Based on the Cancer Genome Atlas Database Development of a prognostic model of RNA binding protein in stomach adenocarcinoma.

The purpose of this study was to identify potential RNA binding proteins associated with the survival of gastric adenocarcinoma, as well as the corresponding biological characteristics and signaling pathways of these RNA binding proteins. RNA sequencing and clinical data were obtained from the cancer genome map (N = 32, T = 375) and the comprehensive gene expression database (GSE84437, N = 433). The samples in The Cancer Genome Atlas were randomly divided into a development group and a test group. A total of 1495 RNA binding protein related genes were extracted. Using nonparametric tests to analyze the difference of RNA binding protein related genes, 296 differential RNA binding proteins were obtained, 166 were up-regulated and 130 were down regulated. Twenty prognosis-related RNA binding proteins were screened using Cox regression, including 14 high-risk genes (hazard ratio > 1.0) and 6 low-risk genes (hazard ratio < 1.0). Seven RNA binding protein related genes were screened from the final prognostic model and used to construct a new prognostic model. Using the development group and test group, the model was verified with survival analysis, receiver operating characteristics curves and prognosis analysis curves. A prediction nomogram was finally developed and showed good prediction performance.

In silico genomic and proteomic analyses of three heat shock proteins (HSP70, HSP90-a, and HSP90-b) in even-toed ungulates

BACKGROUND Heat shock proteins (HSPs) play important roles in the responses to different environmental stresses. In this study, the genomic and proteomic characteristics of three HSPs (HSP70, HSP90-a and HSP90-b) in five even-toed ungulates (sheep, goats, water buffalo, Zebu cattle and cattle) were analyzed using Multiple sequence alignment, SWISS modeling and phylogenetics analysis tools. RESULTS The bioinformatic analysis revealed that the HSP70 gene in cattle, Zebu cattle, and goat is located on chromosome 23, and is intronless, while in water buffalo and sheep it is located on chromosomes 2 and 20, respectively, and contains two exons linked by one intron. The HSP90-a gene is located on chromosome 21 in cattle, Zebu cattle, and goat, while in water buffalo and sheep it is located on chromosomes 20 and 18, respectively. The HSP90-b gene is located on the same chromosome as the HSP70 gene and contains 12 exons interspersed by 11 introns in all studied animals. In silico Expasy translate tool analysis revealed that HSP70, HSP90-a and HSP90-b encode 641, 733, and 724 amino acids, respectively. The data revealed that goat HSP70 protein has seven variable amino acid residues, while in both sheep and cattle only one such amino acid was detected. CONCLUSIONS This study will be supportive in providing new insights into HSPs for adaptive machinery in these studied animals and selection of target genes for molecular adaptation of livestock

Altered milk yield and rumen microbial abundance in response to concentrate supplementation during the cold season in Tibetan sheep

BACKGROUND Weight loss and decline of milk yield in Tibetan sheep was a challenge for the dairy industry in Qinghai-Tibet Plateau, which were considered to be caused by underfeeding of the sheep during the harsh winter. The objective of this study was to assess the role of feed supplementation in the milk performance and rumen microbiome of ewes under forage-based diets. Based on parity, milking period, milk yield, and body weight, ten 1.5-yr-old ewes were allocated randomly into two groups. One group of ewes was fed no supplement Control group (CON) and the other group was fed with concentrate feed supplement (Treatment group, T). Individual milk yield was determined daily; both the milk composition and rumen bacterial characteristics were analyzed after the end of feeding trials. RESULTS Results showed that lactose in the milk of the CON group was significantly lower (P < 0.05) than that of the T group at days 30 and 60. Milk yield in the T group was greater than in the CON group at day 30 (P < 0.05). Additionally, the dominant ruminal bacteria (phyla Bacteroidetes, Firmicutes, and Verrucomicrobia) were shared by both groups through 16S rRNA gene pyrosequencing. Greater relative abundance of Bacteroidales RF16 group in family level, Victivallales in order level, Lentisphaeria in class level, and Lachnospiraceae bacterium in species level were observed in the T group than in the CON group (P < 0.05). CONCLUSIONS These results demonstrated that supplementation of concentrate in the cold season improved milk lactose yield and milk production, and the rumen microbial abundance of Tibetan sheep.

