scholarly journals Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis

Animals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 189 ◽  
Author(s):  
Jie Wu ◽  
Xingwang Wang ◽  
Rongrong Ding ◽  
Jianping Quan ◽  
Yong Ye ◽  
...  
Keyword(s):  
Small Intestine ◽  
Feed Efficiency ◽  
Enrichment Analysis ◽  
Absolute Quantification ◽  
Biological Processes ◽  
Intestinal Movement ◽  
Extreme Phenotypes ◽  
Isobaric Tag ◽  
Important Trait ◽  
Small Intestinal

Feed efficiency is an economically important trait controlled by multiple genes in pigs. The small intestine is the main organ of digestion and nutrient absorption. To explore the biological processes by which small intestine proteomics affects feed efficiency (FE), we investigated the small intestinal tissue proteomes of high-FE and low-FE pigs by the isobaric tag for relative and absolute quantification (iTRAQ) method. In this study, a total of 225 Duroc × (Landrace × Yorkshire) (DLY) commercial pigs were ranked according to feed efficiency, which ranged from 30 kg to 100 kg, and six pigs with extreme phenotypes were selected, three in each of the high and low groups. A total of 1219 differentially expressed proteins (DEPs) were identified between the high-FE and low-FE groups (fold change ≥1.2 or ≤0.84; p ≤ 0.05), of which 785 were upregulated, and 484 were downregulated. Enrichment analysis indicated that the DEPs were mainly enriched in actin filament formation, microvilli formation, and small intestinal movement pathways. Protein functional analysis and protein interaction networks indicated that RHOA, HCLS1, EZR, CDC42, and RAC1 were important proteins that regulate FE in pigs. This study provided new insights into the important pathways and proteins involved in feed efficiency in pigs.

scholarly journals A Transcriptome Analysis Reveals that Hepatic Glycolysis and Lipid Synthesis Are Negatively Associated with Feed Efficiency in DLY Pigs

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Cineng Xu ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
Jie Wu ◽  
Shenping Zhou ◽  
...  
Keyword(s):  
Energy Consumption ◽  
Feed Efficiency ◽  
Molecular Mechanisms ◽  
Lipid Synthesis ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Go Enrichment ◽  
Group A ◽  
Important Trait

Abstract Feed efficiency (FE) is an important trait in the porcine industry. Therefore, understanding the molecular mechanisms of FE is vital for the improvement of this trait. In this study, 6 extreme high-FE and 6 low-FE pigs were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs for transcriptomic analysis. RNA-seq analysis was performed to determine differentially expressed genes (DEGs) in the liver tissues of the 12 individuals, and 507 DEGs were identified between high-FE pigs (HE- group) and low-FE pigs (LE- group). A gene ontology (GO) enrichment and pathway enrichment analysis were performed and revealed that glycolytic metabolism and lipid synthesis-related pathways were significantly enriched within DEGs; all of these DEGs were downregulated in the HE- group. Moreover, Weighted gene co-expression analysis (WGCNA) revealed that oxidative phosphorylation, thermogenesis, and energy metabolism-related pathways were negatively related to HE- group, which might result in lower energy consumption in higher efficiency pigs. These results implied that the higher FE in the HE- group may be attributed to a lower glycolytic, energy consumption and lipid synthesizing potential in the liver. Furthermore, our findings suggested that the inhibition of lipid synthesis and glucose metabolic activity in the liver may be strategies for improving the FE of DLY pigs.

320 Liver Transcriptome Analysis Reveals Important Genes Involved in the Feed Efficiency of Lactating Cows Fed a High and Low Starch Diet

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 177-177
Author(s):  
Xiaoxia Dai ◽  
Wenli Li ◽  
Amelie Fischer ◽  
Kenneth Kalscheur
Keyword(s):  
Gene Expression ◽  
Feed Efficiency ◽  
Enrichment Analysis ◽  
Experimental Period ◽  
Organic Substrate ◽  
Metabolizable Energy ◽  
Gene Set Enrichment Analysis ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Lactating Cows

