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Physiological Genomics

Kari Branham, Hiroko Matsui, Pooja Biswas, Aditya A Guru, Michael Hicks, John J Suk, He Li, David Jakubosky, Tao Long, Amalio Telenti, Naoki Narai, John R Heckenlively, Kelly A Frazar, Paul A Sieving, Radha Ayyagari
While more than 250 genes are known to cause inherited retinal degenerations (IRD), nearly 40-50% of families have the genetic basis for their disease unknown. In this study we sought to identify the underlying cause of inherited retinal degeneration (IRD) in a family by whole genome sequence (WGS) analysis. Clinical characterization including standard ophthalmic examination, fundus photography, visual field testing, electroretinography, and review of medical and family history was performed. WGS was performed on affected and unaffected family members using Illumina HiSeq X10...
October 7, 2016: Physiological Genomics
Jenna F DuMond, Xue Zhang, Yuichiro Izumi, Kevin Ramkissoon, Guanghui Wang, Marjan Gucek, Xujing Wang, Maurice B Burg, Joan D Ferraris
NFAT5 is a transcription factor originally identified because it is activated by hypertonicity and that activation increases expression of genes that protect against the adverse effects of the hypertonicity. However, its targets also include genes not obviously related to tonicity. The transactivating domain of NFAT5 is contained in its c-terminal region, which is predicted to be unstructured. Unstructured regions are common in transcription factors particularly in transactivating domains where they can bind co-regulatory proteins essential to their function...
October 7, 2016: Physiological Genomics
Jeffrey J Widrick, Matthew Alexander, Benjamin Sanchez, Devin Gibbs, Genri Kawahara, Alan Beggs, Louis Kunkel
Sapje zebrafish lack the protein dystrophin and are the smallest vertebrate model of Duchenne muscular dystrophy (DMD). Their small size makes them ideal for large-scale drug discovery screens. However, the extent that sapje mimic the muscle dysfunction of higher vertebrate models of DMD is unclear. We used an optical birefringence assay to differentiate affected dystrophic sapje larvae from their unaffected siblings and then studied trunk muscle contractility at 4-7 days post fertilization. Preparation cross-sectional area (CSA) was similar for affected and unaffected larvae, yet tetanic forces of affected preparations were only 30-60% of normal...
October 7, 2016: Physiological Genomics
Aksone Nouvong, Aaron M Ambrus, Ellen R Zhang, Lucas Hultman, Hilary Ann Coller
Chronic wounds are a common and debilitating complication for the diabetic population. It is challenging to study the development of chronic wounds in hu-man patients; by the time it is clear that a wound is chronic, the early phases of wound healing have passed and can no longer be studied. Because of this limita-tion, mouse models have been employed to better understand the early phases of chronic wound formation. In the past few years, a series of reports have high-lighted the importance of reactive oxygen species and bacterial biofilms in the development of chronic wounds in diabetics...
October 7, 2016: Physiological Genomics
Seung Kyum Kim, Joshua J Avila, Michael P Massett
Understanding the genetic influence on vascular reactivity is important for identifying genes underlying impaired vascular function. The purpose of this study was to characterize the genetic contribution to intrinsic vascular function and to identify loci associated with phenotypic variation in vascular reactivity in mice. Concentration response curves to phenylephrine (PE), potassium chloride (KCl), acetylcholine (ACh), and sodium nitroprusside (SNP) were generated in aortic rings from male mice (12-wk old) from 27 inbred mouse strains...
October 7, 2016: Physiological Genomics
Ryan D Sheldon, Kayla M Kanosky, Kevin D Wells, Lili Miles, James W Perfield, Stavra Xanthakos, Thomas H Inge, R Scott Rector
BACKGROUND: Mechanisms responsible for progression of nonalcoholic fatty liver disease (NAFLD) to steatohepatitis (NASH) remain poorly defined. METHODS: To examine the potential contribution of adipose tissue to NAFLD progression, we performed a complete transcriptomic analysis using RNA-sequencing (RNA-seq) on intra-abdominal adipose tissue (IAT) from severely obese adolescents (Mage 16.9±0.4 yrs; BMI z-score 2.7±0.1) undergoing bariatric surgery and liver biopsy categorized into 3 groups; No steatosis (Normal, n=8), steatosis only (n=13), or NASH (n=10) by liver histology...
October 7, 2016: Physiological Genomics
Andrea Tarallo, Maria Cristina Gambi, Giuseppe D'Onofrio
A comparative analysis of polychaete species, classified as motile and low-motile forms, highlighted that the former were characterized not only by a higher metabolic rate (MR), but also by a higher genomic GC content. The fluctuation of both variables was not affected by the phylogenetic relationship of the species. Thus, present results further support that a very active lifestyle affects at the same time MR and GC, showing an unexpected similarity between invertebrates and vertebrates. In teleost, indeed, a similar pattern has been also observed comparing migratory and non-migratory species...
