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Physiological Genomics

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https://www.readbyqxmd.com/read/28258078/a-short-term-low-magnesium-diet-reduces-autoimmune-arthritis-severity-and-synovial-tissue-gene-expression
#1
Max Brenner, Teresina Laragione, Percio S Gulko
Magnesium has been suggested to have anti-inflammatory properties in short-term mostly in vitro studies. To examined 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 four-week low-magnesium diet, normal diet and a magnesium-supplemented diet. The diets were switched to a normal diet fourteen days after the induction of PIA (typical time of disease onset)...
March 3, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28213571/mir-146a-b-a-family-with-shared-seeds-and-different-roots
#2
Mark Paterson, Alison J Kriegel
MicroRNAs are small, non-coding, 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 miRNAs are located on different chromosomes and exhibit differential regulation in many cases. However, they are nearly identical in sequence and share a seed sequence, thus they are predicted to target the same set of genes. A large proportion of the 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...
February 17, 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
#3
Rafael U Heiss, Fabian 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...
February 17, 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
#4
Lindsey K Manshack, Caroline M Conard, Sara J Bryan, Sharon L Deem, Dawn K Holliday, Nathan J Bivens, Scott A Givan, Cheryl Susan 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...
February 3, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28130429/modeling-diseases-in-multiple-mouse-strains-for-precision-medicine-studies
#5
Andres D Klein
The genetic basis of the phenotypic variability observed in patients can be studied in mice by generating disease models through genetic or chemical interventions in many genetic backgrounds where the clinical phenotypes can be assessed and used for Genome-Wide Association Studies (GWAS). This is particularly relevant for rare disorders, where patients sharing identical mutations can present with a wide variety of symptoms, but there are not enough number of patients to ensure statistical power of GWAS. Inbred strains are homozygous for each loci and their Single Nucleotide Polymorphisms (SNPs) catalogues are known and freely available, facilitating the bioinformatics and reducing the costs of the study since it is not required to genotype every mouse...
January 27, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28130426/genetic-analysis-of-ten-pedigrees-with-inherited-retinal-degeneration-ird-by-exome-sequencing-and-phenotype-genotype-association
#6
Pooja Biswas, Jacque L Duncan, Bruno Maranhao, Igor Kozak, Kari Branham, Luis Gabriel, Jonathan H Lin, Guilio Barteselli, Mili Navani, John J Suk, Michelle Parke, Catherine Schlechter, Richard Weleber, John R Heckenlively, Gislin Dagnelie, Pauline Lee, S Amer Riazuddin, Radha Ayyagari
PURPOSE: To identify causative mutations and characterize the phenotype associated with the genotype in ten unrelated families with autosomal recessive retinal degeneration. METHODS: Ophthalmic evaluation and DNA isolation was carried out in 10 pedigrees with IRD. Exomes of probands from 8 pedigrees were captured using Nimblegen V2/V3 or Agilent V5+UTR kits, and sequencing was performed on Illumina HiSeq. The DHDDS gene was screened for mutations in the remaining two pedigrees with Ashkenazi Jews ancestry...
January 27, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28087757/alternative-transcription-of-sodium-bicarbonate-transporter-slc4a7-gene-enhanced-by-single-nucleotide-polymorphisms
#7
Hae Jeong Park, Soojung Lee, Eunji Ju, Jayre A Jones, Inyeong Choi
Genome-wide association studies have identified the single nucleotide polymorphism (SNP) rs3278 in the human SLC4A7 gene as one of the marker loci for addiction vulnerability. This marker is located in an intron of the gene, and its genomic role has been unknown. In this study, we examined rs3278 and three adjacent SNPs prevalent in alcoholics for their effects on an alternative promoter that would lead to the production of the N-terminally truncated protein NBCn1ΔN450, missing the first 450 amino acids. Analysis of the transcription start site database and a promoter prediction algorithm identified a cluster of three promoters in intron 7 and two short CpG-rich sites in intron 6...
