scholarly journals Transcriptomic analysis for pork color – the ham halo effect in biceps femoris

2021 ◽  
Author(s):  
Dan Nonneman ◽  
Brittney N Keel ◽  
Amanda K Lindholm-Perry ◽  
Gary Rohrer ◽  
Tommy L. Wheeler ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Enrichment Analysis ◽  
Biceps Femoris ◽  
Halo Effect ◽  
Type I ◽  
Muscle Adaptation ◽  
Normal Muscle ◽  
Biceps Femoris Muscle ◽  
Go Enrichment ◽  
Type I Fibers

Pork color is a major indicator of product quality that guides consumerpurchasing decisions. Recently, industry has received an increase in consumercomplaints about the lightness and non-uniformity of ham color, primarilylighter color in the periphery termed “ham halo” that is not caused bymanufacturing procedures. This effect is seen in fresh and processed hams andthe outer, lighter muscle is associated with lower myoglobin concentration, pHand type I fibers. The objective of this study was to identify differences ingene expression profiles between light and normal colored portions of biceps femoris muscle from pork hams.RNA-sequencing was performed for paired light and normal colored muscle samplesfrom 10 animals showing the ham halo effect. Over 50 million paired-end reads(2x75bp) per library were obtained. An average of 99.74% of trimmed high-qualityreads were mapped to the Sscrofa 11.1 genome assembly. Differentially expressedgenes (DEGs) were identified using both the DESeq2 and GFOLD software packages.A total of 14,049 genes were expressed in bicepsfemoris; 13,907 were expressed in both light and normal muscle, while 56and 86 genes were only expressed in light and normal muscle, respectively. Analysiswith DESeq2 identified 392 DEGs with 359 genes being more highly expressed innormal colored muscle. A total of 61 DEGs were identified in the DESeq2analysis and also were identified in at least 7 of the 10 individual animalanalyses. All 61 of these DEGs were up-regulated in normal colored muscle. Geneontology (GO) enrichment analysis of DEGs identified the transition betweenfast and slow fibers, and skeletal muscle adaptation and contraction as themost significant biological process terms. The evaluation of gene expression byRNA-Seq identified DEGs between regions of the biceps femoris with the ham halo effect that are associated with thevariation in pork color.

Influence of rearing conditions and crossbreeding on muscle color in Iberian pigs Influencia de las condiciones de crianza y del cruce en el color de los músculos de cerdos Ibéricos

2000 ◽  
Vol 6 (4) ◽  
pp. 315-321 ◽  
Author(s):  
A.I. Andrés ◽  
J. Ruiz ◽  
A.I. Mayoral ◽  
J.F. Tejeda ◽  
R. Cava
Keyword(s):  
Image Analysis ◽  
Fiber Type ◽  
Biceps Femoris ◽  
Type I ◽  
Biceps Femoris Muscle ◽  
Rearing Conditions ◽  
Hue Angle ◽  
Total Proportion ◽  
Muscle Color ◽  
Femoris Muscle

The effects of pig crossbreeding (Iberian versus Iberian x Duroc 50%) and rearing conditions (out doors versus indoors) on muscle fiber composition, myoglobin content and objective muscle color in biceps femoris and tibialis crancalis muscles have been studied. Muscle fibers were identified as types I, IIA, IIB, oxidative IIB and IIC and the proportion of each fiber type was determined by a computer ized image analysis. Color co-ordinates L*, a*, and b* were measured and both chroma ( C*) and hue angle ( h°) were calculated. Myoglobin content and chroma value were significantly higher in tibialis cranealis muscle than in biceps femoris muscle ( p ≤ 0.001), whereas the former muscle showed the lowest lightness and hue angle values ( p ≤ 0.001). Moreover, tibialis cranealis muscle exhibited a higher total proportion of oxidative fibers, types I, IIA and IIBx ( p ≤ 0.05), and a lower fat content than did biceps femoris muscle ( p ≤ 0.001). The muscles of pigs reared outdoors tended to show a higher per centage of oxidative fibers (type I) than did muscles from indoor reared pigs, although not to a sig nificant extent. Rearing conditions significantly affected color, muscles from outdoor reared pigs ex hibiting higher lightness ( L*), chroma ( C*) and hue angle ( h°) than muscles from indoor reared pigs. However, neither the crossbreeding nor the rearing conditions showed a significant influence on myoglobin concentration of muscles.

