and exposed to heat stress (44 °C for 2.5 h). We employed transcriptome sequencing, CCK-8 assay, electron microscopy, ROS measurement, autophagy detection, Western blot analysis, and lactate concentration measurement. Bioinformatics analyses including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein–protein interaction network analyses were performed on the transcriptome data. Results: Heat stress significantly reduced SC viability, induced oxidative stress and autophagy, and altered gene expression profiles. We identified 1231 significantly differentially expressed genes, with significant enrichment in membrane-related processes and metabolic pathways. Metabolism-related genes, including PKLR, ACOT11, and LPCT12, were significantly downregulated. Protein–protein interaction network analysis revealed ten hub genes potentially crucial in the heat-stress response: HSP90AA1, HSPA5, BAG3, IGF1, HSPH1, IL1A, CCL2, CXCL10, ALB, and CALML4. Conclusions: This study provides comprehensive insights into the molecular mechanisms underlying goat SC response to heat stress. The identified genes and pathways, particularly those related to metabolism and stress response, offer potential targets for developing strategies to mitigate heat-stress effects on livestock reproduction. These findings contribute to our understanding of climate change impacts on animal husbandry and may inform the development of heat-stress resistant livestock lines. Full article

Clinical mastitis (CM) is a prevalent and severe inflammatory disease in dairy cows affecting the mammary glands. Fatty acid (FA) metabolism and associated enzymes are crucial for many physiological and pathological processes in dairy cows. However, the relationships among FA metabolism, FA-associated enzymes, and CM, as well as the mechanisms underlying their interactions, in dairy cows are not fully understood. The aim of this study was to characterize biological process (BP) terms, pathways, and differentially expressed proteins (DEPs) related to FA metabolism from our previous data-independent acquisition proteomic study. Six BPs involving 14 downregulated and 20 upregulated DEPs, and four pathways involving 10 downregulated and 11 upregulated DEPs related to FA synthesis and metabolism were systematically identified. Associated analysis suggested that 12 candidate DEPs obtained from BPs and pathways, especially acyl-CoA thioesterase 7 (ACOT7), regulate long-chain FA (LCFA) elongation and the biosynthesis of unsaturated FAs. Immunohistochemical and immunofluorescence staining results showed that ACOT7 was present mainly in the cytoplasm of mammary epithelial cells. The qRT-PCR and Western blotting results showed that ACOT7 mRNA and protein levels in the mammary glands of the CM group were significantly upregulated compared to those in the healthy group. This evidence indicates that ACOT7 is positively correlated with CM onset and progression in Holstein cows. These findings offer novel insights into the role of FA metabolism and related enzymes in CM and offer potential targets for the development of therapeutic strategies and biomarkers for the prevention and treatment of CM in dairy cows. Full article

Assisted reproduction technologies (ARTs) are generally considered safe; however, emerging evidence highlights the need to evaluate potential risks in adulthood to improve safety further. ART procedures like rederivation of embryos by vitrification differ from natural conditions, causing significant disparities between in vitro and in vivo embryos, affecting foetal physiology and postnatal life. This study aims to investigate whether hepatic transcriptome and metabolome changes observed postnatally are already present in foetal livers at the end of gestation. This study compared fresh and vitrified rabbit embryos, finding differences between foetuses obtained by the transfer of fresh and vitrified embryos at 24 days of gestation. Rederived embryos had reduced foetal and liver weights and crown-rump length. However, the offspring of vitrified embryos tended to be born with higher weight, showing compensatory growth in the final week of gestation (59.2 vs. 49.8 g). RNA-Seq analysis revealed 43 differentially expressed genes (DEGs) in the foetal liver of vitrified embryos compared to the fresh group. Notably, downregulated genes included BRAT1, CYP4A7, CYP2B4, RPL23, RPL22L1, PPILAL1, A1BG, IFGGC1, LRRC57, DIPP2, UGT2B14, IRGM1, NUTF2, MPST, and PPP1R1B, while upregulated genes included ACOT8, ERICH3, UBXN2A, METTL9, ALDH3A2, DERPC-like, NR5A2-like, AP-1, COG8, INHBE, and PLA2G4C. Overall, a functional annotation of these DEGs indicated an involvement in lipid metabolism and the stress and inflammatory process or immune response. Thus, our results suggest that vitrification and embryo transfer manipulation induce an adaptive response that can be observed in the liver during the last week of gestation. Full article

