Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism

Electronic Liquid Crystal Phases of a Doped Mott Insulator

The character of the ground state of an antiferromagnetic insulator is fundamentally altered upon addition of even a small amount of charge. The added charges agglomerate along domain walls at which the spin correlations, which may or may not remain long-ranged, suffer a $\pi$ phase shift. In two dimensions, these domain walls are ``stripes'' which are either insulating, or conducting, i.e. metallic rivers with their own low energy degrees of freedom. However, quasi one-dimensional metals typically undergo a transition to an insulating ordered charge density wave (CDW) state at low temperatures. Here it is shown that such a transition is eliminated if the zero-point energy of transverse stripe fluctuations is sufficiently large in comparison to the CDW coupling between stripes. As a consequence, there exist novel, liquid-crystalline low-temperature phases -- an electron smectic, with crystalline order in one direction, but liquid-like correlations in the other, and an electron nematic with orientational order but no long-range positional order. These phases, which constitute new states of matter, can be either high temperature supeconductors or two-dimensional anisotropic ``metallic'' non-Fermi liquids. Evidence for the new phases may already have been obtained by neutron scattering experiments in the cuprate superconductor, La_{1.6-x}Nd_{0.4}Sr_xCuO_{4}.Comment: 5 pages in RevTex with two figures in ep

Wear resistant solid lubricating coatings via compression molding and thermal spraying technologies

This work combines two industrially friendly processing methods in order to create wear resistant and solid-lubricating composite coatings potentially suitable for high load applications. Layered composite coatings were fabricated over wrought stainless steel 444 (SS444) by compression molding a mixture of solid lubricant polymer, polytetrafluoroethylene (PTFE, 80 wt%), and wear resistant polymer, polyimide (PI, 20 wt%), onto iron aluminide (Fe3Al) thermal spray coatings without the need of either primers or adhesives. The fabrication process consisted of three main steps: deposition of the Fe3Al thermal spray coating onto a SS444 substrate and transfer into a metal mold; transfer, compress, and sinter mixed polymeric powder onto the thermal spray coating; and finally, sample cooling to room temperature. This method takes advantage of the high surface roughness of thermal spray coatings, which increases mechanical adhesion of slippery PTFE to the underlying metallic material. Coatings were produced with and without a small amount of graphite (5 wt%) to analyze its impact on sliding and wear properties. Unlike current coating technologies, the thickness of the coatings presented herein can be easily and quickly tailored by varying the amount of polymer powder added to the mold prior to compression or by grinding after fabrication. We produced and analyzed coatings ~1.3 mm in total thickness that portray coefficient of frictions ~0.1, similar to pure PTFE. The calculated wear rates for both coatings with and without graphite are an order of magnitude lower than what has been previously reported for coatings of similar composition. The influence of graphite on wear properties was found to be minimal due to the high content of self-lubricating PTFE yet can act as a way to lower material costs and increase the coatings load capacity

On the AC spectrum of one-dimensional random Schroedinger operators with matrix-valued potentials

We consider discrete one-dimensional random Schroedinger operators with decaying matrix-valued, independent potentials. We show that if the l^2-norm of this potential has finite expectation value with respect to the product measure then almost surely the Schroedinger operator has an interval of purely absolutely continuous (ac) spectrum. We apply this result to Schroedinger operators on a strip. This work provides a new proof and generalizes a result obtained by Delyon, Simon, and Souillard.Comment: (1 figure

The magnetic nature of disk accretion onto black holes

Although disk accretion onto compact objects - white dwarfs, neutron stars, and black holes - is central to much of high energy astrophysics, the mechanisms which enable this process have remained observationally elusive. Accretion disks must transfer angular momentum for matter to travel radially inward onto the compact object. Internal viscosity from magnetic processes and disk winds can in principle both transfer angular momentum, but hitherto we lacked evidence that either occurs. Here we report that an X-ray-absorbing wind discovered in an observation of the stellar-mass black hole binary GRO J1655-40 must be powered by a magnetic process that can also drive accretion through the disk. Detailed spectral analysis and modeling of the wind shows that it can only be powered by pressure generated by magnetic viscosity internal to the disk or magnetocentrifugal forces. This result demonstrates that disk accretion onto black holes is a fundamentally magnetic process.Comment: 15 pages, 2 color figures, accepted for publication in Nature. Supplemental materials may be obtained by clicking http://www.astro.lsa.umich.edu/~jonmm/nature1655.p

Spinless impurities and Kondo-like behavior in strongly correlated electron systems

We investigate magnetic properties induced by a spinless impurity in strongly correlated electron systems, i.e. the Hubbard model in the spatial dimension $D=1,2,$ and 3. For the 1D system exploiting the Bethe ansatz exact solution we find that the spin susceptibility and the local density of states in the vicinity of a spinless impurity show divergent behaviors. The results imply that the induced local moment is not completely quenched at any finite temperatures. On the other hand, the spin lattice relaxation rate obtained by bosonization and boundary conformal field theory satisfies a relation analogous to the Korringa law, $1/T_1T \sim \chi^2$. In the 2D and 3D systems, the analysis based upon the antiferromagnetically correlated Fermi liquid theory reveals that the antiferromagnetic spin fluctuation developed in the bulk is much suppressed in the vicinity of a spinless impurity, and thus magnetic properties are governed by the induced local moment, which leads to the Korringa law of $1/T_1$.Comment: 9pages,1figure, final version accepted for publication in Phys.Rev.B(Jan2001

The Herschel Exploitation of Local Galaxy Andromeda (HELGA) II: Dust and Gas in Andromeda

