Research in the exercise sciences: where do we go from here?

The Prospective Study of Epigenetic Regulatory Profiles in Sport and Exercise Monitored Through Chromosome Conformation Signatures

The integration of genetic and environmental factors that regulate the gene expression patterns associated with exercise adaptation is mediated by epigenetic mechanisms. The organisation of the human genome within three-dimensional space, known as chromosome conformation, has recently been shown as a dynamic epigenetic regulator of gene expression, facilitating the interaction of distal genomic regions due to tight and regulated packaging of chromosomes in the cell nucleus. Technological advances in the study of chromosome conformation mean a new class of biomarker-the chromosome conformation signature (CCS)-can identify chromosomal interactions across several genomic loci as a collective marker of an epigenomic state. Investigative use of CCSs in biological and medical research shows promise in identifying the likelihood that a disease state is present or absent, as well as an ability to prospectively stratify individuals according to their likely response to medical intervention. The association of CCSs with gene expression patterns suggests that there are likely to be CCSs that respond, or regulate the response, to exercise and related stimuli. The present review provides a contextual background to CCS research and a theoretical framework discussing the potential uses of this novel epigenomic biomarker within sport and exercise science and medicine.

A compendium of physical exercise-related human genes: an 'omic scale analysis

Regular exercise is an exogenous factor of gene regulation with numerous health benefits. The study aimed to evaluate human genes linked to physical exercise in an ‘omic scale, addressing biological questions to the generated database. Three literature databases were searched with the terms ‘exercise’, ‘fitness’, ‘physical activity’, ‘genetics’ and ‘gene expression’. For additional references, papers were scrutinized and a text-mining tool was used. Papers linking genes to exercise in humans through microarray, RNA-Seq, RT-PCR and genotyping studies were included. Genes were extracted from the collected literature, together with information on exercise protocol, experimental design, gender, age, number of individuals, analytical method, fold change and statistical data. The ‘omic scale dataset was characterized and evaluated with bioinformatics tools searching for gene expression patterns, functional meaning and gene clusters. As a result, a physical exercise-related human gene compendium was created, with data from 58 scientific papers and 5.147 genes functionally correlated with 17 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. While 50.9% of the gene set was up-regulated, 41.9% was down-regulated. 743 up- and 530 down-regulated clusters were found, some connected by regulatory networks. To summarize, up- and down-regulation was encountered, with a wide genomic distribution of the gene set and up- and down-regulated clusters possibly assembled by functional gene evolution. Physical exercise elicits a widespread response in gene expression.

Effect of exercise on the skeletal muscle proteome in patients with type 2 diabetes

PURPOSE

Exercise training alters protein abundance in the muscle of healthy individuals, but the effect of exercise on these proteins in patients with type 2 diabetes (T2D) is unknown. The aim of this study was to determine how exercise training alters the skeletal muscle proteome in patients with T2D.

METHODS

Biopsies of the vastus lateralis were obtained before and after 4 wk of exercise training in six patients with T2D (54 ± 4 yr; body mass index (BMI), 29 ± 2) and six age- and BMI-matched control subjects (48 ± 2; BMI, 28 ± 3) studied at the baseline. The proteins were identified and quantified using normalized spectral abundance factors by multidimensional high-resolution mass spectrometry.

RESULTS

Of the 1329 proteins assigned at the baseline, 438 were present in at least half of all the muscle samples; of these, 15 proteins differed significantly between the patients with T2D and control subjects (P < 0.05). In the diabetic patients, the exercise training altered the abundance of 17 proteins (P < 0.05). Key training adaptations included an increase in proteins of the malate-aspartate shuttle and citric acid cycle, reduced the abundance of glycolytic proteins, and altered the abundance of cytoskeleton proteins.

CONCLUSION

The data from this study support the ability of exercise training to alter the abundance of proteins that regulate metabolism and cytoskeletal structure in patients with T2D. These findings open new avenues for future research.

Proteomic approach to aging research

The scope of the current paper is to review existing and potential applications of proteomic analysis to aging research. The focus will lie on the unique opportunities of high-throughput studies for uncovering specific alterations in protein expression, protein complexes or protein modifications caused by biological aging. The result of such studies will outline aging phenotypes and potentially indicate pathways involved in the pathogenesis of age-associated disfunctions. Specific attention is paid to the illustrations of successful applications of proteomic technologies and potential applications of new proteomic concepts to biogerontological studies.

Proteomic responses of skeletal and cardiac muscle to exercise

Regular exercise is effective in the prevention of chronic diseases and confers a lower risk of death in individuals displaying risk factors such as hypertension and dyslipidemia. Thus, knowledge of the molecular responses to exercise provides a valuable contrast for interpreting investigations of disease and can highlight novel therapeutic targets. While exercise is an everyday experience and can be conceptualized in simple terms, it is also a complex physiological phenomenon and investigation of exercise responses requires sophisticated analytical techniques and careful standardization of the exercise stimulus. Proteomic investigation of exercise is in its infancy but the ability to link changes in function with comprehensive changes in protein expression and post-translational modification holds great promise for advancing physiology. This article highlights recent pioneering work investigating the effects of exercise in skeletal and cardiac muscle that has uncovered novel mechanisms underlying the benefits of physical activity.

