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Abstract Background tRNA fragments (tRFs) are small non-coding RNAs generated from cleaved tRNA molecules, playing key roles in gene regulation and cellular processes. Produced by ribonucleases like angiogenin and Dicer, tRFs vary in length and function in gene silencing and stress responses. They interact with Argonaute proteins and affect mRNA levels, and are emerging as potential diagnostic and therapeutic targets for diseases such as cancer and neurodegenerative disorders. Given that the skin is the largest organ in mammals, it serves as an ideal model for studying development and various diseases. Therefore, this study investigates tRF expression in sheep skin tissues to understand their regulatory roles during growth and development. Results This study analyzed skin tissue from five 1-month-old lambs and five 24-month-old adult Tan sheep using small RNA sequencing and proteomics. Raw sequencing data were filtered and aligned to identify various tsRNAs, while proteomic data were assessed for differential expression. Principal Component Analysis (PCA) revealed distinct separation between juvenile and adult samples based on tsRNA expression patterns, indicating intra-group similarity and inter-group differences. Differentially expressed tsRNAs were identified, with 19 highly expressed tsRNAs at 1 month of age. Proteomic screening identified 932 highly expressed and 835 lowly expressed proteins in the 1-month-old group, with functional enrichment highlighting immunity and inflammation pathways. Predictive analysis of tsRNA target genes intersected with 20 differentially expressed proteins involved in mitochondrial metabolism and stress response. Conclusion This study reveals that tsRNAs significantly influence developmental and immune processes in sheep, with distinct expression patterns between juveniles and adults. Future research should validate these findings and further elucidate the functional mechanisms of tsRNA regulation.

To investigate the effect of fresh corn extract (FCE) on chicken meat quality, 135-day-old Jingyuan chicken hens were fed diets containing different doses of FCE (CON, 0.3% FCE, 0.6% FCE and 0.9% FCE) until 180 day-old in this study. Meat performance measurements showed that the 0.6% FCE group of Jingyuan chickens had higher intramuscular fat (IMF), pressing loss (PL), amino acid and fatty acid contents (P < 0.05). Their breasts were collected for transcriptomic and metabolomic analyses (n=8), and 210 Differentially expressed genes (DEGs) and 29 Differentially expressed genes (DEMs) were obtained. Gene Ontology (GO) analyses of DEGs indicate multiple entries involved in IMF synthesis such as skeletal system development and cellular response to amino acid stimulation. Kyoto Encyclopedia of Genes and Genomes (GSEA-KEGG) analysis identified sphingolipid_metabolism and multiple genes affecting IMF deposition including SPHK1, CERS1, CERS6, GLB1L, SGMS2, UGT8, and UGCG. KEGG and metabolite correlation analyses of DEMs identified Aspartate, PI 38:5; PI(18:1/20:4), PI 36:3; PI(18:1/18:2), PI 36:2; PI(18:0/18:2), and PI 34:1; PI(16:0/18:1) as the likely major influences on IMF deposition in the DEMs. Correlation analysis revealed that shear force (SF) was significantly and positively correlated with Aspartate and CERS6; PL was significantly and positively correlated with SPHK1 and UGCG (P < 0.05). IMF was significantly and positively correlated with PI 34:1; PI (16:0/18:1), SPHK1 and UGCG; and flesh colour yellowness b* was significantly and positively correlated with SGMS2 (P < 0.05). The above results indicate that feeding a basal diet containing 0.6% FCE can improve the meat quality of Jingyuan chicken, which provides a theoretical basis for improving the meat quality of Jingyuan chicken.

Milk production traits play an important role in dairy cattle breeding, and single nucleotide polymorphisms can be used as effective molecular markers for milk production trait marker-assisted breeding in dairy cattle. Based on the results of the preliminary GWAS, candidate genes SPP1 and NCAPG associated with milk production traits were screened. In this study, the aim was to screen and characterize the SNPs of SPP1 and NCAPG genes about milk production traits. Two SNPs and one haplotype block of the SPP1 gene and four SNPs and one haplotype block of the NCAPG gene were obtained by amplification, sequencing and association analysis, and all six SNPs were located in the exon region. Association analysis showed that all six SNPs were significantly associated with milk protein percentage. Linkage disequilibrium analysis showed that 2 SNPs of SPP1 (g. 36,700,265 C > T and g. 36,693,596 C > A) constituted a haplotype that correlated with milk protein percentage, and the dominant haplotype was H2H2, which was CCTT. 4 SNPs of NCAPG (g. 37,342,705 C > A, g. 37,343,379 G > T, g. 37,374,314 C > A and g. 37,377,857 G > A) constituted a haplotype associated with milk protein percentage, 305-days milk protein yield and 305 days milk yield. Tissue expression profiling results revealed that SPP1 and NCAPG had the highest expression in mammary tissue. Interference with SPP1 and NCAPG inhibited the proliferation of Bovine mammary epithelial cells. (BMECs), down-regulated the expression of PCNA, CDK2 and CCND1, up-regulated the expression of BAX and BAD, and promoted apoptosis. Reduced triglyceride synthesis in BMECs, down-regulated the expression of DGAT1, DGAT2, LPIN1, and AGPAT6.SPP1 and NCAPG are involved in the synthesis of milk proteins, and interfering with SPP1 and NCAPG decreased the secretion of β-casein, κ-casein, and αs1-casein, as well as up-regulated the CSN2 and CSN3 expression. The above results indicate that the SNP loci of SPP1 and NCAPG can be used as potential molecular markers to improve milk production traits in dairy cows, laying the foundation for marker-assisted selection. It also proves that SPP1 and NCAPG can be used as candidate key genes for milk production traits in dairy cows, providing new insights into the physiological mechanisms of lactation regulation in dairy cows.

