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The placenta is a crucial determinant of fetal survival, growth, and development. Deficiency in placental development directly causes intrauterine growth retardation (IUGR). IUGR can lead to fetal growth restriction and an increase in the mortality rate. The genetic mechanisms underlying IUGR development, however, remain unclear. In the present study, we integrated whole-genome DNA methylation and transcriptomic analyses to determine distinct gene expression patterns in various placental tissues to identify pivotal genes that are implicated with IUGR development. By performing RNA-sequencing analysis, 1487 differentially expressed genes (DEGs), with 737 upregulated and 750 downregulated genes, were identified in IUGR pigs (H_IUGR) compared with that in normal birth weight pigs (N_IUGR) (p < 0.05); furthermore, 77 miRNAs, 1331 lncRNAs, and 61 circRNAs were differentially expressed. The protein–protein interaction network analysis revealed that among these DEGs, the genes GNGT1, ANXA1, and CDC20 related to cellular developmental processes and blood vessel development were the key genes associated with the development of IUGR. A total of 495,870 differentially methylated regions were identified between the N_IUGR and H_IUGR groups, which included 25,053 differentially methylated genes (DMEs); moreover, the overall methylation level was higher in the H_IUGR group than in the N_IUGR group. Combined analysis showed an inverse correlation between methylation levels and gene expression. A total of 1375 genes involved in developmental processes, tissue development, and immune system regulation exhibited methylation differences in gene expression levels in the promoter regions and gene ontology regions. Five genes, namely, ANXA1, ADM, NRP2, SHH, and SMAD1, with high methylation levels were identified as potential contributors to IUGR development. These findings provide valuable insights that DNA methylation plays a crucial role in the epigenetic regulation of gene expression and mammalian development and that DNA-hypermethylated genes contribute to IUGR development in Rongchang pigs.

The sirtuin family, a group of NAD+-dependent class 3 histone deacetylases (HDACs), was extensively studied initially as a group of longevity genes that are activated in caloric restriction and act in concert with nicotinamide adenine dinucleotides to extend the lifespan. Subsequent studies have found that sirtuins are involved in various physiological processes, including cell proliferation, apoptosis, cell cycle progression, and insulin signaling, and they have been extensively studied as cancer genes. In recent years, it has been found that caloric restriction increases ovarian reserves, suggesting that sirtuins may play a regulatory role in reproductive capacity, and interest in the sirtuin family has continued to increase. The purpose of this paper is to summarize the existing studies and analyze the role and mechanism of SIRT1, a member of the sirtuin family, in regulating ovarian function. Research and review on the positive regulation of SIRT1 in ovarian function and its therapeutic effect on PCOS syndrome.

In recent years, software development models have undergone changes. In order to meet user needs and functional changes, open-source software continuously improves its software quality through successive releases. Due to the iterative development process of open-source software, open-source software testing also requires continuous learning to understand the changes in the software. Therefore, the fault detection process of open-source software involves a learning process. Additionally, the complexity and uncertainty of the open-source software development process also lead to stochastically introduced faults when troubleshooting in the open-source software debugging process. Considering the phenomenon of learning factors and the random introduction of faults during the testing process of open-source software, this paper proposes a reliability modeling method for open-source software that considers learning factors and the random introduction of faults. Least square estimation and maximal likelihood estimation are used to determine the model parameters. Four fault data sets from Apache open-source software projects are used to compare the model performances. Experimental results indicate that the proposed model is superior to other models. The proposed model can accurately predict the number of remaining faults in the open-source software and be used for actual open-source software reliability evaluation.

