bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic profiles and predictive biological networks in oxidant-induced atherogenesis
Authors: Johnson C. D. , Balagurunathan Y. , Lu K. P. , Tadesse M. , Falahatpisheh M. H. , Carroll R. J. , Dougherty E. R. , Afshari C. A. , Ramos K. S.
Published: March 2015

Atherogenic stimuli trigger complex responses in vascular smooth muscle cells (VSMCs) that culminate in activation/repression of overlapping signal transduction cascades involving oxidative stress. In the case of benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon present in tobacco smoke, the atherogenic response involves interference with redox homeostasis by oxidative intermediates of BaP metabolism. The present studies were conducted to define genomic profiles and predictive gene biological networks associated with the atherogenic response of murine (aortic) VSMCs to BaP. A combined oxidant-antioxidant treatment regimen was used to identify redox-sensitive targets during the early course of the atherogenic response. Gene expression profiles were defined using cDNA microarrays coupled to analysis of variance and several clustering methodologies. A predictor algorithm was then applied to gain insight into critical gene-gene interactions during atherogenesis. Supervised and nonsupervised analyses identified clones highly regulated by BaP, unaffected by antioxidant, and neutralized by combined chemical treatments. Lymphocyte antigen-6 complex, histocompatibility class I component factors, secreted phosphoprotein, and several interferon-inducible proteins were identified as novel redox-regulated targets of BaP. Predictor analysis confirmed these relationships and identified immune-related genes as critical molecular targets of BaP. Redox-dependent patterns of gene deregulation indicate that oxidative stress plays a prominent role during the early stages of BaP-induced atherogenesis.
Heart transplantation changes the expression of distinct gene families
Authors: NGIMBOUS BEDEL BIYIHA , BOURGEOIS FRANCINE , MAS CHRISTOPHE , SIMONNEAU MICHEL , MOALIC JEAN-MARIE
Published: March 2015

We took advantage of the combination of a rat heart transplantation model with a modified differential display RT-PCR method to identify transcriptome changes in the right atria from transplanted compared with native hearts. Based on sequence homology search, the 37 cDNAs differentially displayed both 2 and 7 days posttransplantation were categorized into 7 unknown transcripts, 16 expressed sequence tags (ESTs), and 14 partially or completely characterized genes. The last group cDNAs, validated by relative RT-PCR, belonged to diverse gene families involved in specific metabolisms, protein synthesis, cell signaling, and transcription. Furthermore, we identified differential transcripts corresponding to denervation and fetal gene reexpression. We found coordinate downregulation of genes involved in energy metabolism and protein synthesis regulation, similar to that reported for senescent skeletal muscle. From these transcriptome changes, we propose that heart transplants and senescent muscles share common molecular mechanisms.
Influence of age, sex, and strength training on human muscle gene expression determined by microarray
Authors: Roth Stephen M. , Ferrell Robert E. , Peters David G. , Metter E. Jeffrey , Hurley Ben F. , Rogers Marc A.
Published: March 2015

The purpose of this study was to determine the influence of age, sex, and strength training (ST) on large-scale gene expression patterns in vastus lateralis muscle biopsies using high-density cDNA microarrays and quantitative PCR. Muscle samples from sedentary young (20–30 yr) and older (65–75 yr) men and women (5 per group) were obtained before and after a 9-wk unilateral heavy resistance ST program. RNA was hybridized to cDNA filter microarrays representing ∼4,000 known human genes and comparisons were made among arrays to determine differential gene expression as a result of age and sex differences, and/or response to ST. Sex had the strongest influence on muscle gene expression, with differential expression (>1.7-fold) observed for ∼200 genes between men and women (∼75% with higher expression in men). Age contributed to differential expression as well, as ∼50 genes were identified as differentially expressed (>1.7-fold) in relation to age, representing structural, metabolic, and regulatory gene classes. Sixty-nine genes were identified as being differentially expressed (>1.7-fold) in all groups in response to ST, and the majority of these were downregulated. Quantitative PCR was employed to validate expression levels for caldesmon, SWI/SNF (BAF60b), and four-and-a-half LIM domains 1. These significant differences suggest that in the analysis of skeletal muscle gene expression issues of sex, age, and habitual physical activity must be addressed, with sex being the most critical variable.
Novel and nondetected human signaling protein polymorphisms
Authors: Lynch Roy A. , Wagoner Lynne , Li Shunan , Sparks Li , Molkentin Jeffery , Dorn Gerald W.
Published: March 2015

The frequency of single nucleotide polymorphisms (SNPs) in downstream signaling proteins was determined by combination heteroduplex HPLC and double-stranded sequencing of genomic DNA from 96–144 congestive heart failure (CHF) patients. Analysis of 56 coding exons in 9 signaling genes revealed 17 novel and 8 previously reported synonymous (no change in amino acid) SNPs, as well as one novel nonsynonymous SNP in the Rad small G protein. Because this initial analysis failed to detect numerous SNPs reported in the NCBI and Celera databases, double-strand sequencing of relevant exons from 74–91 CHF patients was used to confirm the absence of 10 previously reported nonsynonymous SNPs. Our results show that synonymous SNPs are frequent in signaling protein genes, whereas nonsynonymous SNPs are rare, suggesting a high degree of evolutionary conservation among these downstream signaling molecules. Comparisons of our results to the NCBI and Celera databases indicates that 56% of their SNP entries are not detected in our cohort. Importantly, while 31% of database SNPs were verified, 69% of SNPs detected in our cohort are not included in these databases. These findings indicate that caution may be warranted in relying exclusively on SNP databases as catalogs for polymorphic signaling protein genes.
Influence of ethanol on thermoregulation: mapping quantitative trait loci
Authors: CRAWSHAW LARRY I. , WALLACE HELEN L. , CHRISTENSEN ROBIN , CRABBE JOHN C.
Published: March 2015