Abstract The objectives of this study were to identify different gene expression and metabolic pathways in the liver associated with feed efficiency of lactating cows fed high or low starch diets. Ten lactating cows were involved in a cross-over design experiment consisting of two 56-d treatment periods with 11-d diet adaptation fed either high starch (HS; 27% starch) or low starch (LS; 13% starch) diets. Feed efficiency, measured by residual feed intake (RFI), was estimated based on the difference between observed and expected metabolizable energy intake within each experimental period. The 3 highest RFI cows were considered high RFI (HRFI), the 3 lowest RFI cows were considered low (LRFI), and the remaining 4 cows were considered medium (MRFI) in each experimental period. Total RNA was used for next-generation RNA sequencing analysis. Raw reads were mapped to the cattle genome (UMD3.1) using STAR. Differential gene expression analysis was done using Cufflinks. We discovered 642 differentially expressed genes (DEGs) between HS and LS (FDR< 0.05) with 240 genes upregulated and 402 genes downregulated for HS versus LS diet. Via gene-set enrichment analysis (GSEA) analysis (FDR< 0.05), these genes were enriched in 25 gene ontology (GO) pathways related to mitochondria components and 4 GO biological processes involved in peptide metabolism. There were 1427 DEGs impacted by RFI (FDR< 0.05), of which 829 were upregulated, and 598 were downregulated in LRFI compared to HRFI. The 6 GO biological processes enriched by these genes were mainly related to organic substrate metabolism processing and carbon metabolism (FDR< 0.05). Between the DEGs affected by diet and RFI, 522 DGEs were unique to diet and 1307 DEGs were unique to RFI. Our results suggested that genes contributing to different RFIs and the ones associated with the dietary starch treatment may impact distinct pathways. Further functional annotation of these genes may improve feed efficiency.

scholarly journals Systems biology reveals NR2F6 and TGFB1 as key regulators of feed efficiency in beef cattle

2018 ◽  
Author(s):  
Pâmela A. Alexandre ◽  
Marina Naval-Sanchez ◽  
Laercio R. Porto-Neto ◽  
José Bento S. Ferraz ◽  
Antonio Reverter ◽  
...  
Keyword(s):  
Systems Biology ◽  
Beef Cattle ◽  
Feed Efficiency ◽  
Motif Discovery ◽  
Bos Indicus ◽  
Hormonal Control ◽  
Biological Processes ◽  
Tissue Specific ◽  
Complex Phenotypes ◽  
Important Trait

AbstractSystems biology approaches are used as strategy to uncover tissue-specific perturbations and regulatory genes related to complex phenotypes. We applied this approach to study feed efficiency (FE) in beef cattle, an important trait both economically and environmentally. Poly-A selected RNA of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle and pituitary) of eighteen young bulls, selected for high and low FE, were sequenced (100bp, pared-end). From the 17,354 expressed genes, 1,317 were prioritized by five selection categories (differentially expressed, harbouring SNPs associated with FE, tissue-specific, secreted in plasma and key regulators) and used for network construction. NR2F6 and TGFB were identified and validated by motif discovery as key regulators of hepatic inflammatory response and muscle tissue development, respectively, two biological processes demonstrated to be associated to FE. Moreover, we indicated potential biomarkers of FE which are related to hormonal control of metabolism and sexual maturity. By using robust methodologies and validation strategies, we confirmed main biological processes related to FE in Bos indicus and indicated candidate genes as regulators or biomarkers of superior animals.

Application of a dynamic mechanistic model of small intestinal starch digestion in the dairy cow

2002 ◽  
Vol 2002 ◽  
pp. 104-104
Author(s):  
J. A. N. Mills ◽  
E. Kebreab ◽  
L. A. Crompton ◽  
J. Dijkstra ◽  
J. France
Keyword(s):  
Experimental Data ◽  
Small Intestine ◽  
Dairy Cow ◽  
Energy Recovery ◽  
Mechanistic Model ◽  
Biological Knowledge ◽  
Dietary Energy ◽  
Starch Digestion ◽  
High Contribution ◽  
Small Intestinal

The high contribution of postruminal starch digestion (>50%) to total tract starch digestion on certain energy dense diets (Mills et al. 1999) demands that limitations to small intestinal starch digestion are identified. Therefore, a dynamic mechanistic model of the small intestine was constructed and evaluated against published experimental data for abomasal carbohydrate infusions in the dairy cow. The mechanistic structure of the model allowed the current biological knowledge to be integrated into a system capable of identifying restrictions to dietary energy recovery from postruminal starch delivery.

scholarly journals Network pharmacology and molecular docking study on the active ingredients of qidengmingmu capsule for the treatment of diabetic retinopathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mingxu Zhang ◽  
Jiawei Yang ◽  
Xiulan Zhao ◽  
Ying Zhao ◽  
Siquan Zhu
Keyword(s):  
Diabetic Retinopathy ◽  
Molecular Docking ◽  
Molecular Mechanisms ◽  
Hypoxia Inducible Factor ◽  
Enrichment Analysis ◽  
Docking Study ◽  
Network Pharmacology ◽  
Biological Processes ◽  
Active Ingredients ◽  
Molecular Docking Study