October 7, 2016: Physiological Genomics
Niranjana Natarajan, Daijiro Hori, Sheila Flavahan, Jochen Steppan, Nicholas A Flavahan, Dan E Berkowitz, Jennifer L Pluznick
Short chain fatty acid (SCFA) metabolites are byproducts of gut microbial metabolism that are known to affect host physiology via GPCRs. We previously showed that an acute SCFA bolus decreases blood pressure (BP) in anesthetized mice, an effect mediated via Gpr41. In this study, our aims were to identify the cellular localization of Gpr41 and to determine its role in BP regulation. We localized Gpr41 to the vascular endothelium using RT-PCR: Gpr41 is detected in intact vessels, but is absent from denuded vessels...
September 23, 2016: Physiological Genomics
Yo-Han Kim, Noriyuki Touji, Keiichiro Kizaki, Shiro Kushibiki, Toshihiro Ichijo, Shigeru Sato
We investigated the relationship between ruminal pH and transcriptomic adaptation of the rumen epithelium (RE) of calves fed calf starter with and without forage during the weaning transition. Holstein calves were assigned to groups fed calf starter either with forage (HAY group, n = 3) or without forage (CON group, n = 4). Ruminal pH was measured continuously, and rumen fluid and epithelium were collected 3 weeks after weaning. mRNA expression profiles of the RE were examined by one-color microarray. Differentially expressed genes (DEGs) were investigated using the ingenuity pathway analysis (IPA)...
September 23, 2016: Physiological Genomics
Ryoichi Kawamura, Yasuharu Tabara, Akiko Tsukada, Michiya Igase, Jun Ohashi, Ryo Yamada, Yasunori Takata, Ryuichi Kawamoto, Isao Saito, Hiroshi Onuma, Takeshi Tanigawa, Kazuya Yamada, Norihiro Kato, Yasumasa Ohyagi, Tetsuro Miki, Katsuhiko Kohara, Haruhiko Osawa
Resistin is a cytokine inducing insulin resistance in mice. We previously identified single nucleotide polymorphisms (SNPs) at -420 (rs1862513) and -358 (rs3219175) located in the human resistin gene (RETN) promoter as strong determinants for circulating resistin in the Japanese population. The objective was to identify additional functional variants for circulating resistin. We conducted a genome-wide association study in 448 Japanese subjects. A peak association signal was found on chromosome 19 where RETN is located...
September 23, 2016: Physiological Genomics
Yu-Yu Ren, Lauren G Koch, Steven L Britton, Nathan R Qi, Mary K Treutelaar, Charles F Burant, Jun Z Li
Intrinsic aerobic exercise capacity can influence many complex traits including obesity and aging. To study this connection we established two rat lines by divergent selection of untrained aerobic capacity. After 32 generations the high capacity runners (HCR) and low capacity runners (LCR) differed in endurance running distance and body fat, blood glucose, other health indicators, and natural life span. To understand the interplay among genetic differences, chronological age, and acute exercise we performed microarray-based gene expression analyses in skeletal muscle with a 2×2×2 design to simultaneously compare HCR and LCR, old and young animals, and rest and exhaustion...
September 16, 2016: Physiological Genomics
Sara M F Turner, Darin J Falk, Barry J Byrne, David D Fuller
Pompe disease, caused by deficiency of acid alpha-glucosidase (GAA), leads to widespread glycogen accumulation and profound neuromuscular impairments. There has been controversy, however, regarding the role of central nervous system pathology in Pompe motor dysfunction. We hypothesized that absence of GAA protein causes progressive activation of neuropathological signaling, including pathways associated with cell death. To test this hypothesis, genomic data (Affymetrix Mouse Gene Array 2.0ST) from the mid-cervical spinal cord in 6- and 16-mo old Pompe (Gaa(-/-)) were evaluated (Broad Institute Molecular Signature Database), along with spinal cord histology...
September 9, 2016: Physiological Genomics
Andreia Pereira, Roberto Palma Dos Reis, Ricardo Rodrigues, Ana Célia Sousa, Susana Gomes, Sofia Borges, Ilidio Ornelas, Ana Isabel Freitas, Graça Guerra, Eva Henriques, Mariana Rodrigues, Sónia Freitas, Carolina Freitas, António Brehm, Décio Pereira, Maria Isabel Mendonça
Recent genetic studies have revealed an association between polymorphisms at the ADAMTS7 gene locus and coronary artery disease (CAD) risk. Functional studies have shown that a CAD-associated polymorphism (rs3825807) affects ADAMTS7 maturation and VSMC migration. Here, we tested whether ADAMTS7 (A/G) SNP is associated with cardiovascular (CV) survival in patients with established CAD. A cohort of 1128 patients with angiographic proven CAD, who were followed-up prospectively for a mean follow-up of 63 (range 6 -182) months, were genotyped for rs3825807 A/G...
September 9, 2016: Physiological Genomics
Ingrid Eftedal, Arnar Flatberg, Ivan Drvis, Zeljko Dujic
Freedivers hold their breath while diving, causing blood oxygen levels to decrease (hypoxia) while carbon dioxide increases (hypercapnia). Whereas blood gas changes are presumably involved in the progression of respiratory diseases, less is known about their effect on healthy individuals. Here we have used gene expression profiling to analyze elite athletes' immune and inflammatory responses to freediving. Blood was collected before, 1 and 3 h after a series of maximal dynamic and static apneas in a pool, and peripheral blood gene expression was mapped on genome-wide microarrays...
