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muscle RNA-seq

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https://www.readbyqxmd.com/read/28340271/snp-detection-using-rna-sequences-of-candidate-genes-associated-with-puberty-in-cattle
#1
M M Dias, A Cánovas, C Mantilla-Rojas, D G Riley, P Luna-Nevarez, S J Coleman, S E Speidel, R M Enns, A Islas-Trejo, J F Medrano, S S Moore, M R S Fortes, L T Nguyen, B Venus, I S D P Diaz, F R P Souza, L F S Fonseca, F Baldi, L G Albuquerque, M G Thomas, H N Oliveira
Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28338730/genetic-variability-of-the-activity-of-bidirectional-promoters-a-pilot-study-in-bovine-muscle
#2
Cédric Meersseman, Rabia Letaief, Véronique Léjard, Emmanuelle Rebours, Gabriel Guillocheau, Diane Esquerré, Anis Djari, Amanda Chamberlain, Christy Vander Jagt, Christophe Klopp, Mekki Boussaha, Gilles Renand, Abderrahman Maftah, Daniel Petit, Dominique Rocha
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters...
February 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28330496/calcium-dysregulation-functional-calpainopathy-and-endoplasmic-reticulum-stress-in-sporadic-inclusion-body-myositis
#3
David R Amici, Iago Pinal-Fernandez, Davi A G Mázala, Thomas E Lloyd, Andrea M Corse, Lisa Christopher-Stine, Andrew L Mammen, Eva R Chin
Sporadic inclusion body myositis (IBM) is the most common primary myopathy in the elderly, but its pathoetiology is still unclear. Perturbed myocellular calcium (Ca(2+)) homeostasis can exacerbate many of the factors proposed to mediate muscle degeneration in IBM, such as mitochondrial dysfunction, protein aggregation, and endoplasmic reticulum stress. Ca(2+) dysregulation may plausibly be initiated in IBM by immune-mediated membrane damage and/or abnormally accumulating proteins, but no studies to date have investigated Ca(2+) regulation in IBM patients...
March 22, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28329397/resveratrol-improves-vascular-function-and-mitochondrial-number-but-not-glucose-metabolism-in-older-adults
#4
Rena M Pollack, Nir Barzilai, Valentin Anghel, Ameya S Kulkarni, Aaron Golden, Pilib O'Broin, David A Sinclair, Michael S Bonkowski, Alexander J Coleville, Danielle Powell, Sharon Kim, Ruin Moaddel, Daniel Stein, Kehao Zhang, Meredith Hawkins, Jill P Crandall
Background: Resveratrol, a plant-derived polyphenol, has been reported to improve glucose metabolism and vascular function and to extend life span in animal models, but studies in humans have been inconclusive. Methods: In a randomized, double-blind crossover study, we treated older glucose-intolerant adults (n = 30) with resveratrol (2-3 g/daily) or placebo, each for 6 weeks. A standard mixed-meal test was used to assess insulin sensitivity (Matsuda index) and secretion (C-peptide deconvolution) and vascular function by reactive hyperemia peripheral arterial tonometry...
March 16, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28321693/age-at-diagnosis-obesity-smoking-and-molecular-subtypes-in-muscle-invasive-bladder-cancer
#5
Xuezheng Sun, Katherine A Hoadley, William Y Kim, Helena Furberg, Andrew F Olshan, Melissa A Troester
BACKGROUND: Heterogeneity of muscle-invasive bladder cancer (MIBC) has been characterized using whole-genome mRNA expression data, showing distinct molecular and clinicopathological characteristics by subtypes. However, associations between risk factors and molecular subtypes have not been reported. METHODS: Four previously published schemes were used to categorize molecular subtypes in 372 MIBC patients from the Cancer Genome Atlas (TCGA). Data on gene expression (RNA-seq), demographic, and clinicopathological characteristics were retrieved through TCGA data portal...
March 20, 2017: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/28286175/cilia-dependent-gli-processing-in-neural-crest-cells-is-required-for-tongue-development
#6
Grethel Millington, Kelsey Elliott, Ya-Ting Chang, Ching-Fang Chang, Andrzej Dlugosz, Samantha A Brugmann
Ciliopathies are a class of diseases caused by the loss of a ubiquitous, microtubule-based organelle called a primary cilium. Ciliopathies commonly result in defective development of the craniofacial complex, causing midfacial defects, craniosynostosis, micrognathia and aglossia. Herein, we explored how the conditional loss of primary cilia on neural crest cells (Kif3a(f/f);Wnt1-Cre) generated aglossia. On a cellular level, our data revealed that aglossia in Kif3a(f/f);Wnt1-Cre embryos was due to a loss of mesoderm-derived muscle precursors migrating into and surviving in the tongue anlage...
