Dietary supplementation with polyunsaturated fatty acid during pregnancy modulates DNA methylation at IGF2/H19 imprinted genes and growth of infants
This study was based on a randomized intervention trial conducted in Mexican pregnant women supplemented daily with 400 mg of DHA or a placebo from gestation week 18–22 to parturition. We applied quantitative profiling of DNA methylation states at IGF2 promoter 3 (IGF2 P3), IGF2 differentially methylated region (DMR), and H19 DMR in cord blood mononuclear cells of the DHA-supplemented group (n = 131) and the control group (n = 130). In stratified analyses, DNA methylation levels in IGF2 P3 were significantly higher in the DHA group than the control group in preterm infants (P = 0.04). We also observed a positive asso...
Source: Physiological Genomics - December 1, 2014 Category: Genetics & Stem Cells Authors: Lee, H.-S., Barraza-Villarreal, A., Biessy, C., Duarte-Salles, T., Sly, P. D., Ramakrishnan, U., Rivera, J., Herceg, Z., Romieu, I. Tags: Nutrient Gene Interaction Source Type: research
In utero exposure to prepregnancy maternal obesity and postweaning high-fat diet impair regulators of mitochondrial dynamics in rat placenta and offspring
The proportion of pregnant women who are obese at conception continues to rise. Compelling evidence suggests the intrauterine environment is an important determinant of offspring health. Maternal obesity and unhealthy diets are shown to promote metabolic programming in the offspring. Mitochondria are maternally inherited, and we have previously shown impaired mitochondrial function in rat offspring exposed to maternal obesity in utero. Mitochondrial health is maintained by mitochondrial dynamics, or the processes of fusion and fission, which serve to repair damaged mitochondria, remove irreparable mitochondria, and maintai...
Source: Physiological Genomics - December 1, 2014 Category: Genetics & Stem Cells Authors: Borengasser, S. J., Faske, J., Kang, P., Blackburn, M. L., Badger, T. M., Shankar, K. Tags: Call for Papers Source Type: research
TNF-{alpha} alters the release and transfer of microparticle-encapsulated miRNAs from endothelial cells
MicroRNAs (miRNAs) encapsulated within microparticles (MPs) are likely to have a role in cell-to-cell signaling in a variety of diseases, including atherosclerosis. However, little is known about the mechanisms by which different cell types release and transfer miRNAs. Here, we examined TNF-α-induced release of MP-encapsulated miR-126, miR-21, and miR-155 from human aortic endothelial cells (ECs) and their transfer to recipient cells. ECs were treated with TNF-α (100 ng/ml) in the presence or absence of inhibitors that target different MP production pathways. MPs released in response to TNF-α were charact...
Source: Physiological Genomics - November 15, 2014 Category: Genetics & Stem Cells Authors: Alexy, T., Rooney, K., Weber, M., Gray, W. D., Searles, C. D. Tags: MicroRNA Source Type: research
Identification of genes whose expression is altered by obesity throughout the arterial tree
In conclusion, the present study identifies a select number of genes (i.e., 20 genes) whose expression is consistently altered throughout the arterial network in response to obesity and provides further insight into the heterogeneous vascular effects of obesity. Although there is no known direct function of the majority of 20 genes related to vascular health, the obesity-associated upregulation of SREBF2, LGALS3BP, IRF7, and FOLR2 across all arteries is suggestive of an unfavorable vascular phenotypic alteration with obesity. These data may serve as an important resource for identifying novel therapeutic targets against ob...
Source: Physiological Genomics - November 15, 2014 Category: Genetics & Stem Cells Authors: Padilla, J., Jenkins, N. T., Thorne, P. K., Martin, J. S., Rector, R. S., Davis, J. W., Laughlin, M. H. Tags: Regulation of Gene Expression Source Type: research
Using normalization to resolve RNA-Seq biases caused by amplification from minimal input
RNA-Seq has become a widely used method to study transcriptomes, and it is now possible to perform RNA-Seq on almost any sample. Nevertheless, samples obtained from small cell populations are particularly challenging, as biases associated with low amounts of input RNA can have strong and detrimental effects on downstream analyses. Here we compare different methods to normalize RNA-Seq data obtained from minimal input material. Using RNA from isolated medaka pituitary cells, we have amplified material from six samples before sequencing. Both synthetic and real data are used to evaluate different normalization methods to obt...