C/EBPb converts bovine fibroblasts to adipocytes without hormone cocktail induction

BACKGROUND: Adipogenesis and fibrogenesis can be considered as a competitive process in muscle, which may affect the intramuscular fat deposition. The CCAAT/enhancer-binding protein beta (C/EBPb) plays an important role in adipogenesis, which is well-characterized in mice, but little known in bovine so far. RESULTS: In this study, real-time qPCR revealed that the level of C/EBPb was increased during the developmental stages of bovine and adipogenesis process of preadipocytes. Overexpression of C/EBPb promoted bovine fibroblast proliferation through mitotic clonal expansion (MCE), a necessary process for initiating adipogenesis, by significantly downregulating levels of p21 and p27 (p < 0.01). Also, the PPARc expression was inhibited during the MCE stage (p < 0.01). 31.28% of transfected fibroblasts adopted lipid-laden adipocyte morphology after 8 d. Real-time qPCR showed that C/EBPb activated the transcription of early stage adipogenesis markers C/EBPa and PPARc. Expression of ACCa, FASN, FABP4 and LPL was also significantly upregulated, while the expression of LEPR was weakened. CONCLUSIONS: It was concluded C/EBPb can convert bovine fibroblasts into adipocytes without hormone induction by initiating the MCE process and promoting adipogenic genes expression, which may provide new insights into the potential functions of C/EBPb in regulating intramuscular fat deposition in beef cattle.

Identification of genetic variants the CCKAR gene and based on body measurement and carcass quality characteristics in Qinchuan beef cattle (Bos taurus)

BACKGROUND: This study aimed to explore genetic polymorphisms of the CCKAR gene and their relationship with the growth and development of Qinchuan cattle which could be used as molecular markers for the improvement of the breeding of Qinchuan cattle. RESULTS: Here, we have identified seven single nucleotide polymorphisms (SNPs) at loci g. 1463 C>G; g. 1532 T>A; g. 1570 G>A; g. 1594 C>A; g. 1640 T>C; g. 1677 G>C; and g. 1735 C>T in the coding region of the bovine CCKAR gene. The frequencies identified on allelic and genotypic characteristics have shown that all seven SNPs diverged from the Hardy-Weinberg-Equilibrium. The SNP2, SNP3, SNP6 and SNP7 had the lowest polymorphism information content values, and remaining SNPs were found to be moderate (0.25 < PIC < 0.50). The genotype CG in SNP1 at loci g.1463 C>G had the greatest association with WH, HW, CD and CCF, while the genotype TA at the very same loci was associated with BFT, ULA and IMF content in Qinchuan cattle. The CCKAR gene expression level in adipose tissue, small intestine, liver and skeleton muscle was found to be higher, whereas, the expression level of mRNA in organs of other digestive system including reticulum, abomasum and omasum was moderate. Some expression of CCKAR mRNA was found in the large intestine, kidney and rumen. CONCLUSIONS: In summary, our finding suggested that the CCKAR gene could be used as a potential candidate for the improvement of carcass quality and body measurements of Qinchuan cattle.

RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation.