scholarly journals Bioinformatics Analysis of ceRNA Network Related to Polycystic Ovarian Syndrome

2021 ◽  
Vol 2021 ◽  
pp. 1-20
Author(s):  
Yuanqi Li ◽  
Yong Tan
Keyword(s):  
Signaling Pathway ◽  
Type I Diabetes ◽  
Polycystic Ovary ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Type I ◽  
Childbearing Age ◽  
Cerna Network

Introduction. Polycystic ovary syndrome (PCOS) is caused by the hormonal environment in utero, abnormal metabolism, and genetics, and it is common in women of childbearing age. A large number of studies have reported that lncRNA is important to the biological process of cancer and can be used as a potential prognostic biomarker. Thus, we studied lncRNAs’ roles in PCOS in this article. Methods. We obtained mRNAs’, miRNAs’, and lncRNAs’ expression profiles in PCOS specimens and normal specimens from the National Biotechnology Information Gene Expression Comprehensive Center database. The EdgeR software package is used to distinguish the differentially expressed lncRNAs, miRNAs, and mRNAs. Functional enrichment analysis was carried out by the clusterProfiler R Package, and the lncRNA-miRNA-mRNA interaction ceRNA network was built in Cytoscape plug-in BiNGO and Database for Annotation, Visualization, and Integration Discovery (DAVID), respectively. Results. We distinguished differentially expressed RNAs, including 1087 lncRNAs, 14 miRNAs, and 566 mRNAs in PCOS. Among them, 410 lncRNAs, 11 miRNAs, and 185 mRNAs were contained in the ceRNA regulatory network. The outcomes from Gene Ontology (GO) analysis showed that the differentially expressed mRNAs (DEMs) were mainly enriched in response to the maternal process involved in female pregnancy, morphogenesis of embryonic epithelium, and the intracellular steroid hormone receptor signaling pathway. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis data showed that DEMs were primarily enriched in pathways related to the TGF-β signaling pathway, Type I diabetes mellitus, and glycolysis/gluconeogenesis. In addition, we chose NONHSAT123397, ENST00000564619, and NONHSAT077997 as key lncRNAs due to their high bearing on PCOS. Conclusion. ceRNA networks play an important role in PCOS. The research indicated that specific lncRNAs were related to PCOS development. NONHSAT123397, ENST00000564619, and NONHSAT077997 could be regarded as potential diagnostic mechanisms and biomarkers for PCOS. This discovery might provide more effective and more novel insights into the mechanisms of PCOS worthy of further exploration.

Skeletal muscle adaptation in rats flown on Cosmos 1667

1990 ◽  
Vol 68 (1) ◽  
pp. 48-52 ◽  
Author(s):  
D. Desplanches ◽  
M. H. Mayet ◽  
E. I. Ilyina-Kakueva ◽  
B. Sempore ◽  
R. Flandrois
Keyword(s):  
Simultaneous Increase ◽  
Control Group ◽  
Type I ◽  
Muscle Adaptation ◽  
Cross Sectional ◽  
Significant Difference ◽  
Male Wistar Rats ◽  
Hydroxyacyl Coa Dehydrogenase ◽  
Biochemical Analyses ◽  
Type I Fibers

