bluuebunny/crossref_metadata_2025 huggingface dataset:
Concurrent exercise prevents high-fat-diet-induced macrovesicular hepatic steatosis
Authors: Gauthier Marie-Soleil , Couturier Karine , Latour Jean-Gilles , Lavoie Jean-Marc
Published: March 2015

The purpose of the present study was to assess the effect of an exercise training program conducted concurrently with a high-fat (HF)-diet regimen on the induction of hepatic steatosis. Two groups of rats were fed either a standard (SD) or a HF (40% kcal) diet for 8 wk and were additionally assigned either to a sedentary (Sed) or a treadmill-trained (TR) group. Training (5 days/wk) was initiated at the same time as the HF diet and was progressively increased, reaching 60 min at 26 m/min, 10% grade, for the last 4 wk. At the end of the 8-wk period, HF-Sed rats exhibited ∼72% higher liver triacylglycerol concentration than SD-Sed rats (means ± SE: 17.15 ± 1.5 vs. 9.98 ± 1.0 mg/g; P < 0.01). Histological quantification of lipid infiltration, with the use of an image analysis computing system, revealed that, although fat was mainly stored as microvesicles (<1 μm2), the HF-diet-induced hepatic steatosis occurred via the accumulation of macrovesicles (>1 μm2). Concurrent exercise training completely prevented the HF-diet-induced hepatic steatosis. The surface area of liver parenchyma infiltrated by lipid vacuoles was similar in HF-TR as in SD-Sed rats (26.4 ± 1.8 vs. 29.3 ± 5.9 × 103μm2/200,000 μm2of liver parenchyma, respectively; P> 0.05). The different states of liver lipid infiltration after the HF diet in Sed and TR rats were associated with similar changes in plasma free fatty acids and glycerol, as well as with similar changes in fat pad weights, but not with plasma triacylglycerol levels. It is concluded that, after a HF-diet regimen of 8 wk in rats, hepatic steatosis occurs primarily via the accumulation of lipid as macrovesicles. Exercise training pursued at the same time completely prevents the HF-diet-induced macrovesicular hepatic steatosis.
Content of intramyocellular lipids derived by electron microscopy, biochemical assays, and1H-MR spectroscopy
Authors: Howald Hans , Boesch Chris , Kreis Roland , Matter Sibylle , Billeter Rudolf , Essen-Gustavsson Birgitta , Hoppeler Hans
Published: March 2015

Three different methods to determine intramyocellular lipid (IMCL) contents in human skeletal muscle have been compared.1H-magnetic resonance spectroscopy (MRS) was evaluated against electron microscopic morphometry and biochemical assays of biopsy samples from m. tibialis anterior of 10 healthy subjects. The results of1H-MRS and morphometry were strongly correlated, proving the validity of the1H-MRS results for the noninvasive determination of IMCL. Biochemical assays yielded results that did not significantly correlate with the results of the other methods. When IMCL levels obtained from the three methods are expressed in common units, it was found that1H-MRS yielded IMCL average levels that were 1.8 times lower than those found by morphometry. Potential reasons for the discrepancy are discussed. It is expected that1H-MRS will be suitable to replace invasive techniques for IMCL determination, whenever noninvasiveness is crucial, e.g., for repeated investigations in studies of substrate recruitment and recovery in exercise.
Steroid receptor concentration in aged rat hindlimb muscle: effect of anabolic steroid administration
Authors: Carson James A. , Lee Won Jun , McClung Joseph , Hand Gregory A.
Published: March 2015

Skeletal muscle is a target of anabolic steroid action; however, anabolic steroid's affect on aged skeletal muscle is not well understood. The effect of 4 wk of nandrolone decanoate (ND) administration on hindlimb muscles of 5- and 25-mo-old Fischer 344/Brown Norway rats was examined. ND (6 mg/kg body wt) was injected every 7th day for 4 wk. Controls received an oil injection. ND significantly reduced 25-mo-old rat perirenal fat pad mass by 30%. Soleus (Sol) and plantaris (Plan) muscle-to-body weight ratios were reduced in 25-mo-old rats. ND did not affect Sol or Plan muscle-to-body weight ratios at either age. Sol DNA concentration was reduced by 25% in 25-mo-old rats, and ND increased it to 12% greater than 5-mo-old rats. ND did not affect Plan DNA content. Sol androgen receptor (AR) protein in 25-mo-old rats was reduced to 35% of 5-mo-old values. ND increased AR protein by 900% in 25-mo-old rat Sol. Plan AR concentration was not affected by aging but was induced by ND in both age groups. Aging or ND treatment did not affect glucocorticoid receptor levels in either muscle. These data demonstrate that fast- and slow-twitch rat hindlimb muscles differ in their response to aging and ND therapy.
Neonatal sex steroids affect ventilatory responses to aspartic acid and NMDA receptor subunit 1 in rats
Authors: Shi Yijiang , Schlenker Evelyn H.
Published: March 2015

We hypothesized that administration of estradiol benzoate to males and testosterone propionate to female neonatal rat pups alters sex-specific ventilatory responses to aspartic acid with correspondent changes in N-methyl-d-aspartate receptor subunit 1 (NR1) expression determined by Western blot in specific brain regions. One-day-old rat pups received estradiol benzoate, testosterone propionate, or vehicle and were studied at weanling and adulthood. Different groups had distinct patterns of changes in tidal volume and frequency of breathing after aspartic acid administration. NR1 expression in hypothalamus was altered by age, sex, and treatment. Medullary and pontine NR1 expression correlated with baseline ventilation and magnitude of the ventilatory response to aspartic acid in some groups. Thus 1) tidal volume and breathing frequency patterns in response to aspartic acid are gender, age, and treatment dependent; 2) sex, age, and exogenous steroid hormones affect NR1 expression primarily in the hypothalamus; and 3) there is correlation between NR1 expression in pons and medulla with ventilatory parameters.
Exercise-induced bronchodilation in natural and induced asthma: effects on ventilatory response and performance
Authors: Crimi Emanuele , Pellegrino Riccardo , Smeraldi Attilio , Brusasco Vito
Published: March 2015

