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

On How to Extend the NIR Tully-Fisher Relation to be Truly All-Sky

Dust extinction and stellar confusion by the Milky Way reduce the efficiency of detecting galaxies at low Galactic latitudes, creating the so-called Zone of Avoidance. This stands as a stumbling block in charting the distribution of galaxies and cosmic flow fields, and therewith our understanding of the local dynamics in the Universe (CMB dipole, convergence radius of bulk flows). For instance, ZoA galaxies are generally excluded from the whole-sky Tully-Fisher Surveys ($|b| \leq 5^\circ$) even if catalogued. We show here that by fine-tuning the near-infrared TF relation, there is no reason not to extend peculiar velocity surveys deeper into the ZoA. Accurate axial ratios ($b/a$) are crucial to both the TF sample selection and the resulting TF distances. We simulate the effect of dust extinction on the geometrical properties of galaxies. As expected, galaxies appear rounder with increasing obscuration level, even affecting existing TF samples. We derive correction models and demonstrate that we can reliably reproduce the intrinsic axial ratio from the observed value up to extinction level of about $A_J\simeq3$ mag ($A_V\sim11$ mag), we also recover a fair fraction of galaxies that otherwise would fall out of an uncorrected inclination limited galaxy sample. We present a re-calibration of the 2MTF relation in the NIR $J$, $H$, and $K_s$-bands for isophotal rather than total magnitudes, using their same calibration sample. Both TF relations exhibit similar scatter at high Galactic latitudes. However, the isophotal TF relation results in a significant improvement in the scatter for galaxies in the ZoA, and low surface brightness galaxies in general, because isophotal apertures are more robust in the face of significant stellar confusion.Comment: 12 pages, 10 figures, 4 tables, accepted for publication in MNRA

The HI mass function in the Parkes HI Zone of Avoidance survey

An HI mass function (HIMF) was derived for 751 galaxies selected from the deep Parkes HI survey across the Zone of Avoidance (HIZOA). HIZOA contains both the Great Attractor Wall and the Local Void, two of the most extreme environments in the local Universe, making the sample eminently suitable to explore the overall HIMF as well as its dependence on local environment. To avoid any selection bias because of the different distances of these large-scale structures, we first used the two-dimensional stepwise maximum-likelihood method for the definition of an average HIMF. The resulting parameters of a Schechter-type HIMF for the whole sample are $\alpha = -1.33\pm0.05$, $\log(M_{\rm HI}^*/M_{\odot})=9.93\pm0.04$, and $\phi^* = (3.9\pm0.6)\times 10^{-3}$ Mpc$^{-3}$. We then used the $k$-th nearest-neighbour method to subdivide the sample into four environments of decreasing local density and derived the Schechter parameters for each subsample. A strong trend is observed, for the slope $\alpha$ of the low-mass end of the HIMF. The slope changes from being nearly flat, i.e. $\alpha = -0.99\pm0.19$ for galaxies residing in the densest bin, to the steep value of $\alpha = -1.31\pm0.10$ in the lowest density bin. The characteristic mass, however, does not show a clear trend between the highest and lowest density bins. We find similar trends in the low-mass slope when we compare the results for a region dominated by the Great Attractor, and the Local Void, which are found to be over-, respectively underdense by 1.35 and 0.59 compared to the whole sample.Comment: 10 pages, 13 figures, 4 tables, accepted for publication in MNRA

Galaxy peculiar velocities in the Zone of Avoidance

Dust extinction and stellar confusion of the Milky Way hinder the detection of galaxies at low Galactic latitude, creating the so-called Zone of Avoidance (ZoA). This has hampered our understanding of the local dynamics, cosmic flow fields and the origin of the Cosmic Microwave Background dipole. The ZoA ($|b| \le 5^\circ$) is also excluded from the "whole-sky" Two Micron All-Sky Survey (2MASS) Redshift Survey (2MRS) and 2MASS Tully-Fisher Survey (2MTF). The latter aims to provide distances and peculiar velocities for all bright inclined 2MASS galaxies with $K_s^o$ \leq 11\hbox{.\!\!^{\rm m}}25. Correspondingly, knowledge about the density distribution in the ZoA remains limited to statistical interpolations. To improve on this bias we pursued two different surveys to fill in the southern and northern ZoA. These data will allow a direct measurement of galaxy peculiar velocities. In this paper we will present a newly derived optimized Tully-Fisher (TF) relation that allow accurate measures of galaxy distances and peculiar velocities for dust-obscured galaxies. We discuss further corrections for magnitudes and biases and present some preliminary results on flow fields in the southern ZoA.Comment: 6 pages, 3 figures, to appear in Proceedings of SAIP2013, the 58th Annual Conference of the South African Institute of Physics, edited by Roelf Botha and Thulani Jili (SAIP and University of Zululand, 2014). ISBN: 978-0-620-62819-

Lung Circulation Modeling: Status and Prospect

Mathematical modeling has been used to interpret anatomical and physiological data obtained from metabolic and hemodynamic studies aimed at investigating structure-function relationships in the vasculature of the lung, and how these relationships are affected by lung injury and disease. The indicator dilution method was used to study the activity of redox processes within the lung. A steady-state model of the data was constructed and used to show that pulmonary endothelial cells may play an important role in reducing redox active compounds and that those reduction rates can be altered with oxidative stress induced by exposure to high oxygen environments. In addition, a morphometric model of the pulmonary vasculature was described and used to detect, describe,and predict changes in vascular morphology that occur in response to chronic exposure to low-oxygen environments, a common model of pulmonary hypertension. Finally, the model was used to construct simulated circulatory networks designed to aid in evaluation of competing hypotheses regarding the relative contribution of various morphological and biomechanical changes observed with hypoxia. These examples illustrate the role of mathematical modeling in the integration of the emerging metabolic, hemodynamic, and morphometric databases

Optimisasi Penambahan Limbah Drilling Cutting pada Proses Bioremediasi

The company ways to maintain its production of crude oil, by drilling new wells and wells that have done some existing treatments. These activities will generate waste, and called with sludge drilling cutting. Characteristics of drilling cutting waste is similar to petroleum-contaminated soil. Based on the Decree of the Minister of the Environment No. 128 of 2003 on Procedures for the Technical Requirements for Waste Oil and Soil Contaminated by Petroleum Biological, waste oil is classified as hazardous and toxic waste ( B3 ) . One way to improve the quality of petroleum-contaminated soil is bioremediation techniques . In the process of bioremediation, microbes in the soil to degrade hydrocarbons that contaminate the soil. In this study drilling cutting waste is added to the oil- contaminated soil samples, which will be processed in bioremediation using naturally existing microorganisms. The results of the most effective and efficient comparison of the addition of contaminated soil and drilling cutting waste is 3:2 and its supported by the pH value of the sample in neutral pH range ( 6,5 - 7,5 ), because the hydrocarbon degrading bacteria can grow well on the pH