The genetic basis for the effects of ethanol on thermoregulation was investigated by utilizing recombinant inbred mouse strains from C57BL/6J and DBA/2J progenitor strains. Changes in core body temperature (Tc) and the degree of fluctuation of Tcwere monitored in male mice following the administration of ethanol in an environment with cyclic changes in ambient temperature (Ta). Changes in Tcwere utilized to assess ethanol-induced effects on regulated Tc, whereas fluctuations in Tcwere utilized to assess thermoregulatory disruption. Ethanol was administered intraperitoneally at 1.5, 2.5, and 3.5 g/kg for all strains. Change in Tcand increase in tail temperature were also evaluated at 2.5 g/kg ethanol in a constant Taof 26°C. Associations between the measured physiological responses and previously mapped genetic markers were used to identify quantitative trait loci (QTLs). This established probable chromosome locations for a number of genes for the responses. To our knowledge, this is the first report of QTLs that underlie changes in regulation as well as the disruption of a physiological regulatory system.
RNA interference of peroxisome-related genes inC. elegans: a new model for human peroxisomal disorders
Authors: Petriv Oleh I. , Pilgrim David B. , Rachubinski Richard A. , Titorenko Vladimir I.
Published: March 2015

RNA-mediated interference (RNAi) for the posttranscriptional silencing of genes was used to evaluate the importance of various peroxisomal enzymes and peroxins for the development of Caenorhabditis elegans and to compare the roles of these proteins in the nematode to their roles in yeasts and humans. The nematode counterparts of the human ATP-binding cassette half-transporters, the enzymes alkyldihydroxyacetonephosphate synthase and Δ3,5-Δ2,4-dienoyl-CoA isomerase, the receptors for peroxisomal membrane and matrix proteins (Pex19p and Pex5p), and components of the docking and translocation machineries for matrix proteins (Pex13p and Pex12p) are essential for the development of C. elegans. Unexpectedly, RNAi silencing of the acyl-CoA synthetase-mediated activation of fatty acids, the α- and β-oxidation of fatty acids, the intraperoxisomal decomposition of hydrogen peroxide, and the peroxins Pex1p, Pex2p, and Pex6p had no apparent effect on C. elegans development. The described analysis of functional gene knockouts through RNAi provides a basis for the use of C. elegans as a valuable model system with which to study the molecular and physiological defects underlying the human peroxisomal disorders.
MASH-1/RETpathway involvement in development of brain stem control of respiratory frequency in newborn mice
Authors: DAUGER STÉPHANE , GUIMIOT FABIEN , RENOLLEAU SYLVAIN , LEVACHER BÉATRICE , BODA BERNADETTE , MAS CHRISTOPHE , NÉPOTE VIRGINIE , SIMONNEAU MICHEL , GAULTIER CLAUDE , GALLEGO JORGE
Published: March 2015

Respiratory abnormalities have been described in MASH-1 (mammalian achaete-scute homologous gene) and c-RET (“rearranged during transfection”) mutant newborn mice. However, the neural mechanisms underlying these abnormalities have not been studied. We tested the hypothesis that the MASH-1 mutation may impair c-RET expression in brain stem neurons involved in the control of breathing. To do this, we analyzed brain stem c-RET expression and respiratory phenotype in MASH-1 +/+ wild-type, MASH-1 +/− heterozygous, and MASH-1 −/− knock-out newborn mice during the first 2 h of life. In MASH-1 −/− newborns, c-RET gene expression was absent in the noradrenergic nuclei (A2, A5, A6, A7) that contribute to modulate respiratory frequency and in scattered cells of the rostral ventrolateral medulla. The c-RET transcript levels measured by quantitative RT-PCR were lower in MASH-1 −/− and MASH-1 +/− than in MASH-1 +/+ brain stems ( P = 0.001 and P = 0.003, respectively). Breath durations were shorter in MASH-1 −/− and MASH-1 +/− than in MASH-1 +/+ mice ( P = 0.022) and were weakly correlated with c-RET transcript levels ( P = 0.032). Taken together, these results provide evidence that MASH-1 is upstream of c-RET in noradrenergic brain stem neurons important for respiratory rhythm modulation.
Heterogeneous allele expression of pulmonarySP-Dgene in rat large intestine and other tissues
Authors: Lin Zhenwu , Floros Joanna
Published: March 2015

Random allele expression has recently been observed for several genes including interleukins and genes of the lymphoid system. We studied the hypothesis that the surfactant protein D ( SP-D) gene, an innate host defense molecule, exhibits random allele expression in a tissue-specific manner. SP-D gene expression is tissue specific in the 14 tissues studied. Study of SP-D allelic expression in several tissues revealed a balanced biallelic (BB) in lung, and, in several extrapulmonary tissues, a heterogeneous pattern: BB, imbalanced biallelic (IB), and monoallelic (MO). The results from 103 heterozygous rats showed an expression profile in large intestine of BB (22%), IB (58%), and MO (20%). Among eight families, the percent of BB in siblings varied from 0 to 41%, MO from 0 to 33%, and IB from 49 to 83%. The parent-of-origin does not play a role in SP-D allele-specific expression. However, acquired epigenetic factors, family background, or other factors may contribute to the overall pattern of expression.
Of mice and models: improved animal models for biomedical research
Authors: Bockamp Ernesto , Maringer Marko , Spangenberg Christian , Fees Stephan , Fraser Stuart , Eshkind Leonid , Oesch Franz , Zabel Bernhard
Published: March 2015

