Association of the Gut Microbiota with the Host's Health through an Analysis of Biochemical Markers, Dietary Estimation, and Microbial Composition

This research was funded by Centro Tecnológico para el Desarrollo Industrial (CDTI) through the program Consorcio de Investigación Empresarial Nacional (Programa CIEN, BIOFOOD Project) and by CIBERobn (Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CB12/03/30002).This study aims to analyze the relationship between gut microbiota composition and health parameters through specific biochemical markers and food consumption patterns in the Spanish population. This research includes 60 Spanish adults aged 47.3 ± 11.2 years old. Biochemical and anthropometric measurements, and a self-referred dietary survey (food frequency questionnaire), were analyzed and compared with the participant's gut microbiota composition analyzed by 16s rDNA sequencing. Several bacterial strains differed significantly with the biochemical markers analyzed, suggesting an involvement in the participant's metabolic health. Lower levels of Lactobacillaceae and Oscillospiraceae and an increase in Pasteurellaceae, Phascolarctobacterium, and Haemophilus were observed in individuals with higher AST levels. Higher levels of the Christensenellaceae and a decrease in Peptococcaceae were associated with higher levels of HDL-c. High levels of Phascolarctobacterium and Peptococcus and low levels of Butyricicoccus were found in individuals with higher insulin levels. This study also identified associations between bacteria and specific food groups, such as an increase in lactic acid bacteria with the consumption of fermented dairy products or an increase in Verrucomicrobiaceae with the consumption of olive oil. In conclusion, this study reinforces the idea that specific food groups can favorably modulate gut microbiota composition and have an impact on host's health

Innovación abierta en tecnología, diseño y dinámicas sociales

ITESO, A.C

Skittle: A 2-Dimensional Genome Visualization Tool

<p>Abstract</p> <p>Background</p> <p>It is increasingly evident that there are multiple and overlapping patterns within the genome, and that these patterns contain different types of information - regarding both genome function and genome history. In order to discover additional genomic patterns which may have biological significance, novel strategies are required. To partially address this need, we introduce a new data visualization tool entitled Skittle.</p> <p>Results</p> <p>This program first creates a 2-dimensional nucleotide display by assigning four colors to the four nucleotides, and then text-wraps to a user adjustable width. This nucleotide display is accompanied by a "repeat map" which comprehensively displays all local repeating units, based upon analysis of all possible local alignments. Skittle includes a smooth-zooming interface which allows the user to analyze genomic patterns at any scale.</p> <p>Skittle is especially useful in identifying and analyzing tandem repeats, including repeats not normally detectable by other methods. However, Skittle is also more generally useful for analysis of any genomic data, allowing users to correlate published annotations and observable visual patterns, and allowing for sequence and construct quality control.</p> <p>Conclusions</p> <p>Preliminary observations using Skittle reveal intriguing genomic patterns not otherwise obvious, including structured variations inside tandem repeats. The striking visual patterns revealed by Skittle appear to be useful for hypothesis development, and have already led the authors to theorize that imperfect tandem repeats could act as information carriers, and may form tertiary structures within the interphase nucleus.</p

All-particle cosmic ray energy spectrum measured by the HAWC experiment from 10 to 500 TeV

We report on the measurement of the all-particle cosmic ray energy spectrum with the High Altitude Water Cherenkov (HAWC) Observatory in the energy range 10 to 500 TeV. HAWC is a ground based air-shower array deployed on the slopes of Volcan Sierra Negra in the state of Puebla, Mexico, and is sensitive to gamma rays and cosmic rays at TeV energies. The data used in this work were taken from 234 days between June 2016 to February 2017. The primary cosmic-ray energy is determined with a maximum likelihood approach using the particle density as a function of distance to the shower core. Introducing quality cuts to isolate events with shower cores landing on the array, the reconstructed energy distribution is unfolded iteratively. The measured all-particle spectrum is consistent with a broken power law with an index of $-2.49\pm0.01$ prior to a break at $(45.7\pm0.1$) TeV, followed by an index of $-2.71\pm0.01$. The spectrum also respresents a single measurement that spans the energy range between direct detection and ground based experiments. As a verification of the detector response, the energy scale and angular resolution are validated by observation of the cosmic ray Moon shadow's dependence on energy.Comment: 16 pages, 11 figures, 4 tables, submission to Physical Review

