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Physiological Genomics

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https://www.readbyqxmd.com/read/28710295/relationships-between-gastrointestinal-microbiota-and-blood-group-antigens
#1
Anuhya Gampa, Phillip A Engen, Rima Shobar, Ece A Mutlu
FUT2 is a gene for a fucosyltransferase that encodes expression of ABO blood group antigens found on gastrointestinal mucosa and secretions. We hypothesized that the fecal microbiomes of healthy subjects, with blood group antigens A, B and O, have differing compositions. Thirty-three fecal and blood specimens from healthy subjects were analyzed for FUT2 genotype and the fecal microbiome was determined using 454 pyrosequencing. Our data shows that being a blood group secretor is associated with less diversity at higher orders of taxonomy; and the presence of blood group A antigens in the secretor subjects are associated with an expansion families of bacteria within the gut...
July 14, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28698229/changes-in-the-phosphoproteome-of-brown-adipose-tissue-during-hibernation-in-the-ground-squirrel-ictidomys-tridecemlineatus
#2
Didier Vertommen, Gaetan Herinckx, Nusrat Hussain, Fred Opperdoes, Kenneth B Storey, Mark H Rider
Mammalian hibernation is characterized by metabolic rate depression and a strong decrease in core body temperature. Brown adipose tissue (BAT), a thermogenic tissue that uses uncoupled mitochondrial respiration to generate heat instead of ATP, plays a major role in rewarming from deep torpor. In the present study we developed a label-free LC-MS strategy to investigate both differential protein expression and protein phosphorylation in BAT extracts from euthermic versus hibernating ground squirrels. In particular, we incorporated the filter-assisted sample preparation (FASP) protocol, which provides a more in-depth analysis compared with gel-based and other LC-MS proteomics approaches...
July 10, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28698228/perturbations-to-lysyl-oxidase-expression-broadly-influence-the-transcriptome-of-lung-fibroblasts
#3
Ivana Mižíková, Francesco Palumbo, Tamás Tábi, Susanne Herold, István Vadász, Konstantin Mayer, Werner Seeger, Rory E Morty
Lysyl oxidases are credited with pathogenic roles in lung diseases, including cancer, fibrosis, pulmonary hypertension, congenital diaphragmatic hernia, and bronchopulmonary dysplasia (BPD). Lysyl oxidases facilitate the covalent intra- and inter-molecular cross-linking of collagen and elastin fibers, thereby imparting tensile strength to the extracellular matrix (ECM). Alternative ECM-independent roles have recently been proposed for lysyl oxidases, including regulation of growth factor signaling, chromatin remodeling, and transcriptional regulation; all of which impact cell phenotype...
July 10, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28698227/comparative-transcriptomics-of-hepatic-differentiation-of-human-pluripotent-stem-cells-and-adult-human-liver-tissue
#4
Nidal Ghosheh, Barbara Küppers-Munther, Annika Asplund, Josefina Edsbagge, Benjamin Ulfenborg, Tommy B Andersson, Petter Björquist, Christian X Andersson, Helena Carén, Stina Simonsson, Peter Sartipy, Jane Synnergren
Hepatocyte derived from human pluripotent stem cells (hPSC-HEP) have the potential to replace presently used hepatocyte sources applied in liver disease treatment and models of drug discovery and development. Established hepatocyte differentiation protocols are effective and generate hepatocytes, which recapitulate some key features of their in vivo counterparts. However, generating mature hPSC-HEP remains a challenge. In this study, we applied transcriptomics to investigate the progress of in vitro hepatic differentiation of hPSCs at the developmental stages, definitive endoderm (DE), hepatoblasts, early hPSC-HEP, and mature hPSC-HEP, to identify functional targets that enhance efficient hepatocyte differentiation...
July 10, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28626023/microarray-analysis-of-aging-associated-immune-system-alterations-in-the-rostral-ventrolateral-medulla-of-f344-rats
#5
Sivasai Balivada, Chanran K Ganta, Yongqing Zhang, Hitesh N Pawar, Richard J Ortiz, Kevin G Becker, Arshad M Khan, Michael J Kenney
The rostral ventrolateral medulla (RVLM) is an area of the brainstem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts...