Intramuscular fat is a real challenge for the experts of animal science to improve meat quality traits. Research on the mechanism of adipogenesis provides invaluable information for the improvement of meat quality traits. This study investigated the effect of bta-miR-149-5p and its underlying mechanism on lipid metabolism in bovine adipocytes. Bovine adipocytes were differentiated and transfected with bta-miR-149-5p mimics or its negative control (NC). A total of 115 DEGs including 72 upregulated and 43 downregulated genes were identified in bovine adipocytes. The unigenes and GO term biological processes were the most annotated unigene contributor parts at 80.08%, followed by cellular component at 13.4% and molecular function at 6.7%. The KEGG pathways regulated by the DEGs were PI3K-Akt signaling pathway, calcium signaling pathway, pathways in cancer, MAPK signaling pathway, lipid metabolism/metabolic pathway, PPAR signaling pathway, AMPK signaling pathway, TGF-beta signaling pathway, cAMP signaling pathway, cholesterol metabolism, Wnt signaling pathway, and FoxO signaling pathway. In addition to this, the most important reactome enrichment pathways were R-BTA-373813 receptor CXCR2 binding ligands CXCL1 to 7, R-BTA-373791 receptor CXCR1 binding CXCL6 and CXCL8 ligands, R-BTA-210991 basigin interactions, R-BTA-380108 chemokine receptors binding chemokines, R-BTA-445704 calcium binding caldesmon, and R-BTA-5669034 TNFs binding their physiological receptors. Furthermore, the expression trend of the DEGs in these pathways were also exploited. Moreover, the bta-miR-149-5p significantly (p < 0.01) downregulated the mRNA levels of adipogenic marker genes such as CCND2, KLF6, ACSL1, Cdk2, SCD, SIK2, and ZEB1 in bovine adipocytes. In conclusion, our results suggest that bta-miR-149-5p regulates lipid metabolism in bovine adipocytes. The results of this study provide a basis for studying the function and molecular mechanism of the bta-miR-149-5p in regulating bovine adipogenesis.

The interplay between non-coding RNAs and Twist1 signaling contribute to human disorders.

Twist-related protein 1 (Twist1) is a basic helix-loop-helix (bHLH) transcription factor (TF) being coded by the TWIST1 gene. This TF has a fundamental effect on the normal development and in the pathogenesis of various diseases especially cancer. Twist1 has interactions with some long non-coding RNAs and miRNAs. The interactions between this TF and various miRNAs such as miR-16, miR-26b-5p, miR-1271, miR-539, miR-214, miR-200b/c, miR-335, miR-10b, and miR-381 are implicated in the carcinogenic processes. TP73-AS1, LINC01638, ATB, NONHSAT101069, CASC15, H19, PVT1, LINC00339, LINC01385, TANAR, SNHG5, DANCR, CHRF, and TUG1 are among long non-coding RNAs which interact with Twist1 and participate in the carcinogenesis. This review aims at depicting the interaction between these non-coding transcripts and Twist1 and the consequence of these interactions in human neoplasms.

Role of non-coding RNAs in modulating the response of cancer cells to paclitaxel treatment.

Paclitaxel is a chemotherapeutic substance that is administered for treatment of an extensive spectrum of human malignancies. In spite of its potent short-term effects against tumor cells, resistance to paclitaxel occurs in a number of patients precluding its long-term application in these patients. Non-coding RNAs have been shown to influence response of cancer cells to this chemotherapeutic agent via different mechanisms. Mechanistically, these transcripts regulate expression of several genes particularly those being involved in the apoptotic processes. Lots of in vivo and in vitro assays have demonstrated the efficacy of oligonucleotide-mediated microRNAs (miRNA)/ long non-coding RNAs (lncRNA) silencing in enhancement of response of cancer cells to paclitaxel. Therefore, targeted therapies against non-coding RNAs have been suggested as applicable modalities for combatting resistance to this agent. In the present review, we provide a summary of studies which assessed the role of miRNAs and lncRNAs in conferring resistance to paclitaxel.

Transcriptome profiling reveals differential expression of genes potentially involved in muscle and adipose tissue development of cattle

BACKGROUND: To identify differentially expressed genes (DEGs) between muscle and adipose in cattle, we analyzed the data from the RNA sequencing of three Angus×Qinchuan crossbred cattle. RESULTS: Searched the Gene Expression Omnibus (GEO) for a microarray dataset of Yan yellow cattle, GSE49992. After the DEGs were identified, we used STRING and Cytoscape to construct a protein­protein interaction (PPI) network, subsequently analyzing the major modules of key genes. In total, 340 DEGs were discovered, including 21 hub genes, which were mainly enriched in muscle contraction, skeletal muscle contraction, troponin complex, lipid particle, Z disc, tropomyosin binding, and actin filament binding. CONCLUSIONS: In summary, these genes can be regarded as candidate biomarkers for the regulation of muscle and adipose development.

