FOXA2 regulates a network of genes involved in critical functions of human intestinal epithelial cells
The forkhead box A (FOXA) family of pioneer transcription factors is critical for the development of many endoderm-derived tissues. Their importance in regulating biological processes in the lung and liver is extensively characterized, though much less is known about their role in intestine. Here we investigate the contribution of FOXA2 to coordinating intestinal epithelial cell function using postconfluent Caco2 cells, differentiated into an enterocyte-like model. FOXA2 binding sites genome-wide were determined by ChIP-seq and direct targets of the factor were validated by ChIP-qPCR and siRNA-mediated depletion of FOXA1/2...
Source: Physiological Genomics - July 1, 2015 Category: Genetics & Stem Cells Authors: Gosalia, N., Yang, R., Kerschner, J. L., Harris, A. Tags: Regulation of Gene Expression Source Type: research
Development of progressive albuminuria in male Munich Wistar Fromter rats is androgen dependent
Munich Wistar Frömter (MWF) rats develop spontaneous albuminuria that is linked to autosomal genetic loci and inherit a nephron deficit in both female and male animals, respectively. However, albuminuria and kidney damage are clearly more pronounced in males. Here we tested whether androgens and the androgen receptor influence albuminuria in male MWF. We first demonstrated in a pilot study that orchiectomy (Ox) of male MWF led to a significant suppression of urinary albumin excretion (UAE), while continuous testosterone supplementation in MWF Ox led to UAE levels similar to sham-operated (Sham) MWF rats. Subsequently,...
Source: Physiological Genomics - July 1, 2015 Category: Genetics & Stem Cells Authors: Herlan, L., Unland, J., Langer, S., Schulte, L., Schutten, S., Garcia-Prieto, C. F., Kossmehl, P., Fernandez-Alfonso, M. S., Schulz, A., Kreutz, R. Tags: Molecular Genetics of Complex Traits Source Type: research
Identification of quantitative trait transcripts for growth traits in the large scales of liver and muscle samples
In this study, we applied whole genome gene expression and quantitative trait transcript (QTT) analyses in 497 liver and 586 longissimus dorsi muscle samples to identify candidate genes and dissect the genetic basis of pig growth in a white Duroc x Erhualian F2 resource population. A total of 20,108 transcripts in liver and 23,728 transcripts in muscle with expression values were used for association analysis between gene expression level and phenotypic value. At the significance threshold of P < 0.0005, we identified a total of 169 and 168 QTTs for nine growth-related traits in liver and muscle, respectively. We also f...
Source: Physiological Genomics - July 1, 2015 Category: Genetics & Stem Cells Authors: Xiong, X., Yang, H., Yang, B., Chen, C., Huang, L. Tags: Molecular Genetics of Complex Traits Source Type: research
Effect of feed restriction and subsequent re-alimentation on hormones and genes of the somatotropic axis in cattle
The objective of this study was to characterize the effect of feed restriction and compensatory growth during re-alimentation on the functionality of the somatotropic axis. We blocked 60 bulls into one of two groups: 1) restricted feed allowance for 125 days (period 1) (RES, n = 30) followed by ad libitum feeding for 55 days (period 2) or 2) ad libitum access to feed throughout (ADLIB, n = 30). A growth hormone releasing hormone (GHRH) challenge was performed during each period. At the end of each period, 15 animals from each treatment were slaughtered and hepatic tissue collected. Hepatic expression of 13 genes of the som...