Polycystic ovary syndrome (PCOS) is an endocrine disorder characterized by hyperandrogenemia with multiple suspended sinus follicles, thickened cortical tissue, and excessive proliferation of ovarian granulosa cells that severely affects the fertility and quality of life of women. The addition of n-3 PUFA to the diet may slightly reduce body weight and greatly alleviate disturbed blood hormone levels in PCOS mice. We treated KGN as a cell model for n-3 PUFA addition and showed that n-3 PUFA inhibited the proliferation of GCs and promoted ferroptosis in ovarian granulosa cells. We used CCK-8, fluorescence quantitative transmission electron microscopy experiments and ferroptosis marker gene detection and other methods. Furthermore, n-3 PUFA was found to promote YAP1 exocytosis by activating Hippo and weakening the cross-talk between YAP1 and Nrf2 by activating the Hippo signaling pathway. In this study, we found that n-3 PUFA inhibited the over proliferation of granulosa cells in ovarian follicles by activating Hippo, promoting YAP1 exocytosis, weakening the cross-talk between YAP1 and Nrf2, and ultimately activating the ferroptosis sensitivity of ovarian granulosa cells. We demonstrate that n-3 PUFA can alleviate the hormonal and estrous cycle disorder with PCOS by inhibiting the YAP1-Nrf2 crosstalk that suppresses over proliferating ovarian granulosa cells and promotes iron death in GCs. These findings reveal the molecular mechanisms by which n-3 PUFA attenuates PCOS and identify YAP1-Nrf2 as a potential therapeutic target for regulation granulosa cells in PCOS.

Mycotoxins are ubiquitously present in feeds and raw materials and can exert toxicity on animals and humans. Therefore, mycotoxin occurrence should be monitored. We report here a multi-mycotoxin survey of feed samples in China from 2017 to 2021. Concentrations of aflatoxins, trichothecenes type B, fumonisins, and zearalenone were determined in a total of 9392 samples collected throughout China. Regional differences and year-to-year variation of mycotoxin occurrence were also assessed in new-season corn. Generally, Fusarium mycotoxins were prevalent, while mycotoxin contamination in each feed commodity showed a distinct pattern, e.g., wheat and bran were typically affected by trichothecenes type B, peanut meals were highly susceptible to aflatoxins, and finished feeds exhibited a comparatively high prevalence of all mycotoxins. In new-season corn, trichothecenes type B and fumonisins were most prevalent, with positive rates of 84.04% and 87.16%, respectively. Regions exhibited different patterns of mycotoxin occurrence. The Anhui and Jiangsu provinces of East China exhibited a high prevalence and concentrations of aflatoxins with a positive rate and a positive average of 82.61% and 103.08 μg/kg, respectively. Central China obtained high fumonisins levels of 4707.84 μg/kg. Trichothecenes type B and zearalenone occurred more frequently in temperate regions of Northeast China, and their positive rates reached 94.99% and 55.67%, respectively. In these regions, mycotoxin concentrations in new-season corn exhibited pronounced year-to-year variations and this could be due to the unusual changes of rainfall or temperature during sensitive periods of corn growing. A large fraction of new-season corn samples contained multiple mycotoxins with two to three classes (75.42%), and the most frequently observed co-contaminants were the combination of trichothecenes type B and fumonisins (73.52%). Trichothecenes type B and zearalenone concentrations were highly positively correlated with a coefficient of 0.775. In conclusion, mycotoxins contamination and co-contamination of feeds are common. Mycotoxin contamination in new-season corn exhibited regional patterns and year-to-year variations, with climate and weather conditions as determinant factors.

Epigenetic factors, including non-coding RNA regulation, play a vital role in the development of obesity and have been well researched. Transfer RNA-derived small RNA (tsRNA) is a class of non-coding RNA proven to be involved in various aspects of mammalian biology. Here we take pigs as a model for obesity research and use tsRNA-seq to investigate the difference in tsRNA expression in the subcutaneous adipose tissue of obese and lean pigs to elucidate the role of tsRNA in obesity development. A total of 482 tsRNAs were identified in pig adipose tissue, of which 123 were significantly differentially accumulated tsRNAs compared with the control group. The tRF-5c was the main type of these tsRNAs. The largest number of tsRNAs produced was the Gly-carrying tRNA, which produced 81 tsRNAs. Functional enrichment analysis revealed that differential tsRNAs indirectly participated in MAPK, AMPK, insulin resistance, the TNF signaling pathway, adipocytokine signaling pathway, and other signaling pathways by interacting with target genes. These are involved in bioenergetic metabolic regulatory processes, suggesting that tsRNAs may influence these pathways to mediate the regulation of energy metabolism in porcine adipocytes to promote lipid deposition, thus contributing to obesity. Our findings suggest a potential function of tsRNA in regulating obesity development.