The ability to engineer the mouse genome has profoundly transformed biomedical research. During the last decade, conventional transgenic and gene knockout technologies have become invaluable experimental tools for modeling genetic disorders, assigning functions to genes, evaluating drugs and toxins, and by and large helping to answer fundamental questions in basic and applied research. In addition, the growing demand for more sophisticated murine models has also become increasingly evident. Good state-of-principle knowledge about the enormous potential of second-generation conditional mouse technology will be beneficial for any researcher interested in using these experimental tools. In this review we will focus on practice, pivotal principles, and progress in the rapidly expanding area of conditional mouse technology. The review will also present an internet compilation of available tetracycline-inducible mouse models as tools for biomedical research ( http://www.zmg.uni-mainz.de/tetmouse/ ).
Comparison of gene expression profiling during postnatal development of mouse dentate gyrus and cerebellum
Authors: Saito Sakae , Matoba Ryo , Ueno Noriko , Matsubara Kenichi , Kato Kikuya
Published: March 2015

Both the dentate gyrus of the hippocampus and the cerebellar cortex consist mainly of granule cells and develop postnatally. The granule cells in both tissues are presumed to be similar. Changes in gene expression were analyzed during the postnatal development of the dentate gyrus. Altogether, expression patterns of 1,937 genes were determined by adaptor-tagged competitive PCR. More than 90% of the genes belong to groups characterized by elevated expression either at earlier or later stages of development. A majority of the genes expressed showed marked changes during the developmental process, but there was little correlation between gene function and expression, unlike that observed during mouse postnatal cerebellar development. Despite anatomical and physiological similarities between these two processes, the gene expression profiles are completely different.
Increasing the efficiency of fuzzy logic-based gene expression data analysis
Authors: Ressom Habtom , Reynolds Robert , Varghese Rency S.
Published: March 2015

DNA microarray technology can accommodate a multifaceted analysis of the expression of genes in an organism. The wealth of spatiotemporal data generated by this technology allows researchers to potentially reverse engineer a particular genetic network. “Fuzzy logic” has been proposed as a method to analyze the relationships between genes and help decipher a genetic network. This method can identify interacting genes that fit a known “fuzzy” model of gene interaction by testing all combinations of gene expression profiles. This paper introduces improvements made over previous fuzzy gene regulatory models in terms of computation time and robustness to noise. Improvement in computation time is achieved by using a cluster analysis as a preprocessing method to reduce the total number of gene combinations analyzed. This approach speeds up the algorithm by a factor of 50% with minimal effect on the results. The model’s sensitivity to noise is reduced by implementing appropriate methods of “fuzzy rule aggregation” and “conjunction” that produce reliable results in the face of minor changes in model input.
Gene expression profile of human endothelial cells exposed to sustained fluid shear stress
Authors: Wasserman Scott M. , Mehraban Fuad , Komuves Laszlo G. , Yang Ruey-Bing , Tomlinson James E. , Zhang Ying , Spriggs Frank , Topper James N.
Published: March 2015

Biomechanical forces can modulate endothelial phenotype through changes in gene expression. We hypothesized that physiological laminar shear stresses (LSS) act as differentiative stimuli on endothelial cells (EC) to alter gene expression, creating an antioxidant, anti-apoptotic and anti-proliferative environment. The transcriptional profile of cultured human umbilical vein endothelial cells (HUVEC) exposed to LSS was evaluated by GeneCalling; 107 genes demonstrated at least a twofold change in expression at 24 h (LSS vs. static). These flow-responsive genes represent a limited number of functional clusters that include transcription factors, antioxidants, signaling molecules, cell cycle regulators, and genes involved in cellular differentiation. Immunohistochemistry and in situ hybridization confirmed that many of these flow-responsive genes, including the novel basic helix-loop-helix transcription factor Hath6, are expressed in EC in vivo. Thus these data identify a limited set of flow-responsive genes expressed in the endothelium that may be responsible for the establishment and maintenance of the flow-adapted endothelial phenotype in vivo.
Variants of the KCNMB3 regulatory subunit of maxi BK channels affect channel inactivation
Authors: Hu Song , Labuda Malgorzata Z. , Pandolfo Massimo , Goss Greg G. , McDermid Heather E. , Ali Declan W.
Published: March 2015

