Structure of the gut microbiome following colonization with human feces determines colonic tumor burden

Abstract Background A growing body of evidence indicates that the gut microbiome plays a role in the development of colorectal cancer (CRC). Patients with CRC harbor gut microbiomes that are structurally distinct from those of healthy individuals; however, without the ability to track individuals during disease progression, it has not been possible to observe changes in the microbiome over the course of tumorigenesis. Mouse models have demonstrated that these changes can further promote colonic tumorigenesis. However, these models have relied upon mouse-adapted bacterial populations and so it remains unclear which human-adapted bacterial populations are responsible for modulating tumorigenesis. Results We transplanted fecal microbiota from three CRC patients and three healthy individuals into germ-free mice, resulting in six structurally distinct microbial communities. Subjecting these mice to a chemically induced model of CRC resulted in different levels of tumorigenesis between mice. Differences in the number of tumors were strongly associated with the baseline microbiome structure in mice, but not with the cancer status of the human donors. Partitioning of baseline communities into enterotypes by Dirichlet multinomial mixture modeling resulted in three enterotypes that corresponded with tumor burden. The taxa most strongly positively correlated with increased tumor burden were members of the Bacteroides, Parabacteroides, Alistipes, and Akkermansia, all of which are Gram-negative. Members of the Gram-positive Clostridiales, including multiple members of Clostridium Group XIVa, were strongly negatively correlated with tumors. Analysis of the inferred metagenome of each community revealed a negative correlation between tumor count and the potential for butyrate production, and a positive correlation between tumor count and the capacity for host glycan degradation. Despite harboring distinct gut communities, all mice underwent conserved structural changes over the course of the model. The extent of these changes was also correlated with tumor incidence. Conclusion Our results suggest that the initial structure of the microbiome determines susceptibility to colonic tumorigenesis. There appear to be opposing roles for certain Gram-negative (Bacteroidales and Verrucomicrobia) and Gram-positive (Clostridiales) bacteria in tumor susceptibility. Thus, the impact of community structure is potentially mediated by the balance between protective, butyrate-producing populations and inflammatory, mucin-degrading populations.http://deepblue.lib.umich.edu/bitstream/2027.42/109448/1/40168_2014_Article_48.pd

Local Magnetic Field Role in Star Formation

We highlight distinct and systematic observational features of magnetic field morphologies in polarized submm dust continuum. We illustrate this with specific examples and show statistical trends from a sample of 50 star-forming regions.Comment: 4 pages, 3 figures; to appear in the EAS Proceedings of the 6th Zermatt ISM Symposium "Conditions and Impact of Star Formation from Lab to Space", September 201

ASCA Observations of the Thermal Composite Supernova Remnant 3C 391

We present the results from ASCA observations of the centrally enhanced supernova remnant 3C 391 (G31.9+0.0). We use the ASCA SIS data to carry out an investigation of the spatial and spectral properties of the X-ray emission from this remnant. The collisional equilibrium ionization and non-equilibrium ionization spectral fits indicate that the hot gas within the remnant has basically reached ionization equilibrium. The variation of the hydrogen column density across the remnant is in agreement with the presence of a molecular cloud to the northwest. The comparisons of hydrogen column and X-ray hardness between the NW and SE portions of the remnant support a scenario in which the SNR has broken out of a dense region into an adjacent region of lower density. The mean density within the SNR is observed to be much lower than the immediate ambient cloud density. This and the centrally brightened X-ray morphology can be explained either by the evaporation of engulfed cloudlets or by a radiative stage of evolution for the remnant.Comment: 23 pages, 3 figures, accepted for the v563 ApJ 12/10/01 issu

A Candidate Young Massive Planet in Orbit around the Classical T Tauri Star CI Tau

The ~2 Myr old classical T Tauri star CI Tau shows periodic variability in its radial velocity (RV) variations measured at infrared (IR) and optical wavelengths. We find that these observations are consistent with a massive planet in a ~9-day period orbit. These results are based on 71 IR RV measurements of this system obtained over 5 years, and on 26 optical RV measurements obtained over 9 years. CI Tau was also observed photometrically in the optical on 34 nights over ~one month in 2012. The optical RV data alone are inadequate to identify an orbital period, likely the result of star spot and activity induced noise for this relatively small dataset. The infrared RV measurements reveal significant periodicity at ~9 days. In addition, the full set of optical and IR RV measurements taken together phase coherently and with equal amplitudes to the ~9 day period. Periodic radial velocity signals can in principle be produced by cool spots, hot spots, and reflection of the stellar spectrum off the inner disk, in addition to resulting from a planetary companion. We have considered each of these and find the planet hypothesis most consistent with the data. The radial velocity amplitude yields an Msin(i) of ~8.1 M_Jup; in conjunction with a 1.3 mm continuum emission measurement of the circumstellar disk inclination from the literature, we find a planet mass of ~11.3 M_Jup, assuming alignment of the planetary orbit with the disk.Comment: 61 pages, 13 figures, accepted for publication in The Astrophysical Journa

