Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum.

Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host-microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.

Blood transcriptomic differences in the immune response under stressful environmental according to stocking density in pigs.

The implementation of animal welfare in the pig industry is becoming a global trend, and welfare can be improved through livestock management. In modern and intensive farming systems, it has become important to find a reasonable compromise between stocking density and productivity. The simultaneous detection of behavioral and physiological parameters is helpful when considering welfare levels for stocking density. This study aimed to confirm the effect of stocking density through transcriptome linkage. A comparison of three groups according to stocking density (low density, eight pigs and 1.0 m2 per head; normal density, eight pigs and 0.8 m2 per head; and high density, eight pigs and 0.6 m2 per head) was performed, and their transcriptomic changes were observed using the RNA-Seq method. Differentially expressed genes were identified for each comparison group (low density vs. normal density, 95 upregulated genes and 112 downregulated genes; high density vs. normal density, 133 upregulated genes and 217 downregulated genes; and high density vs. low density, 245 upregulated genes and 237 downregulated genes). Biological mechanisms according to stocking density were identified through functional annotation. T-cell differentiation and immune disease pathway enriched in the high-density group caused immune imbalance through dysregulated T-cell signaling. Moreover, oxidative stress, together with DNA damage, can lead to high susceptibility to disease. Our study confirmed the biological mechanisms through immunological expression patterns according to stocking density. The study results are expected to provide comprehensive insight into systematic operation strategies considering stocking density and biomarkers for use in welfare evaluation.

Animal welfare in the pig industry is a worldwide trend, and appropriate livestock management can improve welfare. Balancing stocking density and productivity is crucial in intensive farming systems. This study used behavioral and physiological parameters to assess welfare levels related to stocking density. The study identified biological mechanisms and immunological expression patterns influenced by stocking density by analyzing the transcriptome. These results offer comprehensive insights into operational strategies considering stocking density and biomarkers.

Comparative transcriptome analysis between long- and short-term survival after pig-to-monkey cardiac xenotransplantation reveals differential heart failure development.

Cardiac xenotransplantation is the potential treatment for end-stage heart failure, but the allogenic organ supply needs to catch up to clinical demand. Therefore, genetically-modified porcine heart xenotransplantation could be a potential alternative. So far, pig-to-monkey heart xenografts have been studied using multi-transgenic pigs, indicating various survival periods. However, functional mechanisms based on survival period-related gene expression are unclear. This study aimed to identify the differential mechanisms between pig-to-monkey post-xenotransplantation long- and short-term survivals. Heterotopic abdominal transplantation was performed using a donor CD46-expressing GTKO pig and a recipient cynomolgus monkey. RNA-seq was performed using samples from POD60 XH from monkey and NH from age-matched pigs, D35 and D95. Gene-annotated DEGs for POD60 XH were compared with those for POD9 XH (Park et al. 2021). DEGs were identified by comparing gene expression levels in POD60 XH versus either D35 or D95 NH. 1,804 and 1,655 DEGs were identified in POD60 XH versus D35 NH and POD60 XH versus D95 NH, respectively. Overlapped 1,148 DEGs were annotated and compared with 1,348 DEGs for POD9 XH. Transcriptomic features for heart failure and inhibition of T cell activation were observed in both long (POD60)- and short (POD9)-term survived monkeys. Only short-term survived monkey showed heart remodeling and regeneration features, while long-term survived monkey indicated multi-organ failure by neural and hormonal signaling as well as suppression of B cell activation. Our results reveal differential heart failure development and survival at the transcriptome level and suggest candidate genes for specific signals to control adverse cardiac xenotransplantation effects.

Integrative time-serial networks for genome-wide lncRNA-mRNA interactions reveal interferon-inducible antiviral and T-cell receptor regulations against PRRSV infection.