This study aimed to identify biomarkers for pork quality evaluation. Firstly, the correlation between indicators of pork quality evaluation was investigated. The pH of pork meat at 45 min post slaughter showed a significant negative correlation with meat color indicators (r: −0.4868–−0.3040). Subsequently, porcine plasma samples were further divided into low pH (pH = 6.16 ± 0.22) or high pH (pH = 6.75 ± 0.08) groups. Plasma metabolites in both sample groups were investigated using untargeted metabolomics. In total, 90 metabolites were recognized as differential metabolites using partial least squares discriminant analysis. Pathway enrichment analysis indicated these differential metabolites were enriched in amino acid metabolism and energy metabolism. Correlation analysis revealed that creatinine, L-carnitine, D-sphingosine, citraconic acid, and other metabolites may constitute novel plasma biomarkers with the pH value of pork meat. The current study provides important insights into plasma biomarkers for predicting pork quality based on pH value.

Genistein (GEN), a phytoestrogen, has been reported to regulate skeletal muscle endocrine factor expression and muscle fiber type switching, but its role in skeletal muscle regeneration is poorly understood. As a class of epigenetic regulators widely involved in skeletal muscle development, microRNAs (miRNAs) have the potential to treat skeletal muscle injury. In this study, we identified miR-221 and miR-222 and their target genes MyoG and Tnnc1 as key regulators during skeletal muscle regeneration, and both were regulated by GEN. C2C12 myoblasts and C2C12 myotubes were then used to simulate the proliferation and differentiation of muscle satellite cells during skeletal muscle regeneration. The results showed that GEN could inhibit the proliferation of satellite cells and promote the differentiation of satellite cells by inhibiting the expression of miR-221/222. Subsequent in vitro and in vivo experiments showed that GEN improved skeletal muscle regeneration mainly by promoting satellite cell differentiation in the middle and late stages, by regulating miR-221/222 expression. These results suggest that miR-221/222 and their natural regulator GEN have potential applications in skeletal muscle regeneration.

Intrauterine growth restriction (IUGR) is an important cause of newborn morbidity and mortality in mammals. Transfer RNA-derived small RNA (tsRNA) has become an emerging non-coding RNA in recent years. tsRNA and microRNAs (miRNAs) share similar mechanisms, which are involved in various biological processes. In this study, the pig was used as a model of IUGR, and the tsRNA and miRNA expression profile in the spleen was characterized by RNA sequencing. A total of 361 miRNAs and 620 tsRNAs were identified, of which 22 were differentially expressed miRNA (DEM) and 25 differentially expressed tsRNA (DET). tRF-5c were the primary tsRNA type making up more than 90%, and the most abundantly expressed tsRNAs are from tRNA-Gly-GCC. Functional enrichment analysis found that those DETs and DEMs have been implicated in the immune system process. Protein–protein interaction (PPI) network analysis revealed ssc-miR-370, ssc-miR-206, tiRNA-Ser-TGA-001 and tRF-Val-AAC-034 could be major regulators. TNF, TLR4, CD44, MAPK1 and STAT1 were predicted hub target genes. Those DETs and DEMs may regulate the T-cell receptor signaling pathway and Toll-like receptor signaling pathway to mediate the immunocompromise caused by IUGR. The results discussed in this article uncover the potential role of tsRNAs and miRNAs in IUGR porcine spleen.

As the medium of material exchange between mother and fetus, umbilical cord blood is closely connected with fetal development. microRNA (miRNA) has a wide range of biological functions and has high flow characteristics. Small RNA sequencing of pig umbilical venous blood (UVB) and umbilical arterial blood (UAB) revealed that a total of 302 miRNAs were identified, and 106 and 22 miRNAs were specifically expressed in the UVB and UAB, respectively. Using the two methods of differential expression multiple and differential expression percentage, it is found that only 35% of the highly expressed miRNAs in the UVB by the two analysis modes overlap, but 56.25% of the enriched signal pathways are the same. Only 20% of the highly expressed miRNAs in the UAB overlap, but 62.07% of the signal pathways are the same. Further analysis revealed that miR-423 can be used as a characteristic miRNA of UVB and has the potential to treat muscle-related diseases. miR-122-5p can be used as a characteristic miRNA of UAB and may help to improve liver- and brain-related diseases. In summary, these results enrich understanding of miRNA in mother–fetal communication and provide a reference for the development and application of porcine cord blood products.

