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muscle RNA-seq

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https://www.readbyqxmd.com/read/29777235/response-of-skeletal-muscle-ucp2-expression-during-metabolic-adaptation-to-caloric-restriction
#1
Sascha Heinitz, Paolo Piaggi, Shanshan Yang, Susan Bonfiglio, Jason Steel, Jonathan Krakoff, Susanne B Votruba
BACKGROUND/OBJECTIVES: Spendthrift vs. thrifty individuals expend more energy and experience greater weight loss during caloric restriction (CR). Adaptive mechanisms in skeletal muscle, adipose tissue, and on hormone level modulate energy expenditure (EE) during weight loss. Metabolic mechanisms underlying the variability in EE during CR are unclear. The present study explored whether during long-term CR (i) gene expression changes in skeletal muscle and adipose tissue relate with the individual EE response and weight loss, and (ii) altered catecholamine and FGF21-concentrations are associated with measures of metabolic adaptation...
May 17, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29771332/mechanisms-of-skeletal-muscle-wasting-in-a-mouse-model-for-myotonic-dystrophy-type-1
#2
Ginny R Morriss, Kimal Rajapakshe, Shixia Huang, Cristian Coarfa, Thomas A Cooper
Myotonic dystrophy type 1 (DM1) is a multisystemic disease resulting in severe muscle weakening and wasting. DM1 is caused by expansion of CTG repeats in the 3'-UTR of the DMPK gene. We have developed an inducible, skeletal muscle-specific mouse model of DM1 (CUG960) that expresses 960 CUG repeats in the context of human DMPK exons 11-15. CUG960 RNA-expressing mice induced at PN1, as well as adult-onset animals, show clear, measurable muscle wasting accompanied by severe histological defects including central myonuclei, reduced fiber cross sectional area, increased percentage of oxidative myofibers, and the presence of nuclear RNA foci that colocalize with Mbnl1 protein...
May 16, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29769607/facs-seq-analysis-of-pax3-derived-cells-identifies-non-myogenic-lineages-in-the-embryonic-forelimb
#3
Arun J Singh, Chih-Ning Chang, Hsiao-Yen Ma, Stephen A Ramsey, Theresa M Filtz, Chrissa Kioussi
Skeletal muscle in the forelimb develops during embryonic and fetal development and perinatally. While much is known regarding the molecules involved in forelimb myogenesis, little is known about the specific mechanisms and interactions. Migrating skeletal muscle precursor cells express Pax3 as they migrate into the forelimb from the dermomyotome. To compare gene expression profiles of the same cell population over time, we isolated lineage-traced Pax3+ cells (Pax3 EGFP ) from forelimbs at different embryonic days...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29752288/comparison-of-hepatic-nrf2-and-ahr-binding-in-2-3-7-8-tetrachlorodibenzo-p-dioxin-tcdd-treated-mice-demonstrates-nrf2-independent-pkm2-induction
#4
Rance Nault, Claire M Doskey, Kelly A Fader, Cheryl E Rockwell, Timothy R Zacharewski
2,3,7,8-Tetrachlorodibenzo- p -dioxin (TCDD) induces hepatic oxidative stress following activation of the aryl hydrocarbon receptor (AhR). Our recent studies showed TCDD induced pyruvate kinase muscle isoform 2 ( Pkm2 ) as a novel antioxidant response in normal differentiated hepatocytes. To investigate cooperative regulation between nuclear factor, erythroid derived 2, like 2 ( Nrf2 ) and the AhR in the induction of Pkm2 , hepatic ChIP-seq analyses were integrated with RNA-seq time course data from mice treated with TCDD for 2 - 168h...