Seven male Wistar rats were subjected to 7 days of weightlessness on the Soviet biosatellite Cosmos 1667. Muscle histomorphometry and biochemical analyses were performed on the soleus (SOL) and extensor digitorum longus (EDL) of flight rats (group F) and compared with data from three groups of terrestrial controls: one subjected to conditions similar to group F in space except for the state of weightlessness (group S) and the others living free in a vivarium (V1, V2). Relative to group V2 (its age and weight-matched control group), group F showed a greater decrease of muscle mass in SOL (23%) than in EDL (11%). In SOL a decrease in the percentage of type I fibers was counterbalanced by a simultaneous increase in type IIa fibers. The cross-sectional area of type I fiber was reduced by 24%. No statistically significant difference in capillarization and enzymatic activities was observed between the groups. In EDL a reduction in type I fiber distribution and 3-hydroxyacyl-CoA-dehydrogenase activity (27%) occurred after the flight. The small histochemical and biochemical changes reported suggest the interest in studying muscular adaptation during a flight of longer duration.

Identification of Novel Breast Cancer Genes based on Gene Expression Profiles and PPI Data

2019 ◽  
Vol 16 (5) ◽  
pp. 415-426
Author(s):  
Cheng-Wen Yang ◽  
Huan-Huan Cao ◽  
Yu Guo ◽  
Yuan-Ming Feng ◽  
Ning Zhang
Keyword(s):  
Breast Cancer ◽  
Expression Profiles ◽  
Endocrine Resistance ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Breast Cancer Diagnosis ◽  
Cancer Genes ◽  
Protein Protein Interaction ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Background:Breast cancer is one of the most common malignancies, and a threat to female health all over the world. However, the molecular mechanism of breast cancer has not been fully discovered yet.Objective:It is crucial to identify breast cancer-related genes, which could provide new biomarker for breast cancer diagnosis as well as potential treatment targets.Methods:Here we used the minimum redundancy-maximum relevance (mRMR) method to select significant genes, then mapped the transcripts of the genes on the Protein-Protein Interaction (PPI) network and traced the shortest path between each pair of two proteins.Results:As a result, we identified 24 breast cancer-related genes whose betweenness were over 700. The GO enrichment analysis indicated that the transcription and oxygen level are very important in breast cancer. And the pathway analysis indicated that most of these 24 genes are enriched in prostate cancer, endocrine resistance, and pathways in cancer.Conclusion:We hope these 24 genes might be useful for diagnosis, prognosis and treatment for breast cancer.

scholarly journals Thyroidectomy significantly alters carbonic anhydrase III concentration and fiber distribution in rat muscle.

1987 ◽  
Vol 35 (6) ◽  
pp. 663-668 ◽  
Author(s):  
S Jeffery ◽  
N D Carter ◽  
A Smith
Keyword(s):  
Carbonic Anhydrase ◽  
Type I ◽  
Fiber Distribution ◽  
Normal Muscle ◽  
Dramatic Effect ◽  
Rat Muscle ◽  
Carbonic Anhydrase Iii ◽  
Type I Fibers ◽  
Atpase Staining

Thyroidectomy has a dramatic effect on rat muscle, greatly increasing the number of Type I fibers and the concentrations of carbonic anhydrase III (CAIII) in the muscle. Carbonic anhydrase III is not confined to the Type I fibers, as was previously believed, but also occurs in fibers that exhibit a level of ATPase staining less than that of 2A fibers but greater than 2B. These fibers are rare in normal muscle but become numerous after thyroidectomy, when they stain heavily for CAIII.

scholarly journals Identification of Critical Transcriptomic Signaling Pathways in Patients with H Syndrome and Rosai-Dorfman Disease

2020 ◽  
Author(s):  
Samuel Lara-Reyna ◽  
James A. Poulter ◽  
Elton J.R. Vasconcelos ◽  
Mark Kacar ◽  
Michael F. McDermott ◽  
...  
Keyword(s):  
Gene Expression ◽  
Enrichment Analysis ◽  
Pathological Process ◽  
Type I ◽  
Alternatively Activated Macrophages ◽  
Complex Disorder ◽  
Go Enrichment ◽  
Rosai Dorfman Disease ◽  
Monocytes And Macrophages ◽  
Biallelic Mutations