In Holstein cows, β-casein, one of the most critical proteins in milk, exists in two main genotypes, A1 and A2. Herein, 45 Holstein cows [categorized into three groups based on β-casein A1A1, A1A2, and A2A2 genotypes (N = 15)] with the same feeding management and litter size were enrolled to explore differences in rumen microflora and metabolites across various β-casein genotypes. Rumen fluids were collected for metagenomics and metabolomics analyses. Metabolomics and weighted gene co-expression network analysis (WGCNA) revealed that arachidonic acid (AA), adrenic acid (AdA), glycocholic acid (GCA), and taurocholic acid (TCA) were significantly and positively correlated with milk fat % in dairy cows (p

Abstract Background Cow milk fat is an essential indicator for evaluating and measuring milk quality and cow performance. Growing research has identified the molecular functions of circular RNAs (circRNAs) necessary for mammary gland development and lactation in mammals. Method The present study analyzed circRNA expression profiling data in mammary epithelial cells (MECs) from cows with highly variable milk fat percentage (MFP) using differential expression analysis and weighted gene co-expression network analysis (WGCNA). Results A total of 309 differentially expressed circRNAs (DE-circRNAs) were identified in the high and low MFP groups. WGCNA analysis revealed that the pink module was significantly associated with MFP (r = − 0.85, P = 0.007). Parental genes of circRNAs in this module were enriched mainly in lipid metabolism-related signaling pathways, such as focal adhesion, ECM-receptor interaction, adherens junction and AMPK. Finally, six DE-circRNAs were screened from the pink module: circ_0010571, circ_0007797, circ_0002746, circ_0003052, circ_0004319, and circ_0012840. Among them, circ_0002746, circ_0003052, circ_0004319, and circ_0012840 had circular structures and were highly expressed in mammary tissues. Subcellular localization revealed that these four DE-circRNAs may play a regulatory role in the mammary glands of dairy cows, mainly as competitive endogenous RNAs (ceRNAs). Seven hub target genes (GNB1, GNG2, PLCB1, PLCG1, ATP6V0C, NDUFS4, and PIGH) were obtained by constructing the regulatory network of their ceRNAs and then analyzed by CytoHubba and MCODE plugins in Cytoscape. Functional enrichment analysis revealed that these genes are crucial and most probable ceRNA regulators in milk fat metabolism. Conclusions Our study identified several vital circRNAs and ceRNAs affecting milk fat synthesis, providing new research ideas and a theoretical basis for cow lactation, milk quality, and breed improvement.

The Chinese Tan sheep is a unique breed of sheep that is typical throughout China, mainly used for fur and meat production. They are widely distributed in northwestern China and are famous for their lambskin and shiny white curly wool. In this study, the phenotypic traits of wool length, birth weight, and head coat color were evaluated in 256 Chinese Tan sheep breeds. Whole genome sequencing generated 23.67 million high-quality SNPs for genome-wide association studies (GWAS). We identified 208 significant SNPs associated with birth wool length, implicating RAD50, MACROD2, SAMD5, SASH1, and SPTLC3 as potential candidate genes for this trait. For birth weight, 1056 significant SNPs, with 76.89% of them located on chromosome 2, were identified by GWAS, and XPA, INVS, LOC121818504, GABBR2, LOC101114941, and LOC106990096 were identified as potential candidate genes for birth weight. The GWAS for head coat color identified 1424 significant SNPs across three chromosomes, with 99.65% on chromosome 14, and SPIRE2, TCF25, and MC1R as candidate genes were found to be possibly involved in the development of the black-headed coat color in sheep. Furthermore, we selected head coat color as a representative trait and performed an independent test of our GWAS findings through multiplex PCR SNP genotyping. The findings validated five mutation sites in chromosome 14 (14,251,947 T>A, 14,252,090 G>A, 14,252,158 C>T, 14,252,329 T>G, and 14,252,464 C>T) within the exon1 of the MC1R gene (517 bp), as identified by GWAS in an additional 102 Tan sheep individuals, and revealed that black-headed sheep predominantly exhibited heterozygous genotypes, possibly contributing to their color change. Our results provide a valuable foundation for further study of these three economically important traits, and enhance our understanding of genetic structure and variation in Chinese Tan sheep.

ABSTRACT: Inosine monophosphate (IMP) plays a significant role in meat taste, yet the molecular mechanisms controlling IMP deposition in muscle tissues still require elucidation. The present study systematically and comprehensively explores the molecular network governing IMP deposition in different regions of Jingyuan chicken muscle. Two muscle groups, the breast and leg, were examined as test materials. Using nontargeted metabolomic sequencing, we screened and identified 20 metabolites that regulate IMP-specific deposition. We maintained regular author and institution formatting, used clear, objective, and value-neutral language, and avoided biased or emotional language. We followed a consistent footnote style and formatting features and used precise word choice with technical terms where appropriate. Out of these, 5 were identified as significant contributors to the regulation of IMP deposition. We explained technical term abbreviations when first used and ensured a logical flow of information with causal connections between statements. The results indicate that PGM1, a key enzyme involved in synthesis, is higher in the breast muscle compared to the leg muscle, which may provide an explanation for the increased deposition of IMP in the breast muscle. We aimed for a clear structure with logical progression, avoided filler words, and ensured grammatical correctness. The activity of key enzymes (PKM2, AK1, AMPD1) involved in this process was higher in the breast muscle than in the leg muscle. In the case of IMP degradation metabolism, the activity of its participating enzyme (PurH) was lower in the breast muscle than in the leg muscle. These findings suggest that the increased deposition of IMP in Jingyuan chickens' breast muscle may result from elevated metabolism and reduced catabolism of key metabolites. In summary, a metaomic strategy was utilized to assess the molecular network regulation mechanism of IMP-specific deposition in various segments of Jingyuan chicken. These findings provide insight into genetic improvement and molecular breeding of meat quality traits for top-notch broilers.