May 11, 2018: Molecular Pharmacology
https://www.readbyqxmd.com/read/29748289/regulation-of-insulin-receptor-pathway-and-glucose-metabolism-by-cd36-signaling
#5
Dmitri Samovski, Pallavi Dhule, Terri Pietka, Miriam Jacome-Sosa, Eric Penrose, Ni-Huiping Son, Robert C Flynn, Kooresh I Shoghi, Krzysztof L Hyrc, Ira J Goldberg, Eric R Gamazon, Nada A Abumrad
During reduced energy intake, skeletal muscle maintains homeostasis by rapidly suppressing insulin-stimulated glucose utilization. Loss of this adaptation is observed with deficiency of the fatty acid transporter CD36. A similar loss is also characteristic of the insulin resistant state where CD36 is dysfunctional. To elucidate what links CD36 to muscle glucose utilization we examined whether CD36 signaling might influence insulin action. First, we show that CD36 deletion specific to skeletal muscle reduces expression of insulin signaling and glucose metabolism genes...
May 10, 2018: Diabetes
https://www.readbyqxmd.com/read/29747493/novel-splice-isoforms-of-pig-mynn-and-their-diverse-mrna-expression-patterns
#6
Meng Li, Xiaohong Guo, Pengfei Gao, Guoqing Cao, Zhimin Cheng, Wanfeng Zhang, Jianfeng Liu, Xiaojun Liu, Bugao Li
Objective: The aim of this study was to clone alternative splicing isoforms of pig MYNN, predict the structure and function of coding protein, and study temporal and spatial expression characteristics of each transcript. Methods: Alternative splice isoforms of MYNN were identified using RNA sequencing (RNA-seq) and cloning techniques. Quantitative real-time PCR (qPCR) was employed to detect expression patterns in 11 tissues of Large White (LW) and Mashen (MS) pigs, and to study developmental expression patterns in cerebellum (CE), stomach (ST) and longissimus dorsi (LD)...
April 25, 2018: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/29699519/comprehensive-gene-expression-analysis-of-canine-invasive-urothelial-bladder-carcinoma-by-rna-seq
#7
Shingo Maeda, Hirotaka Tomiyasu, Masaya Tsuboi, Akiko Inoue, Genki Ishihara, Takao Uchikai, James K Chambers, Kazuyuki Uchida, Tomohiro Yonezawa, Naoaki Matsuki
BACKGROUND: Invasive urothelial carcinoma (iUC) is a major cause of death in humans, and approximately 165,000 individuals succumb to this cancer annually worldwide. Comparative oncology using relevant animal models is necessary to improve our understanding of progression, diagnosis, and treatment of iUC. Companion canines are a preferred animal model of iUC due to spontaneous tumor development and similarity to human disease in terms of histopathology, metastatic behavior, and treatment response...
April 27, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29674374/changes-in-free-amino-acid-concentrations-and-associated-gene-expression-profiles-in-the-abdominal-muscle-of-kuruma-shrimp-marsupenaeus-japonicus-acclimated-at-different-salinities
#8
Hiroki Koyama, Nanami Mizusawa, Masataka Hoashi, Engkong Tan, Ko Yasumoto, Mitsuru Jimbo, Daisuke Ikeda, Takehiko Yokoyama, Shuichi Asakawa, Sanit Piyapattanakorn, Shugo Watabe
Shrimps inhabiting the coastal water can survive in a wide range of salinity. However, the molecular mechanisms involved in their acclimation to different environmental salinities have remained largely unknown. In the present study, we acclimated kuruma shrimp Marsupenaeus japonicus at 1.7 %, 3.4 % and 4.0 % salinities. After acclimating for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA-seq analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after acclimating for 24 h...
April 19, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29672513/rna-seq-reveals-differentially-expressed-genes-affecting-polyunsaturated-fatty-acids-percentage-in-the-huangshan-black-chicken-population
#9
Shaohua Yang, Ying Wang, Lulu Wang, Zhaoyuan Shi, Xiaoqian Ou, Dan Wu, Xinmiao Zhang, Hao Hu, Jia Yuan, Wei Wang, Fuhu Cao, Guoqing Liu
Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108-44,901,729 uniquely mapped reads, which covered 74...