Porcine reproductive and respiratory syndrome virus (PRRSV) infection severely affects the swine industry each year. Although the host mechanisms against PRRSV infection have been identified in key target tissues through whole transcriptome sequencing, specific molecular regulators have not been elucidated. Long non-coding RNA (lncRNA) expression is highly specific and could thus be used to effectively identify PRRSV-specific candidates. Here, we identified novel lncRNAs in lungs, bronchial lymph nodes, and tonsils after PRRSV infection and constructed phenotype-based integrative co-expression networks using time-series differentially expressed (DE) lncRNAs and mRNAs. After the analyses, a total of 309 lncRNA-mRNA interactions were identified. During early host innate signalling, interferon-inducible and interferon genes were positively regulated by specific lncRNA. Moreover, T-cell receptor genes in lung adaptive immune signalling were negatively regulated by specific lncRNA. Collectively, our findings provide insights into the genome-wide lncRNA-mRNA interactions and dynamic regulation of lncRNA-mediated mechanisms against PRRSV infection.

Designing multi-epitope-based vaccine targeting surface immunogenic protein of Streptococcus agalactiae using immunoinformatics to control mastitis in dairy cattle.

BACKGROUND: Milk provides energy as well as the basic nutrients required by the body. In particular, milk is beneficial for bone growth and development in children. Based on scientific evidence, cattle milk is an excellent and highly nutritious dietary component that is abundant in vitamins, calcium, potassium, and protein, among other minerals. However, the commercial productivity of cattle milk is markedly affected by mastitis. Mastitis is an economically important disease that is characterized by inflammation of the mammary gland. This disease is frequently caused by microorganisms and is detected as abnormalities in the udder and milk. Streptococcus agalactiae is a prominent cause of mastitis. Antibiotics are rarely used to treat this infection, and other available treatments take a long time to exhibit a therapeutic effect. Vaccination is recommended to protect cattle from mastitis. Accordingly, the present study sought to design a multi-epitope vaccine using immunoinformatics. RESULTS: The vaccine was designed to be antigenic, immunogenic, non-toxic, and non-allergic, and had a binding affinity with Toll-like receptor 2 (TLR2) and TLR4 based on structural modeling, docking, and molecular dynamics simulation studies. Besides, the designed vaccine was successfully expressed in E. coli. expression vector (pET28a) depicts its easy purification for production on a larger scale, which was determined through in silico cloning. Further, immune simulation analysis revealed the effectiveness of the vaccine with an increase in the population of B and T cells in response to vaccination. CONCLUSION: This multi-epitope vaccine is expected to be effective at generating an immune response, thereby paving the way for further experimental studies to combat mastitis.

Integrative methylome and transcriptome analysis of porcine abdominal fat indicates changes in fat metabolism and immune responses during different development.

Fat is involved in synthesizing fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. The samples were collected from the porcine abdominal fat of different developmental stages (10 and 26 weeks of age). Then, the samples were sequenced using MBD-seq and RNA-seq for profiling DNA methylation and RNA expression. In 26 weeks of age pigs, differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified as 2,251 and 5,768, compared with 10 weeks of age pigs, respectively. Gene functional analysis was performed using GO and KEGG databases. In functional analysis results of DMGs and DEGs, immune responses such as chemokine signaling pathways, B cell receptor signaling pathways, and lipid metabolism terms such as PPAR signaling pathways and fatty acid degradation were identified. It is thought that there is an influence between DNA methylation and gene expression through changes in genes with similar functions. The effects of DNA methylation on gene expression were investigated using cis-regulation and trans-regulation analysis to integrate and interpret different molecular layers. In the cis-regulation analysis using 629 overlapping genes between DEGs and DMGs, immune response functions were identified, while in trans-regulation analysis through the TF-target gene network, the co-expression network of lipid metabolism-related functions was distinguished. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.