AbstractBiallelic mutations in SLC29A3 cause histiocytosis-lymphadenopathy plus syndrome, also known as H syndrome (HS). HS is a complex disorder, with ~ 25% of patients developing autoinflammatory complications consisting of unexplained fevers, persistently elevated inflammatory markers, and unusual lymphadenopathies, with infiltrating CD68+, S100+, and CD1a− histiocytes, resembling the immunophenotype found in Rosai-Dorfman disease (RDD). We investigated the transcriptomic profiles of monocytes, non-activated (M0), classically activated (M1), and alternatively activated macrophages (M2) in two patients with HS, one without autoinflammatory (HS1) and one with autoinflammatory complications (HS2). RNA sequencing revealed a dysregulated transcriptomic profile in both HS patients compared to healthy controls (HC). HS2, when compared to HS1, had several differentially expressed genes, including genes associated with lymphocytic-histiocytic predominance (e.g. NINL) and chronic immune activation (e.g. B2M). The transcriptomic and cytokine profiles of HS patients were comparable to patients with SAID with high levels of TNF. SERPINA1 gene expression was found to be upregulated in all patients studied. Moreover, higher levels of IFNγ were found in the serum of both HS patients when compared to HC. Gene ontology (GO) enrichment analysis of the DEGs in HS patients revealed the terms “type I IFN,” “IFNγ signaling pathway,” and “immune responses” as the top 3 most significant terms for monocytes. Gene expression analysis of lymph node biopsies from sporadic and H syndrome-associated RDD suggests common underlying pathological process. In conclusion, monocytes and macrophages from both HS patients showed transcriptomic profiles similar to SAIDs and also uniquely upregulated IFNγ signature. These findings may help find better therapeutic options for this rare disorder.

scholarly journals Effect of Sex and Muscle on the Fiber-Type Composition and Cross-Sectional Area of Springbok (Antidorcas marsupialis) Muscle

2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Megan K. North ◽  
Louw C. Hoffman
Keyword(s):  
Fiber Type ◽  
Biceps Femoris ◽  
Cross Sectional Area ◽  
Type I ◽  
Sectional Area ◽  
Cross Sectional ◽  
Fiber Type Composition ◽  
Type Composition ◽  
Type I Fibers ◽  
Antidorcas Marsupialis

This study aimed to compare the fiber-type composition and fiber cross-sectional area (CSA) of male and female springbok (Antidorcas marsupialis) Longissimus thoracis et lumborum (LTL) and Biceps femoris (BF) muscles. Frozen samples from 4 male and 3 female springbok were fiber-typed immunohistochemically using the primary antibodies A4.74, BA-D5 and BF-35. The CSA of the fibers was determined using the software Image J. Type IIX fibers accounted for 64 to 77% of the fibers in all samples, with type IIA (12.7 to 19.1%), type IIAX (6.4 to 9.3%) and type I (2.4 to 8.5%) making smaller (P < 0.001) contributions. Female springboks’ muscles contained more type IIX fibers than males’ (P = 0.004) and the BF contained more type I fibers and fewer type IIA and IIAX fibers than the LTL (P < 0.001). CSA values did not differ between sexes or muscles; however, they increased with apparent fiber glycolytic capacity (I < IIA < IIAX < IIX; P < 0.001). The glycolytic nature suggested by the fiber-type composition of springbok muscle found in this study is in contrast with previous reports on the physicochemical nature of springbok meat. This casts doubt on the application of standard associations between fiber-type and meat quality to this species. However, it may provide some explanation for the low shear force values found for springbok meat in previous studies.

scholarly journals Analysis of gene expression profiles of Enterococcus faecalis induced by type I collagen