We studied whether bronchodilatation occurs with exercise during the late asthmatic reaction (LAR) to allergen ( group 1, n = 13) or natural asthma (NA; group 2, n = 8) and whether this is sufficient to preserve maximum ventilation (V˙e max), oxygen consumption (V˙o 2 max), and exercise performance (W˙max ). In group 1, partial forced expiratory flow at 30% of resting forced vital capacity increased during exercise, both at control and LAR. W˙max was slightly reduced at LAR, whereasV˙e max, tidal volume, breathing frequency, and V˙o 2 max were preserved. Functional residual capacity and end-inspiratory lung volume were significantly larger at LAR than at control. In group 2, partial forced expiratory flow at 30% of resting forced vital capacity increased greatly with exercise during NA but did not attain control values after appropriate therapy. Compared with control, W˙max was slightly less during NA, whereas V˙o 2 maxand V˙e max were similar. Functional residual capacity, but not end-inspiratory lung volume at maximum load, was significantly greater than at control, whereas tidal volume decreased and breathing frequency increased. In conclusion, remarkable exercise bronchodilation occurs during either LAR or NA and allowsV˙e max andV˙o 2 max to be preserved with small changes in breathing pattern and a slight reduction inW˙max.
Altered frequency responses of sympathetic nerve discharge bursts after IL-1β and mild hypothermia
Authors: Kenney M. J. , Blecha F. , Fels R. J. , Morgan D. A.
Published: March 2015

Although interleukin-1β (IL-1β) administration produces nonuniform changes in the level of sympathetic nerve discharge (SND), the effect of IL-1β on the frequency-domain relationships between discharges in different sympathetic nerves is not known. Autospectral and coherence analyses were used to determine the effect of IL-1β and mild hypothermia (60 min after IL-1β, colonic temperature from 38°C to 36°C) on the relationships between renal-interscapular brown adipose tissue (IBAT) and splenic-lumbar sympathetic nerve discharges in chloralose-anesthetized rats. The following observations were made. 1) IL-1β did not alter renal-IBAT coherence values in the 0- to 2-Hz frequency band or at the cardiac frequency (CF). 2) Peak coherence values relating splenic-lumbar discharges at the CF were significantly increased after IL-1β and during hypothermia. 3) Hypothermia after IL-1β significantly reduced the coupling (0–2 Hz and CF) between renal-IBAT but not splenic-lumbar SND bursts. 4) Combining IL-1β and mild hypothermia had a greater effect on renal-IBAT SND coherence values than did mild hypothermia alone. These data demonstrate functional plasticity in sympathetic neural circuits and suggest complex relationships between immune products and SND regulation.
Invited Review: Heat shock proteins: modifying factors in physiological stress responses and acquired thermotolerance
Authors: Kregel Kevin C.
Published: March 2015

Cells from virtually all organisms respond to a variety of stresses by the rapid synthesis of a highly conserved set of polypeptides termed heat shock proteins (HSPs). The precise functions of HSPs are unknown, but there is considerable evidence that these stress proteins are essential for survival at both normal and elevated temperatures. HSPs also appear to play a critical role in the development of thermotolerance and protection from cellular damage associated with stresses such as ischemia, cytokines, and energy depletion. These observations suggest that HSPs play an important role in both normal cellular homeostasis and the stress response. This mini-review examines recent evidence and hypotheses suggesting that the HSPs may be important modifying factors in cellular responses to a variety of physiologically relevant conditions such as hyperthermia, exercise, oxidative stress, metabolic challenge, and aging.
Time dependence of recruitment and derecruitment in the lung: a theoretical model
Authors: Bates Jason H. T. , Irvin Charles G.
Published: March 2015

Recruitment and derecruitment (R/D) of air spaces within the lung is greatly enhanced in lung injury and is thought to be responsible for exacerbating injury during mechanical ventilation. There is evidence to suggest that R/D is a time-dependent phenomenon. We have developed a computer model of the lung consisting of a parallel arrangement of airways and alveolar units. Each airway has a critical pressure (Pcrit) above which it tends to open and below which it tends to close but at a rate determined by how far pressure is from Pcrit. With an appropriate distribution of Pcrit and R/D velocity characteristics, the model able to produce realistic first and second pressure-volume curves of a lung inflated from an initially degassed state. The model also predicts that lung elastance will increase transiently after a deep inflation to a degree that increases as lung volume decreases and as the lung becomes injured. We conclude that our model captures the time-dependent mechanical behavior of the lung due to gradual R/D of lung units.
Metabolic Myopathy in Heart Failure
Authors: Ventura-Clapier Renée , De Sousa Elvira , Veksler Vladimir
Published: March 2015

Heart failure is a syndrome that also affects the periphery. Exercise intolerance and early fatigue seem to be linked in part to intrinsic alterations of skeletal muscle with decreases in both the production of ATP by mitochondria and the transfer of energy through the phosphotransfer kinases.
Small G Proteins as Novel Therapeutic Targets in Cardiovascular Medicine
Authors: Barandier Christine , Ming Xiu-Fen , Yang Zhihong
Published: March 2015