Source: Physiological Genomics - July 1, 2015 Category: Genetics & Stem Cells Authors: Keogh, K., Waters, S. M., Kelly, A. K., Wylie, A. R. G., Kenny, D. A. Tags: Nutrient Gene Interaction Source Type: research
New insights into the nutritional regulation of gluconeogenesis in carnivorous rainbow trout (Oncorhynchus mykiss): a gene duplication trail
This study demonstrates that Ss4R in trout involved adaptive innovation via gene duplication and via the outcome of the resulting ohnologs. Indeed, maintenance of ohnologous g6pcb2 pair may contribute in a significant way to the glucose-intolerant phenotype of trout and may partially explain its poor use of dietary carbohydrates. (Source: Physiological Genomics)
Source: Physiological Genomics - July 1, 2015 Category: Genetics & Stem Cells Authors: Marandel, L., Seiliez, I., Veron, V., Skiba-Cassy, S., Panserat, S. Tags: Nutrient Gene Interaction Source Type: research
Exoelectrogenic capacity of host microbiota predicts lymphocyte recruitment to the gut
Electrotaxis, directional cell movement in response to an electric potential, has been demonstrated in a wide range of cell types including lymphocytes. Exoelectrogens, microorganisms capable of generating electrical currents, have been identified in microbial fuel cells. However, no studies have investigated exoelectrogenic microbes in fresh feces or the effects of an exoelectrogenic microbiota on the host organism. Here we show that commensal gut microbial populations differ in their capacity for electrical current production by exoelectrogens and that those differences are predictive of increased lymphocyte trafficking ...
Source: Physiological Genomics - July 1, 2015 Category: Genetics & Stem Cells Authors: Ericsson, A. C., Davis, D. J., Franklin, C. L., Hagan, C. E. Tags: Call for Papers: Gut Microbiota in Health and Disease Source Type: research
Physiological genomics - what is in a name?
(Source: Physiological Genomics)
Source: Physiological Genomics - July 1, 2015 Category: Genetics & Stem Cells Authors: Joe, B. Tags: Editorial Source Type: research
Identification of stable reference genes in differentiating human pluripotent stem cells
Reference genes, often referred to as housekeeping genes (HKGs), are frequently used to normalize gene expression data based on the assumption that they are expressed at a constant level in the cells. However, several studies have shown that there may be a large variability in the gene expression levels of HKGs in various cell types. In a previous study, employing human embryonic stem cells (hESCs) subjected to spontaneous differentiation, we observed that the expression of commonly used HKG varied to a degree that rendered them inappropriate to use as reference genes under those experimental settings. Here we present a su...
Source: Physiological Genomics - June 1, 2015 Category: Genetics & Stem Cells Authors: Holmgren, G., Ghosheh, N., Zeng, X., Bogestal, Y., Sartipy, P., Synnergren, J. Tags: Regulation of Gene Expression Source Type: research
Extreme obesity is associated with variation in genes related to the circadian rhythm of food intake and hypothalamic signaling
The hypothalamus is important for regulation of energy intake. Mutations in genes involved in the function of the hypothalamus can lead to early-onset severe obesity. To look further into this, we have followed a strategy that allowed us to identify rare and common gene variants as candidates for the background of extreme obesity from a relatively small cohort. For that we focused on subjects with a well-selected phenotype and on a defined gene set and used a rich source of genetic data with stringent cut-off values. A list of 166 genes functionally related to the hypothalamus was generated. In those genes complete exome s...
Source: Physiological Genomics - June 1, 2015 Category: Genetics & Stem Cells Authors: Mariman, E. C. M., Bouwman, F. G., Aller, E. E. J. G., van Baak, M. A., Wang, P. Tags: Molecular Genetics of Complex Traits Source Type: research
A common variant in the CLDN7/ELP5 locus predicts adiponectin change with lifestyle intervention and improved fitness in obese individuals with diabetes
Overweight/obese individuals with Type 2 diabetes have low adiponectin levels, which may improve with lifestyle changes. We investigated whether genetic variants associated with adiponectin levels in genome-wide association studies (GWAS) would also be related with adiponectin changes in response to an intensive lifestyle intervention (ILI), potentially through mechanisms altering the adipose microenvironment via weight loss and/or improved cardiorespiratory fitness. Look AHEAD was a randomized trial comparing the cardiovascular benefits of ILI-induced weight loss and physical activity compared with diabetes support and ed...
