The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs.

The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression and the landscape of accessible chromatin to reveal the underlying molecular mechanisms controlling muscle development. To address this, skeletal muscle biopsy samples were taken from Landrace pigs at days 0 (D0), 60 (D60), 120 (D120), and 180 (D180) after birth and were then analyzed using RNA-seq and ATAC-seq. The RNA-seq analysis identified 8554 effective differential genes, among which ACBD7, TMEM220, and ATP1A2 were identified as key genes related to the development of porcine skeletal muscle. Some potential cis-regulatory elements identified by ATAC-seq analysis contain binding sites for many transcription factors, including SP1 and EGR1, which are also the predicted transcription factors regulating the expression of ACBD7 genes. Moreover, the omics analyses revealed regulatory regions that become ectopically active after birth during porcine skeletal muscle development after birth and identified 151,245, 53,435, 30,494, and 40,911 peaks. The enriched functional elements are related to the cell cycle, muscle development, and lipid metabolism. In summary, comprehensive high-resolution gene expression maps were developed for the transcriptome and accessible chromatin during postnatal skeletal muscle development in pigs.

Relationship between oxysterols and mild cognitive impairment in the elderly: a case-control study.

BACKGROUND: To investigate the relationship between oxysterols and mild cognitive impairment (MCI) in a matched case-control study. METHODS: The plasma levels of four oxysterols, 27-hydroxycholesterol (27-OHC), 24S-hydroxycholesterol (24S-OHC), 7α-hydroxycholesterol (7α-OHC) and 7ß-hydroxycholesterol (7ß-OHC), were analyzed by High Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS) and compared between 70 MCI patients and 140 matched controls with normal cognition. The odds ratio (OR) was calculated using logistic analyses to assess the association between oxysterols and MCI. RESULTS: Compared with controls with normal cognition, plasma level of 27-OHC was significantly higher in MCI patients. Logistic analyses suggested high plasma level of 27-OHC was significantly associated with MCI even after multivariate adjustment (OR = 2.86, 95 % CI: 1.52 ~ 5.37). CONCLUSIONS: Our findings suggested that the increased plasma level of 27-OHC was associated with MCI, suggesting high plasma levels of 27-OHC may pay an important role in the development of MCI.

The effect of soybean isoflavone on the dysregulation of NMDA receptor signaling pathway induced by ß-amyloid peptides 1-42 in rats.

Synaptic damage is the key factor of cognitive impairment. The purpose of this study was to understand the effect of soybean isoflavone (SIF) on synaptic damage induced by ß-amyloid peptide 1-42 (Aß1-42) in rats. Adult male Wistar rats were randomly divided into control, Aß1-42, SIF, and SIF + Aß1-42 (SIF pretreatment) groups according to body weight. SIF was treated orally by gavage in SIF and SIF + Aß1-42 groups. After 14 days pretreatment with SIF or vehicle, Aß1-42 was injected into the lateral cerebral ventricle of rats in Aß1-42 and SIF + Aß1-42 groups using miniosmotic pump. The level of Aß1-42 and the expression of N-methyl-D-aspartic-acid receptor (NMDAR) were observed by immunohistochemistry. Reverse transcriptase polymerase chain reaction was used to detect the mRNA levels of NMDAR, calmodulin (CaM), calcium/CaM-dependent protein kinase II (CaMKII), cAMP-response element binding protein (CREB), and brain-derived neurotrophic factor (BDNF). The results showed that Aß1-42 down-regulated mRNA and protein expression of the NR1 and NR2B subunits of NMDAR, SIF pretreatment could reverse these changes. The mRNA expression of CaM, CaMKII, CREB, and BDNF were down-regulated by Aß1-42, but they were all regulated by SIF pretreatment. These results suggest that SIF pretreatment could antagonize the neuron damage in rats induced by Aß1-42, and its mechanism might be associated with the NMDA receptor and CaM/CaMKII/CREB/BDNF signaling pathway, which are the synaptic plasticity-related molecules.

Integrated Analysis of the Transcriptome and Microbial Diversity in the Intestine of Miniature Pig Obesity Model.