March 9, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28283548/smooth-muscle-cell-specific-deletion-of-col15a1-unexpectedly-leads-to-impaired-development-of-advanced-atherosclerotic-lesions
#7
Brittany G Durgin, Olga A Cherepanova, Delphine Gomez, Themistoclis Karaoli, Gabriel F Alencar, Joshua T Butcher, Yu-Qing Zhou, Michelle P Bendeck, Brant E Isakson, Gary K Owens, Jessica J Connelly
Atherosclerotic plaque rupture with subsequent embolic events is a major cause of sudden death from myocardial infarction or stroke. Although smooth muscle cells (SMC) produce and respond to collagens in vitro, there is no direct evidence in vivo that SMC are a crucial source of collagens and that this impacts lesion development or fibrous cap formation. We sought to determine how conditional SMC specific knockout of collagen type XV (COL15A1) in SMC lineage tracing mice affects advanced lesion formation given: 1) we previously identified a Col15a1 sequence variant associated with age related atherosclerosis; 2) COL15A1 is a matrix organizer enhancing tissue structural integrity; and 3) siRNA mediated Col15a1 knockdown increased migration and decreased proliferation of cultured human SMC...
March 10, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28276486/a-potential-regulatory-network-underlying-distinct-fate-commitment-of-myogenic-and-adipogenic-cells-in-skeletal-muscle
#8
Wenjuan Sun, Ting He, Chunfu Qin, Kai Qiu, Xin Zhang, Yanhong Luo, Defa Li, Jingdong Yin
Mechanism controlling myo-adipogenic balance in skeletal muscle is of great significance for human skeletal muscle dysfunction and myopathies as well as livestock meat quality. In the present study, two cell subpopulations with particular potency of adipogenic or myogenic differentiation were isolated from neonatal porcine longissimus dorsi using the preplate method to detect mechanisms underlying distinct fate commitment of myogenic and adipogenic cells in skeletal muscle. Both cells share a common surface expression profile of CD29(+)CD31(-)CD34(-)CD90(+)CD105(+), verifying their mesenchymal origin...
March 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265565/the-draft-genome-and-transcriptome-of-the-atlantic-horseshoe-crab-limulus-polyphemus
#9
Stephen D Simpson, Jordan S Ramsdell, Winsor H Watson Iii, Christopher C Chabot
The horseshoe crab, Limulus polyphemus, exhibits robust circadian and circatidal rhythms, but little is known about the molecular mechanisms underlying those rhythms. In this study, horseshoe crabs were collected during the day and night as well as high and low tides, and their muscle and central nervous system tissues were processed for genome and transcriptome sequencing, respectively. The genome assembly resulted in 7.4 × 10(5) contigs with N50 of 4,736, while the transcriptome assembly resulted in 9.3 × 10(4) contigs and N50 of 3,497...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28262958/an-atlas-and-analysis-of-bovine-skeletal-muscle-long-noncoding-rnas
#10
X F Liu, X B Ding, X Li, C F Jin, Y W Yue, G P Li, H Guo
Long noncoding RNAs (lncRNAs) have various biological functions and have been extensively studied in recent years. However, the identification and characterization of bovine lncRNAs in skeletal muscle has been very limited compared with that of lncRNAs in other model organisms. In this study, 7188 bovine skeletal muscle lncRNAs were identified by RNA-Seq and a stringent screening procedure in four different muscle tissues. These lncRNAs shared many characteristics with other mammalian lncRNAs, such as a shorter open reading frame and lower expression level than for mRNAs...
March 6, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28258189/selective-expression-of-tspan2-in-vascular-smooth-muscle-is-independently-regulated-by-tgf-%C3%AE-1-smad-and-myocardin-serum-response-factor
#11
Jinjing Zhao, Wen Wu, Wei Zhang, Yao Wei Lu, Emiley Tou, Jiemei Ye, Ping Gao, David Jourd'heuil, Harold A Singer, Mingfu Wu, Xiaochun Long
Tetraspanins (TSPANs) comprise a large family of 4-transmembrane domain proteins. The importance of TSPANs in vascular smooth muscle cells (VSMCs) is unexplored. Given that TGF-β1 and myocardin (MYOCD) are potent activators for VSMC differentiation, we screened for TGF-β1 and MYOCD/serum response factor (SRF)-regulated TSPANs in VSMC by using RNA-seq analyses and RNA-arrays. TSPAN2 was found to be the only TSPAN family gene induced by TGF-β1 and MYOCD, and reduced by SRF deficiency in VSMCs. We also found that TSPAN2 is highly expressed in smooth muscle-enriched tissues and down-regulated in in vitro models of VSMC phenotypic modulation...