Source: Physiological Genomics - November 1, 2014 Category: Genetics & Stem Cells Authors: Ager-Wick, E., Henkel, C. V., Haug, T. M., Weltzien, F.-A. Tags: Omics Technologies and Applications Source Type: research
Gonadal transcriptomic analysis of yellow catfish (Pelteobagrus fulvidraco): identification of sex-related genes and genetic markers
In this study, the transcriptome of yellow catfish gonad was first sequenced, assembled, and characterized; it provides a valuable genomic resource for better understanding of yellow catfish sex determination as well as development of molecular markers, thereby assisting in the production of monosex yellow catfish for aquaculture. (Source: Physiological Genomics)
Source: Physiological Genomics - November 1, 2014 Category: Genetics & Stem Cells Authors: Lu, J., Luan, P., Zhang, X., Xue, S., Peng, L., Mahbooband, S., Sun, X. Tags: Call for Papers: NextGen Sequencing Technology-based Dissection of Physiological Systems Source Type: research
miR-21 in ischemia/reperfusion injury: a double-edged sword?
MicroRNAs (miRNAs or miRs) are endogenous, small RNA molecules that suppress expression of targeted mRNA. miR-21, one of the most extensively studied miRNAs, is importantly involved in divergent pathophysiological processes relating to ischemia/reperfusion (I/R) injury, such as inflammation and angiogenesis. The role of miR-21 in renal I/R is complex, with both protective and pathological pathways being regulated by miR-21. Preconditioning-induced upregulation of miR-21 contributes to the protection against subsequent renal I/R injury through the targeting of genes such as the proapoptotic gene programmed cell death 4 and ...
Source: Physiological Genomics - November 1, 2014 Category: Genetics & Stem Cells Authors: Xu, X., Kriegel, A. J., Jiao, X., Liu, H., Bai, X., Olson, J., Liang, M., Ding, X. Tags: MicroRNA Source Type: research
Dynamic gene expression patterns in animal models of early and late heart failure reveal biphasic-bidirectional transcriptional activation of signaling pathways
Altered cardiac gene expression in heart failure (HF) has mostly been identified by single-point analysis of end-stage disease. This may miss earlier changes in gene expression that are transient and/or directionally opposite to those observed later. Myocardial datasets from the largest microarray data repository (Gene Expression Omnibus) yielded six HF studies with time-course data. Differentially expressed transcripts between nonfailing controls, early HF (<3 days after cardiac insult) and late HF (usually >2 wk) were determined, and analysis of KEGG pathways and predicted regulatory control elements performed. We ...
Source: Physiological Genomics - October 15, 2014 Category: Genetics & Stem Cells Authors: Rowell, J., Koitabashi, N., Kass, D. A., Barth, A. S. Tags: Systems Biology of Cell State Regulation Source Type: research
Mathematical modeling of light-mediated HPA axis activity and downstream implications on the entrainment of peripheral clock genes
In this work we propose a semimechanistic model that describes the photic signal transduction to the hypothalamic-pituitary-adrenal (HPA) axis that ultimately regulates the synchronization of peripheral clock genes (PCGs). Our HPA axis model predicts that photic stimulation induces a type-1 phase response curve to cortisol's profile with increased cortisol sensitivity to light exposure in its rising phase, as well as the shortening of cortisol's period as constant light increases (Aschoff's first rule). Furthermore, our model provides insight into cortisol's phase and amplitude dependence on photoperiods and reveals that c...
Source: Physiological Genomics - October 15, 2014 Category: Genetics & Stem Cells Authors: Mavroudis, P. D., Corbett, S. A., Calvano, S. E., Androulakis, I. P. Tags: Systems Biology of Cell State Regulation Source Type: research
Multi-omic integrated networks connect DNA methylation and miRNA with skeletal muscle plasticity to chronic exercise in Type 2 diabetic obesity
Epigenomic regulation of the transcriptome by DNA methylation and posttranscriptional gene silencing by miRNAs are potential environmental modulators of skeletal muscle plasticity to chronic exercise in healthy and diseased populations. We utilized transcriptome networks to connect exercise-induced differential methylation and miRNA with functional skeletal muscle plasticity. Biopsies of the vastus lateralis were collected from middle-aged Polynesian men and women with morbid obesity (44 kg/m2 ± 10) and Type 2 diabetes before and following 16 wk of resistance (n = 9) or endurance training (n = 8). Longitudinal trans...