The steady-state and kinetic properties of the KCNMB3 regulatory subunits associated with calcium-activated potassium channels (BK channels) are presented. BK channels containing four sequence variants (V1–V4) in the four different isoforms of the β-subunit (β3a, β3b, β3c, and β3d) were expressed in Xenopus oocytes. Reconstituted BK channel inactivation ranged from none to around 90% inactivation. In particular, channels expressing the β3b-V4 variant displayed a right shift in the potassium current voltage-dependence of activation and inactivated to about 30% of the maximum conductance, compared with wild-type β3b channels that showed no inactivation. When the membrane potential was depolarized, BK channels inactivated with a very rapid time course (∼2–6 ms). This same variant was previously demonstrated to show subtly higher incidence in patients with idiopathic epilepsy (IE) compared with controls, especially when combined with variant V2 (combined heterozygotes). Furthermore, the gene maps to a region containing a susceptibility factor for this disorder. Taken together, these data suggest that neurons expressing BK channels composed of the β3b-V4 variant subunit may experience reduced levels of inhibition and may therefore play permissive roles in high levels of neuronal activity that is characteristic of epilepsy.
Loci of intestinal distress in cystic fibrosis knockout mice
Authors: Haston Christina K. , Tsui Lap-Chee
Published: March 2015

The strain-dependent survival of cystic fibrosis (CF) knockout mice has been used to map a modifier of CF, Cfm1, in mice and, subsequently, in humans. To identify additional modifiers of the CF phenotype, in this study, the survival of F2 CF mice derived from a cross between congenic C57BL/6J CF and BALB/cJ CF heterozygotes was followed up to 12 wk of age. A genome-wide linkage scan completed in F2 CF mice revealed a chromosome 10 locus ( P = 1.2 × 10−4) to predict for intestinal distress in CF male mice. An X chromosome locus for which non-Mendelian inheritance favoring B6 alleles in the surviving CF mice and BALB alleles in mice of a control population, was identified. The survival of female mice, both F2 CF and F2 control, was linked to loci on chromosomes 3 and 5. The identification of additional putative CF modifier loci may permit further genetic dissection of the complex CF phenotype.
Expression imbalance map: a new visualization method for detection of mRNA expression imbalance regions
Authors: Kano Makoto , Nishimura Kunihiro , Ishikawa Shumpei , Tsutsumi Shuichi , Hirota Koichi , Hirose Michitaka , Aburatani Hiroyuki
Published: March 2015

We describe the development of a new visualization method, called the expression imbalance map (EIM), for detecting mRNA expression imbalance regions, reflecting genomic losses and gains at a much higher resolution than conventional technologies such as comparative genomic hybridization (CGH). Simple spatial mapping of the microarray expression profiles on chromosomal location provides little information about genomic structure, because mRNA expression levels do not completely reflect genomic copy number and some microarray probes would be of low quality. The EIM, which does not employ arbitrary selection of thresholds in conjunction with hypergeometric distribution-based algorithm, has a high tolerance of these complex factors. The EIM could detect regionally underexpressed or overexpressed genes (called, here, an expression imbalance region) in lung cancer specimens from their gene expression data of oligonucleotide microarray. Many known as well as potential loci with frequent genomic losses or gains were detected as expression imbalance regions by the EIM. Therefore, the EIM should provide the user with further insight into genomic structure through mRNA expression.
Applications for multifrequency ultrasound biomicroscopy in mice from implantation to adulthood
Authors: Zhou Y. Q. , Foster F. S. , Qu D. W. , Zhang M. , Harasiewicz K. A. , Adamson S. L.
Published: March 2015

A new multifrequency (19–55 MHz) ultrasound biomicroscope with two-dimensional imaging and integrated Doppler ultrasound was evaluated using phantoms and isoflurane-anesthetized mice. Phantoms revealed the biomicroscope’s lateral resolution was between 50 and 100 μm, whereas that of a conventional 13 MHz ultrasound system was 200–500 μm. This difference was apparent in the markedly higher resolution images achieved using the biomicroscope in vivo. Transcutaneous images of embryos in pregnant mice from ∼2 days after implantation (7 days gestation) to near term (17.5 days) were obtained using frequencies from 25 to 40 MHz. The ectoplacental cone and early embryonic cavities were visible as were the placenta and embryonic organs throughout development to term. We also evaluated the ability of the biomicroscope to detect important features of heart development by examining embryos from 8.5 to 17.5 day gestation in exteriorized uteri using 55 MHz ultrasound. Cardiac looping, division of the outflow tract, and ventricular septation were visible. In postnatal imaging, we observed the heart and kidney of neonatal mice at 55 MHz, the carotid artery in juveniles (∼8 g body wt) and adults (∼25 g body wt) at 40 MHz, and the adult heart, aorta, and kidney at 19 MHz. The coefficient of variation of carotid and aortic diameter measurements was 1–3%. In addition, blisters in GRIP1 −/− embryos and aortic valvular stenosis in two adults were readily visualized. Using image-guided Doppler function, low blood velocities in vessels as small as 100 μm in diameter including the primitive heart tube at day 8.5 were measurable, but high blood velocities (>37.5 cm/s) such as in the heart and large arteries in late gestation and postnatal life were off-scale. Accurate cardiac dimension measurements were impeded by poor temporal resolution (4 frames/s). In summary, the multifrequency ultrasound biomicroscope is a versatile tool well suited to detailed study of the morphology of various organ systems throughout development in mice and for hemodynamic measurements in the low velocity range.
Detection of genes with tissue-specific expression patterns using Akaike’s information criterion procedure
Authors: Kadota Koji , Nishimura Shin-Ichiro , Bono Hidemasa , Nakamura Shugo , Hayashizaki Yoshihide , Okazaki Yasushi , Takahashi Katsutoshi
Published: March 2015