Fat is involved in the synthesis of new fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. Modifications in DNA methylation and expression values were confirmed epigenetically with growth. Changed genes in each DNA and RNA showed identical trends in the function of immune response and lipid metabolism. The effects of DNA methylation on gene expression were investigated using cis-regulation (functional enrichment analysis of overlapping genes) and trans-regulation (transcription factor and target gene networking) analysis to integrate and interpret different molecular layers. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.

Integrated transcriptome analysis for the hepatic and jejunal mucosa tissues of broiler chickens raised under heat stress conditions.

BACKGROUND: Heat stress (HS) is one of the most important threats for the current poultry industry. Therefore, many efforts have been made to ameliorate the adverse effect of HS on poultry production; however, physiological and molecular mechanisms pertaining to HS are still limited in poultry. Therefore, the objective of the current study was to investigate functional alterations based on individual and integrated transcriptomes in the liver and jejunal mucosa tissues of broiler chickens exposed to HS conditions. RESULTS: Broiler chickens exposed to HS showed decreased growth performance and increased corticosterone concentrations in the feather. In the transcriptome analysis, the number of differentially expressed genes (DEGs) were identified in the liver and jejunal mucosa by HS conditions. In the liver, genes related to amino acid oxidation, tryptophan metabolism, lipid metabolism, oxidative phosphorylation, and immune responses were altered by HS, which support the reason why heat-stressed poultry had decreased productive performance. In the jejunal mucosa, genes related to defense systems, glutathione metabolism, detoxification of xenobiotics, and immune responses were differently expressed by HS conditions. The integrated transcriptome analysis with DEGs found in the liver and jejunal mucosa showed a considerable connectivity between the core nodes in the constructed networks, which includes glutathione metabolism, xenobiotic metabolism, carbon metabolism, and several amino acid metabolisms. CONCLUSIONS: The core network analysis may indicate that increased requirement of energy and amino acids in the jejunal mucosa of broiler chickens exposed to HS conditions is likely compromised by increased oxidation and synthesis of amino acids in the liver. Therefore, our results may provide comprehensive insights for molecular and metabolic alterations of broiler chickens raised under HS conditions, which can aid in the development of the novel strategies to ameliorate the negative effect of HS on poultry productivity and health.

Investigating Multi-Target Antiviral Compounds by Screening of Phytochemicals From Neem (Azadirachta indica) Against PRRSV: A Vetinformatics Approach.

Porcine reproductive and respiratory syndrome virus (PRRSV) is a global health problem for pigs. PRRSV is highly destructive and responsible for significant losses to the swine industry. Vaccines are available but incapable of providing adequate and long-term protection. As a result, effective and safe strategies are urgently needed to combat the virus. The scavenger receptor cysteine-rich domain 5 (SRCR5) in porcine CD163, non-structural protein 4 (Nsp4), and Nsp10 are known to play significant roles in PRRSV infection and disease development. Therefore, we targeted these proteins to identify multi-target antiviral compounds. To identify potent inhibitors, molecular docking of neem phytochemicals was conducted; three compounds [7-deacetyl-7-oxogedunin (CID:1886), Kulactone (CID:15560423), and Nimocin (CASID:104522-76-1)] were selected based on the lowest binding energy and multi-target inhibitory nature. The efficacy and safety of the selected compounds were revealed through the pharmacokinetics analysis and toxicity assessment. Moreover, 100 ns molecular dynamics (MD) simulation was performed to evaluate the stability and dynamic behavior of target proteins and their docked complexes with selected compounds. Besides, molecular mechanics Poisson-Boltzmann surface area method was used to estimate the binding free energy of each protein-ligand complex obtained from the MD simulations and validate the affinities of selected compounds to target proteins. Based on our analysis, we concluded that the identified multi-target compounds can be utilized as lead compounds for the development of natural drugs against PRRSV. If further validated in clinical studies, these compounds can be used individually or in combination against the virus.

Unraveling structural and conformational dynamics of DGAT1 missense nsSNPs in dairy cattle.

