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.

Bioinformatics role of the WGCNA analysis and co-expression network identifies of prognostic marker in lung cancer.

Lung cancer is the most talked about cancer in the world. It is also one of the cancers that currently has a high mortality rate. The aim of our research is to find more effective therapeutic targets and prognostic markers for human lung cancer. First, we download gene expression data from the GEO database. We performed weighted co-expression network analysis on the selected genes, we then constructed scale-free networks and topological overlap matrices, and performed correlation modular analysis with the cancer group. We screened the 200 genes with the highest correlation in the cyan module for functional enrichment analysis and protein interaction network construction, found that most of them focused on cell division, tumor necrosis factor-mediated signaling pathways, cellular redox homeostasis, reactive oxygen species biosynthesis, and other processes, and were related to the cell cycle, apoptosis, HIF-1 signaling pathway, p53 signaling pathway, NF-κB signaling pathway, and several cancer disease pathways are involved. Finally, we used the GEPIA website data to perform survival analysis on some of the genes with GS > 0.6 in the cyan module. CBX3, AHCY, MRPL12, TPGB, TUBG1, KIF11, LRRC59, MRPL17, TMEM106B, ZWINT, TRIP13, and HMMR was identified as an important prognostic factor for lung cancer patients. In summary, we identified 12 mRNAs associated with lung cancer prognosis. Our study contributes to a deeper understanding of the molecular mechanisms of lung cancer and provides new insights into drug use and prognosis.

RNA-Seq reveals the potential molecular mechanisms of bovine KLF6 gene in the regulation of adipogenesis.

Marbling influences the taste and tenderness of meat and is the main determinant of carcass quality in many countries. This study aims to investigate the influence of KLF6 (Kruppel Like Factor 6) and associated molecular mechanisms on lipid metabolism in bovine adipocytes. In the current study, KLF6 gene expression was down regulated via siRNA (small interfering RNA) in bovine adipocytes in vitro. Subsequently, adipogenic cells were collected from the culture media after 9 days, and subjected to fluorescent imaging and RNA sequencing. After confirming that KLF6 was down regulated in bovine adipocytes by siRNA, differential gene expression analysis was used to characterize the infuence of KLF6 on gene expression profiles in bovine adipocytes. A total of 10,812 genes were characterized as differentially expressed genes (DEGs) of which, 109 were up-regulated and 62 were down-regulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified that the DEGs were associated with lipid metabolism, carbohydrate metabolism, cell growth and death, cancer, and the signaling pathways for calcium, AMPK (Adenosine Monophosphate-Activated Protein Kinase), PI3K-Akt (Phosphatidylinositol 3-kinase), PPAR (Peroxisome proliferator-activated receptors), MAPK (mitogen-activated protein kinase), cAMP (Cyclic adenosine monophosphate), and Wnt (Wingless-related integration site). Similarly, gene ontology analysis indicated that down-regulation of KLF6 gene significantly up regulated the genes that regulate adipogenesis, differentiation and regulation of adipocytes and homeostasis of bovine adipocytes, specifically regulating the cell-type specific apoptotic action, negative regulation of apoptotic pathways, programmed cell death, and growth. Results indicate that KLF6 has a role in regulating lipid metabolism in bovine adipocytes. These findings provide evidence that may inform further investigations into molecular mechanisms that underlie the role of bovine KLF6 gene in regulating adipogenesis.

Beneficial effects and health benefits of Astaxanthin molecules on animal production: A review.

Astaxanthin (AST) is a red pigment of carotenoid and is considered a high-quality keto-carotenoid pigment with food, livestock, cosmetic, therapeutic and nutraceutical proposes. Astaxanthin exists naturally in fish, crustacean, algae, and birds that naturally exists, principally as fatty acid esters. Many investigations have exhibited the beneficial impacts of astaxanthin when utilized as a pharmaceutical agent in animal nutrition. Astaxanthin has a variety of considerable biological actions, such as being antihypertensive, an antioxidant, anti-obesity properties, and anti-carcinogenic. Astaxanthin has recently acquired popularity as a powerful immunomodulator to maintain the health status and well-being of both animals and humans. The use of astaxanthin is broadly utilized in medical sciences and the nutrition pf aquatic species; however, it presently has limited applications in broader animal nutrition. Understanding astaxanthin's structure, source, and mode of action in the body provides a conceptual base for its clinical application and could enhance the screening of compounds associated with the treatment of many diseases. This review article aims to clarify the important aspects of astaxanthin such as its synthesis, bioavailability, and therapeutics actions, with special interest in practical applications. Awareness of this benefits and production is expected to aid the livestock industry to develop nutritional strategies that ensure the protection of animal health.

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.

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.

Adaptive Molecular Evolution of AKT3 Gene for Positive Diversifying Selection in Mammals.

The V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) gene is of the serine/threonine-protein kinase family and influences the production of milk fats and cholesterol by acting on the sterol administrative area restricting protein (SREBP). The AKT3 gene is highly preserved in animals, and during lactation in cattle, its expression increases. The AKT3 gene is expressed in the digestive system, mammary gland, and immune cells. A phylogenetic investigation was performed to clarify the evolutionary role of AKT3, by maximum probability. The AKT3 gene sequence data of various mammalian species was evident even with animals undergoing breeding selection. From 39 mammalian species studied, there was a signal of positive diversifying selection with Hominidae at 13Q, 16G, 23R, 24P, 121P, 294K, 327V, 376L, 397K, 445T, and 471F among other codon sites of the AKT3 gene. These sites were codes for amino acids such as arginine, proline, lysine, and leucine indicating major roles for the function of immunological proteins, and in particular, the study highlighted the importance of changes in gene expression of AKT3 on immunity.