2018: PloS One
https://www.readbyqxmd.com/read/29662503/identification-and-functional-analysis-of-long-intergenic-non-coding-rnas-underlying-intramuscular-fat-content-in-pigs
#10
Cheng Zou, Long Li, Xiaofang Cheng, Cencen Li, Yuhua Fu, Chengchi Fang, Changchun Li
Intramuscular fat (IMF) content is an important trait that can affect pork quality. Previous studies have identified many genes that can regulate IMF. Long intergenic non-coding RNAs (lincRNAs) are emerging as key regulators in various biological processes. However, lincRNAs related to IMF in pig are largely unknown, and the mechanisms by which they regulate IMF are yet to be elucidated. Here we reconstructed 105,687 transcripts and identified 1,032 lincRNAs in pig longissimus dorsi muscle (LDM) of four stages with different IMF contents based on published RNA-seq...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29659518/examining-the-genetic-background-of-porcine-muscle-growth-and-development-based-on-transcriptome-and-mirnaome-data
#11
Katarzyna Ropka-Molik, Klaudia Pawlina-Tyszko, Kacper Żukowski, Katarzyna Piórkowska, Grzegorz Żak, Artur Gurgul, Natalia Derebecka, Joanna Wesoły
Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content...
April 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29658965/a-comprehensive-transcriptome-analysis-of-skeletal-muscles-in-two-polish-pig-breeds-differing-in-fat-and-meat-quality-traits
#12
Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Ropka-Molik, Mirosław Tyra, Artur Gurgul
Pork is the most popular meat in the world. Unfortunately, the selection pressure focused on high meat content led to a reduction in pork quality. The present study used RNA-seq technology to identify metabolic process genes related to pork quality traits and fat deposition. Differentially expressed genes (DEGs) were identified between pigs of Pulawska and Polish Landrace breeds for two the most important muscles (semimembranosus and longissimus dorsi). A total of 71 significant DEGs were reported: 15 for longissimus dorsi and 56 for semimembranosus muscles...
January 2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29622030/mapping-human-pluripotent-stem-cell-differentiation-pathways-using-high-throughput-single-cell-rna-sequencing
#13
Xiaoping Han, Haide Chen, Daosheng Huang, Huidong Chen, Lijiang Fei, Chen Cheng, He Huang, Guo-Cheng Yuan, Guoji Guo
BACKGROUND: Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. RESULTS: We use high throughput single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body system. We present a cellular-state landscape for hPSC early differentiation that covers multiple cellular lineages, including neural, muscle, endothelial, stromal, liver, and epithelial cells...
April 5, 2018: Genome Biology
https://www.readbyqxmd.com/read/29618798/differential-expression-of-micrornas-and-other-small-rnas-in-muscle-tissue-of-patients-with-als-and-healthy-age-matched-controls
#14
Anja Kovanda, Lea Leonardis, Janez Zidar, Blaž Koritnik, Leja Dolenc-Groselj, Stanislava Ristic Kovacic, Tomaž Curk, Boris Rogelj
Amyotrophic lateral sclerosis is a late-onset disorder primarily affecting motor neurons and leading to progressive and lethal skeletal muscle atrophy. Small RNAs, including microRNAs (miRNAs), can serve as important regulators of gene expression and can act both globally and in a tissue-/cell-type-specific manner. In muscle, miRNAs called myomiRs govern important processes and are deregulated in various disorders. Several myomiRs have shown promise for therapeutic use in cellular and animal models of ALS; however, the exact miRNA species differentially expressed in muscle tissue of ALS patients remain unknown...
April 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29618337/gene-co-expression-networks-in-liver-and-muscle-transcriptome-reveal-sex-specific-gene-expression-in-lambs-fed-with-a-mix-of-essential-oils
#15
Marcella Sabino, Victor Adriano Okstoft Carmelo, Gianluca Mazzoni, Katia Cappelli, Stefano Capomaccio, Paolo Ajmone-Marsan, Andrea Verini-Supplizi, Massimo Trabalza-Marinucci, Haja N Kadarmideen
BACKGROUND: Essential oil (EO) dietary supplementation is a new strategy to improve animal health. EO compounds have antiparasitic, antimicrobial, antiviral, antimycotic, antioxidant and anti-inflammatory proprieties. Nutrigenomics investigations represent innovative approaches in understanding the relation between diet effect and gene expression related to the animal performance. Few nutrigenomics studies have used a high-throughput RNA-Sequencing (RNA-Seq) approach, despite great potential of RNA-Seq data in gene expression quantification and in co-expression network analyses...