January 13, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28087756/fine-mapping-of-genes-determining-extrafusal-fiber-properties-in-murine-soleus-muscle
#8
Andrew Carroll, Riyan Cheng, Elaina Collie-Duguid, Caroline Meharg, Michael E Scholz, Steven N Fiering, Jennifer L Fields, Abraham A Palmer, Arimantas Lionikas
INTRODUCTION: Muscle fiber cross-sectional area (CSA) and proportion of different fiber types are important determinants of muscle function and overall metabolism. Genetic variation plays a substantial role in phenotypic variation of these traits, however, the underlying genes remain poorly understood. AIMS: This study aimed to map quantitative trait loci (QTL) affecting differences in soleus muscle fiber traits between the LG/J and SM/J mouse strains. METHODS: Fiber number, CSA, and proportion of oxidative type I fibers were assessed in the soleus of 334 genotyped male and female mice of the F34 generation of advanced intercross lines (AIL) derived from the LG/J and SM/J strains...
January 13, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28062686/the-gstp1-c-313a-g-polymorphism-in-russian-and-polish-athletes
#9
Aleksandra Zarebska, Zbigniew Jastrzębski, Ildus I Ahmetov, Piotr Zmijewski, Pawel Cieszczyk, Agata Leonska-Duniec, Marek Sawczuk, Katarzyna Leznicka, Grzegorz Trybek, Ekaterina A Semenova, Agnieszka Maciejewska-Skrendo
The GSTP1 gene encodes glutathione S-transferase P1 which is a member of glutathione S-transferases (GSTs) that are a family of enzymes playing an important role in detoxification and in the antioxidant defense system. There were some the evidence indicating that GSTP1 c.313A>G polymorphism may be beneficial for exercise performance. Therefore, we have decided to verify the association between the frequency of GSTP1 c.313A>G variants, physical performance and athlete's status in two cohorts: in a group of Russian athletes (n=507) and in an independent population of Polish athletes (n=510) in a replication study...
January 6, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28039431/data-integration-in-physiology-using-bayes-rule-and-minimum-bayes-factors-deubiquitylating-enzymes-in-the-renal-collecting-duct
#10
Zhe Xue, Jia-Xu Chen, Yue Zhao, Barbara Medvar, Mark A Knepper
A major challenge in physiology is to exploit the many large-scale datasets available from "-omic" studies in order to seek answers to key physiological questions. In previous studies, Bayes' Theorem has been used for this purpose. This approach requires a means to map continuously distributed experimental data to probabilities (likelihood values) in order to derive posterior probabilities from the combination of prior probabilities and new data. Here, we introduce the use of Minimum Bayes' Factors for this purpose and illustrate the approach by addressing a physiological question, "Which deubiquitylating enzymes (DUBs) encoded by mammalian genomes are most likely to regulate plasma membrane transport processes in renal cortical collecting duct principal cells?" To do this, we have created a comprehensive online database of 110 DUBs present in the mammalian genome (https://hpcwebapps...
December 30, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/28039430/inflammation-and-vascular-smooth-muscle-cell-dedifferentiation-following-carotid-artery-ligation
#11
Brian Paul Herring, April M Hoggatt, Sarah L Griffith, Jeanette N McClintick, Patricia Jane Gallagher
OBJECTIVE: Following vascular injury medial smooth muscle cells dedifferentiate and migrate through the internal elastic lamina where they form a neointima. The goal of the current study was to identify changes in gene expression that occur prior to the development of neointima and are associated with the early response to injury. Approach and Results: Vascular injury was induced in C57Bl/6 mice and in Myh11-creER(T2) mTmG reporter mice by complete ligation of the left carotid artery...
