Community Dynamics in the Mouse Gut Microbiota: A Possible Role for IRF9-Regulated Genes in Community Homeostasis

Background

Gut microbial communities of mammals are thought to show stable differences between individuals. This means that the properties imparted by the gut microbiota become a unique and constant characteristic of the host. Manipulation of the microbiota has been proposed as a useful tool in health care, but a greater understanding of mechanisms which lead to community stability is required. Here we have examined the impact of host immunoregulatory phenotype on community dynamics.

Methods and Findings

Denaturing gradient gel electrophoresis was used to analyse the faecal bacterial community of BALB/c and C57BL/6 mice and C57BL/6 mice deficient for either type I interferon (IFN) signalling (IRF9 KO mice) or type I and type II IFN signalling (STAT1 KO mice). Temporal variation was found in all mouse strains. A measure of the ability for a community structure characteristic of the host to be maintained over time, the individuality index, varied between mouse strains and available data from pigs and human models. IRF9 KO mice had significantly higher temporal variation, and lower individuality, than other mouse strains. Examination of the intestinal mucosa of the IRF9 KO mice revealed an increased presence of T-cells and neutrophils in the absence of inflammation.

Significance

The high temporal variation observed in the gut microbiota of inbred laboratory mice has implications for their use as experimental models for the human gut microbiota. The distinct IRF9 and STAT1 phenotypes suggest a role for IRF9 in immune regulation within the gut mucosa and that further study of interferon responsive genes is necessary to understand host-gut microbe relationships.     

OnEX: Exploring changes in life science ontologies

Background  

Numerous ontologies have recently been developed in life sciences to support a consistent annotation of biological objects, such as genes or proteins. These ontologies underlie continuous changes which can impact existing annotations. Therefore, it is valuable for users of ontologies to study the stability of ontologies and to see how many and what kind of ontology changes occurred.     

Enzymatically active mammalian ribonucleotide reductase exists primarily as an alpha6beta2 octamer

Ribonucleotide reductase synthesizes deoxyribonucleotides, which are essential building blocks for DNA synthesis. The mammalian ribonucleotide reductase is described as an alpha(2)beta(2) complex consisting of R1 (alpha) and R2 (beta) proteins. ATP stimulates and dATP inhibits enzyme activity by binding to an allosteric site called the activity site on the R1 protein. Despite the opposite effects by ATP and dATP on enzyme activity, both nucleotides induce formation of R1 oligomers. By using a new technique termed Gas-phase Electrophoretic-Mobility Macromolecule Analysis (GEMMA), we have found that the ATP/dATP-induced R1 oligomers have a defined size (hexamers) and can interact with the R2 dimer to form an enzymatically active protein complex (alpha(6)beta(2)). The newly discovered alpha(6)beta(2) complex can either be in an active or an inhibited state depending on whether ATP or dATP is bound. Our results suggest that this protein complex is the major form of ribonucleotide reductase at physiological levels of R1-R2 protein and nucleotides.     

The translocation inhibitor CAM741 interferes with vascular cell adhesion molecule 1 signal peptide insertion at the translocon

The cyclopeptolide CAM741 selectively inhibits cotranslational translocation of vascular cell adhesion molecule 1 (VCAM1), a process that is dependent on its signal peptide. In this study we identified the C-terminal (C-) region upstream of the cleavage site of the VCAM1 signal peptide as most critical for inhibition of translocation by CAM741, but full sensitivity to the compound also requires residues of the hydrophobic (h-) region and the first amino acid of the VCAM1 mature domain. The murine VCAM1 signal peptide, which is less susceptible to translocation inhibition by CAM741, can be converted into a fully sensitive signal peptide by two amino acid substitutions identified as critical for compound sensitivity of the human VCAM1 signal peptide. Using cysteine substitutions of non-critical residues in the human VCAM1 signal peptide and chemical cross-linking of targeted short nascent chains we show that, in the presence of CAM741, the N- and C-terminal segments of the VCAM1 signal peptide could be cross-linked to the cytoplasmic tail of Sec61beta, indicating altered positioning of the VCAM1 signal peptide relative to this translocon component. Moreover, translocation of a tag fused N-terminal to the VCAM1 signal peptide is selectively inhibited by CAM741. Our data indicate that the compound inhibits translocation of VCAM1 by interfering with correct insertion of its signal peptide into the translocon.     

Reducing uncertainty in projections of extinction risk from climate change

Aim Concern over the implications of climate change for biodiversity has led to the use of species–climate ‘envelope’ models to forecast risks of species extinctions under climate change scenarios. Recent studies have demonstrated significant variability in model projections and there remains a need to test the accuracy of models and to reduce uncertainties. Testing of models has been limited by a lack of data against which projections of future ranges can be tested. Here we provide a first test of the predictive accuracy of such models using observed species’ range shifts and climate change in two periods of the recent past. Location Britain. Methods Observed range shifts for 116 breeding bird species in Britain between 1967 and 1972 (t₁) and 1987–91 (t₂) are used. We project range shifts between t₁ and t₂ for each species based on observed climate using 16 alternative models (4 methods × 2 data parameterizations × 2 rules to transform probabilities of occurrence into presence and absence records). Results Modelling results were extremely variable, with projected range shifts varying both in magnitude and in direction from observed changes and from each other. However, using approaches that explore the central tendency (consensus) of model projections, we were able to improve agreement between projected and observed shifts significantly. Conclusions Our results provide the first empirical evidence of the value of species–climate ‘envelope’ models under climate change and demonstrate reduction in uncertainty and improvement in accuracy through selection of the most consensual projections.     

A New Fluorescence Method for the Continuous Determination of Surface Lipid Oxidation in Lipoproteins and Plasma

We report on a new method for the determination of lipid oxidation in lipoproteins and plasma. The biological lipid system is preloaded with a fluorescent analog of phosphatidylcholine containing diphenylhexatriene (DPH) propionic acid covalently linked to the sn-2 position. When externally added, the respective phospholipid label (DPHPC) localizes to the surface monolayer of a lipoprotein. Under oxidative conditions (e.g. in the presence of Cu²⁺ ions) the fluorophore undergoes decomposition, resulting in a continuous decrease of fluorescence intensity which reflects the oxidation of a chemically defined phospholipid molecule with well defined localization. When incorporated into LDL particles, the kinetics of the decrease in DPHPC fluorescence intensity upon exposure to Cu²⁺ is very similar to that of conjugated diene accumulation. Furthermore, our assay can be applied to follow the oxidation of lipids in diluted serum and may also be developed into a suitable test system for clinical studies of susceptibility of plasma lipids to oxidation.