Observation of the Crab Nebula with the HAWC Gamma-Ray Observatory

The Crab Nebula is the brightest TeV gamma-ray source in the sky and has been used for the past 25 years as a reference source in TeV astronomy, for calibration and verification of new TeV instruments. The High Altitude Water Cherenkov Observatory (HAWC), completed in early 2015, has been used to observe the Crab Nebula at high significance across nearly the full spectrum of energies to which HAWC is sensitive. HAWC is unique for its wide field-of-view, nearly 2 sr at any instant, and its high-energy reach, up to 100 TeV. HAWC's sensitivity improves with the gamma-ray energy. Above $\sim$1 TeV the sensitivity is driven by the best background rejection and angular resolution ever achieved for a wide-field ground array. We present a time-integrated analysis of the Crab using 507 live days of HAWC data from 2014 November to 2016 June. The spectrum of the Crab is fit to a function of the form $\phi(E) = \phi_0 (E/E_{0})^{-\alpha -\beta\cdot{\rm{ln}}(E/E_{0})}$. The data is well-fit with values of $\alpha=2.63\pm0.03$, $\beta=0.15\pm0.03$, and log$_{10}(\phi_0~{\rm{cm}^2}~{\rm{s}}~{\rm{TeV}})=-12.60\pm0.02$ when $E_{0}$ is fixed at 7 TeV and the fit applies between 1 and 37 TeV. Study of the systematic errors in this HAWC measurement is discussed and estimated to be $\pm$50\% in the photon flux between 1 and 37 TeV. Confirmation of the Crab flux serves to establish the HAWC instrument's sensitivity for surveys of the sky. The HAWC survey will exceed sensitivity of current-generation observatories and open a new view of 2/3 of the sky above 10 TeV.Comment: Submitted 2017/01/06 to the Astrophysical Journa

Constraining the pˉ/p\bar{p}/p Ratio in TeV Cosmic Rays with Observations of the Moon Shadow by HAWC

An indirect measurement of the antiproton flux in cosmic rays is possible as the particles undergo deflection by the geomagnetic field. This effect can be measured by studying the deficit in the flux, or shadow, created by the Moon as it absorbs cosmic rays that are headed towards the Earth. The shadow is displaced from the actual position of the Moon due to geomagnetic deflection, which is a function of the energy and charge of the cosmic rays. The displacement provides a natural tool for momentum/charge discrimination that can be used to study the composition of cosmic rays. Using 33 months of data comprising more than 80 billion cosmic rays measured by the High Altitude Water Cherenkov (HAWC) observatory, we have analyzed the Moon shadow to search for TeV antiprotons in cosmic rays. We present our first upper limits on the $\bar{p}/p$ fraction, which in the absence of any direct measurements, provide the tightest available constraints of $\sim1\%$ on the antiproton fraction for energies between 1 and 10 TeV.Comment: 10 pages, 5 figures. Accepted by Physical Review

Calibration of the Logarithmic-Periodic Dipole Antenna (LPDA) Radio Stations at the Pierre Auger Observatory using an Octocopter

An in-situ calibration of a logarithmic periodic dipole antenna with a frequency coverage of 30 MHz to 80 MHz is performed. Such antennas are part of a radio station system used for detection of cosmic ray induced air showers at the Engineering Radio Array of the Pierre Auger Observatory, the so-called Auger Engineering Radio Array (AERA). The directional and frequency characteristics of the broadband antenna are investigated using a remotely piloted aircraft (RPA) carrying a small transmitting antenna. The antenna sensitivity is described by the vector effective length relating the measured voltage with the electric-field components perpendicular to the incoming signal direction. The horizontal and meridional components are determined with an overall uncertainty of 7.4^{+0.9}_{-0.3} % and 10.3^{+2.8}_{-1.7} % respectively. The measurement is used to correct a simulated response of the frequency and directional response of the antenna. In addition, the influence of the ground conductivity and permittivity on the antenna response is simulated. Both have a negligible influence given the ground conditions measured at the detector site. The overall uncertainties of the vector effective length components result in an uncertainty of 8.8^{+2.1}_{-1.3} % in the square root of the energy fluence for incoming signal directions with zenith angles smaller than 60{\deg}.Comment: Published version. Updated online abstract only. Manuscript is unchanged with respect to v2. 39 pages, 15 figures, 2 table

Multi-resolution anisotropy studies of ultrahigh-energy cosmic rays detected at the Pierre Auger Observatory

We report a multi-resolution search for anisotropies in the arrival directions of cosmic rays detected at the Pierre Auger Observatory with local zenith angles up to $80^\circ$ and energies in excess of 4 EeV ($4 \times 10^{18}$ eV). This search is conducted by measuring the angular power spectrum and performing a needlet wavelet analysis in two independent energy ranges. Both analyses are complementary since the angular power spectrum achieves a better performance in identifying large-scale patterns while the needlet wavelet analysis, considering the parameters used in this work, presents a higher efficiency in detecting smaller-scale anisotropies, potentially providing directional information on any observed anisotropies. No deviation from isotropy is observed on any angular scale in the energy range between 4 and 8 EeV. Above 8 EeV, an indication for a dipole moment is captured; while no other deviation from isotropy is observed for moments beyond the dipole one. The corresponding $p$-values obtained after accounting for searches blindly performed at several angular scales, are $1.3 \times 10^{-5}$ in the case of the angular power spectrum, and $2.5 \times 10^{-3}$ in the case of the needlet analysis. While these results are consistent with previous reports making use of the same data set, they provide extensions of the previous works through the thorough scans of the angular scales.Comment: Published version. Added journal reference and DOI. Added Report Numbe