Small G proteins are implicated in regulation of endothelial function, smooth muscle cell contraction, proliferation, and migration, as well as cardiomyocyte hypertrophy. Targeting small G proteins and their downstream signaling could constitute promising therapeutic approaches in cardiovascular disorders such as atherosclerosis, restenosis, hypertension, vasospasm, and cardiac hypertrophy.
From the Nucleus Toward the Cell Periphery: a Guided Tour for mRNAs
Authors: Jockusch Brigitte M. , Hüttelmaier Stefan , Illenberger Susanne
Published: March 2015

RNA processing, directed transport along cytoskeletal tracks, and site-specific translation of mRNA at the cell periphery are considered discrete steps in the generation of microfilament-membrane adhesion complexes. A recently identified member of the heterogeneous nuclear ribonucleoprotein family, raver1, may couple these steps and contribute to the assembly and maintenance of these structures.
Central Nervous System Processing of Human Visceral Pain in Health and Disease
Authors: Hobson Anthony R. , Aziz Qasim
Published: March 2015

To understand the pathophysiology of anomalous pain in functional gastrointestinal disorders, we must increase our understanding of how the central nervous system processes visceral pain. Over the past decade, novel application of functional brain imaging and electrophysiological techniques has given us the opportunity to study these processes in humans, and this review summarizes the current body of knowledge.
Mitochondrial Regulation of Apoptosis
Authors: Mayer Bernd , Oberbauer Rainer
Published: March 2015

Mitochondria play a central part in cellular survival and apoptotic death. These processes are highly regulated by pro- and antiapoptotic Bcl-2 superfamily members. A key feature within apoptosis cascades is disruption of mitochondrial transmembrane potential and apoptogenic protein release, caused by opening of the permeability transition pore (PT). New data, however, indicate that mitochondrial apoptosis may occur without PT involvement.
Pulmonary Surfactant: The Key to the Evolution of Air Breathing
Authors: Daniels Christopher B. , Orgeig Sandra
Published: March 2015

Pulmonary surfactant controls the surface tension at the air-liquid interface within the lung. This system had a single evolutionary origin that predates the evolution of the vertebrates and lungs. The lipid composition of surfactant has been subjected to evolutionary selection pressures, particularly temperature, throughout the evolution of the vertebrates.
Patterns of global gene expression in rat skeletal muscle during unloading and low-intensity ambulatory activity
Authors: Bey Lionel , Akunuri Nagabhavani , Zhao Po , Hoffman Eric P. , Hamilton Deborah G. , Hamilton Marc T.
Published: March 2015

Physical inactivity and unloading lead to diverse skeletal muscle alterations. Our goal was to identify the genes in skeletal muscle whose expression is most sensitive to periods of unloading/reduced physical activity and that may be involved in triggering initial responses before phenotypic changes are evident. The ability of short periods of physical activity/loading as an effective countermeasure against changes in gene expression mediated by inactivity was also tested. Affymetrix microarrays were used to compare mRNA levels in the soleus muscle under three experimental treatments ( n = 20–29 rats each): 12-h hindlimb unloading (HU), 12-h HU followed by 4 h of intermittent low-intensity ambulatory and postural activity (4-h reloading), and control (with ambulatory and postural activity). Using a combination of criteria, we identified a small set of genes (∼1% of 8,738 genes on the array or 4% of significant expressed genes) with the most reproducible and largest responses to altered activity. Analysis revealed a coordinated regulation of transcription for a large number of key signaling proteins and transcription factors involved in protein synthesis/degradation and energy metabolism. Most (21 of 25) of the gene expression changes that were downregulated during HU returned at least to control levels during the reloading. In surprising contrast, 27 of 38 of the genes upregulated during HU remained significantly above control, but most showed trends toward reversal. This introduces a new concept that, in general, genes that are upregulated during unloading/inactivity will be more resistant to periodic reloading than those genes that are downregulated. This study reveals genes that are the most sensitive to loading/activity in rat skeletal muscle and indicates new targets that may initiate muscle alterations during inactivity.
Genomic analysis of immediate/early response to shear stress in human coronary artery endothelial cells
Authors: Peters D. G. , Zhang X.-C. , Benos P. V. , Heidrich-O’Hare E. , Ferrell R. E.
Published: March 2015

The involvement of shear stress in the pathogenesis of vascular disease has motivated efforts to define the endothelial cell response to applied shear stress in vitro. A central question has been the mechanisms by which endothelial cells perceive and respond to changes in fluid flow. We have utilized cDNA microarrays to characterize the immediate/early genomic response to applied laminar shear stress (LSS) in primary cultures of human coronary artery endothelial cells (HCAECs). Cells were exposed, in a parallel plate flow chamber, to 0, 15, or 45 dyn/cm2LSS for 1 h, and gene expression profiles were determined using human GEM1 cDNA microarrays. We find that a high proportion of LSS-responsive genes are transcription factors, and these are related by their involvement in growth arrest. These likely play a central role in the reprogramming of endothelial homeostasis following the switch from a static to a shear-stressed environment. LSS-responsive genes were also found to encode factors involved in vasoreactivity, signal transduction, antioxidants, cell cycle-associated genes, and markers of cytoskeletal function and dynamics.
Complexity and species variation of the kidney-type glutaminase gene
Authors: Porter L. David , Ibrahim Hend , Taylor Lynn , Curthoys Norman P.
Published: March 2015