Cattle are domestic animals that have been nourishing humans for thousands of years. Milk from cattle represents a key source of high-quality protein, fat, and other nutrients. The nutritional value of milk and dairy products is closely associated with the fat content, providing up to 30% of the total fat consumed in the human diet. The fat content in cattle milk represents a major concern for the scientific community due to its association with human health. The relationship between milk fat content and diacylglycerol o-acyltransferase 1 gene (DGAT1) is well described in literature. Several studies demonstrated the difference in fat contents and other milk production traits in a wide range of cattle breeds, to be associated with missense non-synonymous single nucleotide polymorphisms (nsSNPs) of the DGAT1 gene. As a result, an nsSNPs analysis is crucial for unraveling the DGAT1 structural and conformational dynamics linked to milk fat content. DGAT1-nsSNPs are yet to be studied in terms of their structural and functional impact. Therefore, state-of-the-art computational and structural genomic methods were used to analyze five selected variants (W128R, W214R, C215G, P245R, and W459G), along with the wild type DGAT1. Significant structural and conformational changes in the variants were observed. We illustrate how single amino acid substitutions affect DGAT1 function, how this contributes to our understanding of the molecular basis of variations in DGAT1, and ultimately its impact in improving fat quality in milk.

Time Series Ovarian Transcriptome Analyses of the Porcine Estrous Cycle Reveals Gene Expression Changes during Steroid Metabolism and Corpus Luteum Development.

The porcine estrous cycle is influenced by reproductive hormones, which affect porcine reproduction and result in physiological changes in the reproductive organs. The ovary is involved in ovulation, luteinization, corpus luteum development, and luteolysis. Here, we aimed to provide a comprehensive understanding of the gene expression patterns in porcine ovarian transcriptomes during the estrous cycle through differentially expressed genes profiling and description of molecular mechanisms. The transcriptomes of porcine ovary were obtained during the estrous cycle at three-day intervals from day 0 to day 18 using RNA-seq. At seven time points of the estrous cycle, 4414 DEG were identified; these were classified into three clusters according to their expression patterns. During the late metestrus and diestrus periods, the expression in cluster 1 increased rapidly, and steroid biosynthesis was significant in the pathway. Cluster 2 gene expression patterns represented the cytokine-cytokine receptor interaction in significant pathways. In cluster 3, the hedgehog signaling pathway was selected as the significant pathway. Our study exhibited dynamic gene expression changes with these three different patterns of cluster 1, 2, and 3. The results helped identify the functions and related significant genes especially during the late metestrus and diestrus periods in the estrous cycle.

Integrated multiple transcriptomes in oviductal tissue across the porcine estrous cycle reveal functional roles in oocyte maturation and transport.

Understanding the changes in the swine female reproductive system is important for solving issues related to reproductive failure and litter size. Elucidating the regulatory mechanisms of the natural estrous cycle in the oviduct under non-fertilisation conditions can improve our understanding of its role in the reproductive system. Herein, whole transcriptome RNA sequencing of oviduct tissue samples was performed. The differentially expressed genes (DEGs) were identified for each time point relative to day 0 and classified into three clusters based on their expression patterns. Clusters 1 and 2 included genes involved in the physiological changes through the estrous cycle. Cluster 1 genes were mainly involved in PI3K-Akt signaling and steroid hormone biosynthesis pathways. Cluster 2 genes were involved in extracellular matrix-receptor interactions and protein digestion pathways. In Cluster 3, the DEGs were downregulated in the luteal phase; they were strongly associated with cell cycle, calcium signaling, and oocyte meiosis. The gene expression in the oviduct during the estrous cycle influenced oocyte transport and fertilization. Our findings provide a basis for successfully breeding pigs and elucidating the mechanisms underlying the changes in the pig oviduct during the estrous cycle.