Source: Physiological Genomics - October 15, 2014 Category: Genetics & Stem Cells Authors: Rowlands, D. S., Page, R. A., Sukala, W. R., Giri, M., Ghimbovschi, S. D., Hayat, I., Cheema, B. S., Lys, I., Leikis, M., Sheard, P. W., Wakefield, S. J., Breier, B., Hathout, Y., Brown, K., Marathi, R., Orkunoglu-Suer, F. E., Devaney, J. M., Leiken, B., Tags: Call for Papers: Physiological Genomics of Exercise in Health and Disease Source Type: research
Expression of microRNAs and their target genes and pathways associated with ovarian follicle development in cattle
This study identified differentially expressed miRNAs in the theca and granulosa cells of dominant and subordinate follicles and implicates them in having important roles in regulating known molecular pathways that determine the fate of ovarian follicle development. (Source: Physiological Genomics)
Source: Physiological Genomics - October 1, 2014 Category: Genetics & Stem Cells Authors: Zielak-Steciwko, A. E., Browne, J. A., McGettigan, P. A., Gajewska, M., Dzięcioł, M., Szulc, T., Evans, A. C. O. Tags: MicroRNA Source Type: research
Acclimatization to long-term hypoxia: gene expression in ovine carotid arteries
Exposure to acute high-altitude hypoxia is associated with an increase in cerebral blood flow (CBF) as a consequence of low arterial O2 tension. However, in response to high altitude acclimatization, CBF returns to levels similar to those at sea level, and tissue blood flow is maintained by an increase in angiogenesis. Of consequence, dysregulation of the acclimatization responses and CBF can result in acute mountain sickness, acute cerebral and/or pulmonary edema. To elucidate the signal transduction pathways involved in successful acclimatization to high altitude, in ovine carotid arteries, we tested the hypothesis that ...
Source: Physiological Genomics - October 1, 2014 Category: Genetics & Stem Cells Authors: Goyal, R., Longo, L. D. Tags: Omics Technologies and Applications Source Type: research
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer
Bioinformatic approaches are intended to provide systems level insight into the complex biological processes that underlie serious diseases such as cancer. In this review we describe current bioinformatic resources, and illustrate how they have been used to study a clinically important example: epithelial-to-mesenchymal transition (EMT) in lung cancer. Lung cancer is the leading cause of cancer-related deaths and is often diagnosed at advanced stages, leading to limited therapeutic success. While EMT is essential during development and wound healing, pathological reactivation of this program by cancer cells contributes to ...
Source: Physiological Genomics - October 1, 2014 Category: Genetics & Stem Cells Authors: Beck, T. N., Chikwem, A. J., Solanki, N. R., Golemis, E. A. Tags: Systems Biology of Cell State Regulation Source Type: research
Maternal PRKAA1 and EDNRA genotypes are associated with birth weight, and PRKAA1 with uterine artery diameter and metabolic homeostasis at high altitude
Low birth weight and intrauterine growth restriction (IUGR) increase the risk of mortality and morbidity during the perinatal period as well as in adulthood. Environmental and genetic factors contribute to IUGR, but the influence of maternal genetic variation on birth weight is largely unknown. We implemented a gene-by-environment study wherein we utilized the growth restrictive effects of high altitude. Multigenerational high-altitude residents (Andeans) are protected from altitude-associated IUGR compared with recent migrants (Europeans). Using a combined cohort of low- and high-altitude European and Andean women, we tes...
Source: Physiological Genomics - September 15, 2014 Category: Genetics & Stem Cells Authors: Bigham, A. W., Julian, C. G., Wilson, M. J., Vargas, E., Browne, V. A., Shriver, M. D., Moore, L. G. Tags: Molecular Genetics of Complex Traits Source Type: research
Structural changes in the gut microbiome of constipated patients
Previous studies using culture-based methods suggested an association between constipation and altered abundance of certain taxa of the colonic microbiome. We aim to examine the global changes in gut microbial composition of constipated patients. A cross-sectional pilot study using 16S rRNA gene pyrosequencing was performed to compare stool microbial composition of eight constipated patients and 14 nonconstipated controls. Only obese children were enrolled so that the microbiome features associated with constipation would not be obscured by those associated with obesity. The sequencing reads were processed by QIIME for qua...
Source: Physiological Genomics - September 15, 2014 Category: Genetics & Stem Cells Authors: Zhu, L., Liu, W., Alkhouri, R., Baker, R. D., Bard, J. E., Quigley, E. M., Baker, S. S. Tags: Call for Papers Source Type: research