BackgroundInosine monophosphate (IMP) is naturally present in poultry muscle and plays a key role in improving meat flavour. However, IMP deposition is regulated by numerous genes and complex molecular networks. In order to excavate key candidate genes that may regulate IMP synthesis, we performed proteome and metabolome analyses on the leg muscle, compared to the breast muscle control of 180-day-old Jingyuan chickens (hens), which had different IMP content. The key candidate genes identified by a differential analysis were verified to be associated with regulation of IMP-specific deposition.ResultsThe results showed that the differentially expressed (DE) proteins and metabolites jointly involve 14 metabolic pathways, among which the purine metabolic pathway closely related to IMP synthesis and metabolism is enriched with four DE proteins downregulated (with higher expression in breast muscles than in leg muscles), including adenylate kinase 1 (AK1), adenosine monophosphate deaminase 1 (AMPD1), pyruvate kinase muscle isoenzyme 2 (PKM2) and phosphoglucomutase 1 (PGM1), six DE metabolites, Hypoxanthine, Guanosine, L-Glutamine, AICAR, AMP and Adenylsuccinic acid. Analysis of PGM1 gene showed that the high expression of PGM1 promoted the proliferation and differentiation of myoblasts and inhibited the apoptosis of myoblasts. ELISA tests have shown that PGM1 reduced adenosine triphosphate (ATP) and IMP and uric acid (UA), while enhancing the biosynthesis of hypoxanthine (HX). In addition, up-regulation of PGM1 inhibited the expression of purine metabolism pathway related genes, and promoted the IMP de novo and salvage synthesis pathways.ConclusionThis study preliminarily explored the mechanism of action of PGM1 in regulating the growth and development of myoblasts and specific IMP deposition in Jingyuan chickens, which provided certain theoretical basis for the development and utilization of excellent traits in Jingyuan chickens.

ABSTRACT: Intramuscular fat (IMF) has a pivotal influence on meat quality, with its deposition being a multifaceted physiological interaction of several regulatory factors. N6-methyladenosine (m6A), the preeminent epigenetic alteration among eukaryotic RNA modifications, holds a crucial role in moderating post-transcriptional gene expression. However, there is a dearth of comprehensive understanding regarding the functional machinery of m6A modification in the context of IMF deposition in poultry. Our current study entails an analysis of the disparities in IMF within the breast and leg of 180-day-old Jingyuan chickens. We implemented methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to delve into the distribution of m6A and its putative regulatory frameworks on IMF deposition in chickens. The findings demonstrated a markedly higher IMF content in leg relative to breast (P < 0.01). Furthermore, the expression of METTL14, WTAP, FTO, and ALKBH5 was significantly diminished in comparison to that of breast (P < 0.01). The m6A peaks in the breast and leg primarily populated 3′untranslated regions (3′UTR) and coding sequence (CDS) regions. The leg, when juxtaposed with the breast, manifested 176 differentially methylated genes (DMGs), including 151 hyper-methylated DMGs and 25 hypo-methylated DMGs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed a pronounced enrichment of DMGs in the biosynthesis of amino acids, peroxisome, Fatty acid biosynthesis, fatty acid elongation, and cell adhesion molecules (CAMs) pathways. Key DMGs, namely ECH1, BCAT1, and CYP1B1 were implicated in the regulation of muscle lipid anabolism. Our study offers substantial insight and forms a robust foundation for further exploration of the functional mechanisms of m6A modification in modulating IMF deposition. This holds profound theoretical importance for improving and leveraging meat quality in indigenous chicken breeds.

Objective Inosine monophosphate (IMP) is a key factor that imparts of meat flavor. Differences in the IMP content in the muscles were evaluated to improve chicken meat quality. Methods For this study, the IMP content was detected by high performance liquid chromatography. The gene expression profiles of Jingyuan chickens with different feeding patterns and different sexes were analyzed by RNA-sequencing (RNA-seq). Results Breast muscle IMP content in free-range chickens was extremely significantly higher than that of caged chickens (p

ABSTRACT: Intramuscular fat (IMF) is an important indicator for determining meat quality, and IMF deposition during muscle development is regulated by a complex molecular network involving multiple genes. The N6-methyladenosine (m6A) modification of mRNA plays an important regulatory role in muscle adipogenesis. However, the distribution of m6A and its role in IMF metabolism in poultry has not been reported. In the present study, a transcriptome-wide m6A profile was constructed using methylated RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq) to explore the potential mechanism of regulating IMF deposition in the breast muscle based on the comparative analysis of IMF differences in the breast muscles of 42 (group G), 126 (group S), and 180-days old (group M) Jingyuan chickens. The findings revealed that the IMF content in the breast muscle increased significantly with the increase in the growth days of the Jingyuan chickens (P < 0.05). The m6A peak in the breast muscles of the 3 groups was highly enriched in the coding sequence (CDS) and 3′ untranslated regions (3′ UTR), which corresponded to the consensus motif RRACH. Moreover, we identified 129, 103, and 162 differentially methylated genes (DMGs) in the breast muscle samples of the G, S, and M groups, respectively. Functional enrichment analyses revealed that DMGs are involved in many physiological activities of muscle fat anabolism. The m6A-induced ferroptosis pathway was identified in breast muscle tissue as a new target for regulating IMF metabolism. In addition, association analysis demonstrated that LMOD2 and its multiple m6A negatively regulated DMGs are potential regulators of IMF differential deposition in muscle. The findings of the present study provide a solid foundation for further investigation into the potential role of m6A modification in regulating chicken fat metabolism.

The present study investigated the effect of different dietary levels (0%, 0.25%, 0.5%, 1%, 2%) of Sophora alopecuroides (S. alopecuroides) on intramuscular fat (IMF) content in Ningxia Tan sheep. Candidate genes affecting IMF deposition were screened by comparing the RNA-Seq profiles of test (2% S. alopecuroides) and control (no S. alopecuroides) groups. The results showed that the intramuscular fat content of the diet supplemented with S. alopecuroides was significantly lower than that of the control group, and the intramuscular fat content decreased significantly with the increase of the dietary content of S. alopecuroides (P < 0.05). The highest IMF content of the control group (group A) was 4.21%, which was significantly higher than that of the other four experimental groups (B, C, D, E) (P < 0.05). Moreover, 66 genes were significantly upregulated and 202 genes were significantly downregulated in the test group compared to the control. Gene Ontology functional annotation revealed that the differentially expressed genes were closely related to plasma lipoprotein particle assembly, plasma lipoprotein particle organization, protein-lipid complex subunit organization, and other biological processes. KEGG pathway analysis showed that the differentially expressed genes belonged to 147 metabolic pathways. Finally, four differential genes which may be related to IMF deposition were screened out in PPAR signalling pathway, fatty acid biosynthesis, fatty acid degradation, and fatty acid metabolism. The quantitative analysis of four differential genes including ACSL3, PLIN2, ABCA1 and ANGPTL4 was carried out by RT-qPCR method, and the results were basically consistent with those of RNA-seq. Among them, the quantitative results of PLIN2 gene were slightly different from the sequencing results, but the difference was not significant, and they may be false positive. This study lays the foundation for understanding the molecular mechanism regulating mutton quality, and provides a theoretical basis for the study of S. alopecuroides as a feed additive to improve mutton meat quality and impact the gene function.