2022 ◽  
Vol 13 (1) ◽  
pp. 129-139
Author(s):  
Yoki Hirakawa ◽  
Sadaomi Sugimoto ◽  
Norimasa Tsuji ◽  
Takeshi Inamoto ◽  
Hiroshi Maeda
Keyword(s):  
Gene Expression ◽  
Enterococcus Faecalis ◽  
High Throughput Sequencing ◽  
Type I Collagen ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Culture Conditions ◽  
Type I ◽  
Go Terms

Enterococcus faecalis is an etiological agent of endodontic infections. The present study was performed to investigate the gene profiles of E. faecalis induced by type I collagen stimulation. E. faecalis ATCC 19433 was cultivated with [collagen (+)] or without type I collagen [collagen (−)], and transcriptome analysis was performed using high-throughput sequencing technology. A total of 3.6 gb of information was obtained by sequence analysis and 77 differentially expressed genes (DEGs) between the two culture conditions were identified. Among the 77 DEGs, 35 genes were upregulated in collagen (+) E. faecalis, whereas 42 genes were downregulated. Gene Ontology (GO) enrichment analysis was performed and 11 GO terms, including metalloendopeptidase activity (GO:0004222) and two related GO terms (GO:0031012, GO:0044421), were significantly enriched in the set of upregulated genes. We focused on an upregulated DEG belonging to the matrixin metalloprotease gene family, and matrix metalloprotease (MMP) activities of the bacterial cell were examined. The generic MMP, MMP-8, and MMP-9 activities of collagen (+) E. faecalis were significantly higher than those of collagen (−) E. faecalis. These results suggested that contact with type I collagen may alter the gene expression profile of E. faecalis, and upregulation of metalloprotease genes may result in enhanced MMP activities in E. faecalis.

scholarly journals Identification of tumor-infiltrating lymphocyte subpopulations correlated with patient prognosis in esophageal squamous cell carcinoma

2021 ◽  
Vol 49 (5) ◽  
pp. 030006052110162
Author(s):  
Lin Peng ◽  
Wenwu He ◽  
Feng Ye ◽  
Yane Song ◽  
Xinying Shi ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Suppressor Cells ◽  
Enrichment Analysis ◽  
Postoperative Chemotherapy ◽  
Th2 Cells

Objective To identify biomarkers related to esophageal squamous cell carcinoma (ESCC) prognosis by analyzing genetic variations and the infiltration levels of tumor-infiltrating lymphocytes (TILs) in patients. Methods The clinical features of 61 patients with ESCC were collected. DNA panel sequencing was performed to screen differentially expressed genes (DEGs). Transcriptome sequencing was performed to identify gene expression profiles, and subsequent enrichment analysis of DEGs was conducted using Metascape. Results We identified 488 DEGs between patients with ESCC with distinct prognoses that were mainly enriched in the human immune response, fibrinogen complex, and protein activation cascade pathways. Among patients with ESCC treated with postoperative chemotherapy, those with a high infiltration level of myeloid-derived suppressor cells (MDSCs) had longer overall survival (OS), and OS was positively correlated with the infiltration level of T helper type 2 (Th2) cells among patients treated without chemotherapy after surgery. Additionally, in the case of MDSCs >0.7059 or Th2 cells <0.6290, patients receiving postoperative chemotherapy had a longer OS than those treated without chemotherapy following surgery. Conclusion The level of MDSCs or Th2 cells can be used as a biomarker for assessing the prognosis of patients with ESCC treated with or without postoperative chemotherapy, respectively.

scholarly journals Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Guoning Wang ◽  
Xingfen Wang ◽  
Yan Zhang ◽  
Jun Yang ◽  
Zhikun Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Verticillium Wilt ◽  
Dynamic Characteristics ◽  
Target Genes ◽  
Acid Metabolism ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Alpha Linolenic Acid ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract Background Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear. Results Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA. Conclusion This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

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