AbstractDiabetic retinopathy (DR) is a leading cause of irreversible blindness globally. Qidengmingmu Capsule (QC) is a Chinese patent medicine used to treat DR, but the molecular mechanism of the treatment remains unknown. In this study, we identified and validated potential molecular mechanisms involved in the treatment of DR with QC via network pharmacology and molecular docking methods. The results of Ingredient-DR Target Network showed that 134 common targets and 20 active ingredients of QC were involved. According to the results of enrichment analysis, 2307 biological processes and 40 pathways were related to the treatment effects. Most of these processes and pathways were important for cell survival and were associated with many key factors in DR, such as vascular endothelial growth factor-A (VEGFA), hypoxia-inducible factor-1A (HIF-1Α), and tumor necrosis factor-α (TNFα). Based on the results of the PPI network and KEGG enrichment analyses, we selected AKT1, HIF-1α, VEGFA, TNFα and their corresponding active ingredients for molecular docking. According to the molecular docking results, several key targets of DR (including AKT1, HIF-1α, VEGFA, and TNFα) can form stable bonds with the corresponding active ingredients of QC. In conclusion, through network pharmacology methods, we found that potential biological mechanisms involved in the alleviation of DR by QC are related to multiple biological processes and signaling pathways. The molecular docking results also provide us with sound directions for further experiments.

Influence of microbial species on small intestinal myoelectric activity and transit in germ-free rats

2001 ◽  
Vol 280 (3) ◽  
pp. G368-G380 ◽  
Author(s):  
Einar Husebye ◽  
Per M. Hellström ◽  
Frank Sundler ◽  
Jie Chen ◽  
Tore Midtvedt
Keyword(s):  
Small Intestine ◽  
Intestinal Microflora ◽  
Burst Activity ◽  
Intestinal Transit ◽  
Myoelectric Activity ◽  
Regular Spike ◽  
Spike Burst ◽  
Germ Free ◽  
Microbial Species ◽  
Small Intestinal

The effect of an intestinal microflora consisting of selected microbial species on myoelectric activity of small intestine was studied using germ-free rat models, with recording before and after specific intestinal colonization, in the unanesthetized state. Intestinal transit, neuropeptides in blood (RIA), and neuromessengers in the intestinal wall were determined. Clostridium tabificum vp 04 promoted regular spike burst activity, shown by a reduction of the migrating myoelectric complex (MMC) period from 30.5 ± 3.9 min in the germ-free state to 21.2 ± 0.14 min ( P < 0.01). Lactobacillus acidophilus A10 and Bifidobacterium bifidum B11 reduced the MMC period from 27.9 ± 4.5 to 21.5 ± 2.1 min ( P < 0.02) and accelerated small intestinal transit ( P < 0.05). Micrococcus luteus showed an inhibitory effect, with an MMC period of 35.9 ± 9.3 min compared with 27.7 ± 6.3 min in germ-free rats ( P < 0.01). Inhibition was indicated also for Escherichia coli X7gnotobiotic rats. No consistent changes in slow wave frequency were observed. The concentration of neuropeptide Y in blood decreased after introduction of conventional intestinal microflora, suggesting reduced inhibitory control. Intestinal bacteria promote or suppress the initiation and aboral migration of the MMC depending on the species involved. Bacteria with primitive fermenting metabolism (anaerobes) emerge as important promoters of regular spike burst activity in small intestine.

Su1211 The Utility of Small Intestine Capsule Endoscopy and Balloon-Assisted Enteroscopy in the Diagnosis of Small Intestinal Tumors

2017 ◽  
Vol 85 (5) ◽  
pp. AB316
Author(s):  
Ryoichi Sawada ◽  
Ryosuke Miyazaki ◽  
Ayako Ishii ◽  
Yusuke Nagata ◽  
Makio Ogawa ◽  
...  
Keyword(s):  
Small Intestine ◽  
Capsule Endoscopy ◽  
Intestinal Tumors ◽  
Small Intestinal

Serum cobalamin concentrations and small intestinal ultrasound changes in 75 cats with clinical signs of gastrointestinal disease: a retrospective study