Abstract Milk fat is the most important and energy-rich substance in milk, and its content and composition are important reference elements in the evaluation of milk quality. However, the current identification of valuable candidate genes affecting milk fat is limited. IlluminaPE150 was used to sequence bovine mammary epithelial cells (BMECs) with high and low milk fat rates (MFP), the weighted gene co-expression network (WGCNA) was used to analyze mRNA expression profile data in this study. As a result, a total of 10,310 genes were used to construct WGCNA, and the genes were classified into 18 modules. Among them, violet (r = 0.74), yellow (r = 0.75) and darkolivegreen (r = − 0.79) modules were significantly associated with MFP, and 39, 181, 75 hub genes were identified, respectively. Combining enrichment analysis and differential genes (DEs), we screened five key candidate DEs related to lipid metabolism, namely PI4K2A, SLC16A1, ATP8A2, VEGFD and ID1, respectively. Relative to the small intestine, liver, kidney, heart, ovary and uterus, the gene expression of PI4K2A is the highest in mammary gland, and is significantly enriched in GO terms and pathways related to milk fat metabolism, such as monocarboxylic acid transport, phospholipid transport, phosphatidylinositol signaling system, inositol phosphate metabolism and MAPK signaling pathway. This study uses WGCNA to form an overall view of MFP, providing a theoretical basis for identifying potential pathways and hub genes that may be involved in milk fat synthesis.

The inosine monophosphate (IMP) content in chicken meat is closely related to muscle quality and is an important factor affecting meat flavor. However, the molecular regulatory mechanisms underlying the IMP-specific deposition in muscle remain unclear. This study performed transcriptome analysis of muscle tissues from different parts, feeding methods, sexes, and breeds of 180-day-old Jingyuan chickens, combined with differential expression and weighted gene co-expression network analysis (WGCNA), to identify the functional genes that regulate IMP deposition. Out of the four comparison groups, 1,775, 409, 102, and 60 differentially expressed genes (DEGs) were identified, of which PDHA2, ACSS2, PGAM1, GAPDH, PGM1, GPI, and TPI1 may be involved in the anabolic process of muscle IMP in the form of energy metabolism or amino acid metabolism. WGCNA identified 11 biofunctional modules associated with IMP deposition. The brown, midnight blue, red, and yellow modules were strongly correlated with IMP and cooking loss (p < 0.05). Functional enrichment analysis showed that glycolysis/gluconeogenesis, arginine and proline metabolism, and pyruvate metabolism, regulated by PYCR1, SMOX, and ACSS2, were necessary for muscle IMP-specific deposition. In addition, combined analyses of DEGs and four WGCNA modules identified TGIF1 and THBS1 as potential candidate genes affecting IMP deposition in muscle. This study explored the functional genes that regulate muscle development and IMP synthesis from multiple perspectives, providing an important theoretical basis for improving the meat quality and molecular breeding of Jingyuan chickens.

BackgroundMilk fat is one of the main reference elements for evaluating milk quality and is a primary objective trait in dairy cattle breeding. In recent years, circular RNAs (circRNAs) have been found to play crucial roles in many biological processes. However, the function and expression profiles of circRNAs in milk fat synthesis in cows are not completely understood. We performed RNA sequencing to analyze the genome-wide expression of circRNA transcripts in bovine mammary epithelial cells (BMECs) from cows with extreme differences in milk fat percentage. We identified candidate differential circRNAs associated with milk fat metabolism using functional enrichment analysis and constructed a lipid metabolism-related competing endogenous RNA (ceRNA) interactive regulatory network.ResultsA total of 290 circRNAs were significantly differentially expressed (DE-circRNAs) in high milk fat percentage (HMF) cows compared to that in low milk fat percentage (LMF) cows. Of the 290 circRNAs, 142 were significantly upregulated and 148 were significantly downregulated. Enrichment analysis (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes) identified four DE-circRNAs (circ_0001122, circ_0007367, circ_0018269, and circ_0015179) that potentially regulate milk fat metabolism. Among them, circ_0001122, circ_0007367, and circ_0015179 had relatively high expression levels in cow mammary gland tissue compared to other tissues (heart, liver, kidney, uterus, ovaries, and small intestine) of cows. The regulatory networks circ_0001122:miR-12043:LIPG, circ_0007367:miR-331-3p:CIDEA/PML, and circ_0018269:miR-11989:RORC/HPX are potential networks to explore the mechanism of milk fat regulation.ConclusionsThese results reveal the possible role of circRNAs in milk fat metabolism in dairy cows. Several important circRNAs and ceRNAs affecting milk fat synthesis were identified, providing insights into the complex biology of milk fat synthesis as well as a novel theoretical perspective for future research on lactation, milk quality, and breed improvement in dairy cows.

Functional cells in embryonic myogenesis and postnatal muscle development undergo multiple stages of proliferation and differentiation, which are strict procedural regulation processes. N6-methyladenosine (m6A) is the most abundant RNA modification that regulates gene expression in specific cell types in eukaryotes and regulates various biological activities, such as RNA processing and metabolism. Recent studies have shown that m6A modification-mediated transcriptional and post-transcriptional regulation plays an essential role in myogenesis. This review outlines embryonic and postnatal myogenic differentiation and summarizes the important roles played by functional cells in each developmental period. Furthermore, the key roles of m6A modifications and their regulators in myogenesis were highlighted, and the synergistic regulation of m6A modifications with myogenic transcription factors was emphasized to characterize the cascade of transcriptional and post-transcriptional regulation during myogenesis. This review also discusses the crosstalk between m6A modifications and non-coding RNAs, proposing a novel mechanism for post-transcriptional regulation during skeletal muscle development. In summary, the transcriptional and post-transcriptional regulatory mechanisms mediated by m6A and their regulators may help develop new strategies to maintain muscle homeostasis, which are expected to become targets for animal muscle-specific trait breeding and treatment of muscle metabolic diseases.

