Global compositional and functional states of the human gut microbiome in health and disease.

The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses.

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.

Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities' compositions of terminal ileum and large intestine in 5 healthy individuals.

Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9.

Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take center stage in regulating this process in To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1. Sites hypo-phosphorylated upon PKA and Sch9 inhibition were preferentially located in RRxS/T-motifs suggesting that many are directly phosphorylated by these enzymes. Interestingly, when inhibiting Ypk1 we not only detected several hypo-phosphorylated sites in the previously reported RxRxxS/T-, but also in an RRxS/T-motif.

Id4 promotes the elimination of the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells.

Quiescence is essential for the long-term maintenance of adult stem cells but how stem cells maintain quiescence is poorly understood. Here, we show that neural stem cells (NSCs) in the adult mouse hippocampus actively transcribe the pro-activation factor Ascl1 regardless of their activated or quiescent states. We found that the inhibitor of DNA binding protein Id4 is enriched in quiescent NSCs and that elimination of Id4 results in abnormal accumulation of Ascl1 protein and premature stem cell activation.

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

Advances in mass spectrometry have made the quantitative measurement of proteins across multiple samples a reality, allowing for the study of complex biological systems such as the metabolic syndrome. Although the deregulation of lipid metabolism and increased hepatic storage of triacylglycerides are known to play a part in the onset of the metabolic syndrome, its molecular basis and dependency on dietary and genotypic factors are poorly characterized. Here, we used an experimental design with two different mouse strains and dietary and metabolic perturbations to generate a compendium of quantitative proteome data using three mass spectrometric techniques.

Target of Rapamycin Complex 2 Regulates Actin Polarization and Endocytosis via Multiple Pathways.

Target of rapamycin is a Ser/Thr kinase that operates in two conserved multiprotein complexes, TORC1 and TORC2. Unlike TORC1, TORC2 is insensitive to rapamycin, and its functional characterization is less advanced. Previous genetic studies demonstrated that TORC2 depletion leads to loss of actin polarization and loss of endocytosis.

Parallel feedback loops control the basal activity of the HOG MAPK signaling cascade.

Tight regulation of the MAP kinase Hog1 is crucial for survival under changing osmotic conditions. Interestingly, we found that Hog1 phosphorylates multiple upstream components, implying feedback regulation within the signaling cascade. Taking advantage of an unexpected link between glucose availability and Hog1 activity, we used quantitative single cell measurements and computational modeling to unravel feedback regulation operating in addition to the well-known adaptation feedback triggered by glycerol accumulation.

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.

Cells respond to environmental stimuli via specialized signaling pathways. Concurrent stimuli trigger multiple pathways that integrate information, predominantly via protein phosphorylation. Budding yeast responds to NaCl and pheromone via two mitogen-activated protein kinase cascades, the high osmolarity, and the mating pathways, respectively.

Phosphoproteomic analysis identifies proteins involved in transcription-coupled mRNA decay as targets of Snf1 signaling.

Stresses, such as glucose depletion, activate Snf1, the Saccharomyces cerevisiae ortholog of adenosine monophosphate-activated protein kinase (AMPK), enabling adaptive cellular responses. In addition to affecting transcription, Snf1 may also promote mRNA stability in a gene-specific manner. To understand Snf1-mediated signaling, we used quantitative mass spectrometry to identify proteins that were phosphorylated in a Snf1-dependent manner.

Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A.

The TORC1 and PKA protein kinases are central elements of signaling networks that regulate eukaryotic cell proliferation in response to growth factors and/or nutrients. In yeast, attenuation of signaling by these kinases following nitrogen and/or carbon limitation activates the protein kinase Rim15, which orchestrates the initiation of a reversible cellular quiescence program to ensure normal chronological life span. The molecular elements linking Rim15 to distal readouts including the expression of Msn2/4- and Gis1-dependent genes involve the endosulfines Igo1/2.

Mid-term evaluation of the effects of dynamic neutralization system on lumbar intervertebral discs using quantitative molecular MR imaging.

Purpose: To evaluate the mid-term effects of implant of dynamic neutralization system (Dynesys) on disc tissue in patients with lumbar discopathy, through the quantification of glycosaminoglycans (GAG) concentration, both in treated and adjacent levels, by analysis of delayed gadolinium-enhanced MRI contrast (dGEMRIC) images.

Materials And Methods: Ten patients with low back pain underwent the dGEMRIC diagnostic protocol before, 6-months and after 2 years from surgery. Each patient was also evaluated with visual analog (VAS), Oswestry, and Prolo scales both at presurgery and during follow-up.

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae.

Nutrient sensing and coordination of metabolic pathways are crucial functions for all living cells, but details of the coordination under different environmental conditions remain elusive. We therefore undertook a systems biology approach to investigate the interactions between the Snf1 and the target of rapamycin complex 1 (TORC1) in Saccharomyces cerevisiae. We show that Snf1 regulates a much broader range of biological processes compared with TORC1 under both glucose- and ammonium-limited conditions.

Magnetic resonance imaging of human endothelial progenitors reveals opposite effects on vascular and muscle regeneration into ischaemic tissues.

Aims: The assessment of progenitor cell survival and efficacy after transplantation is one of the major challenges in cardiovascular cell therapy. Translation of currently used imaging techniques to patients is not immediate. Possible options include iron oxide particle loading into cells to be tracked using magnetic resonance (MR) and by MR-based water diffusion anisotropy analysis.

Division scheme optimization for the molecular evaluation of the intervertebral disc by Gadolinium-Enhanced MRI.

Purpose: To evaluate the effects of reducing the number of segments in which the intervertebral disc (IVD) can be subdivided on the accuracy in estimating its sGAG content by computation of the parameter DeltaT1 from delayed Gadolinium-Enhanced MRI of Cartilage (dGEMRIC) protocol.

Materials And Methods: Twenty-three herniectomy patients underwent dGEMRIC acquisitions for IVD. Thirty-one tissue samples were obtained at herniectomy from the same patients and biochemically analysed for their sGAG content.

Molecular MR imaging for the evaluation of the effect of dynamic stabilization on lumbar intervertebral discs.

The dynamic stabilization of lumbar spine is a non-fusion stabilization system that unloads the disc without the complete loss of motion at the treated motion segment. Clinical outcomes are promising but still not definitive, and the long-term effect on instrumented and adjacent levels is still a matter of discussion. Several experiments have been devised in order to gain a better understanding of the effect of the device on the intervertebral disc.

Quantitative assessment of intervertebral disc glycosaminoglycan distribution by gadolinium-enhanced MRI in orthopedic patients.

Our hypothesis was that the enhanced MRI of cartilage (dGEMRIC) imaging protocol could be used in patients to quantify the sulfated glycosaminoglycan (sGAG) in intervertebral discs (IVD). To test this hypothesis, 23 patients with degenerative disc pathology scheduled for surgery were studied by a specific dGEMRIC protocol: each patient underwent two MRI scans, before and 3.5 hr after Gd(DTPA)2-injection of a nonconventional dose of 40 mL.