Increased expression of rat kidney-type glutaminase (KGA) during metabolic acidosis results from selective mRNA stabilization. This process is mediated by an 8-base AU-sequence that functions as a pH-response element (pHRE). LLC-PK1-FBPase+cells, a pH-responsive porcine kidney cell line, express four distinct GA mRNAs. RNase H mapping indicated that three of the GA mRNAs are generated by use of alternative polyadenylation sites and are homologs of the rat KGA mRNA, while the fourth contains a different COOH-terminal coding and 3′-untranslated sequence. PCR cloning and sequencing established that the latter GA mRNA is the homolog of the human GAC mRNA. A rat GAC cDNA was also cloned from a rat kidney library. The 3′-untranslated regions of the GAC mRNAs, but not the porcine or human KGA mRNAs, contain identifiable pHREs. The human KGA gene spans 82 kb and is composed of 19 exons. The unique sequence from the hGAC cDNA is contained in a single exon. Thus in humans, alternative splicing of the initial transcript could produce two GA mRNAs, only one of which may be increased during acidosis.
Microarray analysis of global changes in gene expression during cardiac myocyte differentiation
Authors: Peng Chang-Fu , Wei Yi , Levsky Jeffrey M. , McDonald Thomas V. , Childs Geoffrey , Kitsis Richard N.
Published: March 2015

Significant progress has been made in defining pathways that mediate the formation of the mammalian heart. Little is known, however, about the genetic program that directs the differentiation of cardiac myocytes from their precursor cells. A major hindrance to this kind of investigation has been the absence of an appropriate cell culture model of cardiac myocyte differentiation. Recently, a subline of P19 cells (P19CL6) was derived that, following dimethyl sulfoxide (DMSO) treatment, differentiate efficiently over 10 days into spontaneously beating cardiac myocytes. We demonstrate that these cells are indeed cardiac myocytes as they express cell type-specific markers and exhibit electrophysiological properties indicative of cardiac myocytes. The requirement for DMSO stimulation in this paradigm was shown to be limited to the first 4 days, suggesting that critical events in the differentiation process occur over this interval. To uncover relationships among known genes and identify novel genes that mediate cardiac myocyte differentiation, a detailed time course of changes in global gene expression was carried out using cDNA microarrays. In addition to the activation of genes encoding cardiac transcription factors and structural proteins, increases were noted in the expression of multiple known genes and expressed sequence tags (ESTs). Analysis of the former suggested the involvement of a variety of signaling pathways in cardiac myocyte differentiation. The 16 ESTs whose expression was increased during the early, stimulus-dependent phase of cardiac myocyte differentiation may be novel regulators of this process. Thus this first report of large-scale changes in gene expression during cardiac myocyte differentiation has delineated relationships among the expression patterns of known genes and identified a number of novel genes that merit further study.
Phenotypic differences in the hemodynamic response during REM sleep in six strains of inbred mice
Authors: Campen Matthew J. , Tagaito Yugo , Jenkins Todd P. , Smith Philip L. , Schwartz Alan R. , O’Donnell Christopher P.
Published: March 2015

The pattern of cardiovascular changes that occur at nighttime can have an impact on morbidity and mortality. Rapid-eye-movement (REM) sleep, in particular, represents a period of increased risk due to marked cardiovascular instability. We hypothesized that genetic differences between inbred strains of mice would affect the phenotypic expression of cardiovascular responses that occur in REM sleep. We monitored polysomnography and arterial blood pressure (PSA) simultaneously in six inbred strains of mice as they naturally cycled through sleep/wake states. Two strains elevated their PSA above non-REM (NREM) levels for 57.9 ± 6.6% (BALB/cJ) and 51.8 ± 8.4% (DBA/2J) of the REM period and exhibited a significant ( P < 0.05) number of PSA surges greater than 10 mmHg (0.78 ± 0.36 surges/min for BALB/cJ; 0.63 ± 0.13 surges/min for DBA/2J). Despite similar PSA responses, the DBA/2J strain exhibited a decreased heart rate and the BALB/cJ strain exhibited an increased heart rate during REM sleep. The four other strains (A/J, C57BL/6J, C3H/HeJ, and CBA/J) exhibited a significant hypotensive response associated with no change in heart rate in three of the strains and a significant decrease in heart rate in the A/J strain. The overall variability in PSA during REM sleep was significantly greater in the C3H/HeJ strain (26.8 ± 2.0 mmHg; P < 0.0125) compared with the other five strains. We conclude that genetic background contributes to the magnitude, variability, and arterial baroreceptor buffering capacity of cardiovascular responses during REM sleep.
In silico data filtering to identify new angiogenesis targets from a large in vitro gene profiling data set
Authors: Gerritsen Mary E. , Soriano Robert , Yang Suya , Ingle Gladys , Zlot Constance , Toy Karen , Winer Jane , Draksharapu Aparna , Peale Franklin , Wu Thomas D. , Williams P. Mickey
Published: March 2015