An electrochemical sensor sensitive to coenzyme A (CoA) was designed using a CoA-responsive polyallylamine–manganese oxide–polymer dot nanogel coated on the electrode surface to detect various genetic models of osteoarthritis (OA). The CoA-responsive nanogel sensor responded to the abundance of CoA in OA, causing the breakage of MnO₂ in the nanogel, thereby changing the electroconductivity and fluorescence of the sensor. The CoA-responsive nanogel sensor was capable of detecting CoA depending on the treatment time and distinguishing the response towards different OA genetic models that contained different levels of CoA (wild type/WT, NudT7 knockout/N7KO, and Acot12 knockout/A12KO). The WT, N7KO, and A12KO had distinct resistances, which further increased as the incubation time were changed from 12 h (R_12h = 2.11, 2.40, and 2.68 MΩ, respectively) to 24 h (R_24h = 2.27, 2.59, and 2.92 MΩ, respectively) compared to the sensor without treatment (R_control = 1.63 MΩ). To simplify its application, the nanogel sensor was combined with a wireless monitoring device to allow the sensing data to be directly transmitted to a smartphone. Furthermore, OA-indicated anabolic (Acan) and catabolic (Adamts5) factor transcription levels in chondrocytes provided evidence regarding CoA and nanogel interactions. Thus, this sensor offers potential usage in simple and sensitive OA diagnostics. Full article

A genome-wide association study of resistance to retained placenta (RETP) using 632,212 Holstein cows and 74,747 SNPs identified 200 additive effects with p-values < 10⁻⁸ on thirteen chromosomes but no dominance effect was statistically significant. The regions of 87.61–88.74 Mb of Chr09 about 1.13 Mb in size had the most significant effect in LOC112448080 and other highly significant effects in CCDC170 and ESR1, and in or near RMND1 and AKAP12. Four non-ESR1 genes in this region were reported to be involved in ESR1 fusions in humans. Chr23 had the largest number of significant effects that peaked in SLC17A1, which was involved in urate metabolism and transport that could contribute to kidney disease. The PKHD1 gene contained seven significant effects and was downstream of another six significant effects. The ACOT13 gene also had a highly significant effect. Both PKHD1 and ACOT13 were associated with kidney disease. Another highly significant effect was upstream of BOLA-DQA2. The KITLG gene of Chr05 that acts in utero in germ cell and neural cell development, and hematopoiesis was upstream of a highly significant effect, contained a significant effect, and was between another two significant effects. The results of this study provided a new understanding of genetic factors underlying RETP in U.S. Holstein cows. Full article

Macrobrachium rosenbergii is a warm water species, and low temperature is a limiting factor for its growth and survival. In order to explore the role of the acetyl-CoA-carboxylase (ACC) gene in response to the cold stress of M. rosenbergii, we investigated the effects of RNA interference (RNAi) with the ACC gene on the expression of fatty acid metabolism-related genes and the mortality of M. rosenbergii under cold stress. The results showed that different siRNA sequences and different injection concentrations had different inhibiting effects on ACC gene expression, and siRNA-III with an injection concentration of 2.0 μg/g (siRNA/prawn body weight) had the best interference effect. With the optimal siRNA and the optimal concentration under cold stress, the expressions of three fatty acid metabolism-related genes, FabD, echA, and ACOT, were generally significantly down-regulated. Compared to negative (scrambled-siRNA) and blank (PBS) control groups, the expression of FabD in the interference group was extremely significantly down-regulated at 12 h in the hepatopancreas and at 18 h in the muscles and gills; EchA was highly significantly down-regulated at 6 and 12 h in the muscles and gills; and ACOT was extremely significantly down-regulated and kept declining in the gills. Within 6–18 h after injection under cold stress, the mortality rate of the siRNA interference group (75%) was much lower than that of the negative (95%) or blank control group (97.5%), and all prawns died after 24 h. In conclusion, RNA interference with the ACC gene inhibited the expression of some fatty acid metabolism-related genes, and could partly improve the tolerance of M. rosenbergii to cold stress, indicating that the ACC gene might play an important role in the response of M. rosenbergii to cold stress. Full article