Obesity, a key contributor to metabolic disorders, necessitates an in-depth understanding of its pathogenesis and prerequisites for prevention. Guangxi Bama miniature pig (GBM) offers an apt model for obesity-related studies. In this research, we used transcriptomics and 16S rRNA gene sequencing to discern the differentially expressed genes (DEGs) within intestinal (jejunum, ileum, and colon) tissues and variations in microbial communities in intestinal contents of GBM subjected to normal diets (ND) and high-fat, high-carbohydrate diets (HFHCD). After a feeding duration of 26 weeks, the HFHCD-fed experimental group demonstrated notable increases in backfat thickness, BMI, abnormal blood glucose metabolism, and blood lipid levels alongside the escalated serum expression of pro-inflammatory factors and a marked decline in intestinal health status when compared to the ND group. Transcriptomic analysis revealed a total of 1669 DEGs, of which 27 had similar differences in three intestinal segments across different groups, including five immune related genes: COL6A6, CYP1A1, EIF2AK2, NMI, and LGALS3B. Further, we found significant changes in the microbiota composition, with a significant decrease in beneficial bacterial populations within the HFHCD group. Finally, the results of integrated analysis of microbial diversity with transcriptomics show a positive link between certain microbial abundance (Solibacillus, norank_f__Saccharimonadaceae, Candidatus_Saccharimonas, and unclassified_f__Butyricicoccaceae) and changes in gene expression (COL6A6 and NMI). Overall, HFHCD appears to co-contribute to the initiation and progression of obesity in GBM by aggravating inflammatory responses, disrupting immune homeostasis, and creating imbalances in intestinal flora.

Changes in Gut Microbiota Associated with Parity in Large White Sows.

As one of the most critical economic traits, the litter performance of sows is influenced by their parity. Some studies have indicated a connection between the gut microbiota and the litter performance of animals. In this study, we examined litter performance in 1363 records of different parities of Large White sows. We observed a marked decline in TNB (Total Number Born) and NBH (Number of Healthy Born) We observed a marked decline in TNB (Total Number Born) and NBH (Number of Healthy Born) among sows with parity 7 or higher. To gain a deeper understanding of the potential role of gut microbiota in this phenomenon, we conducted 16S rRNA amplicon sequencing of fecal DNA from 263 Large White sows at different parities and compared the changes in their gut microbiota with increasing parity. The results revealed that in comparison to sows with a parity from one to six, sows with a parity of seven or higher exhibited decreased alpha diversity in their gut microbiota. There was an increased proportion of pathogenic bacteria (such as Enterobacteriaceae, Streptococcus, and Escherichia-Shigella) and a reduced proportion of SCFA-producing families (such as Ruminococcaceae), indicating signs of inflammatory aging. The decline in sow function may be one of the primary reasons for the reduction in their litter performance.

Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs.

Litter size and teat number are economically important traits in the porcine industry. However, the genetic mechanisms influencing these traits remain unknown. In this study, we analyzed the genetic basis of litter size and teat number in Bama Xiang pigs and evaluated the genomic inbreeding coefficients of this breed. We conducted a genome-wide association study to identify runs of homozygosity (ROH), and copy number variation (CNV) using the novel Illumina PorcineSNP50 BeadChip array in Bama Xiang pigs and annotated the related genes in significant single nucleotide polymorphisms and common copy number variation region (CCNVR). We calculated the ROH-based genomic inbreeding coefficients (F ROH) and the Spearman coefficient between F ROH and reproduction traits. We completed a mixed linear model association analysis to identify the effect of high-frequency copy number variation (HCNVR; over 5%) on Bama Xiang pig reproductive traits using TASSEL software. Across eight chromosomes, we identified 29 significant single nucleotide polymorphisms, and 12 genes were considered important candidates for litter-size traits based on their vital roles in sperm structure, spermatogenesis, sperm function, ovarian or follicular function, and male/female infertility. We identified 9,322 ROHs; the litter-size traits had a significant negative correlation to F ROH. A total of 3,317 CNVs, 24 CCNVR, and 50 HCNVR were identified using cnvPartition and PennCNV. Eleven genes related to reproduction were identified in CCNVRs, including seven genes related to the testis and sperm function in CCNVR1 (chr1 from 311585283 to 315307620). Two candidate genes (NEURL1 and SH3PXD2A) related to reproduction traits were identified in HCNVR34. The result suggests that these genes may improve the litter size of Bama Xiang by marker-assisted selection. However, attention should be paid to deter inbreeding in Bama Xiang pigs to conserve their genetic diversity.