March 3, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28257923/rna-seq-and-deg-based-comparison-of-developmental-toxicity-in-fish-embryos-of-two-species-exposed-to-iranian-heavy-crude-oil
#12
Jee-Hyun Jung, Junsu Ko, Eun-Hee Lee, Kwang-Min Choi, Moonkoo Kim, Un Hyuk Yim, Jae-Seong Lee, Won Joon Shim
To determine and compare the toxic effects of Iranian heavy crude oil (IHCO) on the embryonic development of two fish species, we examined transcriptome profiles using RNA-seq. The assembled contigs were 66,070 unigenes in olive flounder embryos and 76,498 unigenes in spotted seabass embryos. In the differential gene expression (DEG) profiles, olive flounder embryos showed different up- and down-regulated patterns than spotted seabass embryos in response to fresh IHCO (FIHCO) and weathered IHCO (WIHCO). In this work, we categorized DEG profiles into six pathways: ribosome, oxidative phosphorylation, Parkinson's disease, Alzheimer's disease, Huntington's disease, and cardiac muscle contraction, validating the expression patterns of 13 DEGs using real-time quantitative RT-PCR...
February 28, 2017: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
https://www.readbyqxmd.com/read/28247361/bioinformatics-for-novel-long-intergenic-noncoding-rna-lincrna-identification-in-skeletal-muscle-cells
#13
Xianlu Peng, Kun Sun, Jiajian Zhou, Hao Sun, Huating Wang
Long intergenic noncoding RNAs (lincRNAs) have emerged as critical participators in gene regulation in myriads of cell types. The development of the whole transcriptome sequencing technology, or RNA-seq , has enabled novel lincRNA detection, but the bioinformatics analysis toward distinguishing reliable ones remains a challenge. Here, we describe the bioinformatics workflow developed for identifying novel lincRNAs step by step, including read alignment, transcriptome assembly and transcript filtering.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28209124/rna-seq-and-metabolomic-analyses-of-akt1-mediated-muscle-growth-reveals-regulation-of-regenerative-pathways-and-changes-in-the-muscle-secretome
#14
Chia-Ling Wu, Yoshinori Satomi, Kenneth Walsh
BACKGROUND: Skeletal muscle is a major regulator of systemic metabolism as it serves as the major site for glucose disposal and the main reservoir for amino acids. With aging, cachexia, starvation, and myositis, there is a preferential loss of fast glycolytic muscle fibers. We previously reported a mouse model in which a constitutively-active Akt transgene is induced to express in a subset of muscle groups leading to the hypertrophy of type IIb myofibers with an accompanying increase in strength...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28209092/fibroblast-growth-factor-1-fgf-1-promotes-adipogenesis-by-downregulation-of-carboxypeptidase-a4-cpa4-a-negative-regulator-of-adipogenesis-implicated-in-the-modulation-of-local-and-systemic-insulin-sensitivity
#15
Jingjing He, Daniel L Chen, Dorit Samocha-Bonet, Kevin R Gillinder, Johanna L Barclay, Graham W Magor, Andrew C Perkins, Jerry R Greenfield, Gongshe Yang, Jonathan P Whitehead
Fibroblast growth factor-1 (FGF-1) promotes differentiation of human preadipocytes into mature adipocytes via modulation of a BMP and Activin Membrane-Bound Inhibitor (BAMBI)/Peroxisome proliferator-activated receptor (PPARγ)-dependent network. Here, we combined transcriptomic and functional investigations to identify novel downstream effectors aligned with complementary analyses of gene expression in human adipose tissue to explore relationships with insulin sensitivity. RNA-Seq and qRT-PCR analysis revealed significant down-regulation of carboxypeptidase A4 (CPA4) following FGF-1 treatment or induction of differentiation of human preadipocytes in a BAMBI/PPARγ-independent manner...