Understanding the swine female reproductive system is important for solving issues related to reproductive failure and litter size. The oviduct is the site of fertilization. After fertilization, the fertilized egg moves to the uterus for implantation. Elucidating the regulatory mechanisms of the estrous cycle in the oviduct can improve our understanding of their roles. In this study, whole transcriptome RNA sequencing of oviduct tissue samples was performed throughout the estrous cycle to screen for differentially expressed genes (DEGs). The DEGs were classified into three clusters based on their expression patterns. Clusters 1 and 2 included genes involved in the physiological changes observed through the estrous cycle. The expression levels of Cluster 3 genes were downregulated specifically in the luteal phase; this was associated with calcium signalling and oocyte meiosis. In this study, we identified that the expression of genes in the oviduct influences oocyte transport and fertilization, which are the key functions of the oviduct. This study provides a basis for successful breeding in the pig industry and elucidating the mechanisms underlying the changes in the pig oviduct during the estrous cycle.

Regulation of Swine Growth by Backfat Tissue during Growing and Finishing Stages.

Recently, interest in the function of pig backfat (BF) has increased in the field of livestock animals, and many transcriptome-based studies using commercial pig breeds have been conducted. However, there is a lack of comprehensive studies regarding the biological mechanisms of Korean native pigs (KNPs) and Yorkshire pig crossbreeds. In this study, therefore, BF samples of F1 crossbreeds of KNPs and Yorkshire pigs were investigated to identify differentially expressed genes (DEGs) and their related terms using RNA-sequencing analysis. DEG analysis identified 611 DEGs, of which 182 were up-regulated and 429 were down-regulated. Lipid metabolism was identified in the up-regulated genes, whereas growth and maturation-related terminologies were identified in the down-regulated genes. LEP and ACTC1 were identified as highly connected core genes during functional gene network analysis. Fat tissue was observed to affect lipid metabolism and organ development due to hormonal changes driven by transcriptional alteration. This study provides a comprehensive understanding of BF contribution to crossbreeds of KNPs and Yorkshire pigs during growth periods.

Comprehensive Transcriptomic Comparison between Porcine CD8- and CD8+ Gamma Delta T Cells Revealed Distinct Immune Phenotype.

We aimed to comprehensively understand the functional mechanisms of immunity, especially of the CD8+/- subsets of gamma delta (γδ) T cells, using an RNA-sequencing analysis. Herein, γδ T cells were obtained from bronchial lymph node tissues of 38-day-old (after weaning 10-day: D10) and 56-day-old (after weaning 28-day: D28) weaned pigs and sorted into CD8+ and CD8- groups. Differentially expressed genes (DEGs) were identified based on the CD8 groups at D10 and D28 time points. We confirmed 1699 DEGs between D10 CD8+ versus D10 CD8- groups and 1784 DEGs between D28 CD8+ versus D28 CD8- groups; 646 upregulated and 561 downregulated DEGs were common. The common upregulated DEGs were enriched in the cytokine-cytokine receptor interaction and T cell receptor (TCR) signaling pathway, and the common downregulated DEGs were enriched in the B cell receptor signaling pathway. Further, chemokine-related genes, interferon gamma, and CD40 ligand were involved in the cytokine-cytokine receptor interaction and TCR signaling pathway, which are associated with inter-regulation in immunity. We expect our results to form the basic data required for understanding the mechanisms of γδ T cells in pigs; however, further studies are required in order to reveal the dynamic changes in γδ T cells under pathogenic infections, such as those by viruses.

Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle.