June 16, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28600319/microbiome-and-nafld-potential-influence-of-aerobic-fitness-and-lifestyle-modification
#6
Matthew R Panasevich, Willem T Peppler, Daniel B Oerther, David C Wright, R Scott Rector
Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disease with prevalence rates that are on the rise in the US and worldwide. NAFLD encompasses a spectrum of liver pathologies including simple steatosis to nonalcoholic steatohepatitis (NASH) with inflammation and fibrosis. The gut microbiome has emerged as a potential therapeutic target in combating metabolic diseases including obesity, type 2 diabetes, and NAFLD/NASH. Diet-induced obesity/Western style diet feeding causes severe microbial dysbiosis initiating a microbiome signature that promotes metabolite production that directly impacts hepatic metabolism...
June 9, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28550089/advancing-precision-medicine-in-healthcare
#7
Olivia M Dong, Tim Wiltshire
The incorporation of precision medicine into the clinical setting is becoming increasingly feasible with the availability of more affordable genetic sequencing technologies and successful genetic associations with phenotypes, especially in the pharmacogenomic field. Although substantial progress has been made to ensure successful uptake of pharmacogenomic testing in the clinical setting already, many challenges still remain for sustainable implementation. The importance of pharmacogenomic information in patient care, identifying key barriers, and proposed solutions for advancing pharmacogenomic implementation will be discussed...
May 26, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28550088/cardiac-telomere-length-in-heart-development-function-and-disease
#8
Scott A Booth, Fadi J Charchar
Telomeres are repetitive nucleoprotein structures at chromosome ends and a decrease in the number of these repeats, known as a reduction in telomere length (TL), triggers cellular senescence and apoptosis. Heart disease, the worldwide leading cause of death, often results from the loss of cardiac cells which could be explained by decreases in TL. Due to the cell-specific regulation of TL, this review focuses on studies that have measured telomeres in heart cells and critically assesses the relationship between cardiac TL and heart function...
May 26, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28500252/transcriptome-profiling-reveals-novel-bmi-and-sex-specific-gene-expression-signature-for-human-cardiac-hypertrophy
#9
Mackenzie S Newman, Tina Nguyen, Michael J Watson, Robert Hull, Han-Gang Yu
BACKGROUND: How obesity or sex may affect the gene expression profiles of human cardiac hypertrophy is unknown. We hypothesized that body-mass index (BMI) and sex can affect gene expression profiles of cardiac hypertrophy. RESULTS: Human heart tissues were grouped according to sex (male, female), BMI (lean<25 kg/m(2), obese>30 kg/m(2)), or left ventricular hypertrophy (LVH) and non-LVH non-failed controls (NF). We identified 24 DE genes comparing female to male samples...
May 12, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28455310/exercise-induced-modification-of-the-skeletal-muscle-transcriptome-in-arabian-horses
#10
Katarzyna Ropka-Molik, Monika Stefaniuk-Szmukier, Kacper Żukowski, Katarzyna Piórkowska, Monika Bugno-Poniewierska
It has been found that Arabian and Thoroughbred horses differ in muscle fiber structure and thus in physiological changes occurring in muscles during exercise. The aim of the present study was to identify the global gene expression modifications that occur in skeletal muscle following a training regime to prepare for flat racing. Whole transcriptomes of muscle (gluteus medius) were compared between three time points of tissue collection: T0 (untrained horses), T1 (horses after intense gallop phase) and T2 (horses at the end of racing season), 23 samples in total...
April 28, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28455309/molecular-structure-and-function-of-big-calcium-activated-potassium-channels-in-skeletal-muscle-pharmacological-perspectives
#11
Fatima Maqoud, Michela Cetrone, Antonietta Mele, Domenico Tricarico
The large-conductance Ca(2+)-activated K(+) (BK) channel is broadly expressed in various mammalian cells and tissues such as neurons, skeletal muscles (sarco-BK), and smooth muscles. These channels are activated by changes in membrane electrical potential and by increases in the concentration of intracellular calcium ion (Ca(2+)). The large-conductance Ca(2+)-activated K(+) (BK) channel is subjected to many mechanisms that add diversity to the BK channel α subunit gene. These channels are indeed subject to alternative splicing, auxiliary subunits modulation, post-translational modifications and protein-protein interactions...