December 2016: Growth Factors
https://www.readbyqxmd.com/read/28204905/transcriptome-assembly-and-identification-of-genes-and-snps-associated-with-growth-traits-in-largemouth-bass-micropterus-salmoides
#16
Shengjie Li, Hao Liu, Junjie Bai, Xinping Zhu
Growth is one of the most crucial economic traits of all aquaculture species, but the molecular mechanisms involved in growth of largemouth bass (Micropterus salmoides) are poorly understood. The objective of this study was to screen growth-related genes of M. salmoides by RNA sequencing and identify growth-related single-nucleotide polymorphism (SNP) markers through a growth association study. The muscle transcriptomes of fast- and slow-growing largemouth bass were obtained using the RNA-Seq technique. A total of 54,058,178 and 54,742,444 qualified Illumina read pairs were obtained for the fast-growing and slow-growing groups, respectively, giving rise to 4,865,236,020 and 4,926,819,960 total clean bases, respectively...
February 15, 2017: Genetica
https://www.readbyqxmd.com/read/28195222/rna-seq-based-detection-of-differentially-expressed-genes-in-the-skeletal-muscle-of-duroc-pigs-with-distinct-lipid-profiles
#17
T F Cardoso, A Cánovas, O Canela-Xandri, R González-Prendes, M Amills, R Quintanilla
We have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N = 52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and muscle saturated and monounsaturated fatty acid contents, higher serum lipid concentrations and fatness) and LOW pigs (leaner and with an increased muscle polyunsaturated fatty acid content). The number of mRNAs and non-coding RNAs (ncRNAs) expressed in the porcine gluteus medius muscle were 18,104 and 1,558, respectively...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28193870/disruption-of-quercetin-metabolism-by-fungicide-affects-energy-production-in-honey-bees-apis-mellifera
#18
Wenfu Mao, Mary A Schuler, May R Berenbaum
Cytochrome P450 monooxygenases (P450) in the honey bee, Apis mellifera, detoxify phytochemicals in honey and pollen. The flavonol quercetin is found ubiquitously and abundantly in pollen and frequently at lower concentrations in honey. Worker jelly consumed during the first 3 d of larval development typically contains flavonols at very low levels, however. RNA-Seq analysis of gene expression in neonates reared for three days on diets with and without quercetin revealed that, in addition to up-regulating multiple detoxifying P450 genes, quercetin is a negative transcriptional regulator of mitochondrion-related nuclear genes and genes encoding subunits of complexes I, III, IV, and V in the oxidative phosphorylation pathway...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28188264/immortalized-human-myotonic-dystrophy-muscle-cell-lines-to-assess-therapeutic-compounds
#19
Arandel Ludovic, Polay-Espinosa Micaela, Matloka Magdalena, Bazinet Audrey, De Dea Diniz Damily, Naouar Naïra, Rau Frédérique, Jollet Arnaud, Edom-Vovard Frédérique, Mamchaoui Kamel, Tarnopolsky Mark, Puymirat Jack, Battail Christophe, Boland Anne, Deleuze Jean-Francois, Mouly Vincent, Klein F Arnaud, Furling Denis
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are autosomal dominant neuromuscular diseases caused by microsatellite expansions and belong to the family of RNA dominant disorders. Availability of cellular models in which the DM mutation is expressed within its natural context is essential to facilitate efforts to identify new therapeutic compounds. Here we generated immortalized DM1 and DM2 human muscle cell lines that display nuclear RNA-aggregates of expanded repeats, a hallmark of myotonic dystrophy. Selected clones of DM1 and DM2 immortalized myoblasts behave as parental primary myoblasts with a reduced fusion capacity of immortalized DM1 myoblasts when compared to control and DM2 cells...
February 10, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28163789/a-porcine-gluteus-medius-muscle-genome-wide-transcriptome-analysis-dietary-effects-of-omega-6-and-omega-3-fatty-acids-on-biological-mechanisms
#20
Magdalena Ogłuszka, Agnieszka Szostak, Marinus F W Te Pas, Ewa Poławska, Paweł Urbański, Tadeusz Blicharski, Chandra S Pareek, Edyta Juszczuk-Kubiak, Jenelle R Dunkelberger, Jarosław O Horbańczuk, Mariusz Pierzchała
BACKGROUND: The level of omega-6 and omega-3 polyunsaturated fatty acids can affect many cellular systems and function via nuclear receptors or the bioactive lipid regulation of gene expression. The objective of this study was to investigate changes in the muscle transcriptome and the biological functions regulated by increased consumption of omega-3 and omega-6 fatty acids in the pig gluteus medius muscle. RESULTS: The transcriptome of the gluteus medius muscle was studied for pigs subjected to either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid content...
2017: Genes & Nutrition
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