We applied a method based on Akaike’s information criterion (AIC) to detect genes whose expression profile is considerably different in some tissue(s) than in others. Such observations are detected as outliers, and the method we used was originally developed to detect outliers. The main advantage of the method is that objective decisions are possible because the procedure is independent of a significance level. We applied the method to 48 expression ratios corresponding to various tissues in each of 14,610 clones obtained from the RIKEN Expression Array Database (READ; http://read.gsc.riken.go.jp ). As a result, for several tissues (e.g., muscle, heart, and tongue tissues that contain similar cell types) we objectively obtained specific clones without any “thresholding.” Our study demonstrates the feasibility of the method for detecting tissue-specific gene expression patterns.
Age-related impairment of the transcriptional responses to oxidative stress in the mouse heart
Authors: Edwards Michael G. , Sarkar Deepayan , Klopp Roger , Morrow Jason D. , Weindruch Richard , Prolla Tomas A.
Published: March 2015

To investigate the transcriptional response to oxidative stress in the heart and how it changes with age, we examined the cardiac gene expression profiles of young (5-mo-old), middle-aged (15-mo-old), and old (25-mo-old) C57BL/6 mice treated with a single intraperitoneal injection of paraquat (50 mg/kg). Mice were killed at 0, 1, 3, 5, and 7 h after paraquat treatment, and the gene expression profile was obtained with high-density oligonucleotide microarrays. Of 9,977 genes represented on the microarray, 249 transcripts in the young mice, 298 transcripts in the middle-aged mice, and 256 transcripts in the old mice displayed a significant change in mRNA levels (ANOVA, P < 0.01). Among these, a total of 55 transcripts were determined to be paraquat responsive for all age groups. Genes commonly induced in all age groups include those associated with stress, inflammatory, immune, and growth factor responses. Interestingly, only young mice displayed a significant increase in expression of all three isoforms of GADD45, a DNA damage-responsive gene. Additionally, the number of immediate early response genes (IEGs) found to be induced by paraquat was considerably higher in the younger animals. These results demonstrate that, at the transcriptional level, there is an age-related impairment of specific inducible pathways in the response to oxidative stress in the mouse heart.
Pancreatic gene expression during the initiation of acute pancreatitis: identification of EGR-1 as a key regulator
Authors: Ji Baoan , Chen Xue-qing , Misek David E. , Kuick Rork , Hanash Samir , Ernst Steve , Najarian Rebecca , Logsdon Craig D.
Published: March 2015

We hypothesized that genes expressed in pancreatic acinar cells during the initiation of acute pancreatitis determine the severity of the disease. Therefore, we utilized microarrays to identify those genes commonly induced in rat pancreatic acinar cells within 1–4 h in two in vivo models, caerulein and taurocholate administration. This strategy yielded 51 known genes representing a complex array of molecules, including those that are likely to either reduce or increase the severity of the disease. Novel genes identified in the current study included ATF3, BRF1, C/EBPβ, CGRP, EGR-1, ephrinA1, villin2, ferredoxin, latexin, lipocalin, MKP-1, NGFI-B, RhoA, tissue factor (TF), and syndecan. To validate these microarray results, the role of EGR-1 was further investigated using quantitative RT-PCR, Western blotting, and immunocytochemistry. EGR-1 expression occurred within acinar cells and correlated with the development of caerulein-induced acute pancreatitis in rats. Furthermore, the levels of the inflammation-related genes MCP-1, PAI, TF, IL-6, and ICAM-1 and the extent of lung inflammation were reduced during the initiation of caerulein-induced acute pancreatitis in EGR-1-deficient mice. Thus this study identified EGR-1 and several other novel genes likely to be important in the development and severity of acute pancreatitis.
Exercise assessment of transgenic models of human cardiovascular disease
Authors: Bernstein Daniel
Published: March 2015

Exercise provides one of the most severe, yet physiological, stresses to the intact cardiovascular system and is a major determinant of the utilization of metabolic substrates. The adaptations to exercise are the result of a coordinated response of multiple organ systems, including cardiovascular, pulmonary, endocrine-metabolic, immunologic, and skeletal muscle. With the proliferation of genetically altered murine models of cardiovascular disease, the importance of developing methods of accurate physiological phenotyping is critical. There are numerous examples of transgenic models in which the baseline cardiovascular phenotype is unchanged or minimally changed from the wild type, only to become manifest during the stress of exercise testing. In this review, we cover the basics of the murine cardiovascular response to exercise and the importance of attending to strain differences, compare different exercise methodologies (constant workload treadmill, incremental workload treadmill, swimming) and hemodynamic monitoring systems, and examine the murine response to exercise conditioning. Several examples where exercise studies have contributed to the elucidation of cardiovascular phenotypes are reviewed: the β-adrenergic receptor knockouts, phospholamban knockout, dystrophin knockout ( mdx), and the mutant α-myosin heavy chain (R403Q) transgenic.
Nongenomic Steroid Action: Controversies, Questions, and Answers
Authors: LÖSEL RALF M. , FALKENSTEIN ELISABETH , FEURING MARTIN , SCHULTZ ARMIN , TILLMANN HANNS-CHRISTIAN , ROSSOL-HASEROTH KARIN , WEHLING MARTIN
Published: March 2015