Evaluating the association between feed efficiency and the fecal microbiota of early-life Duroc pigs using 16S rRNA sequencing.

Improving the predication efficiency of porcine production performance at early stage will contribute to reducing the breeding and production costs. The intestinal microbiota had received plenty of attention in recent years due to their influence on host health and performance. The purpose of this study was to investigate the relationship between the fecal microbiota at early growth period and porcine feed efficiency (FE) under a commercial feeding environment. Ninety-one pigs were reordered according to the residual feed intake (RFI) values between day 90 on test and day 160 off test, 9 lowest RFI pigs and 9 highest RFI pigs were selected as the LRFI group and the HRFI group, respectively. Fecal samples from pigs in the early grower phase (day 80) were performed for microbial diversity, composition, and predicted functionality by using 16S rRNA sequencing. The results showed that no significant differences in microbial alpha diversity were observed between two RFI groups, whereas, some RFI-associated compositional differences were revealed. In particular, the microbiota of the LRFI group (more feed-efficient) had significantly higher levels of some members of Clostridiales and Bacteroidales (e.g., g_1_68 and g_norank_f_p_2534_18B5), which may promoted FE through protecting gut barrier function, compared with those of the HRFI pigs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis found that the LRFI pigs were likely have microbiota with higher levels of amino acid metabolism. Moreover, redundancy analysis (RDA) showed that litter size, parity, and date of birth had significant effects on the bacterial community structure. These results improved our knowledge of the porcine early-life fecal microbiota and its potential link underlying RFI, which would be useful for future development of microbial biomarkers for predicting and improving porcine FE as well as investigation of targets for dietary strategies.

Dietary intakes and biomarker patterns of folate, vitamin B6, and vitamin B12 can be associated with cognitive impairment by hypermethylation of redox-related genes NUDT15 and TXNRD1.

BACKGROUND: B vitamins in the one-carbon metabolism pathway (folate, vitamin B6, and vitamin B12) have been implicated in DNA methylation, and their deficiency may contribute to cognitive decline through increased homocysteine (Hcy) levels and subsequent oxidative damage. The aim of this study was to investigate whether B vitamin deficiency and increased Hcy could interact with DNA methylation of oxidative-related genes and exacerbate cognitive impairment. METHODS: Participants were selected from a large cohort study entitled the Effects and Mechanism Investigation of Cholesterol and Oxysterol on Alzheimer's disease (EMCOA) study. We included 2533 participants who completed a selection of comprehensive cognitive tests and a semiquantitative food frequency questionnaire (FFQ) and were followed for an average of 2.3 years. The longitudinal effects of B vitamin intake on cognitive decline were examined using linear mixed-effect models. Seven mild cognitive impairment (MCI) patients, in the predementia stage of Alzheimer's disease (AD), and fivev healthy controls were selected for the discovery of genome-wide differentially methylated CpG sites. Candidate oxidative stress-related genes significantly correlated with serum levels of B vitamins were selected for validation in 102 MCI patients and 68 controls. The correlations between DNA methylation levels and serum concentrations of B vitamins and oxidative biomarkers were analyzed with Spearman's correlation. The interactive effects of DNA methylation and B vitamins on cognitive performance were further evaluated by multiple linear regression. RESULTS: In the prospective analysis, inadequate dietary intake of vitamin B12 was significantly associated with accelerated cognitive decline, whereas adequate folate, vitamin B6, and vitamin B12 intakes were significantly associated with better cognitive reserve. In the case-control analysis, the DNA methylation levels of NUDT15 and TXNRD1 were examined, and significantly hypermethylated sites were identified in MCI patients. Significant correlations of hypermethylated sites with serum levels of folate, homocysteine (Hcy), and oxidative biomarkers were observed, and interactive effects of B vitamins and hypermethylated sites were significantly associated with cognitive performance. CONCLUSION: Adequate dietary folate at baseline predicted a better cognitive reserve, while decreased serum levels of B vitamins may contribute to cognitive impairment by affecting methylation levels of specific redox-related genes. TRIAL REGISTRATION: EMCOA, ChiCTR-OOC-17011882, Registered 5th, July 2017-Retrospectively registered, http://www.medresman.org/uc/project/projectedit.aspx?proj=2610.