The objective of this study was to use gene expression data from well-defined cell culture models, in combination with expression data from diagnostic samples of human diseased tissues, to identify potential therapeutic targets and markers of disease. Using Affymetrix oligonucleotide array technology, we identified a common profile of genes upregulated during endothelial morphogenesis into tubelike structures in three in vitro models of angiogenesis. Rigorous data selection criteria were used to identify a list of over 1,000 genes whose expression was increased more than twofold over baseline at either 4, 8, 24, 40 or 50 h. To further refine and prioritize this list, we used standard bioinformatic algorithms to identify potential transmembrane and secreted proteins. We then overlapped this gene set with genes upregulated in colon tumors vs. normal colon, resulting in a subset of 128 genes in common with our endothelial list. We removed from this list those genes expressed in 6 different colon tumor lines, resulting in a list of 24 putative, vascular-specific angiogenesis-associated genes. Three genes, gp34, stanniocalcin-1 (STC-1), and GA733-1, were expressed at levels 10-fold or more in colon tumors compared with normal mucosa. We validated the vascular-specific expression of one of these genes, STC-1, by in situ hybridization. The ability to combine in vitro and in vivo data sets should permit one to identify putative angiogenesis target genes in various tumors, chronic inflammation, and other disorders where therapeutic manipulation of angiogenesis is a desirable treatment modality.
QTL analysis of self-selected macronutrient diet intake: fat, carbohydrate, and total kilocalories
Authors: Smith Richards Brenda K. , Belton Brenda N. , Poole Angela C. , Mancuso James J. , Churchill Gary A. , Li R. , Volaufova Julia , Zuberi Aamir , York Barbara
Published: March 2015

The present study investigated the inheritance of dietary fat, carbohydrate, and kilocalorie intake traits in an F2population derived from an intercross between C57BL/6J (fat-preferring) and CAST/EiJ (carbohydrate-preferring) mice. Mice were phenotyped for self-selected food intake in a paradigm which provided for 10 days a choice between two macronutrient diets containing 78/22% of energy as a composite of either fat/protein or carbohydrate/protein. Quantitative trait locus (QTL) analysis identified six significant loci for macronutrient intake: three for fat intake on chromosomes (Chrs) 8 ( Mnif1), 18 ( Mnif2), and X ( Mnif3), and three for carbohydrate intake on Chrs 17 ( Mnic1), 6 ( Mnic2), and X ( Mnic3). An absence of interactions among these QTL suggests the existence of separate mechanisms controlling the intake of fat and carbohydrate. Two significant QTL for cumulative kilocalorie intake, adjusted for baseline body weight, were found on Chrs 17 ( Kcal1) and 18 ( Kcal2). Without body weight adjustment, another significant kcal locus appeared on distal Chr 2 ( Kcal3). These macronutrient and kilocalorie QTL, with the exception of loci on Chrs 8 and X, encompassed chromosomal regions influencing body weight gain and adiposity in this F2population. These results provide new insight into the genetic basis of naturally occurring variation in nutrient intake phenotypes.
A novel SCN5A mutation associated with long QT-3: altered inactivation kinetics and channel dysfunction
Authors: Rivolta Ilaria , Clancy Colleen E. , Tateyama Michihiro , Liu Huajun , Priori Silvia G. , Kass Robert S.
Published: March 2015

Mutations in the gene ( SCN5A) encoding the α-subunit of the cardiac Na+ channel cause congenital long QT syndrome (LQT-3). Here we describe a novel LQT-3 mutation I1768V (I1768V) located in the sixth transmembrane spanning segment of domain IV. This mutation is unusual in that it is located within a transmembrane spanning domain and does not promote the typically observed sustained inward current corresponding to a gain of channel function (bursting). Rather, I1768V increases the rate of recovery from inactivation and increases the channel availability, observed as a positive shift of the steady-state inactivation curve (+7.6 mV). Using a Markovian model of the cardiac Na+ channel, we simulated these changes in gating behavior and demonstrated that a small increase in the rate of recovery from inactivation is sufficient to explain all of the experimentally observed current changes. The effect of these alterations in channel gating results in an increase in window current that may act to disrupt cardiac repolarization.
Statistical evaluation of SAGE libraries: consequences for experimental design
Authors: Ruijter Jan M. , Van Kampen Antoine H. C. , Baas Frank
Published: March 2015

Since the introduction of serial analysis of gene expression (SAGE) as a method to quantitatively analyze the differential expression of genes, several statistical tests have been published for the pairwise comparison of SAGE libraries. Testing the difference between the number of specific tags found in two SAGE libraries is hampered by the fact that each SAGE library is only one measurement: the necessary information on biological variation or experimental precision is not available. In the currently available tests, a measure of this variance is obtained from simulation or based on the properties of the tag distribution. To help the user of SAGE to decide between these tests, five different pairwise tests have been compared by determining the critical values, that is, the lowest number of tags that, given an observed number of tags in one library, needs to be found in the other library to result in a significant P value. The five tests included in this comparison are SAGE300, the tests described by Madden et al. ( Oncogene 15: 1079–1085, 1997) and by Audic and Claverie ( Genome Res 7: 986–995, 1997), Fisher’s Exact test, and the Z test, which is equivalent to the chi-squared test. The comparison showed that, for SAGE libraries of equal as well as different size, SAGE300, Fisher’s Exact test, Z test, and the Audic and Claverie test have critical values within 1.5% of each other. This indicates that these four tests will give essentially the same results when applied to SAGE libraries. The Madden test, which can only be used for libraries of similar size, is, with 25% higher critical values, more conservative, probably because the variance measure in its test statistic is not appropriate for hypothesis testing. The consequences for the choice of SAGE library sizes are discussed.
Exercise-induced changes in insulin action are associated with ACE gene polymorphisms in older adults
Authors: Dengel Donald R. , Brown Michael D. , Ferrell Robert E. , Reynolds Thomas H. , Supiano Mark A.
Published: March 2015