Inosine monophosphate (IMP) is an indicator of meat taste, and the molecular mechanism underlying IMP deposition in muscle tissues is important to developing superior poultry breeds. The aim of this study was to identify the key proteins regulating IMP deposition in different muscle groups of 180-day-old Jingyuan chickens (Hen) using a proteomics-based approach. We identified 1,300 proteins in the muscle tissues of Jingyuan chickens, of which 322 were differentially expressed between the breast and leg muscles (129 proteins were highly expressed in breast muscles and 193 proteins were highly expressed in leg muscles). PGM1, PKM2, AK1, AMPD1, and PurH/ATIC were among the differentially expressed proteins (DEPs) involved in the purine metabolism pathway, of which purH was highly expressed in leg muscles, while the others were highly expressed in breast muscles. The proteomics screening results were verified by PRM, qPCR, and western blotting, showing consistency with the proteomics results. Our findings are not only significant in terms of protecting the Jingyuan chicken germplasm resources, but also provide the molecular basis for generating high-quality broiler chicken breeds.

Long noncoding RNAs (lncRNAs) play an important regulatory role in various biological processes as a key regulatory factor. However, the complete expression profile of lncRNAs in dairy cows and its function in milk fat synthesis are unknown. In this study, RNA sequencing (RNA-seq) was used to research the whole genome expression of lncRNAs and mRNA transcripts in high and low milk fat percentage (MFP) bovine mammary epithelial cells (BMECs), and joint analysis was carried out. We identified a total of 47 differentially expressed genes (DEGs) and 38 differentially expressed lncRNAs (DELs, Padj

Milk fat is the most important and energy-rich substance in milk and plays an important role in the metabolism of nutrients during human growth and development. It is mainly used in the production of butter and yogurt. Milk fat not only affects the flavor and nutritional value of milk, but also is the main target trait of ruminant breeding. There are many key genes involve in ruminant milk fat synthesis, including ACSS2, FASN, ACACA, CD36, ACSL, SLC27A, FABP3, SCD, GPAM, AGPAT, LPIN, DGAT1, PLIN2, XDH, and BTN1A1. Taking the de novo synthesis of fatty acids (FA) and intaking of long-chain fatty acids (LCFA) in blood to the end of lipid droplet secretion as the mainline, this manuscript elucidates the complex regulation model of key genes in mammary epithelial cells (MECs) in ruminant milk fat synthesis, and constructs the whole regulatory network of milk fat synthesis, to provide valuable theoretical basis and research ideas for the study of milk fat regulation mechanism of ruminants.

Background Ye Mule Aries sheep is one of the most important sheep breeds in Xinjiang, China. This breed is well adapted to harsh environmental conditions and displays strong disease resistance, fast growth, and high cold tolerance. To analyze the clonal expression and immunogenicity of the Ye Mule Aries sheep inhibin gene, total RNA was extracted from sheep ovarian tissue and used as a template to generate a eukaryotic expression vector and study inhibin immunogenicity. Methods Primers were designed to amplify the inhibin A gene via polymerase chain reaction and the amplified product was cloned between the ScalI and EcoRI restriction sites of the expression vector pEGFP-N1 to construct a recombinant plasmid, pEGFP-INHα. Following the validation of successful cloning, the pEGFP-INHα plasmid was transfected into BHK cells to verify expression in eukaryotes and subsequently utilized as an antigen in rabbits. Rabbits were tested for anti-inhibin antibodies and serum follicle-stimulating hormone (FSH) concentrations. Results The analysis of the INHα gene sequence revealed that INHα is 1109 bp long and is translated to an approximately 40 KDa protein. Bioinformatics approach indicated that the INHα gene is highly conserved between organisms. Immunization with the eukaryotic expression vector, pEGFP-INHα, which expresses the INHα gene elicited immune response and generatigeneration on of anti-INHα antibody. The antibody had a significant regulatory effect on the serum concentration of FSH in rabbits and led to higher levels of FSH, indicating increased ovary function. Conclusions The present work resulted in a successful construction of eukaryotic expression plasmid pEGFP-INHα and verified the immunogenicity of this highly conserved protein. Further, the expression of pEGFP-INHα was shown to have a significant impact on the secretion of FSH, indicating a potential regulatory role in ovarian function. In conclusion, our current findings can serve as a working model for studying the effect of INHα on the breeding performance of Ye Mule Aries sheep, providing a novel strategy to improve their reproduction rates.

High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and quality traits in Holstein cattle population from China. These traits included milk yield, fat, and protein. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a linear mixed model. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten single-nucleotide polymorphisms (SNPs) were detected above the genome-wide significant threshold (p < 4.0 × 10−7), including six located in previously reported quantitative traits locus (QTL) regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The study not only identified the effect of DGAT1 gene on milk fat and protein, but also discovered novel genetic loci and candidate genes related to milk traits. These novel genetic loci would be an important basis for molecular breeding in dairy cattle.

In this study, we examined correlations between the deposition of inosine monophosphate (IMP) and mRNA expression of the adenylate kinase 1 (AK1) gene in Jingyuan chicken. The IMP content was determined by high-performance liquid chromatography. Transcriptome sequencing was used to screen the differentially expressed gene AK1 and real-time quantitative polymerase chain reaction (PCR) to determine the expression level of AK1 mRNA associated with IMP synthesis. IMP and inosine content in the breast muscles of both Jingyuan cocks and hens was found to be significantly higher than that in the leg muscles. Similarly, the expression of AK1 mRNA in the breast muscles of cocks and hens was significantly higher than that in the leg muscles. Moreover, AK1 mRNA expression in cock breast muscles was negatively correlated with IMP content, whereas its expression in cock leg muscles was positively correlated with IMP content. In contrast, the expression of AK1 mRNA in hen breast and leg muscles was significantly positively correlated with IMP content. These findings provide a scientific basis for enhancing the meat flavor of Jingyuan chicken and promoting the development and utilization of local variety resources, as well as constituting a basis for screening IMP-regulated genes. Our study will advance our current understanding of AK1 function.