April 28, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28550087/transcriptional-networks-in-rodent-models-support-a-role-for-gut-brain-communication-in-neurogenic-hypertension-a-review-of-the-evidence
#12
REVIEW
Jasenka Zubcevic, Ashley Baker, Christopher J Martyniuk
Hypertension (HTN) is the most prevalent condition observed in primary health care. Hypertension shows complex etiology, and neuroinflammation, overactive sympathetic drive, and the microbiome are each associated with the disease. To obtain mechanistic perspective into neurogenic HTN, we first constructed a framework for transcriptional regulators of the disease using the Comparative Toxicogenomics Database. This approach yielded a core group of 178 transcripts that are prevalent in studies of HTN, including leptin and neuropeptide Y...
July 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28500253/linc00341-exerts-an-anti-inflammatory-effect-on-endothelial-cells-by-repressing-vcam1
#13
Tse-Shun Huang, Kuei-Chun Wang, Sara Quon, Phu Nguyen, Ting-Yu Chang, Zhen Chen, Yi-Shuan Li, Shankar Subramaniam, John Shyy, Shu Chien
The long noncoding RNAs (lncRNAs), which constitute a large portion of the transcriptome, have gained intense research interest because of their roles in regulating physiological and pathophysiological functions in the cell. We identified from RNA-Seq profiling a set of lncRNAs in cultured human umbilical vein endothelial cells (HUVECs) that are differentially regulated by atheroprotective vs. atheroprone shear flows. Among the comprehensively annotated lncRNAs, including both known and novel transcripts, LINC00341 is one of the most abundant lncRNAs in endothelial cells...
July 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28432191/gene-expression-effects-of-glucocorticoid-and-mineralocorticoid-receptor-agonists-and-antagonists-on-normal-human-skeletal-muscle
#14
Jessica A Chadwick, J Spencer Hauck, Celso E Gomez-Sanchez, Elise P Gomez-Sanchez, Jill A Rafael-Fortney
Mineralocorticoid and glucocorticoid receptors are closely related steroid hormone receptors that regulate gene expression through many of the same hormone response elements. However, their transcriptional activities and effects in skeletal muscles are largely unknown. We recently identified mineralocorticoid receptors (MR) in skeletal muscles after finding that combined treatment with the angiotensin-converting enzyme inhibitor lisinopril and MR antagonist spironolactone was therapeutic in Duchenne muscular dystrophy mouse models...
June 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28389524/de-novo-rna-sequence-assembly-during-in-vivo-inflammatory-stress-reveals-hundreds-of-unannotated-lincrnas-in-human-blood-cd14-monocytes-and-in-adipose-tissue
#15
Chenyi Xue, Xuan Zhang, Hanrui Zhang, Jane F Ferguson, Ying Wang, Christine C Hinkle, Mingyao Li, Muredach P Reilly
Long intergenic noncoding RNAs (lincRNAs) have emerged as key regulators of cellular functions and physiology. Yet functional lincRNAs often have low, context-specific and tissue-specific expression. We hypothesized that many human monocyte and adipose lincRNAs would be absent in current public annotations due to lincRNA tissue specificity, modest sequencing depth in public data, limitations of transcriptome assembly algorithms, and lack of dynamic physiological contexts. Deep RNA sequencing (RNA-Seq) was performed in peripheral blood CD14(+) monocytes (monocytes; average ~247 million reads per sample) and adipose tissue (average ~378 million reads per sample) collected before and after human experimental endotoxemia, an in vivo inflammatory stress, to identify tissue-specific and clinically relevant lincRNAs...
