Expression analysis of sex-determining pathway genes during development in male and female Atlantic salmon (Salmo salar)
We studied the expression of 28 genes that are involved in vertebrate sex-determination or sex-differentiation pathways, in male and female Atlantic salmon (Salmo salar) in 11 stages of development from fertilization to after first feeding. Gene expression was measured in half-sibs that shared the same dam. The sire of family 1 was a sex-reversed female (i.e., genetically female but phenotypically male), and so the progeny of this family are all female. The sire of family 2 was a true male, and so the offspring were 50% male and 50% female. Gene expression levels were compared among three groups: 20 female offspring of the...
Source: Physiological Genomics - December 1, 2015 Category: Genetics & Stem Cells Authors: Lubieniecki, K. P., Botwright, N. A., Taylor, R. S., Evans, B. S., Cook, M. T., Davidson, W. S. Tags: Regulation of Gene Expression Source Type: research
Global deletion of BCATm increases expression of skeletal muscle genes associated with protein turnover
Consumption of a protein-containing meal by a fasted animal promotes protein accretion in skeletal muscle, in part through leucine stimulation of protein synthesis and indirectly through repression of protein degradation mediated by its metabolite, α-ketoisocaproate. Mice lacking the mitochondrial branched-chain aminotransferase (BCATm/Bcat2), which interconverts leucine and α-ketoisocaproate, exhibit elevated protein turnover. Here, the transcriptomes of gastrocnemius muscle from BCATm knockout (KO) and wild-type mice were compared by next-generation RNA sequencing (RNA-Seq) to identify potential adaptations a...
Source: Physiological Genomics - November 1, 2015 Category: Genetics & Stem Cells Authors: Lynch, C. J., Kimball, S. R., Xu, Y., Salzberg, A. C., Kawasawa, Y. I. Tags: Nutrient Gene Interaction Source Type: research
Identifying growth hormone-regulated enhancers in the Igf1 locus
Growth hormone (GH) plays a central role in regulating somatic growth and in controlling multiple physiological processes in humans and other vertebrates. A key agent in many GH actions is the secreted peptide, IGF-I. As established previously, GH stimulates IGF-I gene expression via the Stat5b transcription factor, leading to production of IGF-I mRNAs and proteins. However, the precise mechanisms by which GH-activated Stat5b promotes IGF-I gene transcription have not been defined. Unlike other GH-regulated genes, there are no Stat5b sites near either of the two IGF-I gene promoters. Although dispersed GH-activated Stat5b ...
Source: Physiological Genomics - November 1, 2015 Category: Genetics & Stem Cells Authors: Alzhanov, D., Mukherjee, A., Rotwein, P. Tags: Regulation of Gene Expression Source Type: research
High CO2 alters the hypoxia response of the Pacific whiteleg shrimp (Litopenaeus vannamei) transcriptome including known and novel hemocyanin isoforms
Acclimation to low O2 in many organisms involves changes at the level of the transcriptome. Here we used high-throughput RNA sequencing (RNA-Seq) to explore the global transcriptomic response and specific involvement of a suite of hemocyanin (Hc) subunits to low O2 alone and in combination with high CO2, which naturally co-occurs with low O2. Hepatopancreas mRNA of juvenile L. vannamei exposed to air-saturated water, low O2, or low O2/high CO2 for 4 or 24 h was pooled, sequenced (HiSeq 2500) and assembled (Trinity: 52,190 contigs) to create a deep strand-specific reference transcriptome. Annotation of the assembly revealed...
Source: Physiological Genomics - November 1, 2015 Category: Genetics & Stem Cells Authors: Johnson, J. G., Paul, M. R., Kniffin, C. D., Anderson, P. E., Burnett, L. E., Burnett, K. G. Tags: Regulation of Gene Expression Source Type: research
Systemic PPAR{gamma} deletion causes severe disturbance in fluid homeostasis in mice
The pharmacological action of peroxisome proliferator-activated receptor (PPAR) in promoting sodium and water retention is well documented as highlighted by the major side-effect of body weight gain and edema associated with thiazolidinedione use. However, a possible physiological role of PPAR in regulation of fluid metabolism has not been reported by previous studies. Here we analyzed fluid metabolism in inducible whole-body PPAR knockout mice. The null mice developed severe polydipsia and polyuria, reduced urine osmolality, and modest hyperphagia. The phenomenon persisted during 3 days of pair feeding and pair drinking, ...