Subcutaneous fat deposition is an important index with which to evaluate meat-producing ducks, and affects their meat quality and feed conversion rate. Studying the differentially expressed genes in subcutaneous fat will help to comprehensively understand the potential mechanisms regulating fat deposition in ducks. In this study, 72 Nankou 1 Pekin Ducks and 72 Jingdian Pekin Ducks (half male and half female) at 42 days of age were selected for slaughter performance and transcriptome analysis. The results showed that the breast-muscle yield of Nankou 1 ducks was significantly higher than that of Jingdian ducks, but that the abdominal fat yield and subcutaneous fat yield were higher than that of Jingdian ducks. Thousands of DEGs, including many important genes involved in fat metabolism regulation, were detected by transcriptome. KEGG enrichment analysis showed that the DEGs were significantly enriched on pathways such as regulation of lipolysis in adipocytes, primary bile acid biosynthesis, and biosynthesis of unsaturated fatty acids. SCD, FGF7, LTBP1, PNPLA3, ADCY2, and ACOT8 were selected as candidate genes for regulating subcutaneous fat deposition. The results indicated that Nankou 1 had superior fat deposition ability compared to Jingdian ducks, and that the candidate genes regulated fat deposition by regulating fat synthesis and decomposition. Full article

Concurrent chemo-radiotherapy (CCRT) is linked with accelerated disease progression and early death (ED) in various cancers. This study aimed to assess the association of plasma levels of exosomal non-coding ribonucleic acid (RNA) (ncRNA) and blood cell dynamics with ED prediction in patients with cervical cancer undergoing CCRT. Using propensity score matching, a comparison of complete blood counts (CBCs) was performed among 370 CCRT-treated patients. Differences in ncRNA and messenger RNA (mRNA) expression before and after CCRT in 84 samples from 42 patients (cohort 2) were represented as logarithmic fold change (log₂FC). Networks were constructed to link the CBCs to the RNAs whose expression correlated with ED. From the key RNAs selected using multiple regression of all RNA combinations in the network, CBC dynamics-associated ncRNAs were functionally characterized using an enrichment analysis. Cohort 1 (120 patients) exhibited a correlation between elevated absolute neutrophil counts (ANC) and ED. Cohort 2 exhibited a prevalence of microRNA (miR)-574-3p and long intergenic non-protein coding (LINC)01003 ncRNA, whose expression correlated with ANC and hemoglobin values, respectively. Conversely, acyl-coenzyme A thioesterase 9 (ACOT9) mRNA was relevant to all CBC components. An integrative analysis of post-CCRT ncRNA levels and CBC values revealed that the patients with miR-574-3p-LINC01003-ACOT9 log₂FC) < 0 had a better prospect of 30-month disease-specific survival. These findings indicate that miR-574-3p and LINC01003 could serve as ED prognostic biomarkers. Full article

Maritime emergency materials distribution is a key aspect of maritime emergency responses. To effectively deal with the challenges brought by the uncertainty of the maritime transport environment, the multi-agent joint decision-making location-routing problem of maritime emergency materials distribution (MEMD-LRP) under an uncertain decision-making environment is studied. First, two robust bi-level optimization models of MEMD-LRP are constructed based on the effect of the uncertainty of the ship’s sailing time and demand of emergency materials at the accident point, respectively, on the premise of considering the rescue time window and priority of emergency materials distribution. Secondly, with the help of robust optimization theory and duality theory, the robust optimization models are transformed into robust equivalent models that are easy to solve. Finally, a hybrid algorithm based on the ant colony and tabu search (ACO-TS) algorithm solves multiple sets of numerical cases based on the case design of the Bohai Sea area, and analyzes the influence of uncertain parameters on the decision making of MEMD-LRP. The study of MEMD-LRP under uncertain decision-making environments using bi-level programming and robust optimization methods can help decision makers at different levels of the maritime emergency logistics system formulate emergency material reserve locations and emergency material distribution schemes that can effectively deal with the uncertainty in maritime emergencies. Full article