Lösel, Ralf M., Elisabeth Falkenstein, Martin Feuring, Armin Schultz, Hanns-Christian Tillmann, Karin Rossol-Haseroth, and Martin Wehling. Nongenomic Steroid Action: Controversies, Questions, and Answers. Physiol Rev 83: 965–1016, 2003; 10.1152/physrev.00003.2003.—Steroids may exert their action in living cells by several ways: 1) the well-known genomic pathway, involving hormone binding to cytosolic (classic) receptors and subsequent modulation of gene expression followed by protein synthesis. 2) Alternatively, pathways are operating that do not act on the genome, therefore indicating nongenomic action. Although it is comparatively easy to confirm the nongenomic nature of a particular phenomenon observed, e.g., by using inhibitors of transcription or translation, considerable controversy exists about the identity of receptors that mediate these responses. Many different approaches have been employed to answer this question, including pharmacology, knock-out animals, and numerous biochemical studies. Evidence is presented for and against both the participation of classic receptors, or proteins closely related to them, as well as for the involvement of yet poorly understood, novel membrane steroid receptors. In addition, clinical implications for a wide array of nongenomic steroid actions are outlined.
Role of Endogenous Cannabinoids in Synaptic Signaling
Authors: FREUND TAMÁS F. , KATONA ISTVÁN , PIOMELLI DANIELE
Published: March 2015

Freund, Tamás F., István Katona, and Daniele Piomelli. Role of Endogenous Cannabinoids in Synaptic Signaling. Physiol Rev 83: 1017–1066, 2003; 10.1152/physrev.00004.2003.—Research of cannabinoid actions was boosted in the 1990s by remarkable discoveries including identification of endogenous compounds with cannabimimetic activity (endocannabinoids) and the cloning of their molecular targets, the CB1and CB2receptors. Although the existence of an endogenous cannabinoid signaling system has been established for a decade, its physiological roles have just begun to unfold. In addition, the behavioral effects of exogenous cannabinoids such as delta-9-tetrahydrocannabinol, the major active compound of hashish and marijuana, await explanation at the cellular and network levels. Recent physiological, pharmacological, and high-resolution anatomical studies provided evidence that the major physiological effect of cannabinoids is the regulation of neurotransmitter release via activation of presynaptic CB1receptors located on distinct types of axon terminals throughout the brain. Subsequent discoveries shed light on the functional consequences of this localization by demonstrating the involvement of endocannabinoids in retrograde signaling at GABAergic and glutamatergic synapses. In this review, we aim to synthesize recent progress in our understanding of the physiological roles of endocannabinoids in the brain. First, the synthetic pathways of endocannabinoids are discussed, along with the putative mechanisms of their release, uptake, and degradation. The fine-grain anatomical distribution of the neuronal cannabinoid receptor CB1is described in most brain areas, emphasizing its general presynaptic localization and role in controlling neurotransmitter release. Finally, the possible functions of endocannabinoids as retrograde synaptic signal molecules are discussed in relation to synaptic plasticity and network activity patterns.
Mammalian Hibernation: Cellular and Molecular Responses to Depressed Metabolism and Low Temperature
Authors: CAREY HANNAH V. , ANDREWS MATTHEW T. , MARTIN SANDRA L.
Published: March 2015

Carey, Hannah V., Matthew T. Andrews, and Sandra L. Martin. Mammalian Hibernation: Cellular and Molecular Responses to Depressed Metabolism and Low Temperature. Physiol Rev 83: 1153-1181, 2003; 10.1152/physrev. 00008.2003.—Mammalian hibernators undergo a remarkable phenotypic switch that involves profound changes in physiology, morphology, and behavior in response to periods of unfavorable environmental conditions. The ability to hibernate is found throughout the class Mammalia and appears to involve differential expression of genes common to all mammals, rather than the induction of novel gene products unique to the hibernating state. The hibernation season is characterized by extended bouts of torpor, during which minimal body temperature (Tb) can fall as low as −2.9°C and metabolism can be reduced to 1% of euthermic rates. Many global biochemical and physiological processes exploit low temperatures to lower reaction rates but retain the ability to resume full activity upon rewarming. Other critical functions must continue at physiologically relevant levels during torpor and be precisely regulated even at Tbvalues near 0°C. Research using new tools of molecular and cellular biology is beginning to reveal how hibernators survive repeated cycles of torpor and arousal during the hibernation season. Comprehensive approaches that exploit advances in genomic and proteomic technologies are needed to further define the differentially expressed genes that distinguish the summer euthermic from winter hibernating states. Detailed understanding of hibernation from the molecular to organismal levels should enable the translation of this information to the development of a variety of hypothermic and hypometabolic strategies to improve outcomes for human and animal health.
Na+-K+Pump Regulation and Skeletal Muscle Contractility
Authors: CLAUSEN TORBEN
Published: March 2015