We evaluated the association between insulin resistance and the angiotensin-converting enzyme (ACE) insertion (I)/deletion (D) gene polymorphism in a group of older hypertensive subjects (63 ± 1 yr, n = 35) before and after a 6-mo aerobic exercise program (AEX). Insulin sensitivity index (SI), assessed by the frequently sampled intravenous glucose tolerance test, was significantly ( P = 0.0001) increased following AEX. In addition, there was a significant ( P = 0.001) interaction between AEX and ACE genotype. SI increased significantly ( P < 0.05) more in those with the II (2.5 ± 0.8 μU × 10−4 · min−1 · ml−1) ACE genotype compared with both the DD and ID (0.7 ± 0.1 and 0.7 ± 0.2 μU × 10−4 · min−1 · ml−1, respectively) ACE genotypes. Similarly, there was a significant ( P = 0.036) decrease in the acute insulin response to glucose (AIRG) and a significant ( P = 0.05) interaction between AEX and ACE genotype. AIRG decreased significantly ( P < 0.05) more in those with the II (−17.6 ± 5.6 mU/ml) ACE genotype compared with both the DD and ID (−1.4 ± 6.2 and −3.6 ± 2.5 mU/ml) ACE genotypes. In conclusion, we demonstrated that those older hypertensives with the ACE II genotype have the greatest improvement in insulin action following AEX.
Physical exercise and blood pressure with reference to the angiotensinogen M235T polymorphism
Authors: Rauramaa Rainer , Kuhanen Raimo , Lakka Timo A. , Väisänen Sari B. , Halonen Pirjo , Alén Markku , Rankinen Tuomo , Bouchard Claude
Published: March 2015

We investigated the role of the angiotensinogen (AGT) gene M235T polymorphism in determining blood pressure (BP) response to moderate intensity exercise in a 6-yr randomized controlled trial in 140 middle-aged men. Sitting, supine, and standing blood pressures were measured annually. Of the randomized men, 86% participated in the trial for 6 yr. Submaximal cardiorespiratory fitness increased by 16% in the exercise group. In the M homozygotes, sitting systolic BP decreased by 1.0 mmHg in the exercise but increased by 14.6 mmHg in the reference group ( P = 0.007 for net effect). Sitting and supine diastolic BP decreased by 6.2 and 3.3 mmHg in the exercise but increased by 2.8 and 3.2 mmHg in the reference group ( P = 0.026 and 0.024 for net effects), respectively. Regular moderate intensity exercise attenuates aging-related increase in systolic BP and decreases diastolic BP among the M homozygotes of the AGT gene M235T polymorphism.
Transcriptional profiling and regulation of the extracellular matrix during muscle regeneration
Authors: Goetsch Sean C. , Hawke Thomas J. , Gallardo Teresa D. , Richardson James A. , Garry Daniel J.
Published: March 2015

Muscle regeneration is a complex process requiring the coordinated interaction between the myogenic progenitor cells or satellite cells, growth factors, cytokines, inflammatory components, vascular components and the extracellular matrix (ECM). Previous studies have elegantly described the physiological modulation of the regenerative process in response to muscle injury, but the molecular response that characterizes stages of the repair process remains ill-defined. The recent completion of the Human and Mouse Genome Projects and the advent of technologies such as high-density oligonucleotide array analysis facilitate an expanded analysis of complex processes such as muscle regeneration. In the present study, we define cellular and molecular events that characterize stages of muscle injury and regeneration. Utilization of transcriptional profiling strategies revealed coordinated expression of growth factors [i.e., Tgfb1, Igf1, Egf, chemokine (C-C motif) ligand 6 and 7], the fetal myogenic program (Myod1, Myf5, Myf6), and the biomatrix (procollagen genes, Mmp3, Mmp9, biglycan, periostin) during muscle regeneration. Corroboration of the transcriptional profiling analysis included quantitative real-time RT-PCR and in situ hybridization analyses of selected candidate genes. In situ hybridization studies for periostin [osteoblast-specific factor 2 (fasciclin I-like)] and biglycan revealed that these genes are restricted to mesenchymal derivatives during embryogenesis and are significantly regulated during regeneration of the injured hindlimb skeletal muscle. We conclude that muscle regeneration is a complex process that requires the coordinated modulation of the inflammatory response, myogenic progenitor cells, growth factors, and ECM for complete restoration of muscle architecture.
A splice variant of the G protein β3-subunit implicated in disease states does not modulate ion channels
Authors: Ruiz-Velasco Victor , Ikeda Stephen R.
Published: March 2015

A single-nucleotide polymorphism (C825T) in the GNB3 gene produces an alternative splice variant of the heterotrimeric G protein β3 subunit (Gβ3). Translation of the alternatively spliced mRNA results in a protein product, Gβ3-s, in which 41 amino acids are deleted from Gβ3. Interestingly, previous studies indicate that the C825T allele occurs with a high frequency in patients with certain vascular disorders. However, little information is available regarding the functional role Gβ3-s might play in ion channel modulation. To examine this aspect, Gβ3 or Gβ3-s, along with either Gγ2 or Gγ5, were expressed in rat sympathetic neurons by nuclear microinjection of vector encoding the desired protein. In contrast to Gβ3, expression of Gβ3-s did not modulate N-type Ca2+or G protein-gated inwardly rectifying K+channels. In addition, Gβ3-s did not appear to complex with a pertussis toxin-insensitive mutant of Gαi2or couple to natively expressed α2-adrenergic receptors. Finally, fluorescence resonance energy transfer (FRET) measurements indicated that enhanced yellow fluorescent protein (EYFP)-labeled Gβ3-s does not form a Gβγ heterodimer when coexpressed with enhanced cyan fluorescent protein (ECFP)-labeled Gγ2. Therefore, when expressed in sympathetic neurons, Gβ3-s appears to lack biological activity-hence pathological conditions in patients carrying the homozygous C825T allele may result from a functional knockout of Gβ3.
A smooth response surface algorithm for constructing a gene regulatory network
Authors: Xu Hongquan , Wu Peiru , Wu C. F. Jeff , Tidwell Carl , Wang Yixin
Published: March 2015