Patterns of cognitive function in middle-aged and elderly Chinese adults-findings from the EMCOA study.

BACKGROUND: The principal aim of this study was to demonstrate the gender-specific cognitive patterns among middle-aged and elderly Chinese adults, investigate the risk factors on global and domain-specific cognitive performance in men and women, respectively, and report demographically adjusted norms for cognitive tests. METHODS: The Effects and Mechanism of Cholesterol and Oxysterol on Alzheimer's disease (EMCOA) study enrolled 4573 participants aged 50-70 years in three Chinese cities. All participants underwent an extensive neuropsychological test battery. Composite scores for specific domains were derived from principal component analysis (PCA). Multivariate linear regression models were used to determine gender-specific risk factors and demographically adjusted normative data. RESULTS: Three cognitive domains of verbal memory, attention/processing speed/executive function, and cognitive flexibility were extracted. A female advantage in verbal memory was observed regardless of age, whereas men tended to outperform women in global cognition and attention/processing speed/executive function. The effects of education on women were more substantial than men for general cognition and attention/processing speed/executive function. For all the cognitive tests, regression-based and demographically adjusted normative data were calculated. CONCLUSIONS: There is a need for gender-specific intervention strategies for operationalizing cognitive impairment. TRIAL REGISTRATION: EMCOA, ChiCTR-OOC-17011882 . Retrospectively registered on 5 July 2017.

High­cholesterol diet results in elevated amyloid­ß and oxysterols in rats.

The aim of the present study was to investigate the effects of diet cholesterol on oxysterol levels and amyloid­ß (Aß) production in the peripheral blood and the brains of Sprague­Dawley (SD) rats. SD rats were randomly divided into five groups and fed 0.015, 0.05, 0.2, 0.5 and 1.6% cholesterol­containing diets for 8 weeks. The effect of the different diets on the levels of cholesterol, oxysterols [including 27­hydroxycholesterol (OHC), 24S­OHC, 7α­OHC and 7ß­OHC], and the Aß1­40 and Aß1­42 peptides were examined in the plasma and the brain of the rats. The results demonstrated that diet cholesterol increased the levels of plasma cholesterol in a dose­dependent manner. The plasma levels of 27­OHC, 7α­OHC and 7ß­OHC significantly increased in the 0.5 and 1.6% cholesterol diet groups and the brain levels of 27­OHC significantly increased in the 1.6% cholesterol diet group. Increased concentration of cholesterol in the diet had no significant influence on plasma and brain levels of 24S­OHC in the rats. In addition, Aß1­40 and Aß1­42 levels in plasma and brain were significantly elevated following administration of 0.5 and 1.6% diet cholesterol. The present study revealed that high diet cholesterol contributed to increased level of oxysterols, especially 27­OHC, in the peripheral blood and the brain, which may be the link between increased peripheral cholesterol and brain Aß production.

Association between Exposure to the Chinese Famine in Different Stages of Early Life and Decline in Cognitive Functioning in Adulthood.