tRNA-derived fragments (tRFs), a novel type of non-coding RNA derived from tRNAs, play an important part in governing gene expressions at a post-transcriptional level. To date, the regulatory mechanism of tRFs governing fat deposition and adipogenesis is completely unknown. In this study, high fat diet was employed to induce an obese rat model, and tRFs transcriptome sequencing was conducted to identify differentially expressed tRFs that response to obesity. We found out that tRFGluTTC, which promoted preadipocyte proliferation by increasing expressions of cell cycle regulatory factors, had the highest fold change in the 296 differentially expressed tRFs. Moreover, tRFGluTTC also suppressed preadipocyte differentiation by reducing triglyceride content and lipid accumulation, and by decreasing expressions of genes that related to fatty acid synthesis. According to results of luciferase activity analysis, tRFGluTTC directly targeted Kruppel-like factor (KLF) 9, KLF11, and KLF12, thus significantly suppressing mRNA expressions of these target genes. Moreover, tRFGluTTC suppressed adipogenesis, accompanying by suppressing expressions of adipogenic transcription factors (aP2, PPARγ, and C/EBPα). In conclusion, these results imply that tRFGluTTC may act as a novel epigenetic molecule regulating adipogenesis and could provide a new strategy for the intervention treatment of obesity.

The biochemical and functional differences between oxidative and glycolytic muscles could affect human muscle health and animal meat quality. However, present understanding of the epigenetic regulation with respect to lncRNAs and circRNAs is rudimentary. Here, porcine oxidative and glycolytic skeletal muscles, which were at the growth curve inflection point, were sampled to survey variant global expression of lncRNAs and circRNAs using RNA-seq. A total of 4046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including the oxidation-reduction process, glycolytic process, and fatty acid metabolic. All these were closely related to different phenotypes between oxidative and glycolytic muscles. Additionally, 810 circRNAs were identified, of which 137 were differentially expressed (p < 0.05). Interestingly, some circRNA-miRNA-mRNA networks were found, which were closely linked to muscle fiber-type switching and mitochondria biogenesis in muscles. Furthermore, 44.69%, 39.19%, and 54.01% of differentially expressed mRNAs, lncRNAs, and circRNAs respectively were significantly enriched in pig quantitative trait loci (QTL) regions for growth and meat quality traits. This study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological functions, which may improve understanding of muscle metabolism and development from an epigenetic perspective.

Intermuscular adipose tissue is located between the muscle fiber bundles in skeletal muscles, and has similar metabolic features to visceral adipose tissue, which has been found to be related to a number of obesity-related diseases. Although various miRNAs are known to play crucial roles in adipose deposition and adipogenesis, the microRNA transcriptome of intermuscular adipose tissue has not, until now, been studied. Here, we sequenced the miRNA transcriptomes of porcine intermuscular adipose tissue by small RNA-sequencing and compared it to a representative subcutaneous adipose tissue. We found that the inflammation- and diabetes-related miRNAs were significantly enriched in the intermuscular rather than in the subcutaneous adipose tissue. A functional enrichment analysis of the genes predicted to be targeted by the enriched miRNAs also indicated that intermuscular adipose tissue was associated mainly with immune and inflammation responses. Our results suggest that the intermuscular adipose tissue should be recognized as a potential metabolic risk factor of obesity.

tRNA-derived fragments (tRFs) are a new class of non-coding RNA that play an important role in regulating cellular RNA processing and protein translation. However, there is currently no study reporting the influence of tRFs on myocardial hypertrophy. In this study, we used an isoproterenol (ISO)-induced myocardial hypertrophy rat model. Small RNA (