We performed a genome-wide association study and fine mapping using two methods (single marker regression: frequentist approach and Bayesian C (BayesC): fitting selected single nucleotide polymorphisms (SNPs) in a Bayesian framework) through three high-density SNP chip platforms to analyze milk production phenotypes in Korean Holstein cattle (n = 2780). We identified four significant SNPs for each phenotype in the single marker regression model: AX-311625843 and AX-115099068 on Bos taurus autosome (BTA) 14 for milk yield (MY) and adjusted 305-d fat yield (FY), respectively, AX-428357234 on BTA 18 for adjusted 305-d protein yield (PY), and AX-185120896 on BTA 5 for somatic cell score (SCS). Using the BayesC model, we discovered significant 1-Mb window regions that harbored over 0.5% of the additive genetic variance effects for four milk production phenotypes. The concordant significant SNPs and 1-Mb window regions were characterized into quantitative trait loci (QTL). Among the QTL regions, we focused on a well-known gene (diacylglycerol O-acyltransferase 1 (DGAT1)) and newly identified genes (phosphodiesterase 4B (PDE4B), and anoctamin 2 (ANO2)) for MY and FY, and observed that DGAT1 is involved in glycerolipid metabolism, fat digestion and absorption, metabolic pathways, and retinol metabolism, and PDE4B is involved in cAMP signaling. Our findings suggest that the candidate genes in QTL are strongly related to physiological mechanisms related to the fat production and consequent total MY in Korean Holstein cattle.

Comprehensive Analysis of Cardiac Xeno-Graft Unveils Rejection Mechanisms.

Porcine heart xenotransplantation is a potential treatment for patients with end-stage heart failure. To understand molecular mechanisms of graft rejection after heart transplantation, we transplanted a 31-day-old alpha-1,3-galactosyltransferase knockout (GTKO) porcine heart to a five-year-old cynomolgus monkey. Histological and transcriptome analyses were conducted on xenografted cardiac tissue at rejection (nine days after transplantation). The recipient monkey's blood parameters were analyzed on days -7, -3, 1, 4, and 7. Validation was conducted by quantitative real-time PCR (qPCR) with selected genes. A non-transplanted GTKO porcine heart from an age-matched litter was used as a control. The recipient monkey showed systemic inflammatory responses, and the rejected cardiac graft indicated myocardial infarction and cardiac fibrosis. The transplanted heart exhibited a total of 3748 differentially expressed genes compared to the non-transplanted heart transcriptome, with 2443 upregulated and 1305 downregulated genes. Key biological pathways involved at the terminal stage of graft rejection were cardiomyopathies, extracellular interactions, and ion channel activities. The results of qPCR evaluation were in agreement with the transcriptome data. Transcriptome analysis of porcine cardiac tissue at graft rejection reveals dysregulation of the key molecules and signaling pathways, which play relevant roles on structural and functional integrities of the heart.

Estimation of Variance Components and Genomic Prediction for Individual Birth Weight Using Three Different Genome-Wide SNP Platforms in Yorkshire Pigs.

This study estimates the individual birth weight (IBW) trait heritability and investigates the genomic prediction efficiency using three types of high-density single nucleotide polymorphism (SNP) genotyping panels in Korean Yorkshire pigs. We use 38,864 IBW phenotypic records to identify a suitable model for statistical genetics, where 698 genotypes match our phenotypic records. During our genomic analysis, the deregressed estimated breeding values (DEBVs) and their reliabilities are used as derived response variables from the estimated breeding values (EBVs). Bayesian methods identify the informative regions and perform the genomic prediction using the IBW trait, in which two common significant window regions (SSC8 27 Mb and SSC15 29 Mb) are identified using the three genotyping platforms. Higher prediction ability is observed using the DEBV-including parent average as a response variable, regardless of the SNP genotyping panels and the Bayesian methods, relative to the DEBV-excluding parent average. Hence, we suggest that fine-mapping studies targeting the identified informative regions in this study are necessary to find the causal mutations to improve the IBW trait's prediction ability. Furthermore, studying the IBW trait using a genomic prediction model with a larger genomic dataset may improve the genomic prediction accuracy in Korean Yorkshire pigs.

The Association between Major Dietary Pattern and Low Muscle Mass in Korean Middle-Aged and Elderly Populations: Based on the Korea National Health and Nutrition Examination Survey.