April 4, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29618046/draft-genome-assembly-of-the-bengalese-finch-lonchura-striata-domestica-a-model-for-motor-skill-variability-and-learning
#16
Bradley M Colquitt, David G Mets, Michael S Brainard
Background: Vocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic underpinnings of this variability and the learning it supports are poorly understood...
March 1, 2018: GigaScience
https://www.readbyqxmd.com/read/29617656/impaired-spermatogenesis-muscle-and-erythrocyte-function-in-u12-intron-splicing-defective-zrsr1-mutant-mice
#17
Keiko Horiuchi, Serafín Perez-Cerezales, Panagiotis Papasaikas, Priscila Ramos-Ibeas, Angela Patricia López-Cardona, Ricardo Laguna-Barraza, Noelia Fonseca Balvís, Eva Pericuesta, Raul Fernández-González, Benjamín Planells, Alberto Viera, Jose Angel Suja, Pablo Juan Ross, Francisco Alén, Laura Orio, Fernando Rodriguez de Fonseca, Belén Pintado, Juan Valcárcel, Alfonso Gutiérrez-Adán
The U2AF35-like ZRSR1 has been implicated in the recognition of 3' splice site during spliceosome assembly, but ZRSR1 knockout mice do not show abnormal phenotypes. To analyze ZRSR1 function and its precise role in RNA splicing, we generated ZRSR1 mutant mice containing truncating mutations within its RNA-recognition motif. Homozygous mutant mice exhibited severe defects in erythrocytes, muscle stretch, and spermatogenesis, along with germ cell sloughing and apoptosis, ultimately leading to azoospermia and male sterility...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29587858/hla-and-proteasome-expression-body-map
#18
Sebastian Boegel, Martin Löwer, Thomas Bukur, Patrick Sorn, John C Castle, Ugur Sahin
BACKGROUND: The presentation of HLA peptide complexes to T cells is a highly regulated and tissue specific process involving multiple transcriptionally controlled cellular components. The extensive polymorphism of HLA genes and the complex composition of the proteasome make it difficult to map their expression profiles across tissues. METHODS: Here we applied a tailored gene quantification pipeline to 4323 publicly available RNA-Seq datasets representing 55 normal tissues and cell types to examine expression profiles of (classical and non-classical) HLA class I, class II and proteasomal genes...
March 27, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29565464/comprehensive-analysis-of-differential-expression-profiles-of-mrnas-and-lncrnas-and-identification-of-a-14-lncrna-prognostic-signature-for-patients-with-colon-adenocarcinoma
#19
Yanwei Xing, Zhiwei Zhao, Yuekun Zhu, Liangliang Zhao, Anlong Zhu, Daxun Piao
The objective of this study was to identify potentially significant genes and long non-coding RNAs (lncRNAs) in colon cancer for a panel of lncRNA signatures that could be used as prognostic markers for colon adenocarcinoma (COAD) based on the data from The Cancer Genome Atlas (TCGA). RNA-seq V2 exon data of COAD were downloaded from the TCGA data portal for 285 tumor samples and 41 normal tissue samples adjacent to tumors. Differentially expressed mRNAs and lncRNAs were identified. A functional enrichment analysis of differentially expressed mRNAs was performed, followed by protein-protein interaction (PPI) network construction and significant module selection...
May 2018: Oncology Reports
https://www.readbyqxmd.com/read/29531190/screening-for-candidate-genes-related-with-histological-microstructure-meat-quality-and-carcass-characteristic-in-pig-based-on-rna-seq-data
#20
Katarzyna Ropka-Molik, Anna Bereta, Kacper Żukowski, Mirosław Tyra, Katarzyna Piórkowska, Grzegorz Żak, Maria Oczkowicz
Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of SNPs significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to QTLs regions...
March 13, 2018: Asian-Australasian Journal of Animal Sciences
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