September 9, 2016: Physiological Genomics
Jane Synnergren, Lauren Drowley, Alleyn T Plowright, Gabriella Brolén, Marie-Josè Goumans, Adriana C Gittenberger-de Groot, Peter Sartipy, Qing-Dong Wang
Comparative transcriptomic analysis identifies genes differentially expressed in human epicardial progenitor cells and hiPSC-derived cardiac progenitor cells: effects of hypoxic vs normoxic culture conditions.
September 2, 2016: Physiological Genomics
Hayk Simonyan, Chansol Hurr, Colin N Young
Bioluminescence imaging is an effective tool for in vivo investigation of molecular processes. We have demonstrated the applicability of bioluminescence imaging to spatiotemporally monitor gene expression in cardioregulatory brain nuclei during the development of cardiovascular disease, via incorporation of firefly luciferase into living animals, combined with exogenous d-luciferin substrate administration. Nevertheless, d-luciferin uptake into the brain tissue is low, which decreases the sensitivity of bioluminescence detection, particularly when considering small changes in gene expression in tiny central areas...
October 1, 2016: Physiological Genomics
Long Zhao, Jun Zhao, Xueling Wang, Zhixin Chen, Kexin Peng, Xiaohan Lu, Linghang Meng, Gang Liu, Guangju Guan, Fei Wang
We investigated the expression and function of serum response factor (SRF) in endothelial-mesenchymal transition (EndMT) in glomerular endothelial cells (GEnCs) of diabetic nephropathy (DN). The expression of SRF, endothelial markers (VE-cadherin, CD31), and mesenchymal markers (α-SMA, FSP-1, fibronectin) was examined in GEnCs following high glucose or in renal cortex tissues of DN rats. SRF was upregulated by SRF plasmids and downregulated by CCG-1423 (a small molecule inhibitor of SRF) to investigate how SRF influenced EndMT in GEnCs of DN...
October 1, 2016: Physiological Genomics
Yan Bai, Jian Wu, Daxiang Li, Eric E Morgan, Jiang Liu, Xiaochen Zhao, Aaron Walsh, Jagannath Saikumar, Jodi Tinkel, Bina Joe, Rajesh Gupta, Lijun Liu
Binding of ouabain to cardiac Na(+)/K(+)-ATPase initiates cell signaling and causes contractility in cardiomyocytes. It is widely accepted that caveolins, structural proteins of caveolae, have been implicated in signal transduction. It is known that caveolae play a role in Na(+)/K(+)-ATPase functions. Regulation of caveolin-1 in ouabain-mediated cardiac signaling and contractility has never been reported. The aim of this study is to compare ouabain-induced cardiac signaling and contractility in wild-type (WT) and caveolin-1 knockout (cav-1 KO) mice...
October 1, 2016: Physiological Genomics
Sandra Guauque-Olarte, Arnaud Droit, Joël Tremblay-Marchand, Nathalie Gaudreault, Dimitri Kalavrouziotis, Francois Dagenais, Jonathan G Seidman, Simon C Body, Philippe Pibarot, Patrick Mathieu, Yohan Bossé
The molecular mechanisms leading to premature development of aortic valve stenosis (AS) in individuals with a bicuspid aortic valve are unknown. The objective of this study was to identify genes differentially expressed between calcified bicuspid aortic valves (BAVc) and tricuspid valves with (TAVc) and without (TAVn) AS using RNA sequencing (RNA-Seq). We collected 10 human BAVc and nine TAVc from men who underwent primary aortic valve replacement. Eight TAVn were obtained from men who underwent heart transplantation...
October 1, 2016: Physiological Genomics
Daniel L Hertz, N Lynn Henry, Kelley M Kidwell, Dafydd Thomas, Audrey Goddard, Faouzi Azzouz, Kelly Speth, Lang Li, Mousumi Banerjee, Jacklyn N Thibert, Celina G Kleer, Vered Stearns, Daniel F Hayes, Todd C Skaar, James M Rae
Hormone receptor-positive (HR+) breast cancers express the estrogen (ERα) and/or progesterone (PgR) receptors. Inherited single nucleotide polymorphisms (SNPs) in ESR1, the gene encoding ERα, have been reported to predict tamoxifen effectiveness. We hypothesized that these associations could be attributed to altered tumor gene/protein expression of ESR1/ERα and that SNPs in the PGR gene predict tumor PGR/PgR expression. Formalin-fixed paraffin-embedded breast cancer tumor specimens were analyzed for ESR1 and PGR gene transcript expression by the reverse transcription polymerase chain reaction based Oncotype DX assay and for ERα and PgR protein expression by immunohistochemistry (IHC) and an automated quantitative immunofluorescence assay (AQUA)...
September 1, 2016: Physiological Genomics
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