We present an analysis of the dust and gas in Andromeda, using Herschel images sampling the entire far-infrared peak. We fit a modified-blackbody model to ~4000 quasi-independent pixels with spatial resolution of ~140pc and find that a variable dust-emissivity index (beta) is required to fit the data. We find no significant long-wavelength excess above this model suggesting there is no cold dust component. We show that the gas-to-dust ratio varies radially, increasing from ~20 in the center to ~70 in the star-forming ring at 10kpc, consistent with the metallicity gradient. In the 10kpc ring the average beta is ~1.9, in good agreement with values determined for the Milky Way (MW). However, in contrast to the MW, we find significant radial variations in beta, which increases from 1.9 at 10kpc to ~2.5 at a radius of 3.1kpc and then decreases to 1.7 in the center. The dust temperature is fairly constant in the 10kpc ring (ranging from 17-20K), but increases strongly in the bulge to ~30K. Within 3.1kpc we find the dust temperature is highly correlated with the 3.6 micron flux, suggesting the general stellar population in the bulge is the dominant source of dust heating there. At larger radii, there is a weak correlation between the star formation rate and dust temperature. We find no evidence for 'dark gas' in M31 in contrast to recent results for the MW. Finally, we obtained an estimate of the CO X-factor by minimising the dispersion in the gas-to-dust ratio, obtaining a value of (1.9+/-0.4)x10^20 cm^-2 [K kms^-1]^-1.Comment: 19 pages, 18 figures. Submitted to ApJ April 2012; Accepted July 201

Social and Physical Environments and Disparities in Risk for Cardiovascular Disease: The Healthy Environments Partnership Conceptual Model

The Healthy Environments Partnership (HEP) is a community-based participatory research effort investigating variations in cardiovascular disease risk, and the contributions of social and physical environments to those variations, among non-Hispanic black, non-Hispanic white, and Hispanic residents in three areas of Detroit, Michigan. Initiated in October 2000 as a part of the National Institute of Environmental Health Sciences’ Health Disparities Initiative, HEP is affiliated with the Detroit Community–Academic Urban Research Center. The study is guided by a conceptual model that considers race-based residential segregation and associated concentrations of poverty and wealth to be fundamental factors influencing multiple, more proximate predictors of cardiovascular risk. Within this model, physical and social environments are identified as intermediate factors that mediate relationships between fundamental factors and more proximate factors such as physical activity and dietary practices that ultimately influence anthropomorphic and physiologic indicators of cardiovascular risk. The study design and data collection methods were jointly developed and implemented by a research team based in community-based organizations, health service organizations, and academic institutions. These efforts include collecting and analyzing airborne particulate matter over a 3-year period; census and administrative data; neighborhood observation checklist data to assess aspects of the physical and social environment; household survey data including information on perceived stressors, access to social support, and health-related behaviors; and anthropometric, biomarker, and self-report data as indicators of cardiovascular health. Through these collaborative efforts, HEP seeks to contribute to an understanding of factors that contribute to racial and socioeconomic health inequities, and develop a foundation for efforts to eliminate these disparities in Detroit

Ages for exoplanet host stars

Age is an important characteristic of a planetary system, but also one that is difficult to determine. Assuming that the host star and the planets are formed at the same time, the challenge is to determine the stellar age. Asteroseismology provides precise age determination, but in many cases the required detailed pulsation observations are not available. Here we concentrate on other techniques, which may have broader applicability but also serious limitations. Further development of this area requires improvements in our understanding of the evolution of stars and their age-dependent characteristics, combined with observations that allow reliable calibration of the various techniques.Comment: To appear in "Handbook of Exoplanets", eds. Deeg, H.J. & Belmonte, J.A, Springer (2018

Selection of optimal reference genes for normalization in quantitative RT-PCR

<p>Abstract</p> <p>Background</p> <p>Normalization in real-time qRT-PCR is necessary to compensate for experimental variation. A popular normalization strategy employs reference gene(s), which may introduce additional variability into normalized expression levels due to innate variation (between tissues, individuals, etc). To minimize this innate variability, multiple reference genes are used. Current methods of selecting reference genes make an assumption of independence in their innate variation. This assumption is not always justified, which may lead to selecting a suboptimal set of reference genes.</p> <p>Results</p> <p>We propose a robust approach for selecting optimal subset(s) of reference genes with the smallest variance of the corresponding normalizing factors. The normalizing factor variance estimates are based on the estimated unstructured covariance matrix of all available candidate reference genes, adjusting for all possible correlations. Robustness is achieved through bootstrapping all candidate reference gene data and obtaining the bootstrap upper confidence limits for the variances of the log-transformed normalizing factors. The selection of the reference gene subset is optimized with respect to one of the following criteria: (A) to minimize the variability of the normalizing factor; (B) to minimize the number of reference genes with acceptable upper limit on variability of the normalizing factor, (C) to minimize the average rank of the variance of the normalizing factor. The proposed approach evaluates all gene subsets of various sizes rather than ranking individual reference genes by their stability, as in the previous work. In two publicly available data sets and one new data set, our approach identified subset(s) of reference genes with smaller empirical variance of the normalizing factor than in subsets identified using previously published methods. A small simulation study indicated an advantage of the proposed approach in terms of sensitivity to identify the true optimal reference subset in the presence of even modest, especially negative correlation among the candidate reference genes.</p> <p>Conclusions</p> <p>The proposed approach performs comprehensive and robust evaluation of the variability of normalizing factors based on all possible subsets of candidate reference genes. The results of this evaluation provide flexibility to choose from important criteria for selecting the optimal subset(s) of reference genes, unless one subset meets all the criteria. This approach identifies gene subset(s) with smaller variability of normalizing factors than current standard approaches, particularly if there is some nontrivial innate correlation among the candidate genes.</p