Research in the exercise sciences: where we are and where do we go from here--Part II

This decadal perspective summarizes novel, insightful observations achieved in exercise science. The topics span genomics and gene function, epigenetics, cell signaling, epidemiological phenomena, and other important areas. A future strategy is presented along two parallel, integrated paths involving the following: 1) a continuance of genomic discovery and gene function, and 2) classical biochemical/physiological approaches toward solving biological- and health/disease-related phenomena.

Proteomics and systems biology in exercise and sport sciences research

A systems biology approach toward biological research seeks to model all concurrent processes in a cell, tissue, or organism by global measurements. In this review, we describe recent advances in mass spectrometry-based proteomics and their application toward interpreting the physiological adaptations of skeletal muscle with exercise and obesity.

Inactivity and Inflammation in the Critically Ill Patient

Bed rest is a commonly prescribed activity restriction among patients in the ICU. Although bed rest may promote rest, recovery and safety, inactivity related to bed rest also may lead to complications and adverse outcomes. The biological mechanisms that lead to immediate and long-term sequelae from bed rest have not been elucidated. It may be the inflammatory factors common to critical illness combined with bed rest lead to a positive feedback loop, contributing to inflammatory disequilibrium. This disequilibrium has a profound affect on muscles. Muscle decay has serious and long-term adverse outcomes on survivors of critical illness. Mobility therapy may improve inflammatory disequilibrium and preserve muscles, leading to improved functional outcome. Investigations in the laboratory, in healthy people and among patients with systemic inflammatory disease, suggest that activity does not exacerbate inflammation. Clinically, exercise is beneficial to patients with various chronic inflammatory diseases. Further study is needed to best understand the role, duration, and frequency of activity in promoting recovery for critically ill patients.

Transcriptional profiling of tissue plasticity: role of shifts in gene expression and technical limitations

Reprogramming of gene expression has been recognized as a main instructive modality for the adjustments of tissues to various kinds of stress. The recent application of gene expression profiling has provided a powerful tool to elucidate the molecular pathways underlying such tissue remodeling. However, the biological interpretations of expression profiling results critically depend on normalization of transcript signals to mRNA standards before statistical evaluation. A hypothesis is proposed whereby the “fluctuating nature” of gene expression represents an inherent limitation of the test system used to quantify RNA levels. Misinterpretation of gene expression data occurs when RNA quantities are normalized to a subset of mRNAs that are subject to strong regulation. The contention of contradictory biological outcomes using different RNA-normalization schemes is demonstrated in two models of skeletal muscle plasticity with data from custom-designed microarrays and biochemical and ultrastructural evidence for correspondingly altered RNA content and nucleolar activity. The prevalence of these biological constraints is underlined by a literature survey in different models of tissue plasticity with emphasis on the unique malleability of skeletal muscle. Finally, recommendations on the optimal experimental layout are given to control biological and technical variability in microarray and RT-PCR studies. It is proposed to approach normalization of transcript signals by measuring total RNA and DNA content per sample weight and by correcting for concurrently estimated endogenous standards such as major ribosomal RNAs and spiked RNA and DNA species. This allows for later conversion to diverse tissue-relevant references and should improve the physiological interpretations of phenotypic plasticity.

Human and rat skeletal muscle adaptations to spinal cord injury

Results of studies of rodent skeletal muscle plasticity are often extrapolated to humans. However, responses to "disuse" may be species specific, in part because of different inherent properties of anatomically similar muscles. Thus, this study quantified human and rat m. vastus lateralis (VL) fiber adaptations to 11 weeks of spinal cord injury (SCI). The m. VL was taken from 8 young (54 d) male Charles River rats after T-9 laminectomy (n = 4) or sham surgery (n = 4). In addition, the m. VL was biopsied in 7 able-bodied and in 7 SCI humans (31.3 +/- 4.7 years, mean +/- SE). Samples were sectioned and fibers were analyzed for type (I, IIa, IIb/x), cross-sectional area (CSA), succinate dehydrogenase (SDH), alpha-glycerol-phosphate dehydrogenase (GPDH), and actomyosin adenosine triphosphatase (qATPase) activities. Rat fibers had 1.5- to 2-fold greater SDH and GPDH activities while their fibers were 60% the size of those in humans. The most striking differences, however, were the absence of slow fibers in the rat and its four-fold greater proportion of IIb/x fibers (80% vs. 16% of the CSA) compared to humans. SCI decreased SDH activity more in rats whereas atrophy and IIa to IIb/x fiber shift occurred to a greater extent in humans. It is suggested that the rat is a reasonable model for studying the predominant response to SCI, atrophy. However, its high proportion of IIb/x fibers limits evaluation of the mechanical consequences of shifting to "faster" contractile machinery after SCI.