Excessive accumulation of adipose tissue is a main cause of obesity or overweight, which is significantly involved in increasing the risk of diseases. Recently, numerous studies have proved that microRNAs (miRNAs) play important roles in adipogenesis by negatively regulating gene expression at posttranscriptional levels. In this study, we showed that miR-125a-5p was expressed at lower levels in the adipose tissues of high-fat diet (HFD)-fed mice than the normal chow (NCW)-fed mice. MiR-125a-5p expression were strongly up-regulated by nearly five-fold, when 3T3-L1 preadipocyte were induced and differentiated into mature adipocytes. Functional analysis indicated that overexpression of miR-125a-5p promoted 3T3-L1 preadipocyte proliferation and inhibited its differentiation. By contrast, inhibition of miR-125a-5p repressed 3T3-L1 preadipocyte proliferation and accelerated its differentiation. Furthermore, a dual-luciferase reporter assay demonstrated that signal transducer and activator of transcription 3 (STAT3) is a direct target gene of miR-125a-5p during 3T3-L1 preadipocyte differentiation. Further analysis confirmed that the process of miR-125a-5p inhibiting 3T3-L1 preadipocyte differentiation might be associated with the regulation of fatty acid metabolism related genes. Taken together, our results indicated that miR-125a-5p might promote 3T3-L1 preadipocyte proliferation, whereas inhibiting 3T3-L1 preadipocyte differentiation by negatively regulating STAT3.

Intramuscular fat (IMF) content and composition are considered crucial indicators of porcine meat quality. However, the molecular mechanism of porcine IMF development is still mostly unclear. Recently, new evidence suggested that microRNA (miRNAs) play important roles in porcine intramuscular adipogenesis. Previously, microRNA-125a-5p (miR-125a-5p) was identified as an important regulator of adipogenesis. In the present study, we found that the expression of miR-125a-5p is dynamically regulated during porcine intramuscular preadipocytes differentiation and that its expression levels in different porcine muscle tissues were negatively involved with IMF content. To investigate the potential function role of miR-125a-5p in IMF development, porcine intramuscular preadipocytes were collected and transfected with miR-125a-5p mimics, inhibitors, or a negative control (NC), respectively. The results showed that overexpression of miR-125a-5p promoted proliferation and inhibited differentiation of porcine intramuscular preadipocytes while inhibition of miR-125a-5p had the opposite effects. Furthermore, a luciferase reporter assay demonstrated that porcine kruppel like factor 3 (KLF13) is a target gene of miR-125a-5p during porcine intramuscular preadipocytes differentiation. Interestingly, porcine ELOVL fatty acid elongase 6 (ELOVL6), a regulator of fatty acid composition, was also identified as a target gene of miR-125a-5p during porcine intramuscular adipogenesis. Further studies show that miR-125a-5p overexpression reduced total saturated fatty acids (SFA) content and monounsaturated fatty acids (MUFA)/SFA ratios while having no significant impact on polyunsaturated fatty acids (PUFA)/SFA and n-6/n-3 ratios. Taken together, our results identified that miR-125a-5p may be a novel regulator of porcine intramuscular adipogenesis and the fatty acid composition of porcine IMF.

Obesity is a major driver of metabolic diseases such as nonalcoholic fatty liver disease, certain cancers, and insulin resistance. However, there are no effective drugs to treat obesity. Betaine is a nontoxic, chemically stable and naturally occurring molecule. This study shows that dietary betaine supplementation significantly inhibits the white fat production in a high-fat diet (HFD)-induced obese mice. This might be due to betaine preventing the formation of new white fat (WAT), and guiding the original WAT to burn through stimulated mitochondrial biogenesis and promoting browning of WAT. Furthermore, dietary betaine supplementation decreases intramyocellular lipid accumulation in HFD-induced obese mice. Further analysis shows that betaine supplementation reduced intramyocellular lipid accumulation might be associated with increasing polyunsaturated fatty acids (PUFA), fatty acid oxidation, and the inhibition of fatty acid synthesis in muscle. Notably, by performing insulin-tolerance tests (ITTs) and glucose-tolerance tests (GTTs), dietary betaine supplementation could be observed for improvement of obesity and non-obesity induced insulin resistance. Together, these findings could suggest that inhibiting WAT production, intramyocellular lipid accumulation and inflammation, betaine supplementation limits HFD-induced obesity and improves insulin resistance.