Reduced skeletal muscle mass in older populations is independently associated with functional impairment and disability, resulting in increased risk of mortality and various comorbidities. This study aimed to examine the association between major dietary pattern and low muscle mass among Korean middle-aged and elderly populations. A total of 8136 participants aged ≥50 years were included from a cross-sectional study based on the 2008-2011 Korea National Health and Nutrition Examination Survey. The following four distinct dietary patterns were derived using factor analysis: "Condiment, vegetables, and meats"; "wheat flour, bread, fruits, milk, and dairy products"; "white rice, fish, and seaweeds"; and "whole grain, bean products, and kimchi". A higher "white rice, fish, and seaweeds" pattern score was associated with a lower prevalence of low muscle mass in both men and women, whereas a higher "condiment, vegetables, and meats" pattern score was associated with a higher prevalence of low muscle mass in men. A dietary pattern based on white rice, fish, and seaweeds can be helpful in protecting against loss of skeletal muscle mass in Korean middle-aged and elderly populations. Future research is paramount to confirm the causal association between dietary pattern and the risk of low muscle mass.

Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection.

Porcine reproductive and respiratory syndrome virus (PRRSV) infection is the most important viral disease causing severe economic losses in the swine industry. However, mechanisms underlying gene expression control in immunity-responsible tissues at different time points during PRRSV infection are poorly understood. We constructed an integrated gene co-expression network and identified tissue- and time-dependent biological mechanisms of PRRSV infection through bioinformatics analysis using three tissues (lungs, bronchial lymph nodes [BLNs], and tonsils) via RNA-Seq. Three groups with specific expression patterns (i.e., the 3-dpi, lung, and BLN groups) were discovered. The 3 dpi-specific group showed antiviral and innate-immune signalling similar to the case for influenza A infection. Moreover, we observed adaptive immune responses in the lung-specific group based on various cytokines, while the BLN-specific group showed down-regulated AMPK signalling related to viral replication. Our study may provide comprehensive insights into PRRSV infection, as well as useful information for vaccine development.

Effect of polymorphisms in porcine guanylate-binding proteins on host resistance to PRRSV infection in experimentally challenged pigs.

Guanylate-binding proteins (GBP1 and GBP5) are known to be important for host resistance against porcine reproductive and respiratory syndrome virus (PRRSV) infection. In this study, the effects of polymorphisms in GBP1 (GBP1E2 and WUR) and GBP5 on host immune responses against PRRSV were investigated to elucidate the mechanisms governing increased resistance to this disease. Seventy-one pigs [pre-genotyped based on three SNP markers (GBP1E2, WUR, and GBP5)] were assigned to homozygous (n = 36) and heterozygous (n = 35) groups and challenged with the JA142 PRRSV strain. Another group of nineteen pigs was kept separately as a negative control group. Serum and peripheral blood mononuclear cells (PBMCs) were collected at 0, 3, 7, 14, 21 and 28 days post-challenge (dpc). Viremia and weight gain were measured in all pigs at each time point, and a flow cytometry analysis of PBMCs was performed to evaluate T cell activation. In addition, 15 pigs (5 pigs per homozygous, heterozygous and negative groups) were sacrificed at 3, 14 and 28 dpc, and the local T cell responses were evaluated in the lungs, bronchoalveolar lavage cells (BALc), lymph nodes and tonsils. The heterozygous pigs showed lower viral loads in the serum and lungs and higher weight gains than the homozygous pigs based on the area under the curve calculation. Consistently, compared with the homozygous pigs, the heterozygous pigs exhibited significantly higher levels of IFN-α in the serum, proliferation of various T cells (γδT, Th1, and Th17) in PBMCs and tissues, and cytotoxic T cells in the lungs and BALc. These results indicate that the higher resistance in the pigs heterozygous for the GBP1E2, WUR and GBP5 markers could be mediated by increased antiviral cytokine (IFN-α) production and T cell activation.