A smooth response surface (SRS) algorithm is developed as an elaborate data mining technique for analyzing gene expression data and constructing a gene regulatory network. A three-dimensional SRS is generated to capture the biological relationship between the target and activator-repressor. This new technique is applied to functionally describe triplets of activators, repressors, and targets, and their regulations in gene expression data. A diagnostic strategy is built into the algorithm to evaluate the scores of the triplets so that those with low scores are kept and a regulatory network is constructed based on this information and existing biological knowledge. The predictions based on the identified triplets in two yeast gene expression data sets agree with some experimental data in the literature. It provides a novel model with attractive mathematical and statistical features that make the algorithm valuable for mining expression or concentration information, assist in determining the function of uncharacterized proteins, and can lead to a better understanding of coherent pathways.
Angiotensin II is associated with activation of NF-κB-mediated genes and downregulation of PPARs
Authors: Tham Doris M. , Martin-McNulty Baby , Wang Yi-xin , Wilson Dennis W. , Vergona Ronald , Sullivan Mark E. , Dole William , Rutledge John C.
Published: March 2015

Angiotensin II (ANG II) promotes vascular inflammation through nuclear factor-κB (NF-κB)-mediated induction of pro-inflammatory genes. The role of peroxisome proliferator-activated receptors (PPARs) in modulating vascular inflammation and atherosclerosis in vivo is unclear. The aim of the present study was to examine the effects of ANG II on PPARs and NF-κB-dependent pro-inflammatory genes in the vascular wall in an in vivo model of atherosclerosis and aneurysm formation. Six-month-old male apolipoprotein E-deficient (apoE-KO) mice were treated with ANG II (1.44 mg/kg per day for 30 days). ANG II enhanced vascular inflammation, accelerated atherosclerosis, and induced formation of abdominal aortic aneurysms. These effects of ANG II in the aorta were associated with downregulation of both PPAR-α and PPAR-γ mRNA and protein and an increase in transcription of monocyte chemotactic protein-1 (MCP-1), macrophage-colony stimulating factor (M-CSF), endothelial-selectin (E-selectin), intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1), inducible nitric oxide synthase (iNOS), and cyclooxygenase-2 (COX-2) throughout the entire aorta. ANG II also activated NF-κB with increases in both p52 and p65 NF-κB subunits. In summary, these in vivo results indicate that ANG II, through activation of NF-κB-mediated pro-inflammatory genes, promotes vascular inflammation, leading to acceleration of atherosclerosis and induction of aneurysm in apoE-KO mice. Downregulation of PPAR-α and -γ by ANG II may diminish the anti-inflammatory potential of PPARs, thus contributing to enhanced vascular inflammation.
Transcriptional and physiological responses of HepG2 cells exposed to diethyl maleate: time course analysis
Authors: Casey Warren , Anderson Steve , Fox Tony , Dold Karen , Colton Heidi , Morgan Kevin
Published: March 2015

Expression levels of 767 genes were measured in HepG2 cells at eight time points (0, 0.5, 1, 6, 12, 16, 20, and 24 h) following exposure to the oxidizing agent, diethyl maleate (DEM). DEM treatment caused an immediate and sustained loss of intracellular GSH, with a concomitant increase in GSSG. From 6–12 h after exposure, there was a substantial increase in the percentage of cells undergoing S phase arrest and apoptosis. Expression profiles of ∼90% of the genes fell into one of five clusters generated using hierarchical-clustering software, indicating the well-ordered nature of the stress response. The directional movement and timing of induction for many genes matched closely the known physiological role of the proteins they encode. Inhibitors of the cell cycle (CDKN1, CDKN4D, ATM) were induced, whereas cyclins [proliferating cell nuclear antigen (PCNA), cyclin A, cyclin D1, cyclin K] were downregulated during the period from 6–20 h. Likewise, pro-apoptotic genes such as the caspases (CASP9, CASP3, CASP2) and apoptotic protease activating factor (APAF) were induced during the same period. Results of this study indicate that there is a good correlation between time-dependant physiological, biochemical, and gene expression data.
Fatty acid binding protein-2 gene variants and insulin resistance: gene and gene-environment interaction effects
Authors: Weiss Edward P. , Brown Michael D. , Shuldiner Alan R. , Hagberg James M.
Published: March 2015