June 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28389525/role-of-renal-transporters-and-novel-regulatory-interactions-in-the-tal-that-control-blood-pressure
#16
REVIEW
Lesley A Graham, Anna F Dominiczak, Nicholas R Ferreri
Hypertension (HTN), a major public health issue is currently the leading factor in the global burden of disease, where associated complications account for 9.4 million deaths worldwide every year. Excessive dietary salt intake is among the environmental factors that contribute to HTN, known as salt sensitivity. The heterogeneity of salt sensitivity and the multiple mechanisms that link high salt intake to increases in blood pressure are of upmost importance for therapeutic application. A continual increase in the kidney's reabsorption of sodium (Na(+)) relies on sequential actions at various segments along the nephron...
May 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28258078/short-term-low-magnesium-diet-reduces-autoimmune-arthritis-severity-and-synovial-tissue-gene-expression
#17
Max Brenner, Teresina Laragione, Pércio S Gulko
Magnesium has been suggested to have anti-inflammatory properties in short-term, mostly in vitro studies. To examine the effect of dietary magnesium modifications in arthritis severity and joint damage DA rats were placed on one of three diet regimens before the induction of autoimmune pristane-induced arthritis (PIA): a 4 wk low-magnesium diet, normal diet, and a magnesium-supplemented diet. The diets were switched to a normal diet 14 days after the induction of PIA (typical time of disease onset). Arthritis severity was scored for 38 days, and joints were examined by histology and quantitative PCR for proinflammatory genes...
April 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28213571/mir-146a-b-a-family-with-shared-seeds-and-different-roots
#18
REVIEW
Mark R Paterson, Alison J Kriegel
MicroRNAs are small, noncoding, RNAs known for their powerful modulation of molecular processes, making them a major focus for studying pathological mechanisms. The human miR-146 family of microRNAs consists of two member genes, MIR146A and MIR146B These two microRNAs are located on different chromosomes and exhibit differential regulation in many cases. However, they are nearly identical in sequence, sharing a seed region, and are thus predicted to target the same set of genes. A large proportion of the microRNA (miR)-146 literature focuses on its role in regulating the innate immune response in the context of various pathologies by modulating two widely studied target genes in the toll-like receptor signaling cascade...
April 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28213570/blunted-transcriptional-response-to-skeletal-muscle-ischemia-in-rats-with-chronic-kidney-disease-potential-role-for-impaired-ischemia-induced-angiogenesis
#19
Rafael U Heiss, Fabian B Fahlbusch, Johannes Jacobi, Christoph Daniel, Arif B Ekici, Nada Cordasic, Kerstin Amann, Andrea Hartner, Karl F Hilgers
Chronic kidney disease (CKD) is associated with increased cardiovascular morbidity and mortality. Previous studies indicated an impairment of ischemia-induced angiogenesis in skeletal muscle of rats with CKD. We performed a systematic comparison of early gene expression in response to ischemia in rats with or without CKD to identify potential molecular mechanisms underlying impaired angiogenesis in CKD. CKD was induced in male rats by 5/6 nephrectomy (SNX); control rats were sham operated (sham). Eight weeks later, ischemia of the right limb was induced by ligation and resection of the femoral artery...
April 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28159858/transcriptomic-alterations-in-the-brain-of-painted-turtles-chrysemys-picta-developmentally-exposed-to-bisphenol-a-or-ethinyl-estradiol
#20
Lindsey K Manshack, Caroline M Conard, Sara J Bryan, Sharon L Deem, Dawn K Holliday, Nathan J Bivens, Scott A Givan, Cheryl S Rosenfeld
Developmental exposure of turtles and other reptiles to endocrine-disrupting chemicals (EDCs), including bisphenol A (BPA) and ethinyl estradiol (EE), can stimulate partial to full gonadal sex-reversal in males. We have also recently shown that in ovo exposure to either EDC can induce similar sex-dependent behavioral changes typified by improved spatial learning and memory or possibly feminized brain responses. Observed behavioral changes are presumed to be due to BPA- and EE-induced brain transcriptomic alterations during development...
April 1, 2017: Physiological Genomics
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