Effects of overexpression of ACSL1 gene on the synthesis of unsaturated fatty acids in adipocytes of bovine.

There exists a positive correlation between the unsaturated fatty acids (UFA) content in the bovine species and their taste and nutritional significance. Long-chain acyl-CoA synthetase 1 (ACSL1) is known to be involved in lipid synthesis as well as fatty acid transport and degradation. This gene has been identified as the key candidate gene for regulating lipid composition in the bovine skeletal muscle; however, its mechanism of action in regulating UFA synthesis in bovine adipocytes is unclear. In this study, we used a recombinant adenovirus vector (Ad-ACSL1) to overexpress the ACSL1 gene using Ad-NC (recombinant adenovirus of green fluorescent protein) as the control. Quantitative real-time PCR (qRT-PCR) was done to examine the gene expression associated with the synthesis of UFA, followed by the analysis of the fatty acid composition. Oil red O staining was done to examine the aggregation of lipid droplets. We found that ACSL1 overexpression was associated with an upregulated expression of PPARγ, FABP3, ACLY, SCD1, and FASN, and downregulated expression of CPT1A. Additionally, ACSL1 overexpression resulted in elevated saturated fatty acid content, especially C16:0 and C18:0, than the control group (Ad-NC cells) (p < 0.05). Furthermore, the overexpression of ACSL1 enhanced the proportion of eicosapentaenoic acid (EPA), decreased the proportion of C22:4, and significantly upregulated polyunsaturated fatty acid (PUFA) content. These results were supported by oil red O staining, which revealed an increase in the lipid droplets in bovine adipocytes after the overexpression of the ACSL1 gene. Thus, the results of this study indicated that ACSL1 positively regulated PUFA synthesis in bovine adipocytes.

Cichoric acid from extracted Echinacea purpurea induces the proliferation and apoptosis of peripheral blood mononuclear cells from yaks

BACKGROUND: Cichoric acid (CA) is extracted from Echinacea purpurea. It is well known and widely used for its immunological function. However, the effect of CA on peripheral blood mononuclear cells (PBMCs) from yaks is still unclear. This study investigated the potential influences of CA on the proliferation, cytokine induction, and apoptosis of PBMCs from Datong yak in vivo, and aimed to provide a basis for exploring the pharmacological activities of CA on yaks. RESULTS: In this study, CA promoted PBMCs proliferation by combining concanavalin A (Con A) and exhibited a dose-dependent effect as demonstrated by a Cell Counting Kit-8. The concentration of 60 µg/ml CA was the best and promoted the transformation from the G0/G1 phase to the S and G2/M phases with Con A. Furthermore, 60 µg/ml CA significantly increased IL-2, IL-6, and IFN-γ levels and PCNA, CDK4 and Bcl-2 expression levels, but it significantly inhibited the TP53, Bax, and Caspase-3 expression levels. Transcriptome analysis revealed a total of 6807 differentially expressed genes (DEGs) between the CA treatment and control groups. Of these genes, 3788 were significantly upregulated and 3019 were downregulated. Gene Ontology and pathway analysis revealed that DEGs were enriched in cell proliferation and immune function signaling pathways. The expression level of some transcription factors (BTB, Ras, RRM_1, and zf-C2H2) and genes (CCNF, CCND1, and CDK4) related to PBMCs proliferation in yaks were significantly promoted after CA treatment. By contrast, anti-proliferation-associated genes (TP53 and CDKN1A) were inhibited. CONCLUSIONS: In summary, CA could regulate the immune function of yaks by promoting proliferation and inhibiting inflammation and apoptosis of PBMCs.

Integration of gene expression profile data to screen and verify immune-related genes of chicken erythrocytes involved in Marek's disease virus.