Flavonoid bioactive compounds of hawthorn extract can promote growth, regulate electrocardiogram waves, and improve cardiac parameters of pulmonary hypertensive chickens.

The effect of orally administered hawthorn flavonoid extract (HFE) on growth, electrocardiographic waves, and cardiac parameters of pulmonary hypertensive chickens reared at high altitude (2,100 m above sea level) was examined. A total of 225 one-day-old, mixed broiler chicks (3 treatments with 5 replicates and 15 chicks per each, totally 75 birds/treatment) were assigned to 3 experimental groups: 0, 0.1, and 0.2 ml of HFE per 1 L of drinking water. Birds were administered the drinking water HFE treatments for 42 D. At an age of 28 and 42 D, electrocardiograms were undertaken and cardiac parameters such as the RV:TV, RV:BW, and TV:BW, and indicators of PHS on selected birds were measured. The final BW of chickens receiving the HFE at 0.2 ml/L was greater (2,579 ± 64 g) than that of birds receiving 0.1 ml/L (2,497 ± 62 g) and 0 ml/L (2,323 ± 57 g). Therefore, no supplemented group had a lower final BW than others (P < 0.05). Amplitudes of S and T waves in 0.1- and 0.2-ml/L HFE consumed groups at 28 and 42 D of age decreased compared with that in the control group (P < 0.05). The HFE reduced the heart weight and RV:TV, RV:BW, and TV:BW ratios when supplemented in drinking water at 0.1 and 0.2 mL/L compared with 0 mL/L (P < 0.05). In conclusion, supplementation of HFE in drinking water can reduce the PHS and incidence of cardiac disorders. Owing to the positive effect of HFE on cardiac parameters that mediated through flavonoids bioactive compounds, this product can be used to prevent complications of pulmonary hypertension and disarray of electrocardiographic waves in broiler chickens reared at high altitude.

Function and characterization of the promoter region of perilipin 1 (PLIN1): Roles of E2F1, PLAG1, C/EBPß, and SMAD3 in bovine adipocytes.

Perilipin 1 (PLIN1) protein, also known as lipid droplet-associated protein, is encoded by the PLIN1 gene and is able to anchor itself to the membranes of lipid droplets. The phosphorylation of PLIN1 is critical for the mobilization of fat in adipose tissue and plays an important role in regulating lipolysis and lipid storage in adipocytes. However, research on the synthesis and lipid metabolism of lipid droplets by PLIN1 in bovine adipocytes is limited. In the present study, we found that bovine PLIN1 was highly expressed in subcutaneous adipose tissue. The highest level of PLIN1 mRNA expression in bovine adipocytes was observed on day 6 of differentiation. Moreover, the cytoplasmic subcellular localization of PLIN1 was observed in bovine preadipocytes. To elucidate the molecular mechanism of bovine PLIN1 transcriptional regulation, we cloned eight fragments containing the 5' regulatory region of the PLIN1 gene. The results showed that the -209/-17 bp region of the bovine PLIN1 gene was the core promoter region. Based on the transcriptional activities of the promoter vector fragments, the luciferase activity of the mutated fragment, the siRNA interference, and the results of the electrophoretic mobility shift assay (EMSA), we identified the binding sites of E2F transcription factor 1 (E2F1), pleiomorphic adenoma gene 1 (PLAG1), CCAAT enhancer binding protein beta (C/EBPß), and SMAD family member 3 (SMAD3) as the transcriptional activators or repressors of the core promoter region. Further experiments confirmed that the knockdown of the PLIN1 gene affected the ability of these transcription factors to regulate the lipid metabolism in bovine adipocytes. In conclusion, our results reveal a potential mechanism for the transcriptional regulation of PLIN1 in bovine adipocytes.

Effects of five cryoprotectants on proliferation and differentiation-related gene expression of frozen-thawed bovine calf testicular tissue.

The cryopreservation of testicular tissue is a potential method for preserving male fertility. However, the effect of cryopreservation on bovine calf testicular tissue is scarce. This study investigated the effect of different cryoprotectants on bovine calf testicular tissue at the molecular level. Testicular tissue from ten immature bovine calves (6 months) was collected after slaughter and cryopreserved in an extender containing different concentrations of the following five cryopreservation solutions (CP): bovine serum albumin (BSA) with 5% dimethyl sulfoxide (DMSO), trehalose with 5% DMSO, DMSO and glycerol and ethylene glycol (EG). After 7-day cryopreservation, the expression levels of three spermatogonial stem cell (SSC)-related genes, octamer-4 (OCT4), KIT ligand (MGF/SCF) and kit oncogene (C-KIT), were investigated by quantitative PCR (qPCR). The cell viability was highest for the tissues preserved with 30 mg/ml BSA (77.82% ± 1.22) and 40 mg/ml trehalose (74.23% ± 1.16) compared with other groups (p < 0.05), and the level of expression of the three genes was highest with 30 mg/ml BSA (p < 0.05). Compared with other CPs, the 30 mg/ml BSA and 40 mg/ml trehalose have the better cryopreserve protection. The 30 mg/ml BSA is the most viable media for the cryopreservation of testicular tissue from cattle.