Mice in the ENCODE spotlight

Response of adult stem cell populations to a high-fat/high-fiber diet in skeletal muscle and adipose tissue of growing pigs divergently selected for feed efficiency

PURPOSE

The control of body composition by genetics and dietary nutrients is of the upmost importance for both human and animal physiology. Adult stem cells (aSC) may represent a relevant level of tissue adaptation. The purpose of this study was to determine the impact of macronutrient composition on aSC populations isolated from adipose tissue or muscle in growing pigs.

METHODS

Pigs from two lines divergently selected for feed efficiency were fed ad libitum either a high-fat/high-fiber (HF) diet or a low-fat/low-fiber (LF) diet (n = 6 per line and diet) from 74 to 132 days of age. Stroma vascular cells were isolated from adipose tissue and muscle and characterized with cell surface markers.

RESULTS

In both lines, pigs fed the HF diet exhibited a reduced adiposity (P < 0.001) compared with pigs fed the LF diet. In the four groups, CD90 and PDGFRα markers were predominantly expressed in adipose cells, whereas CD90 and CD56 markers were highly expressed in muscle cells. In adipose tissue, the proportions of CD56+/PDGFRα + and of CD90+/PDGFRα + cells were lower (P < 0.05) in HF pigs than in LF pigs. On the opposite, in muscle, these proportions were higher (P < 0.001) in HF pigs.

CONCLUSION

This study indicates that dietary nutrients affected the relative proportions of CD56+/PDGFRα + cells with opposite effects between muscle and adipose tissue. These cell populations exhibiting adipogenic potential in adipose tissue and myogenic potential in muscle may be a target to modulate body composition.

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells

Transposable elements (TEs) are thought to have helped establish gene regulatory networks. Both the embryonic and extraembryonic lineages of the early mouse embryo have seemingly co-opted TEs as enhancers, but there is little evidence that they play significant roles in gene regulation. Here we tested a set of long terminal repeat TE families for roles as enhancers in mouse embryonic and trophoblast stem cells. Epigenomic and transcriptomic data suggested that a large number of TEs helped to establish tissue-specific gene expression programmes. Genetic editing of individual TEs confirmed a subset of these regulatory relationships. However, a wider survey via CRISPR interference of RLTR13D6 elements in embryonic stem cells revealed that only a minority play significant roles in gene regulation. Our results suggest that a subset of TEs are important for gene regulation in early mouse development, and highlight the importance of functional experiments when evaluating gene regulatory roles of TEs.

Recent developments in severe sepsis research: from bench to bedside and back

Severe sepsis remains a worldwide threat, not only in industrialized countries, due to their aging population, but also in developing countries where there still are numerous cases of neonatal and puerperal sepsis. Tools for early diagnosis, a prerequisite for rapid and appropriate antibiotic therapy, are still required. In this review, we highlight some recent developments in our understanding of the associated systemic inflammatory response that help deciphering pathophysiology (e.g., epigenetic, miRNA, regulatory loops, compartmentalization, apoptosis and synergy) and discuss some of the consequences of sepsis (e.g., immune status, neurological and muscular alterations). We also emphasize the challenge to better define animal models and discuss past failures in clinical investigations in order to define new efficient therapies.

Application of Functional Genomics for Bovine Respiratory Disease Diagnostics

Bovine respiratory disease (BRD) is the most common economically important disease affecting cattle. For developing accurate diagnostics that can predict disease susceptibility/resistance and stratification, it is necessary to identify the molecular mechanisms that underlie BRD. To study the complex interactions among the bovine host and the multitude of viral and bacterial pathogens, as well as the environmental factors associated with BRD etiology, genome-scale high-throughput functional genomics methods such as microarrays, RNA-seq, and proteomics are helpful. In this review, we summarize the progress made in our understanding of BRD using functional genomics approaches. We also discuss some of the available bioinformatics resources for analyzing high-throughput data, in the context of biological pathways and molecular interactions. Although resources for studying host response to infection are avail-able, the corresponding information is lacking for majority of BRD pathogens, impeding progress in identifying diagnostic signatures for BRD using functional genomics approaches.

NMR-based metabolomics highlights differences in plasma metabolites in pigs exhibiting diet-induced differences in adiposity

PURPOSE

A better understanding of the control of body fat mass and distribution is required for both human health and animal production. The current study investigates plasma parameters in response to changes in body fat mass.

METHODS

Pigs from two lines divergently selected for residual feed intake were fed diets contrasted in energy sources and nutrients. Between 74 and 132 days of age, pigs (n = 12 by diet and by line) received isoproteic and isoenergetic diets, either rich in starch (LF) or in lipids and fibres (HF). At the end of the feeding trial, plasma samples were analysed by (1)H NMR spectroscopy and standard hormonal and biochemical assays.

RESULTS

Pigs fed the HF diet had lower (P < 0.01) perirenal and subcutaneous adipose tissue relative masses than pigs fed the LF diet. Metabolomic approach showed a clear discrimination between diets, with lower (P < 0.05) plasma levels of creatinine-lysine, creatine, tyrosine, proline, histidine, lysine, phenylalanine and formate but higher (P < 0.001) plasma VLDL-LDL levels in HF pigs than in LF pigs. Plasma concentrations of triglycerides were higher (P < 0.001), while plasma concentrations of β-hydroxybutyrate, leptin, glucose, insulin and urea were lower (P ≤ 0.05) in HF pigs than in LF pigs. Plasma levels of leptin, creatine and urea were positively correlated (r = 0.3, P < 0.05) with relative adipose tissue masses.

CONCLUSION

These data indicate that metabolites associated with energy and protein metabolism were involved in the response to a high-fat, high-fibre diet. Relevant plasma indicators of metabolic flexibility related to changes in body adiposity were then proposed.

Analysis of RNA from Alzheimer's Disease Post-mortem Brain Tissues

Alzheimer's disease (AD) is a uniquely human, age-related central nervous system (CNS) disorder for which there is no adequate experimental model. While well over 100 transgenic murine models of AD (TgAD) have been developed that recapitulate many of the neuropathological features of AD, key pathological features of AD such as progressive neuronal atrophy, neuron cell loss, and neurofibrillary tangle (NFT) formation have not been observed in any TgAD model to date. To more completely analyze and understand the neuropathology, altered neuro-inflammatory and innate-immune signaling pathways, and the complex molecular-genetics and epigenetics of AD, it is therefore necessary to rigorously examine short post-mortem interval (PMI) human brain tissues to gain a deeper and more thorough insight into the neuropathological mechanisms that characterize the AD process. This perspective-methods paper will highlight some important recent findings on the utilization of short PMI tissues in sporadic (idiopathic; of unknown origin) AD research with focus on the extraction and quantification of RNA, and in particular microRNA (miRNA) and messenger RNA (mRNA) and analytical strategies, drawing on the authors' combined 125 years of laboratory experience into this investigative research area. We sincerely hope that new investigators in the field of "gene expression analysis in neurological disease" will benefit from the observations presented here and incorporate these recent findings and observations into their future experimental planning and design.