Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction

SummaryProtein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized

Long Term Survival and Infectivity of Salmonella Choleraesuis

It is believed that Salmonella cho leraesuis, the host-adapted serotype of swine, does not survive well outside the host. Pigs were infected with S. Choleraesuis and feces was collected and pooled on days 2, 4, 7 and 10 post inoculation (PI). Feces was stored in a wet and a dry form and survival was measured over 13 months. Salmonella Choleraesuis was recovered from wet feces through 3 months of storage. In a desiccated (dry) form, S. Choleraesuis was recovered from at least 13 months. Direct PCR analysis did not detect S. Choleraesuis subsequent to culture. We also examined the infectivity of S. Choleraesu is resident in dry feces. Six or 13 week old pigs were inoculated with dry feces that had been stored either 2 months or 4 months, respectively. Pigs were inoculated either intranasally or by mixing dry feces with feed. Although clinical signs were mild, S. Choleraesuis was widely disseminated among the tissues of all the pigs inoculated. This study demonstrates that S. Choleraesuis remains viab le and infective in the environment. Contaminated fecal matter can serve as a reservoir for S. Choleraesuis

Enhancing the stability of Organic Photovoltaics through Machine Learning

A machine learning approach for extracting information from organic photovoltaic (OPV) solar cell data is presented. A database consisting of 1850 entries of device characteristics, performance and stability data is utilised and a sequential minimal optimisation regression (SMOreg) model is employed as a means of determining the most influential factors governing the solar cell stability and power conversion efficiency (PCE). This is achieved through the analysis of the acquired SMOreg model in terms of the attribute weights. Significantly, the analysis presented allows for identification of materials which could lead to improvements in stability and PCE for each thin film in the device architecture, as well as highlighting the role of different stress factors in the degradation of OPVs. It is found that, for tests conducted under ISOS-L protocols the choice of light spectrum and the active layer material significantly govern the stability, whilst for tests conducted under ISOS-D protocols, the primary attributes are material and encapsulation dependent. The reported approach affords a rapid and efficient method of applying machine learning to enable material identification that possess the best stability and performance. Ultimately, researchers and industries will be able to obtain invaluable information for developing future OPV technologies so that can be realised in a significantly shorter period by reducing the need for time-consuming experimentation and optimisation

Isolation of Escherichia coli O157:H7 from Intact Colon Fecal Samples of Swine1

Escherichia coli O157:H7 was recovered from colon fecal samples of pigs. Polymerase chain reaction confirmed two genotypes: isolates harboring the eaeA, stx1, and stx2 genes and isolates harboring the eaeA, stx1, and hly933 genes. We demonstrate that swine in the United States can harbor potentially pathogenic E. coli O157:H7

Synergism between Porcine Reproductive and Respiratory

This study was conducted to investigate the effects of exposure to porcine reproductive and respiratory syndrome virus, Salmonella choleraesuis, and stress on young swine. Five-week-old segregated early weaned pigs were randomly assigned to one of eight treatments consisting of all possible combinations of three factors: S. choleraesuis (SC) on day zero, porcine reproductive and respiratory syndrome virus (PRRSV) on day three, and dexamethasone (DEX) on days three to seven. DEX was used as a proxy for stress. Treatment differences were seen in performance parameters, levels and duration of SC shedding, level and distribution of SC in tissues, clinical disease, and mortality. The results of this study provided evidence to support field observations that clinical outbreaks of PRRS are the result of interactions among concurrent infections and stressors

Salmonella Immunity: Development of a Neutrophil Phagocytosis Assay and Stress Model in Swine