December 30, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/28039429/limited-potential-of-genetic-predisposition-scores-to-predict-muscle-mass-and-strength-performance-in-flemish-caucasians-between-19-73-years-of-age
#12
Ruben Charlier, Maarten Caspers, Sara Knaeps, Evelien Mertens, Diether Lambrechts, Johan Lefevre, Martine Thomis
Since both muscle mass and strength performance are polygenic in nature, the current study compared four Genetic Predisposition Scores (GPS) in their ability to predict these phenotypes. Data were gathered within the framework of the first generation Flemish Policy Research Centre 'Sport, Physical Activity and Health' (2002-2004). Results are based on muscle characteristics data of 565 Flemish Caucasians (19-73 yr, 365 men). Skeletal muscle mass (SMM) was determined using bioelectrical impedance. The Biodex dynamometer was used to measure isometric (PTstatic120°) and isokinetic strength (PTdynamic60° and PTdynamic240°), ballistic movement speed (S20%) and muscular endurance (Work) of the knee extensors...
December 30, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/28130428/hla-gene-expression-is-altered-in-whole-blood-and-placenta-from-women-who-later-developed-preeclampsia
#13
Heather Y Small, Christine Akehurst, Liliya Sharafetdinova, Martin W McBride, John D McClure, Scott W Robinson, David M Carty, Dilys J Freeman, Christian Delles
Preeclampsia is a multisystem disease that significantly contributes to maternal and fetal morbidity and mortality. In this study, we used a non-biased microarray approach to identify dysregulated genes in maternal whole blood samples which may be associated with the development of preeclampsia. Whole blood samples were obtained at 28 wk of gestation from 5 women who later developed preeclampsia (cases) and 10 matched women with normotensive pregnancies (controls). Placenta samples were obtained from an independent cohort of 19 women with preeclampsia matched with 19 women with normotensive pregnancies...
March 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28130427/nephron-number-hypertension-and-ckd-physiological-and-genetic-insight-from-humans-and-animal-models
#14
REVIEW
Xuexiang Wang, Michael R Garrett
The kidneys play a vital role in the excretion of waste products and the regulation of electrolytes, maintenance of acid-base balance, regulation of blood pressure, and production of several hormones. Any alteration in the structure of the nephron (basic functional unit of the kidney) can have a major impact on the kidney's ability to work efficiently. Progressive decline in kidney function can lead to serious illness and ultimately death if not treated by dialysis or transplantation. While there have been numerous studies that implicate lower nephron numbers as being an important factor in influencing susceptibility to developing hypertension and chronic kidney disease, a direct association has been difficult to establish because of three main limitations: 1) the large variation in nephron number observed in the human population; 2) no established reliable noninvasive methods to determine nephron complement; and 3) to date, nephron measurements have been done after death, which doesn't adequately account for potential loss of nephrons with age or disease...
March 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28011883/single-cell-transcriptomic-profiling-of-mouse-pancreatic-progenitors
#15
Diana E Stanescu, Reynold Yu, Kyoung-Jae Won, Doris A Stoffers
The heterogeneity of the developing pancreatic epithelium and low abundance of endocrine progenitors limit the information derived from traditional expression studies. To identify genes that characterize early developmental tissues composed of multiple progenitor lineages, we applied single-cell RNA-Seq to embryonic day (e)13.5 mouse pancreata and performed integrative analysis with single cell data from mature pancreas. We identified subpopulations expressing macrophage or endothelial markers and new pancreatic progenitor markers...
February 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28011881/alterations-in-the-gut-microbiota-can-elicit-hypertension-in-rats
#16
Sareema Adnan, James W Nelson, Nadim J Ajami, Venugopal R Venna, Joseph F Petrosino, Robert M Bryan, David J Durgan
Gut dysbiosis has been linked to cardiovascular diseases including hypertension. We tested the hypothesis that hypertension could be induced in a normotensive strain of rats or attenuated in a hypertensive strain of rats by exchanging the gut microbiota between the two strains. Cecal contents from spontaneously hypertensive stroke prone rats (SHRSP) were pooled. Similarly, cecal contents from normotensive WKY rats were pooled. Four-week-old recipient WKY and SHR rats, previously treated with antibiotics to reduce the native microbiota, were gavaged with WKY or SHRSP microbiota, resulting in four groups; WKY with WKY microbiota (WKY g-WKY), WKY with SHRSP microbiota (WKY g-SHRSP), SHR with SHRSP microbiota (SHR g-SHRSP), and SHR with WKY microbiota (SHR g-WKY)...
