Tenotomy immobilization as a model to investigate skeletal muscle fibrosis (with emphasis on Secreted frizzled-related protein 2)
The pathological endpoint of congenital and senile myopathies is chronic muscle degeneration characterized by the atrophy of contractile elements, accompanied by fibrosis and fatty infiltration of the interstitium. Tenotomy is the release of preload that causes abrupt shortening of the muscle and models atrophy and fibrosis without prominent inflammatory response. Fibrosis in the skeletal muscle is known to be triggered by transforming growth factor (TGF)-β, which is activated by inflammatory events. As these were lacking, tenotomy provided an opportunity to investigate transcriptional events on a background without i...
Source: Physiological Genomics - May 31, 2016 Category: Genetics & Stem Cells Authors: Akpulat, U., Onbasılar, I., Kocaefe, Y. C. Tags: Comparative, Statistical, and Computational Genomics and Model Organism Databases Source Type: research
Analysis of microRNA expression during the torpor-arousal cycle of a mammalian hibernator, the 13-lined ground squirrel
In this study, we profiled the expression of 117 conserved microRNAs in the heart, muscle, and liver of the 13-lined ground squirrel (Ictidomys tridecemlineatus) across four stages of the torpor-arousal cycle (euthermia, early torpor, late torpor, and interbout arousal) by real-time PCR. We found significant differential regulation of numerous microRNAs that were both tissue specific and torpor stage specific. Among the most significant regulated microRNAs was miR-208b, a positive regulator of muscle development that was found to be upregulated by fivefold in the heart during late torpor (13-fold during arousal), while dec...
Source: Physiological Genomics - May 31, 2016 Category: Genetics & Stem Cells Authors: Wu, C.-W., Biggar, K. K., Luu, B. E., Szereszewski, K. E., Storey, K. B. Tags: General Interest Source Type: research
Functional phosphorylation sites in cardiac myofilament proteins are evolutionarily conserved in skeletal myofilament proteins
Protein phosphorylation plays an important role in regulating cardiac contractile function, but phosphorylation is not thought to play a regulatory role in skeletal muscle. To examine how myofilament phosphorylation arose in the human heart, we analyzed the amino acid sequences of 25 cardiac phosphorylation sites in animals ranging from fruit flies to humans. These analyses indicated that of the 25 human phosphorylation sites examined, 11 have been conserved across vertebrates and four have been sporadically present in vertebrates. Furthermore, all 11 of the cardiac sites found across vertebrates were present in skeletal m...
Source: Physiological Genomics - May 31, 2016 Category: Genetics & Stem Cells Authors: Gross, S. M., Lehman, S. L. Tags: Genome-Wide Assocation Studies and Function Source Type: research
FABP4 is a leading candidate gene associated with residual feed intake in growing Holstein calves
Ecological and economic concerns drive the need to improve feed utilization by domestic animals. Residual feed intake (RFI) is one of the most acceptable measures for feed efficiency (FE). However, phenotyping RFI-related traits is complex and expensive and requires special equipment. Advances in marker technology allow the development of various DNA-based selection tools. To assimilate these technologies for the benefit of RFI-based selection, reliable phenotypic measures are prerequisite. In the current study, we identified single nucleotide polymorphisms (SNPs) associated with RFI phenotypic consistency across different...
Source: Physiological Genomics - April 30, 2016 Category: Genetics & Stem Cells Authors: Cohen-Zinder, M., Asher, A., Lipkin, E., Feingersch, R., Agmon, R., Karasik, D., Brosh, A., Shabtay, A. Tags: Genome-Wide Assocation Studies and Function Source Type: research
Human cerebrospinal fluid microRNA: temporal changes following subarachnoid hemorrhage
Aneurysmal subarachnoid hemorrhage (aSAH) is a devastating form of hemorrhagic stroke with 30-day mortality between 33 and 45%. Delayed cerebral ischemia (DCI) is the chief cause of morbidity and mortality in patients who survive the initial aSAH. DCI accounts for almost 50% of deaths in patients surviving to treatment of the ruptured aneurysm. The mechanisms for brain injury after aSAH and the brain's response to this injury are not fully understood in humans. MicroRNAs (miRs) are 22- to 25-nucleotide single-stranded RNA molecules that inhibit the expression of specific messenger RNA targets. In this work, miR profiling o...