Our laboratory is interested in the immunomodulation of porcine defense mechanisms against bacterial intracellular pathogens such as Salmonella typhimurium and S. choleraesuis. Past studies indicate that levels of serum tumor necrosis factor-a (TNF-a) increase after intranasal challenge with S. typhimurium but not after oral inoculation. Challenge with S. choleraesuis has no effect on serum TNF-a concentration in the blood, regardless of route. Route of inoculation with S. choleraesuis has been shown to affect levels of lymphocyte proliferation. Both oral and intranasal routes of inoculation stimulate peripheral blood B-cells while the intranasal route is more effective at stimulating peripheral blood T-cells. The inoculum dose of S. typhimurium or S. choleraesuis can also play an important role in the host immune response. TNF-a concentrations in the blood are much greater after a 106 S. typhimurium challenge than after a 104 S. typhimurium challenge. At high doses (;:o:l09 CFU) S. choleraesuis causes signs of lymphocyte suppression, which may affect the ability of the immune system to eliminate the bacteria. Pigs administered an intranasal dose of 108 CFU S. choleraesuis have similar immune responses as naturally infected animals

Pathogenesis, Transmission, and Control of Salmonellosis in Swine

The objectives of our project at the National Animal Disease Center are: 1. To identify virulence factors important in the pathogenesis of Salmonella choleraesuis and Salmonella typhimurium in swine 2. To define the epidemiology and transmission of Salmonella in swine 3. To define the porcine immune response to acute and chronic Salmonella infection focusing on mechanisms to reduce or eliminate the pathogenic organism 4. To identify methods to control Salmonella in swine

Expression divergence measured by transcriptome sequencing of four yeast species

<p>Abstract</p> <p>Background</p> <p>The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial.</p> <p>Results</p> <p>We quantified gene expression with whole-transcriptome sequencing in four diploid, prototrophic strains of <it>Saccharomyces </it>species grown under the same condition to investigate the evolution of gene expression. We found that variation in expression is gene-dependent with large variations in each gene's expression between replicates of the same species. This confounds the identification of genes differentially expressed across species. To address this, we developed a statistical approach to establish significance bounds for inter-species differential expression in RNA-Seq data based on the variance measured across biological replicates. This metric estimates the combined effects of technical and environmental variance, as well as Poisson sampling noise by isolating each component. Despite a paucity of large expression changes, we found a strong correlation between the variance of gene expression change and species divergence (R²= 0.90).</p> <p>Conclusion</p> <p>We provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects.</p> <p>GEO Accession Number: GSE32679</p

Efficient Photometric Selection of Quasars from the Sloan Digital Sky Survey: 100,000 z<3 Quasars from Data Release One

We present a catalog of 100,563 unresolved, UV-excess (UVX) quasar candidates to g=21 from 2099 deg^2 of the Sloan Digital Sky Survey (SDSS) Data Release One (DR1) imaging data. Existing spectra of 22,737 sources reveals that 22,191 (97.6%) are quasars; accounting for the magnitude dependence of this efficiency, we estimate that 95,502 (95.0%) of the objects in the catalog are quasars. Such a high efficiency is unprecedented in broad-band surveys of quasars. This ``proof-of-concept'' sample is designed to be maximally efficient, but still has 94.7% completeness to unresolved, g<~19.5, UVX quasars from the DR1 quasar catalog. This efficient and complete selection is the result of our application of a probability density type analysis to training sets that describe the 4-D color distribution of stars and spectroscopically confirmed quasars in the SDSS. Specifically, we use a non-parametric Bayesian classification, based on kernel density estimation, to parameterize the color distribution of astronomical sources -- allowing for fast and robust classification. We further supplement the catalog by providing photometric redshifts and matches to FIRST/VLA, ROSAT, and USNO-B sources. Future work needed to extend the this selection algorithm to larger redshifts, fainter magnitudes, and resolved sources is discussed. Finally, we examine some science applications of the catalog, particularly a tentative quasar number counts distribution covering the largest range in magnitude (14.2<g<21.0) ever made within the framework of a single quasar survey.Comment: 35 pages, 11 figures (3 color), 2 tables, accepted by ApJS; higher resolution paper and ASCII version of catalog available at http://sdss.ncsa.uiuc.edu/qso/nbckde