NON-FOULING AFFINITY PLATFORMS FOR PROTEIN IMMOBILIZATION IN ELECTRON MICROSCOPY

Single-particle reconstruction has grown significantly with the improvements in various data collection and computational strategies including CTF fitting, the use of vitrified samples and the utilization of ultra-sensitive direct electron detectors. Although these improvements have contributed significantly to the recent evolution of 3D reconstruction analysis, the way samples are prepared for electron microscopy has remained largely unchanged. We report the development of TEM grids that are modified with non-fouling coatings bearing surface grafted nitrilotriacetic acid substituents that promotes specific capture of protein targets for high resolution TEM analysis. The utilization of these grids for specific adsorption of the targeted protein onto the grid surface results in well-controlled surface concentration enhancements and a days-to-minutes reduction in time required for the preparation of a purified sample for cryoEM analysis from an E. coli expression system. The selective and reversible capture of his-tag T7 bacteriophage, RplL, and GroEL from crude lysates, as well as purified nanodisc-solubilized his-malFGK2, on these NTA-modified grids with an exceptionally low level of adsorption by non-target proteins has been observed. Our data illustrates the utility of these grids for selective capture from complex mixtures, detergent-solubilized membrane protein isolates, and expression systems yielding low copy numbers of the desired target in a manner that is well-suited for single particle reconstruction analysis

Ethanol plant location and intensification vs. extensification of corn cropping in Kansas

This is the author final draft. Copyright 2014 Elsevier.Farmers' cropping decisions are a product of a complex mix of socio-economic, cultural, and natural environments in which factors operating at a number of different spatial scales affect how farmers ultimately decide to use their land in any given year or over a set of years. Some environmentalists are concerned that increased demand for corn driven by ethanol production is leading to conversion of non-cropland into corn production (which we label as “extensification”). Ethanol industry advocates counter that more than enough corn supply comes from crop switching to corn and increased yields (which we label as “intensification”). In this study, we determine whether either response to corn demand – intensification or extensification – is supported. This is determined through an analysis of land-use/land-cover (LULC) data that covers the state of Kansas and a measure of a corn demand shifter related to ethanol production – distance to the closest ethanol plant – between 2007 and 2009

Deep ugrizY imaging and DEEP2/3 spectroscopy: a photometric redshift testbed for LSST and public release of data from the DEEP3 Galaxy Redshift Survey

We present catalogues of calibrated photometry and spectroscopic redshifts in the Extended Groth Strip, intended for studies of photometric redshifts (photo-z’s). The data includes ugriz photometry from Canada–France–Hawaii Telescope Legacy Survey (CFHTLS) and Y-band photometry from the Subaru Suprime camera, as well as spectroscopic redshifts from the DEEP2, DEEP3, and 3D-HST surveys. These catalogues incorporate corrections to produce effectively matched-aperture photometry across all bands, based upon object size information available in the catalogue and Moffat profile point spread function fits. We test this catalogue with a simple machine learning-based photometric redshift algorithm based upon Random Forest regression, and find that the corrected aperture photometry leads to significant improvement in photo-z accuracy compared to the original SEXTRACTOR catalogues from CFHTLS and Subaru. The deep ugrizY photometry and spectroscopic redshifts are well suited for empirical tests of photometric redshift algorithms for LSST. The resulting catalogues are publicly available at http://d-scholarship.pitt.edu/36064/. We include a basic summary of the strategy of the DEEP3 Galaxy Redshift Survey to accompany the recent public release of DEEP3 data

Genetic risk prediction of atrial fibrillation

Background—Atrial fibrillation (AF) has a substantial genetic basis. Identification of individuals at greatest AF risk could minimize the incidence of cardioembolic stroke. Methods—To determine whether genetic data can stratify risk for development of AF, we examined associations between AF genetic risk scores and incident AF in five prospective studies comprising 18,919 individuals of European ancestry. We examined associations between AF genetic risk scores and ischemic stroke in a separate study of 509 ischemic stroke cases (202 cardioembolic [40%]) and 3,028 referents. Scores were based on 11 to 719 common variants (≥5%) associated with AF at P-values ranging from <1x10-3 to <1x10-8 in a prior independent genetic association study. Results—Incident AF occurred in 1,032 (5.5%) individuals. AF genetic risk scores were associated with new-onset AF after adjusting for clinical risk factors. The pooled hazard ratio for incident AF for the highest versus lowest quartile of genetic risk scores ranged from 1.28 (719 variants; 95%CI, 1.13-1.46; P=1.5x10-4) to 1.67 (25 variants; 95%CI, 1.47-1.90; P=9.3x10-15). Discrimination of combined clinical and genetic risk scores varied across studies and scores (maximum C statistic, 0.629-0.811; maximum ΔC statistic from clinical score alone, 0.009-0.017). AF genetic risk was associated with stroke in age- and sex-adjusted models. For example, individuals in the highest versus lowest quartile of a 127-variant score had a 2.49-fold increased odds of cardioembolic stroke (95%CI, 1.39-4.58; P=2.7x10-3). The effect persisted after excluding individuals (n=70) with known AF (odds ratio, 2.25; 95%CI, 1.20-4.40; P=0.01). Conclusions—Comprehensive AF genetic risk scores were associated with incident AF beyond associations for clinical AF risk factors, though offered small improvements in discrimination. AF genetic risk was also associated with cardioembolic stroke in age- and sex-adjusted analyses. Efforts are warranted to determine whether AF genetic risk may improve identification of subclinical AF or help distinguish between stroke mechanisms

The Speed of Sound in Methane under Conditions of the Thermal Boundary Layer of Uranus

We present the first direct observations of acoustic waves in warm dense matter. We analyze wavenumber- and energy-resolved X-ray spectra taken from warm dense methane created by laser-heating a cryogenic liquid jet. X-ray diffraction and inelastic free electron scattering yield sample conditions of 0.3$\pm$0.1 eV and 0.8$\pm$0.1 g/cm$^3$, corresponding to a pressure of $\sim$13 GPa and matching the conditions predicted in the thermal boundary layer between the inner and outer envelope of Uranus. Inelastic X-ray scattering was used to observe the collective oscillations of the ions. With a highly improved energy resolution of $\sim$50 meV, we could clearly distinguish the Brillouin peaks from the quasi-elastic Rayleigh feature. Data at different wavenumbers were used to obtain a sound speed of 5.9$\pm$0.5 km/s, which enabled us to validate the use of Birch's law in this new parameter regime.Comment: 7 pages, 4 figures with supplementary informatio

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes