scholarly journals Dietary Enteromorpha Polysaccharides Supplementation Improves Breast Muscle Yield and Is Associated With Modification of mRNA Transcriptome in Broiler Chickens

2021 ◽  
Vol 8 ◽  
Author(s):  
Yue Zhao ◽  
Balamuralikrishnan Balasubramanian ◽  
Yan Guo ◽  
Sheng-Jian Qiu ◽  
Rajesh Jha ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Broiler Chickens ◽  
Molecular Mechanisms ◽  
Carcass Traits ◽  
Enrichment Analysis ◽  
Dietary Supplementation ◽  
Breast Muscle ◽  
Rna Seq ◽  
Feeding Trial ◽  
Mrna Transcriptome

The present study evaluated the effects of dietary supplementation of Enteromorpha polysaccharides (EP) on carcass traits of broilers and potential molecular mechanisms associated with it. This study used RNA-Sequencing (RNA-Seq) to detect modification in mRNA transcriptome and the cognate biological pathways affecting the carcass traits. A total of 396 one-day-old male broilers (Arbor Acres) were randomly assigned to one of six dietary treatments containing EP at 0 (CON), 1000 (EP_1000), 2500 (EP_2500), 4000 (EP_4000), 5500 (EP_5500), and 7000 (EP_7000) mg/kg levels for a 35-d feeding trial with 6 replicates/treatment. At the end of the feeding trial, six birds (one bird from each replicate cage) were randomly selected from each treatment and slaughtered for carcass traits analysis. The results showed that the dietary supplementation of EP_7000 improved the breast muscle yield (p < 0.05). Subsequently, six breast muscle samples from CON and EP_7000 groups (three samples from each group) were randomly selected for RNA-Seq analysis. Based on the RNA-Seq results, a total of 154 differentially expressed genes (DEGs) were identified (p < 0.05). Among the DEGs, 112 genes were significantly upregulated, whereas 42 genes were significantly down-regulated by EP_7000 supplementation. Gene Ontology enrichment analysis showed that the DEGs were mainly enriched in immune-related signaling pathways, macromolecule biosynthetic, DNA-templated, RNA biosynthetic, and metabolic process (p < 0.05). Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the DEGs were enriched in signaling pathways related to viral infectious diseases and cell adhesion molecules (p < 0.05). In conclusion, dietary inclusion of EP_7000 improves the breast muscle yield, which may be involved in improving the immunity and the cell differentiation of broilers, thus promoting the muscle growth of broilers. These findings could help understand the molecular mechanisms that enhance breast muscle yield by dietary supplementation of EP in broilers.

scholarly journals Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

2019 ◽  
Author(s):  
Guodong Ge ◽  
Yong Long ◽  
Lianyu Shi ◽  
Jing Ren ◽  
Junjun Yan ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Cold Acclimation ◽  
Cold Tolerance ◽  
Drug Transport ◽  
Molecular Mechanisms ◽  
Secondary Alcohol ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Rna Seq ◽  
Mirror Carp

Abstract Background Closely related species of the carp family ( Cyprinidae ) have evolved distinctive abilities to survive under cold stress, but molecular mechanisms underlying the generation of cold resistance remain largely unknow. In this study, we compared transcriptomic profiles of two carp species to identify key factors and pathways for cold tolerance and acclimation. Results Larvae of Songpu mirror carp and Barbless carp that were pretreated at 18°C for 24 hours significantly improved their survival rates under lethal cold temperature at 8°C or 10°C, indicating that two carp species possess the ability of cold acclimation. However, Songpu mirror carp exhibited stronger abilities of cold tolerance and acclimation than Barbless carp. Transcriptomic profiles of Songpu mirror carp and Barbless carp larvae at 28°C and 18°C were compared during cold acclimation through RNA-seq. Differentially expressed genes that are closely associated with the differences in cold acclimation between two carp species were identified through bioinformatics and Venn's diagram analysis. GO enrichment analysis of these genes indicated that cellular component assembly involved in morphogenesis, secondary alcohol metabolism and drug transport were the most up-regulated biological processes during cold acclimation of Songpu mirror carp. Conversely, positive regulation of macroautophagy, intracellular protein transport, and organonitrogen compound catabolism were the most down-regulated biological processes during cold acclimation of Barbless carp. KEGG enrichment analysis revealed that factors in the FoxO-related signaling pathways are mainly responsible for the development of differences in cold tolerance and acclimation between two carp species since altering the phosphorylation of key proteins in the FoxO-related signaling pathways with inhibitors or an activator significantly decreased the cold tolerance and acclimation of Songpu mirror carp. These data provided key clues for dissection of molecular mechanisms underlying the development of cold tolerance and acclimation in carps. Conclusions These findings indicate that larvae of two carp species possess different abilities of cold tolerance and can build cold acclimation under mild low temperature. Multiple biological processes and FoxO-related signaling pathways are closely associated with the development of differences in cold tolerance and acclimation between two carp species. Keywords: Carp; cold tolerance; cold acclimation; RNA-Seq; biological process; signaling pathways

scholarly journals Effects of Dietary Probiotic (Bacillus subtilis) Supplementation on Carcass Traits, Meat Quality, Amino Acid, and Fatty Acid Profile of Broiler Chickens

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiaopeng Tang ◽  
Xuguang Liu ◽  
Hu Liu
Keyword(s):  
Bacillus Subtilis ◽  
Fatty Acid ◽  
Amino Acid ◽  
Meat Quality ◽  
Fatty Acid Profile ◽  
Broiler Chickens ◽  
Carcass Traits ◽  
Dietary Supplementation ◽  
Breast Muscle ◽  
Thigh Muscle

The aim of the present study was to evaluate the effects of dietary supplementation with or without Bacillus subtilis (B. subtilis) on carcass traits, meat quality, amino acids, and fatty acids of broiler chickens. In total, 160 1-day-old Arbor Acres male broiler chicks were divided into two groups with eight replicates of 10 chicks each. Chickens received basal diets without (CN group) or with 500 mg/kg B. subtilis (BS group) for 42 days. Eight chickens from each group were slaughtered at the end of the trial, and carcass traits, meat quality, chemical composition, amino acid, and fatty acid profile of meat were measured. The results showed that the breast muscle (%) was higher in BS than in CN (p < 0.05), while abdominal fat decreased (p < 0.05). The pH24h of thigh muscle was increased (p < 0.05) when supplemented with BS; however, drip loss, cooking loss of breast muscle, and shear force of thigh muscle decreased (p < 0.05). Lysine (Lys), methionine (Met), glutamic acid (Glu), and total essential amino acid (EAA) in breast muscle and Glu in thigh muscle were greater in BS than in CN (p < 0.05). C16:1, C18:1n9c, and MUFA in breast muscle and thigh muscle were greater in BS than in CN (p < 0.05). In conclusion, dietary supplementation with B. subtilis could improve the carcass traits and meat quality of broilers, which is beneficial for the consumers due to the improved fatty acid profile and amino acid composition.

Effects of feeding Isomaltooligosaccharides on the growth performance, carcass traits and immune response of broiler chickens

2014 ◽  
Vol 3 (1) ◽  
pp. 150-157
Author(s):  
Khalid M. Gaafar
Keyword(s):  
Immune Response ◽  
Growth Performance ◽  
Broiler Chickens ◽  
Carcass Traits ◽  
Dietary Supplementation ◽  
Control Group ◽  
Broiler Chicks ◽  
Feed Conversion ◽  
Flu Vaccine ◽  
Lipids Profile

The research was conducted to study the effect of feeding broiler chickens on diets containing isomaltooligosaccharides on the growth performance, carcass traits and immune response. 90-one day old broiler chicks were used according to completely randomized two treatment groups and one control, 30 birds each. Birds fed ad-libitum on basal starter and grower-finisher diets for 35 day. Diets of treatment`s groups contained 0.5 g/Kg and 1 g/Kg of Isomaltooligosaccharides, while the control group fed on the basal diets without Isomaltooligosaccharides supplementation. Dietary supplementation of broiler chickens with Isomaltooligosaccharides improved body weight, feed conversion, carcass traits, two lymphoid organs weight and log antibody titer against avian flu vaccine. Most of the highest values were for birds fed low levels of Isomaltooligosaccharides. Feed intake decreases as Isomaltooligosaccharides level increases. Dietary supplementation with Isomaltooligosaccharides did not affect the lipids profile (triglycerides, total cholesterol, LDL and HDL), however the blood VLDL levels decreased with increased levels of Malondialdehyde and Glutathione reductase. Collectively, Dietary supplementation of broiler chickens with 0.5 g/Kg diet of Isomaltooligosaccharides improved growth performance, carcass traits and immune status.

Analysis of Expression Profiles of mRNA and lncRNA in Oviduct During Estrus Phase of Sheep (Ovis Aries) with Two Fecundity (FecB Gene) Genotypes

2021 ◽  
Author(s):  
Weihao Chen ◽  
Zhifeng Li ◽  
Wei Sun ◽  
Mingxing Chu
Keyword(s):  
Embryo Development ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Ovis Aries ◽  
Functional Enrichment ◽  
Saga Complex ◽  
Rna Seq ◽  
Estrus Phase

Abstract Background:In sheep, FecB is the essential biomarker of the fertility, previous researches have provided a detailed insight on the regulation involved estrus phase and FecB in the reproductive-related tissues including hypothalamus, pituitary, and ovary. However, as the host of embryo development and connection between the ovary and the uterus, little is known about the interaction between mRNAs and lncRNAs in sheep oviduct. In the present study, RNA-Seq was performed to identify the transcriptomic profiles of mRNAs and lncRNAs in oviduct during estrus phase of sheep with FecBBB/++ genotypes.Results:In total, 21,863 lncRNAs and 43,674 mRNAs were identified, 57 DE lncRNAs and 637 DE mRNAs were revealed in the comparisons between follicular phase and luteal phase, 26 DE lncRNAs and 421 DE lncRNAs were revealed in the comparisons between FecB BB genotype and FecB ++ genotype. Functional enrichment analysis suggested that GO and KEGG terms related to reproduction such as SAGA complex, ATP-binding cassette (ABC), Nestin, and Hippo signalling pathway. DE-interaction network suggested that LNC_018420 maybe the key regulators related to embryo development in sheep oviduct.Conclusion:This was the first study to reveal the transcriptomic profiles of mRNAs and lncRNAs in the oviduct of FecB BB/++ sheep at estrus phase using RNA-Seq. Our findings can provide new understanding on the molecular mechanisms of mRNAs and lncRNAs underlying sheep embryo development and also opening new lines of investigation in sheep reproduction.

scholarly journals Analysis of the Molecular Mechanisms of the Effects of Prunella vulgaris against Subacute Thyroiditis Based on Network Pharmacology

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Xin Shen ◽  
Rui Yang ◽  
Jianpeng An ◽  
Xia Zhong
Keyword(s):  
Signaling Pathways ◽  
Molecular Mechanisms ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Subacute Thyroiditis ◽  
Network Pharmacology ◽  
Pharmacokinetic Parameters ◽  
Pathway Enrichment Analysis ◽  
Prunella Vulgaris ◽  
Protein Protein Interaction

Prunella vulgaris (PV) has a long history of application in traditional Chinese and Western medicine as a remedy for the treatment of subacute thyroiditis (SAT). This study applied network pharmacology to elucidate the mechanism of the effects of PV against SAT. Components of the potential therapeutic targets of PV and SAT-related targets were retrieved from databases. To construct a protein-protein interaction (PPI) network, the intersection of SAT-related targets and PV-related targets was input into the STRING platform. Gene ontology (GO) analysis and KEGG pathway enrichment analysis were carried out using the DAVID database. Networks were constructed by Cytoscape for visualization. The results showed that a total of 11 compounds were identified according to the pharmacokinetic parameters of ADME. A total of 126 PV-related targets and 2207 SAT-related targets were collected, and 83 overlapping targets were subsequently obtained. The results of the KEGG pathway and compound-target-pathway (C-T-P) network analysis suggested that the anti-SAT effect of PV mainly occurs through quercetin, luteolin, kaempferol, and beta-sitosterol and is most closely associated with their regulation of inflammation and apoptosis by targeting the PIK3CG, MAPK1, MAPK14, TNF, and PTGS2 proteins and the PI3K-Akt and TNF signaling pathways. The study demonstrated that quercetin, luteolin, kaempferol, and beta-sitosterol in PV may play a major role in the treatment of SAT, which was associated with the regulation of inflammation and apoptosis, by targeting the PI3K-Akt and TNF signaling pathways.

P5398CircRNAs deregulation in heart failure patients

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
S Greco ◽  
A Made' ◽  
M Longo ◽  
R Tikhomirov ◽  
S Castelvecchio ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Functional Characterization ◽  
Enrichment Analysis ◽  
Host Gene ◽  
Circular Rnas ◽  
Amplification Efficiency ◽  
Rna Seq ◽  
Bioinformatics Pipeline

Abstract Background Circular RNAs (circRNAs) are an emerging class of noncoding RNAs stemming from the splicing and circularization of pre-mRNAs exons. CircRNAs can regulate transcription and splicing, sequester microRNAs acting as “sponge” and inducing the respective targets, and bind to RNA binding proteins. Recently, they have been found deregulated in dilated cardiomyopathies (DCM), one of the cardiovascular diseases with the worst rate of morbidity and mortality, and whose molecular mechanisms are only partially known. Purpose Therein, we will evaluate in ischemic DCM patients the modulation of 17 circRNAs, 14 out of them obtained from literature data on DCM ischemic or not, while the other 3 were circRNAs not characterized in the heart previously. The study aims to identify circRNAs candidates for further functional characterization in DCM. In addition, as differential expression (DE) analysis is not easily performed for circRNAs in RNA-seq datasets, the validated circRNAs will be used to set up the most specific and sensitive bioinformatics pipeline for circRNA-DE analysis. Methods We designed divergent and convergent specific primers for 17 circRNAs and their host gene, respectively, and their amplification efficiency was measured by RT-qPCR. Transcripts expression was measured in left ventricle biopsies of 12 patients affected by non end-stage ischemic HF and of 12 matched controls. Results We identified cPVT1, cANKRD17, cBPTF as DE, and validated the modulation of 5 out of the 14 DCM-related circRNAs (cHIPK3, cALPK2, cPCMTD1, cNEBL, cSLC8A1), while cPDRM5, cTTN1 showed opposite modulation, which may be due to the specific disease condition. All of them were modulated differently from the respective host gene. CircRNA/miRNA interactions were predicted using Starbase 3.0. Next, mRNAs-targets of the identified miRNAs were predicted by mirDIP 4.1 and intersected with gene expression datasets of the same patients, previously obtained by microarray analysis. We found that cBPTF and cANKRD17 might sponge 12 and 2 miRNAs, respectively. Enrichment analysis of the relevant targets identified several important pathways implicated in DCM, such as MAPK, FoxO, EGFR, VEGF and Insulin/IGF pathways. In addition, deep RNA-Seq analysis that is currently ongoing and the validated circRNAs will be used to optimize the bioinformatics pipeline for circRNA DE analysis. Conclusions We identified a subset of circRNAs deregulated in ischemic HF potentially implicated in HF pathogenesis.

Effect of Dietary Supplementation of Organic Chromium on Performance, Carcass Traits, Oxidative Parameters, and Immune Responses in Commercial Broiler Chickens

2012 ◽  
Vol 147 (1-3) ◽  
pp. 135-141 ◽  
Author(s):  
S. V. Rama Rao ◽  
M. V. L. N. Raju ◽  
A. K. Panda ◽  
N. S. Poonam ◽  
O. Krishna Murthy ◽  
...  
Keyword(s):  
Immune Responses ◽  
Broiler Chickens ◽  
Carcass Traits ◽  
Dietary Supplementation ◽  
Commercial Broiler

scholarly journals The complexity and robustness of gene network inside the story between miRNAs and splicing isoforms in sacred lotus

2019 ◽  
Author(s):  
Yue Zhang ◽  
Razgar Seyed Rahmani ◽  
Xingyu Yang ◽  
Jinming Chen ◽  
Tao Shi
Keyword(s):  
Gene Network ◽  
Molecular Mechanisms ◽  
Functional Divergence ◽  
Enrichment Analysis ◽  
Flowering Plant ◽  
Transcript Isoforms ◽  
Function Enrichment Analysis ◽  
Splicing Isoforms ◽  
Gene Inhibition ◽  
Mrna Transcriptome

Abstract BACKGROUND. Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, coordination of interaction between miRNAs with different splicing isoforms, and the role of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus ( Nelumbo nucifera ), an economically important flowering plant. RESULTS. Through RNA-seq expression analyses among six lotus tissues, the negative regulatory roles of most miRNAs are reflected by their tissue-biased expression and the negative correlation with their targets in expression. Further, the central roles of miRNAs in the gene network was unveiled as there are more frequent interactions between miRNAs and hub isoforms than between miRNAs and non-hub isoforms. Surprisingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. The gene function enrichment analysis of miRNA targeted reveals that miRNAs are involved in regulation of lotus growth and development by regulating plant hormone-related pathway genes. CONCLUSION. Taken together, we carry out a comprehensive and deep analysis between miRNA and mRNA transcriptome to study coordination of interaction between miRNAs with different splicing isoforms. Our study on lotus highlights not only the complicate interactions between the miRNAs and transcript isoforms but also functional divergence of many transcript isoforms from the same locus in plant.

scholarly journals Identification and verification of the molecular mechanisms and prognostic values of the cadherin gene family in gastric cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shanshan Luo ◽  
Rujing Lin ◽  
Xiwen Liao ◽  
Daimou Li ◽  
Yuzhou Qin
Keyword(s):  
Gastric Cancer ◽  
Signaling Pathways ◽  
Risk Score ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Study Data ◽  
The Cancer Genome Atlas ◽  
Risk Scores ◽  
Phosphoinositide 3 Kinase ◽  
Functional Mechanisms

AbstractWhile cadherin (CDH) genes are aberrantly expressed in cancers, the functions of CDH genes in gastric cancer (GC) remain poorly understood. The clinical significance and molecular mechanisms of CDH genes in GC were assessed in this study. Data from a total of 1226 GC patients included in The Cancer Genome Atlas (TCGA) and Kaplan–Meier plotter database were used to independently explore the value of CDH genes in clinical application. The TCGA RNA sequencing dataset was used to explore the molecular mechanisms of CDH genes in GC. Using enrichment analysis tools, CDH genes were found to be related to cell adhesion and calcium ion binding in function. In TCGA cohort, 12 genes were found to be differentially expressed between GC para-carcinoma and tumor tissue. By analyzing GC patients in two independent cohorts, we identified and verified that CDH2, CDH6, CDH7 and CDH10 were significantly associated with a poor GC prognosis. In addition, CDH2 and CDH6 were used to construct a GC risk score signature that can significantly improve the accuracy of predicting the 5-year survival of GC patients. The GSEA approach was used to explore the functional mechanisms of the four prognostic CDH genes and their associated risk scores. It was found that these genes may be involved in multiple classic cancer-related signaling pathways, such as the Wnt and phosphoinositide 3-kinase signaling pathways in GC. In the subsequent CMap analysis, three small molecule compounds (anisomycin, nystatin and bumetanide) that may be the target molecules that determine the risk score in GC, were initially screened. In conclusion, our current study suggests that four CDH genes can be used as potential biomarkers for GC prognosis. In addition, a prognostic signature based on the CDH2 and CDH6 genes was constructed, and their potential functional mechanisms and drug interactions explored.

scholarly journals Systems Biology Unraveled the Relationship of lncRNA OIP5-AS1 with CD25 and its Co-Expression Analysis in Cancers

2020 ◽  
Author(s):  
Moein Dehbashi ◽  
Zohreh Hojati ◽  
Majid Motovali-bashi ◽  
C. S. Cho ◽  
Akihiro Shimosaka ◽  
...  
Keyword(s):  
Systems Biology ◽  
Signaling Pathways ◽  
Expression Analysis ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Treg Cells ◽  
Rna Seq ◽  
Cd25 Expression ◽  
High Level ◽  
The Relationship

Abstract Background: Treg cells function in the immune homeostasis, these cells express high level of CD25. Even though the molecular mechanisms of CD25-mediated signaling pathways has been reported, some questions are still unclear, e.g. the relationship and function of the relative lncRNA. It is known that the CD25 expression levels are various among different cancers. Thus, we intended to dissect systems biology of a lncRNA pertained to CD25 and CD25 protein interactors-targeting miRNAs. Methods: Apart from using the available RNA-seq data, the co-expression analysis of the lncRNA pertained to some cancers was performed. Our analysis was done for protein interactors of CD25 by STRING 11.0, ShinyGO v0.60 and KEGG web servers were used for enrichment and network analysis of CD25. TargetScan 7.2, miRTargetLink Human and mirDIP were applied for determining the CD25 and CD25 interactors-targeting miRNAs. To find the lncRNA-miRNA and lncRNA-protein interactions, starBase v3.0, LncBase Predicted v.2 and SFPEL-LPI were recruited, respectively. Also, using Co-LncRNA, the co-expressed lncRNA analysis and the relative signaling pathways in some cancers including bladder, breast, head and neck, kidney, liver, lung, prostate and thyroid cancers using RNA-seq data were achieved. Results: OIP5-AS1 was shown to have the interaction with CD25 and CD25 protein interactors-targeting miRNAs. In addition, the co-expression of OIP5-AS1 in cancers and their signaling pathways was identified. Conclusions: Possibly, OIP5-AS1 can effect on CD25 expression in all relative signaling pathways of these cancers.

Sign in / Sign up

Export Citation Format

Share Document