Source: Physiological Genomics - April 30, 2016 Category: Genetics & Stem Cells Authors: Powers, C. J., Dickerson, R., Zhang, S. W., Rink, C., Roy, S., Sen, C. K. Tags: MicroRNA Source Type: research
Dynamic macrophage polarization-specific miRNA patterns reveal increased soluble VEGF receptor 1 by miR-125a-5p inhibition
Dynamic, epigenetic mechanisms can regulate macrophage phenotypes following exposure to different stimulating conditions and environments. However, temporal patterns of microRNAs (miRNAs or miRs) across multiple macrophage polarization phenotypes have not been defined. We determined miRNA expression in bone marrow-derived murine macrophages over multiple time points (0.5, 1, 3, 24 h) following exposure to cytokines and/or LPS. We hypothesized that dynamic changes in miRNAs regulate macrophage phenotypes. Changes in macrophage polarization markers were detected as early as 0.5 and as late as 24 h; however, robust responses ...
Source: Physiological Genomics - April 30, 2016 Category: Genetics & Stem Cells Authors: Melton, D. W., Lei, X., Gelfond, J. A. L., Shireman, P. K. Tags: Physiological Genomics of Cell States and Their Regulation and Single Cell Genomics Source Type: research
Age-dependent differences in microglial responses to systemic inflammation are evident as early as middle age
Whereas age increases microglial inflammatory activities and impairs their ability to effectively regulate their immune response, it is unclear at what age these exaggerated responses begin. We tested the hypotheses that augmented microglial responses to inflammatory challenge are present as early as middle age and that repeated stimulation of primed microglia in vivo would reveal microglial senescence. Microglial gene expression was investigated in a mouse model of repeated systemic inflammation induced by intraperitoneal injection of bacterial lipopolysaccharide (LPS). Following LPS, microglia from middle-aged mice (9&nd...
Source: Physiological Genomics - April 30, 2016 Category: Genetics & Stem Cells Authors: Nikodemova, M., Small, A. L., Kimyon, R. S., Watters, J. J. Tags: Physiological and Genetic Control of Neural Function Source Type: research
Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region
Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlat...
Source: Physiological Genomics - April 30, 2016 Category: Genetics & Stem Cells Authors: Staiger, E. A., Al Abri, M. A., Pflug, K. M., Kalla, S. E., Ainsworth, D. M., Miller, D., Raudsepp, T., Sutter, N. B., Brooks, S. A. Tags: Call for Papers: Systems Biology and Polygenic Traits Source Type: research
MicroRNA expression profiling in skeletal muscle reveals different regulatory patterns in high and low responders to resistance training
In this study, we investigated how RE affects miRNA expression and whether the variability of muscle hypertrophy to RE training may be attributed to differential miRNA regulation in the skeletal muscle. To screen high and low responders to RE, we had 18 young men perform arm curl exercise training. After screening, all the men performed 12 wk of lower body RE training, but only the high or low responders participated in the acute RE test before training. Muscle biopsies were obtained from the vastus lateralis muscle at baseline, 3 h after acute RE, and after the training period. Total RNA was extracted from the skeletal mu...
Source: Physiological Genomics - March 31, 2016 Category: Genetics & Stem Cells Authors: Ogasawara, R., Akimoto, T., Umeno, T., Sawada, S., Hamaoka, T., Fujita, S. Tags: Systems Biology of Exercise Source Type: research
Endometrial gene expression in high- and low-fertility heifers in the late luteal phase of the estrous cycle and a comparison with midluteal gene expression
This study highlights some of the pathways and mechanisms underpinning late luteal bovine endometrial physiology and endometrial-related conception rate variance. (Source: Physiological Genomics)
Source: Physiological Genomics - March 31, 2016 Category: Genetics & Stem Cells Authors: Killeen, A. P., Diskin, M. G., Morris, D. G., Kenny, D. A., Waters, S. M. Tags: Omics Technologies and Applications Source Type: research
Peptide affinity analysis of proteins that bind to an unstructured NH2-terminal region of the osmoprotective transcription factor NFAT5
NFAT5 is an osmoregulated transcription factor that particularly increases expression of genes involved in protection against hypertonicity. Transcription factors often contain unstructured regions that bind co-regulatory proteins that are crucial for their function. The NH2-terminal region of NFAT5 contains regions predicted to be intrinsically disordered. We used peptide aptamer-based affinity chromatography coupled with mass spectrometry to identify protein preys pulled down by one or more overlapping 20 amino acid peptide baits within a predicted NH2-terminal unstructured region of NFAT5. We identify a total of 467 uni...