Background: Inosine monophosphate (IMP) is naturally present in poultry muscle and plays a key role in improving meat flavour. However, IMP deposition is regulated by numerous genes and complex molecular networks. In order to excavate key candidate genes that may regulate IMP synthesis, we performed proteome and metabolome analyses on the leg muscle, compared to the breast muscle control of 180-day-old Jingyuan chickens (hens), which had different IMP content. The key candidate genes identified by a differential analysis were verified to be associated with regulation of IMP-specific deposition. Results: The results showed that the differentially expressed (DE) proteins and metabolites jointly involve 14 metabolic pathways, among which the purine metabolic pathway closely related to IMP synthesis and metabolism is enriched with four DE proteins downregulated (with higher expression in breast muscles than in leg muscles), including adenylate kinase 1 (AK1), adenosine monophosphate deaminase 1 (AMPD1), pyruvate kinase muscle isoenzyme 2 (PKM2) and phosphoglucomutase 1 (PGM1), six DE metabolites, Hypoxanthine, Guanosine, L-Glutamine, AICAR, AMP and Adenylsuccinic acid. Analysis of PGM1 gene showed that the high expression of PGM1 promoted the proliferation and differentiation of myoblasts and inhibited the apoptosis of myoblasts. ELISA tests have shown that PGM1 reduced adenosine triphosphate (ATP) and IMP and uric acid (UA), while enhancing the biosynthesis of hypoxanthine (HX). In addition, up-regulation of PGM1 inhibited the expression of purine metabolism pathway related genes, and promoted the IMP de novo and salvage synthesis pathways. Conclusion: This study preliminarily explored the mechanism of action of PGM1 in regulating the growth and development of myoblasts and specific IMP deposition in Jingyuan chickens, which provided certain theoretical basis for the development and utilization of excellent traits in Jingyuan chickens. [ABSTRACT FROM AUTHOR]

Diacetylmorphine (DA) abuse can result in severe arrhythmias and even sudden death. Although previous research has connected ion channel proteins to arrhythmia occurrences, the precise mechanism underlying DA-induced arrhythmias remains poorly understood. This study conducted a comprehensive analysis of the myocardial toxicity of DA by applying proteomic and histopathological approaches and investigated the underlying mechanisms using in vitro experiments. In vivo experiments confirmed that DA induces cardiac arrhythmias, as evidenced by electrocardiographic analyses of rats. Additionally, Masson staining, wheat germ agglutinin staining (WGA) staining, and western blotting of myocardial tissues revealed significant myocardial damage. Tandem mass tag proteomics analysis identified syntrophin alpha 1 (SNTA1) as a pivotal target molecule linked to myocardial toxicity. Ex vivo experiments showed specific upregulation of SNTA1 in rat cardiomyocytes following DA exposure. Furthermore, in vitro experiments indicated that DA caused disruption of potassium channels and activated the arrhythmia-related PI3K/AKT signaling pathway. Silencing and overexpression studies of SNTA1 highlighted its role in ion channel abnormalities and that of the PI3K/AKT signaling pathway expression in cardiomyocytes, underscoring the crucial role of mitochondrial function in cardiac arrhythmias. This research indicates that SNTA1 is integral to arrhythmia development by influencing the PI3K/AKT signaling pathway, leading to mitochondrial dysfunction and ion channel irregularities. SNTA1 is a potential therapeutic target for DA-induced arrhythmias. This study enhances our understanding of DA-induced myocardial toxicity and offers valuable insights for assessing the risks of DA exposure in humans.

To explore the effects of fresh leaves harvested at different picking periods on aroma quality and chemical characteristics of oolong tea, morning leaves and evening leaves of Tieguanyin were selected as materials and turned into morning tea and evening tea according to the traditional technology. The volatile components of fresh leaves and oolong tea were analyzed by the method of gas chromatography-mass spectrometer (GC-MS), in order to compare their differences between morning oolong tea and evening oolong tea. The results showed that total volatile components of evening tea were 28.3% less than that of morning tea. The content and proportion of alcohol compounds were superior, especially isophytol and trans-nerolidol. The characteristics of volatile components in fresh leaves were different from that in oolong tea. The rate of alcohol compounds was close to that of acid compounds in fresh leaves, while in oolong teas the difference was large. Two kinds of fresh leaves had 56 identical components, that were 4 more than the two kinds of oolong tea. However, among 42 common components of fresh leaves and oolong tea, palmitic acid, dihydroactinidiolide, trans-nerolidol and isophytol were obviously affected by the manufacture technology, and their variation amplitudes were large. It can be seen that the distribution characteristics of volatile compounds of evening leaves and morning ones were different, and the aroma quality of evening tea was better than that of morning tea, especially the refreshing aroma.

Ten percent of non-small cell lung cancer patients with epidermal growth factor receptor (EGFR) mutations harbor uncommon variants. These mutations are mainly involved in lung adenocarcinomas but are rare in lung squamous cell carcinoma (LSCC). In 2018, the Food and Drug Administration-approved afatinib for this specific patient population. However, there is limited information regarding the effectiveness of afatinib for LSCC with EGFR mutations. This case report documented a unique case of a patient with LSCC, which had a rare compound EGFR mutation (G719C and S768I) and showed significant response to afatinib treatment, with 10 months of progression-free survival. New NTRK1 and RET gene mutations may play a potential role in the development of acquired resistance to afatinib following clinical progression. This case highlights the importance of genetic profiling in patients with LSCC. Although these patients have a low positive rate of EGFR mutations, searching for EGFR mutations in these patients might broaden their treatment options.