Clausen, Torben. Na+-K+Pump Regulation and Skeletal Muscle Contractility. Physiol Rev 83: 1269-1324, 2003; 10.1152/physrev.00011.2003.—In skeletal muscle, excitation may cause loss of K+, increased extracellular K+([K+]o), intracellular Na+([Na+]i), and depolarization. Since these events interfere with excitability, the processes of excitation can be self-limiting. During work, therefore, the impending loss of excitability has to be counterbalanced by prompt restoration of Na+-K+gradients. Since this is the major function of the Na+-K+pumps, it is crucial that their activity and capacity are adequate. This is achieved in two ways: 1) by acute activation of the Na+-K+pumps and 2) by long-term regulation of Na+-K+pump content or capacity. 1) Depending on frequency of stimulation, excitation may activate up to all of the Na+-K+pumps available within 10 s, causing up to 22-fold increase in Na+efflux. Activation of the Na+-K+pumps by hormones is slower and less pronounced. When muscles are inhibited by high [K+]oor low [Na+]o, acute hormone- or excitation-induced activation of the Na+-K+pumps can restore excitability and contractile force in 10-20 min. Conversely, inhibition of the Na+-K+pumps by ouabain leads to progressive loss of contractility and endurance. 2) Na+-K+pump content is upregulated by training, thyroid hormones, insulin, glucocorticoids, and K+overload. Downregulation is seen during immobilization, K+deficiency, hypoxia, heart failure, hypothyroidism, starvation, diabetes, alcoholism, myotonic dystrophy, and McArdle disease. Reduced Na+-K+pump content leads to loss of contractility and endurance, possibly contributing to the fatigue associated with several of these conditions. Increasing excitation-induced Na+influx by augmenting the open-time or the content of Na+channels reduces contractile endurance. Excitability and contractility depend on the ratio between passive Na+-K+leaks and Na+-K+pump activity, the passive leaks often playing a dominant role. The Na+-K+pump is a central target for regulation of Na+-K+distribution and excitability, essential for second-to-second ongoing maintenance of excitability during work.
Ryanodine Receptor Calcium Release Channels
Authors: Fill Michael , Copello Julio A.
Published: March 2015

The ryanodine receptors (RyRs) are a family of Ca2+release channels found on intracellular Ca2+storage/release organelles. The RyR channels are ubiquitously expressed in many types of cells and participate in a variety of important Ca2+signaling phenomena (neurotransmission, secretion, etc.). In striated muscle, the RyR channels represent the primary pathway for Ca2+release during the excitation-contraction coupling process. In general, the signals that activate the RyR channels are known (e.g., sarcolemmal Ca2+influx or depolarization), but the specific mechanisms involved are still being debated. The signals that modulate and/or turn off the RyR channels remain ambiguous and the mechanisms involved unclear. Over the last decade, studies of RyR-mediated Ca2+release have taken many forms and have steadily advanced our knowledge. This robust field, however, is not without controversial ideas and contradictory results. Controversies surrounding the complex Ca2+regulation of single RyR channels receive particular attention here. In addition, a large body of information is synthesized into a focused perspective of single RyR channel function. The present status of the single RyR channel field and its likely future directions are also discussed.
Molecular Physiology of P2X Receptors
Authors: North R. Alan
Published: March 2015

P2X receptors are membrane ion channels that open in response to the binding of extracellular ATP. Seven genes in vertebrates encode P2X receptor subunits, which are 40–50% identical in amino acid sequence. Each subunit has two transmembrane domains, separated by an extracellular domain (∼280 amino acids). Channels form as multimers of several subunits. Homomeric P2X1, P2X2, P2X3, P2X4, P2X5, and P2X7channels and heteromeric P2X2/3and P2X1/5channels have been most fully characterized following heterologous expression. Some agonists (e.g., αβ-methylene ATP) and antagonists [e.g., 2′,3′- O-(2,4,6-trinitrophenyl)-ATP] are strongly selective for receptors containing P2X1and P2X3subunits. All P2X receptors are permeable to small monovalent cations; some have significant calcium or anion permeability. In many cells, activation of homomeric P2X7receptors induces a permeability increase to larger organic cations including some fluorescent dyes and also signals to the cytoskeleton; these changes probably involve additional interacting proteins. P2X receptors are abundantly distributed, and functional responses are seen in neurons, glia, epithelia, endothelia, bone, muscle, and hemopoietic tissues. The molecular composition of native receptors is becoming understood, and some cells express more than one type of P2X receptor. On smooth muscles, P2X receptors respond to ATP released from sympathetic motor nerves (e.g., in ejaculation). On sensory nerves, they are involved in the initiation of afferent signals in several viscera (e.g., bladder, intestine) and play a key role in sensing tissue-damaging and inflammatory stimuli. Paracrine roles for ATP signaling through P2X receptors are likely in neurohypophysis, ducted glands, airway epithelia, kidney, bone, and hemopoietic tissues. In the last case, P2X7receptor activation stimulates cytokine release by engaging intracellular signaling pathways.
Cell Biology of the Glomerular Podocyte
Authors: Pavenstädt Hermann , Kriz Wilhelm , Kretzler Matthias
Published: March 2015

Glomerular podocytes are highly specialized cells with a complex cytoarchitecture. Their most prominent features are interdigitated foot processes with filtration slits in between. These are bridged by the slit diaphragm, which plays a major role in establishing the selective permeability of the glomerular filtration barrier. Injury to podocytes leads to proteinuria, a hallmark of most glomerular diseases. New technical approaches have led to a considerable increase in our understanding of podocyte biology including protein inventory, composition and arrangement of the cytoskeleton, receptor equipment, and signaling pathways involved in the control of ultrafiltration. Moreover, disturbances of podocyte architecture resulting in the retraction of foot processes and proteinuria appear to be a common theme in the progression of acquired glomerular disease. In hereditary nephrotic syndromes identified over the last 2 years, all mutated gene products were localized in podocytes. This review integrates our recent physiological and molecular understanding of the role of podocytes during the maintenance and failure of the glomerular filtration barrier.
Transport of Exogenous Growth Factors and Cytokines to the Cytosol and to the Nucleus
Authors: Olsnes Sjur , Klingenberg Olav , Wie˛dłocha Antoni
Published: March 2015