Source: Physiological Genomics - November 1, 2015 Category: Genetics & Stem Cells Authors: Zhou, L., Panasiuk, A., Downton, M., Zhao, D., Yang, B., Jia, Z., Yang, T. Tags: Genetic and Genomics Investigation of Structure and Function of the Kidney Source Type: research
Critical role of PPAR{gamma} in water balance
(Source: Physiological Genomics)
Source: Physiological Genomics - November 1, 2015 Category: Genetics & Stem Cells Authors: Li, N. Tags: Genetic and Genomics Investigation of Structure and Function of the Kidney Source Type: research
Chromosome Y genetic variants: impact in animal models and on human disease
Chromosome Y (chrY) variation has been associated with many complex diseases ranging from cancer to cardiovascular disorders. Functional roles of chrY genes outside of testes are suggested by the fact that they are broadly expressed in many other tissues and correspond to regulators of basic cellular functions (such as transcription, translation, and protein stability). However, the unique genetic properties of chrY (including the lack of meiotic crossover and the presence of numerous highly repetitive sequences) have made the identification of causal variants very difficult. Despite the prior lack of reliable sequences an...
Source: Physiological Genomics - November 1, 2015 Category: Genetics & Stem Cells Authors: Prokop, J. W., Deschepper, C. F. Tags: Comparative, Statistical, and Computational Genomics and Model Organism Databases Source Type: research
High-fat diet caused widespread epigenomic differences on hepatic methylome in rat
A high-fat (HF) diet is associated with progression of liver diseases. To illustrate genome-wide landscape of DNA methylation in liver of rats fed either a control or HF diet, two enrichment-based methods, namely methyl-DNA immunoprecipitation assay with high-throughput sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq), were performed in our study. Rats fed with the HF diet exhibited an increased body weight and liver fat accumulation compared with that of the control group when they were 12 wk of age. Genome-wide analysis of differentially methylated regions (DMRs) showed that 12,494...
Source: Physiological Genomics - October 1, 2015 Category: Genetics & Stem Cells Authors: Zhang, Y., Wang, H., Zhou, D., Moody, L., Lezmi, S., Chen, H., Pan, Y.-X. Tags: Nutrient Gene Interaction Source Type: research
RNA-Seq analysis of high NaCl-induced gene expression
High extracellular NaCl is known to change expression of numerous genes, many of which are regulated by the osmoprotective transcription factor nuclear factor of activated T cells-5 (NFAT5). In the present study we employed RNA-Seq to provide a comprehensive, unbiased account of genes regulated by high NaCl in mouse embryonic fibroblast cells (MEFs). To identify genes regulated by NFAT5 we compared wild-type MEFs (WT-MEFs) to MEFs in which mutation of the NFAT5 gene inhibits its transcriptional activity (Null-MEFs). In WT-MEFs adding NaCl to raise osmolality from 300 to 500 mosmol/kg for 24 h increases expression of 167 ge...
Source: Physiological Genomics - October 1, 2015 Category: Genetics & Stem Cells Authors: Izumi, Y., Yang, W., Zhu, J., Burg, M. B., Ferraris, J. D. Tags: Regulation of Gene Expression Source Type: research
Responses of the mammary transcriptome of dairy cows to altered photoperiod during late gestation
Cows exposed to short day photoperiod (SD, 8L:16D) during the 60-day nonlactating period prior to parturition produce more milk in their subsequent lactation compared with cows exposed to long day photoperiod (LD, 16L:8D). Although this response is well established in dairy cows, the underlying mechanisms are not understood. We hypothesized that differential gene expression in cows exposed to SD or LD photoperiods during the dry period could be used to identify the functional basis for the subsequent increase in milk production during lactation. Pregnant, multiparous cows were maintained on an SD or LD photoperiod for 60 d...
Source: Physiological Genomics - October 1, 2015 Category: Genetics & Stem Cells Authors: Bentley, P. A., Wall, E. H., Dahl, G. E., McFadden, T. B. Tags: Regulation of Gene Expression Source Type: research
Role of the Na+/H+ exchanger 3 in angiotensin II-induced hypertension
The renal mechanisms responsible for angiotensin II (ANG II)-induced hypertension remain incompletely understood. The present study tested the hypothesis that the Na+/H+ exchanger 3 (NHE3) is required for ANG II-induced hypertension in mice. Five groups of wild-type (Nhe3+/+) and Nhe3–/– mice were treated with vehicle or high pressor doses of ANG II (1.5 mg/kg/day ip, via minipump for 2 wk, or 10 pmol/min iv for 30 min). Under basal conditions, Nhe3–/– mice had significantly lower systolic blood pressure (SBP) and mean intra-arterial pressure (MAP) (P < 0.01), 24 h urine (P < 0.05), urinary Na...