2016 ◽  
Vol 19 (1) ◽  
pp. 48-56 ◽  
Author(s):  
Maria C Jugan ◽  
John R August
Keyword(s):  
Small Intestine ◽  
Gastrointestinal Disease ◽  
Clinical Signs ◽  
Small Animal ◽  
Abdominal Ultrasound ◽  
Wall Layer ◽  
Normal Serum ◽  
Definitive Diagnosis ◽  
Albumin Concentration ◽  
Small Intestinal

Objectives The aim of the study was to evaluate ultrasonographic changes in the small intestine of cats with clinical signs of gastrointestinal disease and low or low–normal serum cobalamin concentrations. Methods Records for client-owned cats presenting to the small animal hospital with signs of gastrointestinal disease and in which serum cobalamin concentrations were measured from 2000–2013 were reviewed. Inclusion criteria were cobalamin concentrations <500 ng/l, abdominal ultrasound within 1 month of cobalamin testing and definitive diagnosis. Results Of 751 serum cobalamin measurements, hypocobalaminemia or low–normal cobalamin was identified in 270 cats, abdominal ultrasound was performed in 207 of those cats and a diagnosis was available for 75 of them. Small intestinal ultrasound changes were detected in 49/75 (65%) cats. Abnormalities included thickening, loss of wall layer definition, echogenicity alterations and discrete masses. Serum cobalamin concentrations <500 ng/l were observed with diagnoses of inflammatory disease, neoplasia, infectious disease and normal histopathology. Cobalamin concentration was significantly lower in cats with lymphoma or inflammatory bowel disease compared with other gastrointestinal neoplasia ( P = 0.031). No difference was found between cobalamin concentration and the presence of ultrasound abnormalities, specific ultrasound changes or albumin concentration. Conclusions and relevance One-third of symptomatic cats with hypocobalaminemia or low–normal cobalamin concentrations may have an ultrasonographically normal small intestine. For the majority of cats in this study, histopathologic abnormalities were observed in the small intestine, regardless of ultrasound changes. These findings suggest gastrointestinal disease should not be excluded based on low–normal cobalamin concentrations, even with a concurrent normal ultrasound examination. Additional studies are needed in cats with low–normal serum cobalamin concentrations, as a definitive diagnosis was not pursued consistently in those cats. However, data from this study suggest that careful monitoring, histopathologic evaluation and future cobalamin supplementation may be warranted.

scholarly journals A breakdown in communication? Understanding the effects of aging on the human small intestine epithelium

2015 ◽  
Vol 129 (7) ◽  
pp. 529-531 ◽  
Author(s):  
Neil A. Mabbott
Keyword(s):  
Small Intestine ◽  
Barrier Function ◽  
Intestinal Barrier ◽  
Intestinal Barrier Function ◽  
Human Small Intestine ◽  
Small Intestinal ◽  
Effects Of Aging ◽  
Insight Into

A new study by Man and colleagues provides further insight into the effects of aging on small intestinal barrier function in humans. Here, their findings are briefly summarised and the wider implications discussed.

scholarly journals Circulating or tissue microRNAs and extracellular vesicles as potential lung cancer biomarkers: a systematic review

2017 ◽  
Vol 33 (1) ◽  
pp. 3-9 ◽  
Author(s):  
Yan Song ◽  
Xiuli Yu ◽  
Zongmei Zang ◽  
Guijuan Zhao
Keyword(s):  
Lung Cancer ◽  
Systematic Review ◽  
Cancer Patients ◽  
Extracellular Vesicles ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Cancer Biomarkers ◽  
Biological Processes ◽  
Lung Cancer Patients ◽  
Prediction Of Prognosis

For both lung cancer patients and clinical physicians, tumor biomarkers for more efficient early diagnosis and prediction of prognosis are always wanted. Biomarkers in circulating serum, including microRNAs (miRNAs) and extracellular vesicles, hold the greatest possibilities to partially substitute for tissue biopsy. In this systematic review, studies on circulating or tissue miRNAs and extracellular vesicles as potential biomarkers for lung cancer patients were reviewed and are discussed. Furthermore, the target genes of the miRNAs indicated were identified through the miRTarBase, while the relevant biological processes and pathways of miRNAs in lung cancer were analyzed through MiRNA Enrichment Analysis and Annotation (MiEAA). In conclusion, circulating or tissue miRNAs and extracellular vesicles provide us with a window to explore strategies for diagnosing and assessing prognosis and treatment in lung cancer patients.

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