Chicken erythrocytes participated in immunity, but the role of erythrocytes in the immunity of Marek's disease virus (MDV) has not been reported related to the immunity genes. The purpose of this study was to screen and verify the immune-related genes of chicken erythrocytes which could be proven as a biomarker in MDV. The datasets (GPL8764-Chicken Gene Expression Microarray) were downloaded from the GEO profile database for control and MDV infected chickens to obtain differentially expressed genes (DEGs) through bioinformatics methods. Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed to find enriched pathways, including Gene Ontology (GO). Based on enriched pathways, the top 19 immune-related genes were screened-out and process further to construct the protein-protein interaction (PPI) networks. The screened genes were validated on RT-PCR and qPCR. Results suggested that the mRNA transcription of Toll-like receptors 2, 3, 4, 6 (TLR2, TLR3, TLR4, TLR6), major histocompatibility complex-II (MHCII), interleukin-7 (IL-7), interferon-ßeta (IFN-ß), chicken myelomonocytic growth factor (cMGF) and myeloid differentiation primary response 88 (MyD88) were significantly up-regulated. The expression of toll-like receptor 5, 7 (TLR5, TLR7) interleukin-12 (IL-12 p40), interleukin-13 (IL-13), and interferon-αlpha (IFN-α) were significantly down-regulated in the erythrocytes of the infected group (P < 0.05). In contrast, the expression of toll-like receptor-1, 15, 21 (TLR1, TLR15, TLR21), major histocompatibility complex I (MHCI) and Tumor necrosis factor receptor (TNFR)-associated factor 6 (TRAF6) were not significant. In conclusion, it has been verified on qRT-PCR results that 19 immune-related genes, which included TLRs, cytokines and MHC have immune functions in MDV infected chickens.

SIRT6 cooperates with SIRT5 to regulate bovine preadipocyte differentiation and lipid metabolism via the AMPKα signaling pathway.

Preadipocyte differentiation and lipid synthesis are critical steps for intramuscular fat (IMF) deposition and lipid metabolism homeostasis. IMF content of beef not only determines the ratio of muscle to adipose, but also determines the beef quality, flavor, and sensory characteristics. Maintaining lipid metabolism homeostasis is the key means of preventing and treating diabetes, obesity, and other metabolic diseases. SIRT6, which is an ADP-ribosyltransferase and NAD+-dependent deacetylase of acetyl and long-chain fatty acyl groups, playing central roles in lipid and glucose metabolism, is closely related to the occurrence of diabetes and obesity caused by overnutrition and aging. This study was based on bovine preadipocyte differentiation and an obese mice model, and comprehensively used transcriptome sequencing (RNA-seq) and morphological identification methods to explore the effects of inhibition of SIRT6 on differentiation and lipid synthesis, and related molecular mechanisms. Additionally, the feedback synergistic regulation of SIRT5 and SIRT6 on differentiation and lipid deposition was analyzed. The results showed that in the differentiation process of bovine preadipocytes, inhibition of SIRT5 significantly promoted SIRT6 expression. In addition, SIRT6 inhibited bovine preadipocyte differentiation and lipid synthesis, cooperating with SIRT5 to decrease lipid deposition, and repressed cell cycle arrest of preadipocytes. Moreover, in vivo verification experiments also obtained consistent results. Furthermore, SIRT6 inhibited preadipocyte differentiation and lipid deposition by activating the adenosine monophosphate activated protein kinase alpha (AMPKα) pathway. The above results provided a novel approach for understanding the functions of SIRT6 in regulating bovine adipocyte differentiation and lipid metabolism, as well as a new target for the treatment of diabetes and obesity in a clinical setting.

Review: Molecular structure and functions of zinc binding metallothionein-1 protein in mammalian body system.