The intestinal fatty acid binding protein (FABP2) gene is proposed as a candidate gene for diabetes because the protein it codes is involved in fatty acid (FA) absorption and metabolism and may, therefore, affect insulin sensitivity and glucose metabolism. Numerous studies have assessed FABP2 gene variants and their association with insulin resistance and type 2 diabetes. Some weak evidence indicates that the silent variants and those in the noncoding regions of the gene (codon 118, 3′ noncoding region, intron 2 trinucleotide repeat) might be associated with insulin resistance/type 2 diabetes. The most extensively studied variant is the missense Ala54Thr variation, which is common in diverse populations and results in increased FA absorption in vivo. Some evidence indicates that this variant may be associated with insulin sensitivity/type 2 diabetes. However, the large majority of studies assessing the potential association between the Ala54Thr FABP2 variant and insulin resistance/type 2 diabetes did not account for the independent and substantial effects of body composition, habitual physical activity (PA) levels, and diet on insulin resistance. We recently reported that there was an association between Ala54Thr FABP2 genotypes and insulin sensitivity after accounting for the independent effects of body composition and habitual PA levels on insulin sensitivity. Furthermore, others have demonstrated that Ala54Thr FABP2 may associate with insulin sensitivity, but only if individuals are consuming a high-fat diet. These results highlight the importance of including behavioral and environmental factors in the design of studies seeking to assess the impact of genes on physiological and clinical outcome phenotypes.
Relation ofPvuII site polymorphism in the COL1A2 gene to the risk of fractures in prepubertal Finnish girls
Authors: Suuriniemi Miia , Mahonen Anitta , Kovanen Vuokko , Alén Markku , Cheng Sulin
Published: March 2015

Genetic susceptibility to fractures may be detectable in early childhood. We evaluated the associations between the polymorphic PvuII site of the COL1A2 gene and bone properties assessed by different modalities (dual-energy X-ray absorptiometry; peripheral quantitative computed tomography; gel coupling scanning quantitative ultrasonometry; ultrasound bone sonometry), bone turnover markers, and the occurrence of fractures in 244 prepubertal Finnish girls. Tanner stage and physical characteristics did not differ significantly among girls with different COL1A2 genotypes. The polymorphism was not significantly associated with different bone properties or any of the bone turnover markers when girls at Tanner stage I (prepuberty) and stage II (early puberty) were considered together, but there was a significant association with spine bone mineral content (BMC) and bone mineral density (BMD), as well as with speed of sound (SOS) ( P < 0.05), when girls at Tanner stage I were considered separately, as a purpose to avoid the confounding effect that the pubertal growth spurt has on skeletal development. The distribution of fractures was different between the three genotype groups ( P = 0.023). The P alleles were over-represented in girls who had been fractured at least once; 88% of them had at least one copy of the P allele (either PP or Pp). Girls with the PP genotype had 4.9 times higher relative risk for fractures than girls with the pp genotype (95% CI, 1.4 to 17.4; P = 0.015). No significant difference was found between fractured and nonfractured girls in anthropometric measurements, physical activity, or bone mass. However, BMD of the spine and SOS at the radius and tibia were significantly lower in the fractured girls. We conclude that the COL1A2 polymorphism is associated with nonosteoporotic fractures in prepubertal girls independently of bone density.
Exploring genetic regulatory networks in metazoan development: methods and models
Authors: Halfon Marc S. , Michelson Alan M.
Published: March 2015

One of the foremost challenges of 21st century biological research will be to decipher the complex genetic regulatory networks responsible for embryonic development. The recent explosion of whole genome sequence data and of genome-wide transcriptional profiling methods, such as microarrays, coupled with the development of sophisticated computational tools for exploiting and analyzing genomic data, provide a significant starting point for regulatory network analysis. In this article we review some of the main methodological issues surrounding genome annotation, transcriptional profiling, and computational prediction of cis-regulatory elements and discuss how the power of model genetic organisms can be used to experimentally verify and extend the results of genomic research.
Gene expression profiling of acute spinal cord injury reveals spreading inflammatory signals and neuron loss
Authors: CARMEL JASON B. , GALANTE ANTHONY , SOTEROPOULOS PATRICIA , TOLIAS PETER , RECCE MICHAEL , YOUNG WISE , HART RONALD P.
Published: March 2015

We have completed the first large-scale gene expression study of acute spinal cord injury (SCI) in rat. Oligonucleotide microarrays containing 1,200 gene-specific probes were used to quantify mRNA levels, relative to uninjured controls, in spinal cords injured using a standard contusion model. Our results revealed a marked loss of neuron-specific mRNAs at the injury site. The surviving cells showed a characteristic inflammatory response that started at the injury site and spread to the distal cord. Changes in several mRNA levels were associated with putative regenerative responses in the spinal cord. Notably, phosphodiesterase 4, nestin, glia-derived neurite promoting factor, and GAP-43 mRNAs increased significantly. Other mRNAs clustered temporally and spatially with these regeneration-associated genes. Thus we have described global patterns of gene expression following acute SCI, and we have identified targets for future study and possible therapeutic intervention.
Differentially abundant mRNAs in rat liver in response to diets containing soy protein isolate
Authors: Iqbal M.J. , Yaegashi S. , Ahsan R. , Lightfoot D.A. , Banz W.J.
Published: March 2015

Soy diets influence cell growth, regulate lipid metabolism to lower blood cholesterol, and prevent bone losses. These biological effects are most likely due to effects of soy phytochemicals on the expression of genes. In this study, we fed 12 female obese Zucker rats ( fa/ fa) with a low- or a high-isoflavone soy protein diet and compared the gene expression with animals on a casein diet. Rat livers were compared by differential display of mRNA, and 62 unique sequences were identified. The change in mRNA abundance of these sequences was quantified by cDNA macroarray analysis. Thirty-three mRNAs showed more than twofold increase in abundance on soy diets compared with the control. The corresponding genes include carnitine palmitoyltransferase I, stromal cell-derived factor 1, a protein associated with MYC mRNA, basic transcription element binding protein, and expressed sequence tags (ESTs) of unknown function. Twenty-nine mRNAs showed a less than twofold change in abundance in the two diet treatments. For majority of the genes identified, there was not significant difference between the low- and high-isoflavone diet treatments. Therefore, the contrast between soy protein and casein caused the changes observed in mRNA abundance.