February 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28011880/roles-of-estrogen-receptor-alpha-in-mediating-life-span-the-hypothalamic-deregulation-hypothesis
#17
REVIEW
Arvin M Gouw, Gizem Efe, Rita Barakat, Andrew Preecha, Morvarid Mehdizadeh, Steven A Garan, George A Brooks
In several species caloric restriction (CR) extends life span. In this paper we integrate data from studies on CR and other sources to articulate the hypothalamic deregulation hypothesis by which estrogen receptor-alpha (ER-α) signaling in the hypothalamus and limbic system affects life span under the stress of CR in mammals. ER-α is one of two principal estrogen-binding receptors differentially expressed in the amygdala, hippocampus, and several key hypothalamic nuclei: the arcuate nucleus (ARN), preoptic area (POA), ventromedial nucleus (VMN), antero ventral periventricular nucleus (AVPV), paraventricular nucleus (PVN), supraoptic nucleus (SON), and suprachiasmatic nucleus (SCN)...
February 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/27940566/glucose-regulates-the-intrinsic-inflammatory-response-of-the-heart-to-surgically-induced-hypothermic-ischemic-arrest-and-reperfusion
#18
Ahmed S Bux, Merry L Lindsey, Hernan G Vasquez, Heinrich Taegtmeyer, Romain Harmancey
We investigated the isolated working rat heart as a model to study early transcriptional remodeling induced in the setting of open heart surgery and stress hyperglycemia. Hearts of male Sprague Dawley rats were cold-arrested in Krebs-Henseleit buffer and subjected to 60 min normothermic reperfusion in the working mode with buffer supplemented with noncarbohydrate substrates plus glucose (25 mM) or mannitol (25 mM; osmotic control). Gene expression profiles were determined by microarray analysis and compared with those of nonperfused hearts...
January 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/27815535/pattern-analysis-uncovers-a-chronic-ethanol-induced-disruption-of-the-switch-like-dynamics-of-c-ebp-%C3%AE-and-c-ebp-%C3%AE-genome-wide-binding-during-liver-regeneration
#19
Lakshmi Kuttippurathu, Biswanath Patra, Daniel Cook, Jan B Hoek, Rajanikanth Vadigepalli
Chronic ethanol intake impairs liver regeneration through a system-wide alteration in the regulatory networks driving the response to injury. Our study focused on the initial phase of response to 2/3rd partial hepatectomy (PHx) to investigate how adaptation to chronic ethanol intake affects the genome-wide binding profiles of the transcription factors C/EBP-β and C/EBP-α. These factors participate in complementary and often opposing functions for maintaining cellular differentiation, regulating metabolism, and governing cell growth during liver regeneration...
January 1, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/27815534/biological-roles-of-micrornas-in-the-control-of-insulin-secretion-and-action
#20
REVIEW
Sophie Calderari, Malika R Diawara, Alois Garaud, Dominique Gauguier
microRNAs (miRNAs) are intracellular and circulating molecular components contributing to genome expression control through binding mRNA targets, which generally results in downregulated mRNA expression. One miRNA can target several mRNAs, and one transcript can be targeted by several miRNAs, resulting in complex fine-tuning of regulation of gene networks and signaling pathways. miRNAs regulate metabolism, adipocyte differentiation, pancreatic development, β-cell mass, insulin biosynthesis, secretion, and signaling, and their role in diabetes and obesity is emerging...
January 1, 2017: Physiological Genomics
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