Zinc a major trace element; perform diverse roles in genetics and physiology in almost every vital body system of the mammalian body. Zinc regulates the expression of almost all essential genes responsible for performing pivotal functions in mammal cells through provision of structural integrity to the major transcriptional factors Zn finger Proteins (ZnF) and gene regulation for production of metallothionein protein. Zinc performed at least eight vital functions in living organisms including gene regulation e.g., as a promoter through metal response elements, structural i.e. zinc-finger motifs, catalytic e.g., metalloenzymes, DNA and RNA polymerase, DNA replication, Growth promotion, antioxidant, regulate functions of central nervous system and also act as hepato-protectant and detoxifying agent. Almost all of these vital functions are regulated through metallothionein protein, a cysteine rich Zn binding protein. These functions are basic mechanism for sustaining life. Therefore, this review paper was planned with the objective to highlight the important functions of Zn inside the mammal's body with particular reference to the metallothionein protein. Bioinformatics study performed for estimation of conservation and evolution of this important protein shows its greater conservancies in six important mammalian species.

OmpW expressed by recombinant Lactobacillus casei elicits protective immunity against Aeromonas veronii in common carp.

Aeromonas veronii is an opportunistic pathogen that is capable of infecting both aquatic livestock and mammals. Natural infection in fishes results in irreparable damage to the aquaculture industry. In this study, we sought to investigate whether recombinant Lactobacillus casei expressing the outer membrane protein W (OmpW) of A.veronii could elicit protective immunity against A.veronii infections. We generated two recombinant Lactobacillus casei (L.casei) strains expressing the OmpW of A.veronii (surface-displayed or secreted) and evaluated the effect on immune responses in a fish model. A 600-bp gene fragment was subcloned into the L.casei expression plasmids pPG-1 (surface-displayed) and pPG-2 (secreted). Expression of the recombinant OmpW protein was also confirmed by Western blot and immunofluorescence assays. Common carp immunized with Lc-pPG-1- OmpW and Lc-pPG-2- OmpW via oral administration elicited high serum specific antibody titers and high LZM, ACP, and SOD activities. High levels of the IL-10, IL-ß, IFN-γ, and TNF-α genes in different organs indicated that the inflammatory response and cell immune response were triggered. Additionally, when immunized fish were challenged with A.veronii, Lc-pPG1-OmpW and Lc-pPG2-OmpW demonstrated 40% and 50% protective efficacy. These data indicate that the combination of OmpW delivery and the lactic acid bacteria (LAB) approach may be a promising mucosal therapeutic strategy for treatment of A.veronii.

Effects of Matricaria chamomilla Extract on Growth and Maturation of Isolated Mouse Ovarian Follicles in a Three-dimensional Culture System.

BACKGROUND: The aim of this study was to design and assess the effects of hydroalcoholic extract of Matricaria chamomilla (MC) on preantral follicle culture of mouse ovaries in a three-dimensional culture system. METHODS: Isolated preantral follicles were randomly divided into three main groups: the control group containing 10% fetal bovine serum without MC extract (G1), the first experimental group supplemented with 25 µg/ml hydroalcoholic extract of chamomile (G2), and the second experimental group supplemented with 50 µg/ml hydroalcoholic extract of chamomile (G3). RESULTS: After 12 days of culture, the survival rate (P < 0.05), antrum formation (P < 0.01), metaphase two oocytes (P < 0.01), and the expression of PCNA (P < 0.05) and FSHR (P < 0.05) genes significantly decreased in G3 as compared with G1. On the other hand, at the last day of culture (day 12), the mean diameter of follicles cultured in the medium which was supplemented with 50 µg/ml hydroalcoholic extract of chamomile significantly decreased as compared with the G1 (P < 0.05). In addition, the levels of progesterone and dehydroepiandrosterone hormones significantly increased in the medium of G3 relative to G1 (P < 0.01), while in the medium of G1, the level of 17ß-estradiol was significantly higher than that of other groups (P < 0.01). Reactive oxygen species levels of metaphase II oocytes were significantly decreased in G2 as compared with G1 (P < 0.01). CONCLUSION: Adding chamomile extract to culture media appeared to decrease follicular function and development.