Acne vulgaris ranks as the second most prevalent dermatological condition worldwide, and there are still insufficient safe and reliable drugs to treat it. Cryptotanshinone (CTS), a bioactive compound derived from traditional Chinese medicine Salvia miltiorrhiza, has shown promise for treating acne vulgaris due to its broad-spectrum antimicrobial and significant anti-inflammatory properties. Nevertheless, its local application is hindered by its low solubility and poor skin permeability. To overcome these challenges, a carrier-free pure drug self-assembled nanosystem is employed, which can specifically modify drug molecules based on the disease type and microenvironment, offering a potential for more effective treatment. We designed and synthesized three distinct structures of cationic CTS-peptide conjugates, creating self-assembled nanoparticles. This study has explored their self-assembly behavior, skin permeation, cellular uptake, and both in vitro and in vivo anti-acne effects. Molecular dynamics simulations revealed these nanoparticles form through intermolecular hydrogen bonding and π-π stacking interactions. Notably, self-assembled nanoparticles demonstrated enhanced bioavailability with higher skin permeation and cellular uptake rates. Furthermore, the nanoparticles exhibited superior anti-acne effects compared to the parent drug, attributed to heightened antimicrobial activity and significant downregulation of the MAPK/NF-κB pathway, leading to reduced expression of pro-inflammatory factors including TNF-α, IL-1β and IL-8. In summary, the carrier-free self-assembled nanoparticles based on CTS-peptide conjugate effectively address the issue of poor skin bioavailability, offering a promising new approach for acne treatment.

Abstract Although opioids are necessary for the treatment of acute pain, cancer pain, and palliative care, opioid abuse is a serious threat to society. Heroin (Diacetylmorphine) is the most commonly abused opioid, and it can have a variety of effects on the body's tissues and organs, including the well-known gastrointestinal depression and respiratory depression; however, there is little known about the effects of diacetylmorphine on cardiac damage. Here, we demonstrate that diacetylmorphine induces abnormal electrocardiographic changes in rats and causes damage to cardiomyocytes in vitro by an underlying mechanism of increased autophosphorylation of CaMKII and concomitant regulation of myocardial contractile protein TPM1 and MYOM2 protein expression. The CaMKII inhibitor KN-93 was first tested to rescue the toxic effects of heroin on cardiomyocytes in vitro and the abnormal ECG changes caused by heroin in SD rats, followed by the TMT relative quantitative protein technique to analyze the proteome changes. Diacetylmorphine causes increased phosphorylation at the CaMKII Thr287 site in myocardium, resulting in increased autophosphorylation of CaMKII and subsequent alterations in myocardial contractile proteins, leading to myocardial rhythm abnormalities. These findings provide a theoretical basis for the treatment and prevention of patients with arrhythmias caused by diacetylmorphine inhalation and injection.

Abstract To examine the protecting effect of jasmine tea extract (JTE) against ultraviolet B (UVB) induced damage on human retinal pigment epithelial (RPE) cells, the RPE cells were subjected to UVB exposure and sequential JTE administration. The cell viability, intracellular reactive oxygen species (ROS), and apoptosis were determined by MTT, 2ʹ,7ʹ-dichlorodihydrofluorescein diacetate and flow cytometer assays, respectively. Further, the cells treated with UVB irradiation and sequential JTE administration were subjected to RNA-sequencing analysis in order to identify genes and pathways involved in the UVB-induced damage and JTE protecting mechanisms. The results showed that JTE effectively attenuated the UVB-induced cell injury by reducing the excessive intracellular ROS generation, and inhibiting the expression of apoptotic genes such as Bax, Caspase-3/9. This finding may offer a promising candidate for the prevention of UVB exposure related eye diseases.

Abstract Objective The effects of Otubain-2 (OTUB2) on the proliferation, invasion, and migration of esophageal squamous cell carcinoma (ESCC) were investigated by interfering with OTUB2 expression. Methods Bioinformatics analysis was used to analyze OTUB2 expression in esophageal carcinoma and interactions between OTUB2 and YAP1/TAZ. Paraffin-embedded ESCC tissues (n = 183) were selected for immunohistochemical staining to detect OTUB2, YAP1, TAZ, CTGF and their relationship with clinicopathological parameters, then the survival prognosis of ESCC patients was analyzed. Immunofluorescence, western blotting, and qRT-PCR were used to evaluate OTUB2 in ESCC cell lines. Cell lines with the highest expression of OTUB2 were transfected with lentivirus to knockdown OTUB2 levels. Changes in KYSE150 cell proliferation, migration, and invasion were measured using CCK-8, wound healing, and clone formation assays. The Transwell test and flow cytometry identified OTUB2 targets and explored roles and mechanisms involved in ESCC. Effects of OTUB2 on YAP1/TAZ signaling were also observed. Results Bioinformatics analysis revealed OTUB2 was highly expressed in esophageal cancer and was associated with YAP1/TAZ. Immunohistochemistry showed that OTUB2 expression was increased in ESCC samples compared to parcancerous tissue. YAP1 and TAZ were higher expression in ESCC tissues, mainly localized in the nucleus. Compared with controls, the proliferation, migration, and invasion ability of KYSE150 cells after OTUB2 knockdown were significantly reduced (P

Objective To evaluate the clinical efficacy and safety of leflunomide (LEF) combined with prednisone for the treatment of PLA2R-associated primary membranous nephropathy (PMN) and changes in anti-PLA2R antibody titers after treatment. Methods Sixty patients with nephrotic syndrome, biopsy-proven MN and anti-PLA2R antibody positivity were included in this study conducted from December 2017 to February 2019. The patients were randomly divided into an experimental group (n = 30) and a control group (n = 30). The patients in the experimental group were treated with LEF combined with prednisone, whereas the patients in the control group were treated with cyclophosphamide (CTX) combined with prednisone. We assessed 24-h urinary protein and serum albumin levels, kidney function markers, blood lipid levels and anti-PLA2R antibody titers before and after treatment. Adverse reactions during treatment were recorded. Results After 16 weeks of treatment, there were 2 cases of complete remission and 6 cases of partial remission in the experimental group, with a total effective rate of 26.67%. In the control group, there were 4 cases of complete remission and 8 cases of partial remission, with a total effective rate of 40% (p > .05). After 24 weeks of treatment, the total effective rates of the experimental and control groups were 66.67% and 76.67%, respectively (p > .05). There were no significant differences in 24-h urinary protein, serum albumin, kidney function marker or blood lipid levels between the two groups after treatment (p > .05). However, there were fewer adverse reactions in the experimental group than in the control group (p .05). Conclusion LEF combined with prednisone has a certain efficacy for the treatment of PLA2R-associated PMN and provokes few adverse reactions. A large-sample randomized double-blind controlled study with a long follow-up period is needed to verify the efficacy of LEF combined with prednisone.