Source: Physiological Genomics - June 1, 2015 Category: Genetics & Stem Cells Authors: Belalcazar, L. M., Papandonatos, G. D., McCaffery, J. M., Peter, I., Pajewski, N. M., Erar, B., Allred, N. D., Balasubramanyam, A., Bowden, D. W., Brautbar, A., Pi-Sunyer, F. X., Ballantyne, C. M., Huggins, G. S., and the Look AHEAD Research Group Tags: General Interest Source Type: research
Expression of three topologically distinct membrane proteins elicits unique stress response pathways in the yeast Saccharomyces cerevisiae
Misfolded membrane proteins are retained in the endoplasmic reticulum (ER) and are subject to ER-associated degradation, which clears the secretory pathway of potentially toxic species. While the transcriptional response to environmental stressors has been extensively studied, limited data exist describing the cellular response to misfolded membrane proteins. To this end, we expressed and then compared the transcriptional profiles elicited by the synthesis of three ER retained, misfolded ion channels: The α-subunit of the epithelial sodium channel, ENaC, the cystic fibrosis transmembrane conductance regulator, CFTR, ...
Source: Physiological Genomics - June 1, 2015 Category: Genetics & Stem Cells Authors: Buck, T. M., Jordan, R., Lyons-Weiler, J., Adelman, J. L., Needham, P. G., Kleyman, T. R., Brodsky, J. L. Tags: Model Organisms Source Type: research
Evidence for a link between gut microbiota and hypertension in the Dahl rat
This study was designed to evaluate whether gut microbial composition affects hypertension. 16S rRNA genes obtained from cecal samples of Dahl salt-sensitive (S) and Dahl salt-resistant (R) rats were sequenced. Bacteria of the phylum Bacteroidetes were higher in the S rats compared with the R rats. Furthermore, the family S24-7 of the phylum Bacteroidetes and the family Veillonellaceae of the phylum Firmicutes were higher in the S rats compared with the R rats. Analyses of the various phylogenetic groups of cecal microbiota revealed significant differences between S and R rats. Both strains were maintained on a high-salt d...
Source: Physiological Genomics - June 1, 2015 Category: Genetics & Stem Cells Authors: Mell, B., Jala, V. R., Mathew, A. V., Byun, J., Waghulde, H., Zhang, Y., Haribabu, B., Vijay-Kumar, M., Pennathur, S., Joe, B. Tags: Call for Papers: Gut Microbiota in Health and Disease Source Type: research
Similarities and differences of X and Y chromosome homologous genes, SRY and SOX3, in regulating the renin-angiotensin system promoters
The renin-angiotensin system (RAS) is subject to sex-specific modulation by hormones and gene products. However, sex differences in the balance between the vasoconstrictor/proliferative ACE/ANG II/AT1 axis, and the vasodilator/antiproliferative ACE2/ANG-(1–7)/MAS axis are poorly known. Data in the rat have suggested the male-specific Y-chromosome gene Sry to contribute to balance between these two axes, but why the testis-determining gene has these functions remains unknown. A combination of in silico genetic/protein comparisons, functional luciferase assays for promoters of the human RAS, and RNA-Seq profiling in ra...
Source: Physiological Genomics - May 1, 2015 Category: Genetics & Stem Cells Authors: Araujo, F. C., Milsted, A., Watanabe, I. K. M., Del Puerto, H. L., Santos, R. A. S., Lazar, J., Reis, F. M., Prokop, J. W. Tags: Molecular Genetics of Complex Traits Source Type: research
Downregulation of growth hormone 1 gene in the cerebellum and prefrontal cortex of rats with depressive-like behavior
This study indicates that the depressive-like behavior may be related to the decrease of Gh1 expression in the cerebellum and PFC. (Source: Physiological Genomics)
Source: Physiological Genomics - May 1, 2015 Category: Genetics & Stem Cells Authors: Yamamoto, Y., Ueyama, T., Ito, T., Tsuruo, Y. Tags: Omics Technologies and Applications Source Type: research
Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax)
We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA. (Source: Physiological Genomics)
Source: Physiological Genomics - May 1, 2015 Category: Genetics & Stem Cells Authors: Kaitetzidou, E., Xiang, J., Antonopoulou, E., Tsigenopoulos, C. S., Sarropoulou, E. Tags: Regulation of Gene Expression Source Type: research