Crystal size and oxygen segregation for polycrystalline GaN

The grain size for polycrystallineGaN,grown in low-temperature gallium-rich conditions, is shown to be correlated to the oxygen content of the films. Films with lower oxygen content were observed to have larger crystals with an increased tendency to a single-preferred crystal orientation.Elastic recoil detection analysis with heavy ions (i.e., 200 MeV ¹⁹⁷Au ions) was used to determine the composition of the GaN films grown for the study, including the hydrogen, carbon, gallium, nitrogen, and oxygen content. Atomic force microscopy and x-ray diffraction were used to study the sample morphology. From these measurements, the available surface area of the films was found to be sufficient for a significant proportion of the oxygen present in the films to segregate at the grain boundaries. This interpretation is consistent with earlier theoretical studies of the formation and segregation of the VGa-(ON)₃defect complex at dislocation sites in gallium-rich GaN. For this work, however, the defect complex is believed to segregate at the grain boundary of the polycrystallineGaN.The authors would like to acknowledge the support of a U. S. NICOP Contract, No. N00014-99-1-GO17 sponsored through the U. S. Office of Naval Research. One of the authors (K.S.A.B.) would like to further acknowledge the support of a Macquarie University Research Fellowship

Gemini Deep Deep Survey VI: Massive Hdelta-strong galaxies at z=1

We show that there has been a dramatic decline in the abundance of massive galaxies with strong Hdelta stellar absorption lines from z=1.2 to the present. These ``Hdelta-strong'', or HDS, galaxies have undergone a recent and rapid break in their star-formation activity. Combining data from the Gemini Deep Deep and the Sloan Digital Sky Surveys to make mass-matched samples (M*>=10^10.2 Msun), with 25 and 50,255 galaxies, respectively), we find that the fraction of galaxies in an HDS phase has decreased from about 50% at z=1.2 to a few percent today. This decrease in fraction is due to an actual decrease in the number density of massive HDS systems by a factor of 2-4, coupled with an increase in the number density of massive galaxies by about 30 percent. We show that this result depends only weakly on the threshold chosen for the Hdelta equivalent width to define HDS systems (if greater than 4 A) and corresponds to a (1+z)^{2.5\pm 0.7} evolution. Spectral synthesis studies of the high-redshift population using the PEGASE code, treating Hdelta_A, EW[OII], Dn4000, and rest-frame colors, favor models in which the Balmer absorption features in massive Hdelta-strong systems are the echoes of intense episodes of star-formation that faded about 1 Gyr prior to the epoch of observation. The z=1.4-2 epoch appears to correspond to a time at which massive galaxies are in transition from a mode of sustained star formation to a relatively quiescent mode with weak and rare star-formation episodes. We argue that the most likely local descendants of the distant massive HDS galaxies are passively evolving massive galaxies in the field and small groups.Comment: 16 pages, 12 figures, 3 tables, uses emulateapj.sty; updated to match the version accepted by ApJ. One figure added, conclusions unchange

Genome-scale gene/reaction essentiality and synthetic lethality analysis

Synthetic lethals are to pairs of non-essential genes whose simultaneous deletion prohibits growth. One can extend the concept of synthetic lethality by considering gene groups of increasing size where only the simultaneous elimination of all genes is lethal, whereas individual gene deletions are not. We developed optimization-based procedures for the exhaustive and targeted enumeration of multi-gene (and by extension multi-reaction) lethals for genome-scale metabolic models. Specifically, these approaches are applied to iAF1260, the latest model of Escherichia coli, leading to the complete identification of all double and triple gene and reaction synthetic lethals as well as the targeted identification of quadruples and some higher-order ones. Graph representations of these synthetic lethals reveal a variety of motifs ranging from hub-like to highly connected subgraphs providing a birds-eye view of the avenues available for redirecting metabolism and uncovering complex patterns of gene utilization and interdependence. The procedure also enables the use of falsely predicted synthetic lethals for metabolic model curation. By analyzing the functional classifications of the genes involved in synthetic lethals, we reveal surprising connections within and across clusters of orthologous group functional classifications