Factors that alter body fat, body mass, and fat-free mass in pediatric obesity

PURPOSE

The purpose of this study was to quantify the effects of exercise treatment programs on changes in body mass, fat-free mass, and body fat in obese children and adolescents.

METHODS

By using the meta-analytic approach, studies that met the following criteria were included in our analyses: 1) at least six subjects per group; 2) subject groups consisting of children in the 5- to 17-yr age range; 3) pretest and posttest values for either body mass, percent body fat, or fat-free mass (FFM); 4) used exercise as a mode of treatment (e.g., walking, jogging, cycle ergometry, high-repetition resistance exercise, and combinations); 6) training programs >or= 3 wk; 7) full-length publications (not conference proceedings); 8) apparently "healthy" children (i.e., free from endocrine diseases and disorders); and 9) published studies in English language journals only.

RESULTS

A total of 120 investigations were located that addressed the issue of exercise as a method of treatment in pediatric obesity. Of those, 30 met our criteria for inclusion. Across all designs and categories, fixed-effects modeling yielded significant decreases in the following dependent variables: 1) percent body fat (mean = 0.70 +/- 0.35; 95% CI = 0.21 to 1.1); 2) FFM (mean = 0.50 +/- 0.38; 95% CI = 0.03 to 0.57); 3) body mass (mean = 0.34 +/- 0.18; 95% CI = 0.01 to 0.46); 4) BMI (mean = 0.76 +/- 0.55; 95% CI = 4.24 to 1.7), and 5) VO2max (mean = 0.52 +/- 0.16; 95% CI = 0.18 to 0.89), respectively. Significant differences were found as a function of the type intervention groups (exercise vs exercise + behavioral modification; P < 0.04); body composition assessment methods (skinfold vs hydrostatic weighing, DEXA, and total body water; P < 0.006); exercise intensity (60-65%, vs >or= 71% VO2max; P < 0.01); duration (<or= 30 min vs > 30 min; P < 0.03); and mode (aerobic vs aerobic + resistance training; P < 0.02). Stepwise linear regression suggested that initial body fat levels (or body mass), type of treatment intervention, exercise intensity, and exercise mode accounted for most of the variance associated with changes in body composition after training.

CONCLUSIONS

Exercise is efficacious for reducing selected body composition variables in children and adolescents. The most favorable alterations in body composition occurred with 1) low-intensity, long-duration exercise; 2) aerobic exercise combined with high-repetition resistance training; and 3) exercise programs combined with a behavioral-modification component.

Mass-spectrometry-linked screening of protein fractions for enzymatic activities--a tool for functional genomics

A simple and rapid strategy is described to screen protein fractions for defined enzymatic activity. A protein fraction from a porcine kidney extract was immobilized by covalent coupling to activated affinity beads. The immobilized proteins were incubated with probes specific for different enzyme activities. The reaction products were analyzed by matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry. The MALDI spectra indicate the presence of 5'-nucleotidase, phosphatase, kinase, glutathione reductase, and renin activities in the kidney protein extract. Furthermore, the method can be used to screen for inhibitors of enzymatic reactions. The method is adaptable to high-throughput sample handling and automated mass spectrometric analysis and therefore suited for functional genomics.

Invited review: gravitational biology of the neuromotor systems: a perspective to the next era

Earth's gravity has had a significant impact on the designs of the neuromotor systems that have evolved. Early indications are that gravity also plays a key role in the ontogenesis of some of these design features. The purpose of the present review is not to assess and interpret a body of knowledge in the usual sense of a review but to look ahead, given some of the general concepts that have evolved and observations made to date, which can guide our future approach to gravitational biology. We are now approaching an era in gravitational biology during which well-controlled experiments can be conducted for sustained periods in a microgravity environment. Thus it is now possible to study in greater detail the role of gravity in phylogenesis and ontogenesis. Experiments can range from those conducted on the simplest levels of organization of the components that comprise the neuromotor system to those conducted on the whole organism. Generally, the impact of Earth's gravitational environment on living systems becomes more complex as the level of integration of the biological phenomenon of interest increases. Studies of the effects of gravitational vectors on neuromotor systems have and should continue to provide unique insight into these mechanisms that control and maintain neural control systems designed to function in Earth's gravitational environment. A number of examples are given of how a gravitational biology perspective can lead to a clearer understanding of neuromotor disorders. Furthermore, the technologies developed for spaceflight studies have contributed and should continue to contribute to studies of motor dysfunctions, such as spinal cord injury and stroke. Disorders associated with energy support and delivery systems and how these functions are altered by sedentary life styles at 1 G and by space travel in a microgravity environment are also discussed.