OBJECTIVE: To investigate whether exposure to the Chinese Famine in different life stages of early life is associated with cognitive functioning decline in adulthood. METHODS: We recruited 1366 adults born between 1950 and 1964 and divided them into fetal-exposed, early childhood-exposed (1-3 years old during the famine), mid childhood-exposed (4-6 years old during the famine), late childhood-exposed (7-9 years old during the famine), and non-exposed groups. A selection of cognitive tests was administered to assess their cognitive performance. Association between malnutrition in different famine exposure periods and adult cognitive performance was estimated by multivariate logistic and multiple linear regression analyses. RESULTS: There were significant differences in cognitive performance between subjects exposed to famine during different life stages. For the general cognitive tests, fetal-exposed period was associated with decreased scores of the Mini-Mental State Examination (MMSE), and late childhood-exposed with decreased scores of the Montreal Cognitive Assessment (MoCA). We also found exposure to famine during mid and late childhood was associated with worse performance on the Stroop color and word test. CONCLUSION: Famine exposure in utero and during childhood is associated with overall and specific cognitive decline, affecting selective attention and response inhibition particularly.

The cytotoxicity of 27-hydroxycholesterol in co-cultured SH-SY5Y cells and C6 cells.

BACKGROUND: Diverse physiological and pathological functions of 27-hydroxycholesterol (27-OHC) were proved. However, cytotoxicity and potential influence of 27-OHC on cholesterol metabolism in neurons are unclear. DESIGN AND METHODS: In the vitro co-culture system, SH-SY5Y cells and C6 cells were applied to explore the potential cytotoxicity of 27-OHC. MTT assay was used to detect the cell proliferation. Cell vitality was measured by using the Annexin-FITC/PI test. Immunofluorescence technique was applied to observe the changes of mitochondria membrane potential. The expression of mRNA and protein (including SREBP-1, HMGCR, LXR-α, ABCA1) were measured by real-time PCR and western blot method respectively. RESULTS: 27-OHC induced apoptosis in co-cultured SH-SY5Y cells and C6 cells. 27-OHC treatment significantly inhibited cell viability and proliferation (p<0.05). Compared with control group, 27-OHC caused the reduction of mitochondrial membrane potential (p<0.05). Additionally, the mRNA and protein expression of cholesterol synthesis-related factors, such as SREBP-1, HMGCR, were down-regulated (p<0.05), while the mRNA and protein expression of cholesterol transport-related factors (LXR-α, ABCA1) were up-regulated (p<0.05). CONCLUSIONS: Cytotoxicity and cholesterol metabolism disorder induced by 27-OHC may contribute to the pathogenesis of neurodegenerative disease.

Effects of GSTM1/GSTT1 gene polymorphism and fruit & vegetable consumption on antioxidant biomarkers and cognitive function in the elderly: a community based cross-sectional study.

BACKGROUND: It was reported that Glutathione S-transferase (GST) gene polymorphism and fruit and vegetable (FV) intake were associated with body antioxidant capacity. The oxidative/anti-oxidative imbalance played an important role in the pathogenesis of AD. However, the association of GST genotype, dietary FV consumption with body antioxidant biomarkers and cognitive function in the elderly is not clear. OBJECTIVE: The aim of the present study was to determine the association of GST genotype, and dietary FV intake, with antioxidant biomarkers and cognitive function in the elderly. METHODS: Food frequency questionnaire was used to collect data of dietary FV intakes in 504 community dwelling elderly aged from 55 to 75 years old. GSTM1 and GSTT1 genotypes were determined by using multiple-PCR method. Plasma and erythrocyte antioxidant biomarkers were measured. Cognitive function was measured by using Montreal Cognitive Assessment. Statistical analysis was applied for exploring the association of GST genotype and FV intake with antioxidant biomarkers level and cognitive function in the elderly. RESULTS: Individual GSTM1 or GSTT1 gene deletion affects body antioxidant biomarkers levels, including erythrocyte GST activity, plasma total antioxidant capacity, and glutathione levels. GSTM1and/or GSTT1 gene deletion have no effects on cognitive function in the surveyed participants. The effect of GST genotype on antioxidant biomarkers are FV intake dependent. There is interaction of FV intake and GST genotype on cognitive function in the elderly. CONCLUSION: GST genotype or daily FV consumption impact body antioxidant biomarkers, but not cognitive function in the elderly. There were combined effects of GST genotype and FV consumption on cognitive function in the elderly population. Large scale perspective population study is required to explore the association of GST genetic polymorphism, FV consumption and antioxidant biomarkers and cognitive function in the elderly.