Source: Physiological Genomics - October 1, 2015 Category: Genetics & Stem Cells Authors: Li, X. C., Shull, G. E., Miguel-Qin, E., Zhuo, J. L. Tags: Molecular Genetics of Complex Traits Source Type: research
PBMC transcriptomic responses to primary and secondary vaccination differ due to divergent lean growth and antibody titers in a pig model
This study aims to show differences of transcript abundance changes during the time intervals before and after two tetanus toxoid (TT) vaccinations in domestic pigs differing in lean growth (LG) and anti-TT-antibody titers (AB) parameters of performance and immunocompetence. During response to the first vaccination all animals had a general decrease in transcript abundances related to various functional pathways as measured by comparative Affymetrix microarray hybridization and Ingenuity Pathway analyses. Low-AB phenotypes had predominantly decreased immune response transcripts. Combined phenotypes high-AB/high-LG had decr...
Source: Physiological Genomics - October 1, 2015 Category: Genetics & Stem Cells Authors: Adler, M., Murani, E., Ponsuksili, S., Wimmers, K. Tags: Molecular Genetics of Complex Traits Source Type: research
Interaction of long noncoding RNAs and microRNAs in the pathogenesis of idiopathic pulmonary fibrosis
Long noncoding RNAs (lncRNAs) are transcribed RNAs with more than 200 nucleotides in length. A growing body of evidence supports the notion that lncRNAs act as competitive endogenous RNAs for microRNAs and play roles in physiological and pathological processes. Several studies have demonstrated the roles of microRNAs in the pathogenesis of idiopathic pulmonary fibrosis (IPF). However, it is unknown whether lncRNAs are involved in IPF. To investigate the roles of lncRNAs in IPF, we determined the interaction of lncRNAs and microRNAs by motif search and manual comparison. The sequences of the dysregulated microRNAs in IPF in...
Source: Physiological Genomics - October 1, 2015 Category: Genetics & Stem Cells Authors: Huang, C., Yang, Y., Liu, L. Tags: MicroRNA Source Type: research
Integrated microRNA and mRNA responses to acute human left ventricular ischemia
In this study, we performed next-generation miRNA and mRNA sequencing on LV tissue from nine patients undergoing cardiac surgery with cardiopulmonary bypass and cardioplegic arrest. Samples were obtained immediately after aortic cross clamping (baseline) and before aortic cross clamp removal (postischemic). Of 1,237 identified miRNAs, 21 were differentially expressed between baseline and postischemic LV samples including the upregulated miRNAs miR-339-5p and miR-483-3p and the downregulated miRNA miR-139-5p. Target prediction analysis of these miRNAs was integrated with mRNA expression from the same LV samples to identify ...
Source: Physiological Genomics - October 1, 2015 Category: Genetics & Stem Cells Authors: Saddic, L. A., Chang, T.-W., Sigurdsson, M. I., Heydarpour, M., Raby, B. A., Shernan, S. K., Aranki, S. F., Body, S. C., Muehlschlegel, J. D. Tags: MicroRNA Source Type: research
AZT-induced mitochondrial toxicity: an epigenetic paradigm for dysregulation of gene expression through mitochondrial oxidative stress
Mitochondrial dysfunction causes oxidative stress and cardiomyopathy. Oxidative stress also is a side effect of dideoxynucleoside antiretrovirals (NRTI) and is observed in NRTI-induced cardiomyopathy. We show here that treatment with the NRTI AZT {1-[(2R,4S,5S)-4-azido-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione} modulates cardiac gene expression epigenetically through production of mitochondrially derived reactive oxygen species. Transgenic mice with ubiquitous expression of mitochondrially targeted catalase (MCAT) and C57Bl/6 wild-type mice littermates (WT) were administered AZT (0.22 mg/day po, 35 days), ...
Source: Physiological Genomics - October 1, 2015 Category: Genetics & Stem Cells Authors: Koczor, C. A., Jiao, Z., Fields, E., Russ, R., Ludaway, T., Lewis, W. Tags: Call for Papers: Epigenetics and Epigenomics Source Type: research