Source: Physiological Genomics - March 31, 2016 Category: Genetics & Stem Cells Authors: DuMond, J. F., Ramkissoon, K., Zhang, X., Izumi, Y., Wang, X., Eguchi, K., Gao, S., Mukoyama, M., Burg, M. B., Ferraris, J. D. Tags: Physiological Genomics of Cell States and Their Regulation and Single Cell Genomics Source Type: research
Gene expression profiling of the effects of organic dust in lung epithelial and THP-1 cells reveals inductive effects on inflammatory and immune response genes
The intensification and concentration of animal production operations expose workers to high levels of organic dusts in the work environment. Exposure to organic dusts is a risk factor for the development of acute and chronic respiratory symptoms and diseases. Lung epithelium plays important roles in the control of immune and inflammatory responses to environmental agents to maintain lung health. To better understand the effects of organic dust on lung inflammatory responses, we characterized the gene expression profiles of A549 alveolar and Beas2B bronchial epithelial and THP-1 monocytic cells influenced by exposure to po...
Source: Physiological Genomics - March 31, 2016 Category: Genetics & Stem Cells Authors: Boggaram, V., Loose, D. S., Gottipati, K. R., Natarajan, K., Mitchell, C. T. Tags: Genomic and ' Polyomic Studies of Cardiovascular and Inflammatory Diseases Source Type: research
Mitochondrial polymerase gamma dysfunction and aging cause cardiac nuclear DNA methylation changes
We examined the relationship between mitochondrial dysfunction and cardiac epigenetic DNA methylation changes in both young and old mice. We used genetically engineered C57Bl/6 mice transgenic for a cardiac-specific mutant of the mitochondrial polymerase- (termed Y955C). Y955C mice undergo left ventricular hypertrophy (LVH) at a young age (~94 days old), and LVH decompensated to CHF at old age (~255 days old). Results found 95 genes differentially expressed as a result of Y955C expression, while 4,452 genes were differentially expressed as a result of aging hearts. Moreover, cardiac DNA methylation patterns differed betwee...
Source: Physiological Genomics - March 31, 2016 Category: Genetics & Stem Cells Authors: Koczor, C. A., Ludlow, I., Fields, E., Jiao, Z., Ludaway, T., Russ, R., Lewis, W. Tags: Genomic and ' Polyomic Studies of Cardiovascular and Inflammatory Diseases Source Type: research
Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells
Region and cell-type specific differences in the molecular make up of colon epithelial cells have been reported. Those differences may underlie the region-specific characteristics of common colon epithelial diseases such as colorectal cancer and inflammatory bowel disease. DNA methylation is a cell-type specific epigenetic mark, essential for transcriptional regulation, silencing of repetitive DNA and genomic imprinting. Little is known about any region-specific variations in methylation patterns in human colon epithelial cells. Using purified epithelial cells and whole biopsies (n = 19) from human subjects, we generated e...
Source: Physiological Genomics - March 31, 2016 Category: Genetics & Stem Cells Authors: Barnicle, A., Seoighe, C., Golden, A., Greally, J. M., Egan, L. J. Tags: Call for Papers: Epigenetics and Epigenomics Source Type: research
Biosynthesis of milk fat, protein, and lactose: roles of transcriptional and posttranscriptional regulation
The demand for high-quality milk is increasing worldwide. The efficiency of milk synthesis can be improved by taking advantage of the accumulated knowledge of the transcriptional and posttranscriptional regulation of genes coding for proteins involved in the synthesis of fat, protein, and lactose in the mammary gland. Research in this area is relatively new, but data accumulated in the last 10 years provide a relatively clear picture. Milk fat synthesis appears to be regulated, at least in bovines, by an interactive network between SREBP1, PPAR, and LXRα, with a potential role for other transcription factors, such as...
Source: Physiological Genomics - March 31, 2016 Category: Genetics & Stem Cells Authors: Osorio, J. S., Lohakare, J., Bionaz, M. Tags: Nutrient Gene Interaction Source Type: research