Objective: By copying the uric acid nephropathy rat model, the oxidative stress injury of mitochondria was caused in renal tubular epithelial cells and the relationship between the injury and the induction of cell apoptosis was identified. Methods: All rats were randomly divided into NC (normal control, NC) group, HUA (high uric acid, HUA) group and GSH (reductive glutathione, GSH) group. The values were quantitatively tested in the kidney tissues, including 24-h urinary protein quantity, serum creatinine, blood uric acid, the MDA (malondialdehyde, MDA) and SOD (superoxide dismutase, SOD) oxidative stress indicators. The expression of p53, Bax and caspase-9/-3 were detected by immunoblotting. TUNEL assays were used to detect the apoptosis of renal tubular epithelial cells. Result: In HUA and GSH groups, the 24-h urinary protein(24UTP), serum creatinine, and blood uric acid increased gradually with the increase of the replication cycle and the increase was significant compared to the NC group (p

Fatty acids (FAs) are important precursors of oolong tea volatile substances, and their famous derivatives have been shown to be the key aroma components. However, the relationship between fatty acids and their derivatives during oolong tea production remains unclear. In this study, fresh Tieguanyin leaves were manufactured into oolong tea and green tea (control), and fatty acids and fatty acid-derived volatiles (FADV) were extracted from processed samples by the sulfuric acid–methanol method and solvent-assisted flavor evaporation (SAFE), respectively. The results showed that unsaturated fatty acids were more abundant than saturated fatty acids in fresh leaves and decreased significantly during tea making. Relative to that in green tea, fatty acids showed larger variations in oolong tea, especially at the green-making stage. Unlike fatty acids, the FADV content first increased and then decreased. During oolong tea manufacture, FADV contents were significantly and negatively correlated with total fatty acids; during the green-making stage, methyl jasmonate (MeJA) content was significantly and negatively correlated with abundant fatty acids except steric acid. Our data suggest that the aroma quality of oolong tea can be improved by manipulating fatty acid transformation.

Background: Previous studies have shown that podocyte autophagy is an important trigger for proteinuria and glomerulosclerosis. The mammalian rapamycin target protein (mTOR) occupies a pivotal position in the autophagy pathway. In this study, we planned to clarify the mechanism of mTOR regulation of podocyte autophagy and the effect of rapamycin (RAPA). Methods: All rats were randomly divided into normal control group (n = 8), DN group (n = 8), and RAPA group (n = 8). Blood and urine samples were collected at the 4th, 8th, and 12th weeks of the experiment. The serum creatinine (Scr), urine volume levels, and the 24 h urine protein (UP) levels were examined. The nephrin, podocin, mTOR, ribosomal S6 kinase 1 (S6K1), and autophagy marker light chain 3 (LC3II) expression levels were evaluated by immunohistochemistry, quantitative PCR, and immunoblotting. Results: The urine volume, 24 h UP, and Scr of the DN and RAPA groups increased significantly compared with the NC group (p

As a semifermented tea, oolong is exceedingly popular worldwide for its elegant, flowery aroma and mellow, rich taste. However, recent marketing trends for old oolong teas and their chemical quality largely remain unexplored. In this study, we applied widely targeted metabolomics using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) combined with multivariate analysis to investigate the chemical change of oolong teas in the aging process. With the increasing of store time, most nongalloylated catechins; tannins, including TFs and proanthocyanidins; flavonols and glycosylated flavonols; amino acids and their derivatives; nucleotides and their derivatives; and lots of alkaloids and phospholipids declined, while most fatty acids and organic acids increased, and galloylated catechins, GA, and caffeine were almost stable. The result also suggested that approximately seven years (but not an infinite extension) was a special period for oolong tea storage, which brings about excellent taste.

Characteristic aroma is a well-appreciated feature contributing to tea quality. Although extensive studies have been made to investigate aroma biosynthesis and gene expressions during tea making processes, it remains unclear whether the endogenous volatile biosynthesis during postharvest tea processing contributes to the aroma quality of made tea. To critically evaluate this question, we used the same batch of fresh tea leaves and produced three different types of tea with different degrees of fermentation (green tea, oolong tea, and black tea). Total volatiles were extracted by solvent-assisted-flavor evaporation, then quantified by gas chromatography-flame ionization detector combined with response factor correction for quantitative measurement. Compared with fresh tea leaves, the volatile profiles of the made teas were dramatically altered, with significant loss for the majority of endogenous volatiles and simultaneous gain for non-endogenous volatiles. By calculation of odor-activity values, the potential volatiles contributing to the aroma characteristics of each tea type were identified. Our data suggest that postharvest synthesis of endogenous volatiles did not contribute to the aroma quality of made tea.

A moral concept involves two main factors: moral cognition (indicated by morality) and emotion (indicated by emotionality). The cognitive mechanism underlying moral metaphors on the vertical dimension (e.g., moral-up, immoral-down) was investigated in three experiments using implicit association tests. The results of Experiment 1 show a stronger association of “moral-up, immoral-down” between words high in morality and vertical space than between words low in morality and vertical space, which indicates that cognitive factors of morality facilitate the processing of vertical spatial metaphors of moral concepts. Experiment 2, employing moral words different in emotionality, reveals a stronger association of “moral-up, immoral-down” between words high in emotionality and vertical space than between words low in emotionality and vertical space, which shows that emotional factors of morality facilitate the processing of vertical spatial metaphors of moral concepts. A comparison between the two experiments suggests a faster response to emotion than to moral cognition and similar association strengths of the two factors with verticality. Using words high in morality and emotionality, Experiment 3 shows that a combination of the two conditions (i.e., high morality and high emotionality) leads to a stronger tie with verticality than either condition. The above three experiments indicate that both moral cognition and emotion facilitate the processing of vertical spatial metaphor of moral concepts, and the forces of the two, which jointly affect the metaphorical connection between morality and verticality, are basically equal, although the processing of emotionality is faster than that of morality.