In recent years a number of growth factors, cytokines, protein hormones, and other proteins have been found in the nucleus after having been added externally to cells. This review evaluates the evidence that translocation takes place and discusses possible mechanisms. As a demonstration of the principle that extracellular proteins can penetrate cellular membranes and reach the cytosol, a brief overview of the penetration mechanism of protein toxins with intracellular sites of action is given. Then problems and pitfalls in attempts to demonstrate the presence of proteins in the cytosol and in the nucleus as opposed to intracellular vesicular compartments are discussed, and some new approaches to study this are described. A detailed overview of the evidence for translocation of fibroblast growth factor, HIV-Tat, interferon-γ, and other proteins where there is evidence for intracellular action is given, and translocation mechanisms are discussed. It is concluded that although there are many pitfalls, the bulk of the experiments indicate that certain proteins are indeed able to enter the cytosol and nucleus. Possible roles of the internalized proteins are discussed.
From Genes to Integrative Physiology: Ion Channel and Transporter Biology inCaenorhabditis elegans
Authors: Strange Kevin
Published: March 2015

The stunning progress in molecular biology that has occurred over the last 50 years drove a powerful reductionist approach to the study of physiology. That same progress now forms the foundation for the next revolution in physiological research. This revolution will be focused on integrative physiology, which seeks to understand multicomponent processes and the underlying pathways of information flow from an organism's “parts” to increasingly complex levels of organization. Genetically tractable and genomically defined nonmammalian model organisms such as the nematode Caenorhabditis elegansprovide powerful experimental advantages for elucidating gene function and the molecular workings of complex systems. This review has two main goals. The first goal is to describe the experimental utility of C. elegans for investigating basic physiological problems. A detailed overview of C. elegans biology and the experimental tools, resources, and strategies available for its study is provided. The second goal of this review is to describe how forward and reverse genetic approaches and direct behavioral and physiological measurements in C. elegans have generated novel insights into the integrative physiology of ion channels and transporters. Where appropriate, I describe how insights from C. elegans have provided new understanding of the physiology of membrane transport processes in mammals.
Actin Binding Proteins: Regulation of Cytoskeletal Microfilaments
Authors: Dos Remedios C. G. , Chhabra D. , Kekic M. , Dedova I. V. , Tsubakihara M. , Berry D. A. , Nosworthy N. J.
Published: March 2015

The actin cytoskeleton is a complex structure that performs a wide range of cellular functions. In 2001, significant advances were made to our understanding of the structure and function of actin monomers. Many of these are likely to help us understand and distinguish between the structural models of actin microfilaments. In particular, 1) the structure of actin was resolved from crystals in the absence of cocrystallized actin binding proteins (ABPs), 2) the prokaryotic ancestral gene of actin was crystallized and its function as a bacterial cytoskeleton was revealed, and 3) the structure of the Arp2/3 complex was described for the first time. In this review we selected several ABPs (ADF/cofilin, profilin, gelsolin, thymosin β4, DNase I, CapZ, tropomodulin, and Arp2/3) that regulate actin-driven assembly, i.e., movement that is independent of motor proteins. They were chosen because 1) they represent a family of related proteins, 2) they are widely distributed in nature, 3) an atomic structure (or at least a plausible model) is available for each of them, and 4) each is expressed in significant quantities in cells. These ABPs perform the following cellular functions: 1) they maintain the population of unassembled but assembly-ready actin monomers (profilin), 2) they regulate the state of polymerization of filaments (ADF/cofilin, profilin), 3) they bind to and block the growing ends of actin filaments (gelsolin), 4) they nucleate actin assembly (gelsolin, Arp2/3, cofilin), 5) they sever actin filaments (gelsolin, ADF/cofilin), 6) they bind to the sides of actin filaments (gelsolin, Arp2/3), and 7) they cross-link actin filaments (Arp2/3). Some of these ABPs are essential, whereas others may form regulatory ternary complexes. Some play crucial roles in human disorders, and for all of them, there are good reasons why investigations into their structures and functions should continue.
Bile Salt Transporters: Molecular Characterization, Function, and Regulation
Authors: Trauner Michael , Boyer James L.
Published: March 2015

Molecular medicine has led to rapid advances in the characterization of hepatobiliary transport systems that determine the uptake and excretion of bile salts and other biliary constituents in the liver and extrahepatic tissues. The bile salt pool undergoes an enterohepatic circulation that is regulated by distinct bile salt transport proteins, including the canalicular bile salt export pump BSEP (ABCB11), the ileal Na+-dependent bile salt transporter ISBT (SLC10A2), and the hepatic sinusoidal Na+- taurocholate cotransporting polypeptide NTCP (SLC10A1). Other bile salt transporters include the organic anion transporting polypeptides OATPs (SLC21A) and the multidrug resistance-associated proteins 2 and 3 MRP2,3 (ABCC2,3). Bile salt transporters are also present in cholangiocytes, the renal proximal tubule, and the placenta. Expression of these transport proteins is regulated by both transcriptional and posttranscriptional events, with the former involving nuclear hormone receptors where bile salts function as specific ligands. During bile secretory failure (cholestasis), bile salt transport proteins undergo adaptive responses that serve to protect the liver from bile salt retention and which facilitate extrahepatic routes of bile salt excretion. This review is a comprehensive summary of current knowledge of the molecular characterization, function, and regulation of bile salt transporters in normal physiology and in cholestatic liver disease and liver regeneration.