Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine

Background: The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract. Results: In coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small intestine bile acid pool, and, importantly, could not be inferred from analyzing large intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine. Conclusions: Future studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small intestine microbiome and to small intestine dysbiosis

Impact of anthropogenic disturbances on beetle communities of French Mediterranean coastal dunes

In coastal dunes, influenced by anthropogenic activities such as tourism, it is important to determine the relative influence of environmental factors at different spatial scales to evaluate the sensitivity of local communities to disturbances. We analyzed beetle communities of 14 dunes of the French Mediterranean coast: four in the relatively preserved Camargue area, and ten in the Var department, where tourism is intensive. Beetle communities were studied three times in early spring using sand sampling. Species-environment relationships were evaluated at the regional, landscape and local scale using redundancy analysis (RDA) and variability partitioning. About 28 species were identified, of which 15 were sand-specialist species, which accounted for more than 93% of total abundance. The beetle communities of Camargue were significantly different from those of the Var department owing to the pullulation of a Tenebrionid species (Trachyscelis aphodioides Latr.) in the Var, except for one restored dune where the community was very similar to those of Camargue. Our results showed no longitudinal gradient between the two regions. Local factors (dune height, preservation and disturbance index) significantly explained most of the variation in the dominance of T. aphodioides, while some other local factors were important for other psammophilous species. This study also suggests that dune beetle communities are strongly affected on beaches intensively managed for tourism, but beetles are still abundant in much disturbed sites

Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification

Isothermal amplification assays, such as loop-mediated isothermal amplification (LAMP), show great utility for the development of rapid diagnostics for infectious diseases because they have high sensitivity, pathogen-specificity and potential for implementation at the point of care. However, elimination of non-specific amplification remains a key challenge for the optimization of LAMP assays. Here, using chlamydia DNA as a clinically relevant target and high-throughput sequencing as an analytical tool, we investigate a potential mechanism of non-specific amplification. We then develop a real-time digital LAMP (dLAMP) with high-resolution melting temperature (HRM) analysis and use this single-molecule approach to analyze approximately 1.2 million amplification events. We show that single-molecule HRM provides insight into specific and non-specific amplification in LAMP that are difficult to deduce from bulk measurements. We use real-time dLAMP with HRM to evaluate differences between polymerase enzymes, the impact of assay parameters (e.g. time, rate or florescence intensity), and the effect background human DNA. By differentiating true and false positives, HRM enables determination of the optimal assay and analysis parameters that leads to the lowest limit of detection (LOD) in a digital isothermal amplification assay

Première approche par l'analyse anthracologique de la végétation de Tin Ouaffadene (gisement archéologique de l'holocène ancien, Niger nord-oriental)

Dans le site archéologique de Tin Ouaffadene (Niger nord-oriental), dont l'étude de la faune a fait l'objet d'une publication antérieure, un paléolac daté d'environ 9000 ans a recouvert une zone d'occupation humaine riche en fragments de charbons de bois. L'analyse anthracologique a révélé la présence de Calotropis procera et Leptadenia pyrotechnica. Ces deux espèces, rarement utilisées comme bois de chauffage, servent essentiellement à des constructions légères. Ces charbons correspondraient donc aux restes d'un abri. Ces données montrent bien l'intérêt des déterminations anthracologiques en archéologie. (Résumé d'auteur

Brans-Dicke-type theories and avoidance of the cosmological singularity

We tudy flat Friedmann-Robertson-Walker cosmology in Brans-Dicke-type theories of gravitation with minimal coupling between the scalar field and the matter fields in the Einstein frame (general relativity with an extra scalar field) for arbitrary values of the Brans-Dicke parameter $\omega>-{3/2}$. It is shown that the cosmological singularity occuring in the Einstein frame formulation of this theory is removed in the Jordan frame in the range $-{3/2}<\omega<\leq-{4/3}$. This result is interpreted in the ligth of a viewpoint (first presented in reference gr-qc/9905071) asserting that both Jordan frame and Einstein frame formulations of general relativity are physically equivalent. The implications of the obtained result for string theory are outlined.Comment: 9 pages, LaTeX, no figures. Improved version accepted for publication in PR

The Bangkok Declaration and Strategy for Aquaculture Development Beyond 2000 and Philippine Aquaculture

This paper reviews the Philippine aquaculture sector in light of the Bangkok Declaration and Strategy for Aquaculture Development Beyond 2000, an internationally produced document that strongly encourages the incorporation of key strategy elements into the national aquaculture development programs. The purpose of the paper is to identify constraints to the full incorporation of the key strategy elements into the local aquaculture program and recommend measures for addressing them. The paper found that the various key strategies mentioned in the Bangkok Declaration have already been implemented in the aquaculture sector to a significant extent. While so, however, much remains to be done to hasten the implementation of the strategies. In general, they will be better pursued if the Philippine Fisheries Code and the Agriculture and Fisheries Modernization Act are fully implemented. Adequate funding for the two laws must be provided to allow the establishment and operations of the different aquaculture institutions, programs, projects and activities they envisioned. Review of the contentious provisions of the two laws must also be conducted and amendments made at the appropriate time, if necessary. Streamlining of the different government institutions and functions involved in fisheries and aquaculture should be pursued to effect coordinated operations. Furthermore, increased support for training and extension is needed. In particular, the strengthening of regional offices of the Bureau of Fisheries and Aquatic Resources and the offices of the Local Government Units involved in extension must be given priority

Students And Faculty Perceptions Of Communications Channels: A Comparison Of Survey Results

Individual communication between faculty and students outside of the classroom is one of the cornerstones of education. This survey examines the students and faculty perceptions of three communications media for several communication tasks that occur between students and faculty. A random sample of 449 students (undergraduate and graduate, full-time and part-time) which represents 10% of the population at a small Texas state university were invited to participate in a survey that elicited their perceptions on the effectiveness of face-to-face (office hours), e-mail and telephone communication. Similarly a random sample of 49 professors, which represents 32 % of the faculty population, was used to test several hypotheses. In this survey, the relevant results supported by some nonparametric statistical analyses are that at each media channel the "bootstrapped" confidence intervals estimates for the percentages in communications-time preferences of students and faculty were very similar, or without a significant difference. In addition, students and faculty expressed simultaneously (criteria of convergence) the same preference-level about e-mail for convenience and efficiency. Office hours were preferred for confidentiality, confrontation and emotional support. Equal preference about e-mail and office hours was expressed by both groups of study for the criteria: accuracy and overall effectiveness

Parameter Estimation with Mixed-State Quantum Computation

We present a quantum algorithm to estimate parameters at the quantum metrology limit using deterministic quantum computation with one bit. When the interactions occurring in a quantum system are described by a Hamiltonian $H= \theta H_0$, we estimate $\theta$ by zooming in on previous estimations and by implementing an adaptive Bayesian procedure. The final result of the algorithm is an updated estimation of $\theta$ whose variance has been decreased in proportion to the time of evolution under H. For the problem of estimating several parameters, we implement dynamical-decoupling techniques and use the results of single parameter estimation. The cases of discrete-time evolution and reference-frame alignment are also discussed within the adaptive approach.Comment: 12 pages. Improved introduction and technical details moved to Appendi