Development of Electron Microscopy Analysis and Simulation tools for nanoHUB

Electron microscopy has a crucial role in the field of materials science and structural biology. Although electron microscopy gives lots of important results and findings, some additional simulations and image processing/reconstruction is required to get more information from the data that are collected from the experiments. For this purpose, researchers are using IMOD1 and QSTEM2 for electron microscopy analysis and simulation. IMOD is a set of programs used for tomographic reconstruction and 3D visualization and QSTEM is used for quantitative simulations of TEM and STEM images. However, IMOD and QSTEM are hard to install or use for beginners who are not familiar with computational skills. To overcome this issue, we have developed “Online IMOD and STEM tools” to allow users to perform microscopy analysis and simulation with ease. We applied several ways to launch or combine tools. Based on the original source codes of the software, we used the graphical interface builder Rappture to build a new interface to launch several tools. Also, we used the nanowhim window manager to combine and organize tools. The online version of IMOD and QSTEM will enable researchers from all over the world to use IMOD and QSTEM programs directly and easily on the nanoHUB website

Estimating genomic breeding values and detecting QTL using univariate and bivariate models

Background Genomic selection is particularly beneficial for difficult or expensive to measure traits. Since multi-trait selection is an important tool to deal with such cases, an important question is what the added value is of multi-trait genomic selection. Methods The simulated dataset, including a quantitative and binary trait, was analyzed with four univariate and bivariate linear models to predict breeding values for juvenile animals. Two models estimated variance components with REML using a numerator (A), or SNP based relationship matrix (G). Two SNP based Bayesian models included one (BayesA) or two distributions (BayesC) for estimated SNP effects. The bivariate BayesC model sampled QTL probabilities for each SNP conditional on both traits. Genotypes were permuted 2,000 times against phenotypes and pedigree, to obtain significance thresholds for posterior QTL probabilities. Genotypes were permuted rather than phenotypes, to retain relationships between pedigree and phenotypes, such that polygenic effects could still be estimated. Results Correlations between estimated breeding values (EBV) of different SNP based models, for juvenile animals, were greater than 0.93 (0.87) for the quantitative (binary) trait. Estimated genetic correlation was 0.71 (0.66) for model G (A). Accuracies of breeding values of SNP based models were for both traits highest for BayesC and lowest for G. Accuracies of breeding values of bivariate models were up to 0.08 higher than for univariate models. The bivariate BayesC model detected 14 out of 32 QTL for the quantitative trait, and 8 out of 22 for the binary trait. Conclusions Accuracy of EBV clearly improved for both traits using bivariate compared to univariate models. BayesC achieved highest accuracies of EBV and was also one of the methods that found most QTL. Permuting genotypes against phenotypes and pedigree in BayesC provided an effective way to derive significance thresholds for posterior QTL probabilitie

Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae

Background: In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study. Results: Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15% divergence (88 to 85% ANI and 92 to 91% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95% and AAI <96% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59%) and 2058 ORFs (56%) with the published core genome of V. cholerae and 2956 (82%) and 3048 ORFs (84%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81% Vibrio sp. RC341 and 81% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp. Conclusions: Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.

Boosting NAD preferentially blunts Th17 inflammation via arginine biosynthesis and redox control in healthy and psoriasis subjects

Acknowledgments We thank Myron Waclawiw of the NHLBI Biostatistics Branch for assistance with the clinical protocol design, Chromadex for supplying NR and matching placebo capsules for the in vivo study and NR powder for the cell culture studies, and an NIH Bench-to-Bedside award for supplemental funding. We additionally thank Dr. Nina Klimova, formerly of the NHLBI, and Dr. Yun-Wei A. Hsu for their support of the metabolomics analysis at the Northwest Metabolomics Research Center of the University of Washington (NIH grant 1S10OD021562-01). We thank and acknowledge the assistance of the NHLBI DNA Sequencing and Genomics Core in performing the RNA library sequencing and Dr. Pradeep Dagur in the NHLBI Flow Cytometry Core for performing the immunophenotyping. Trial registration was as follows: ClinicalTrials.gov: NCT01934660, NCT02812238, and NCT01143454 and NIH Clinical Center blood bank (ClinicalTrials.gov: NCT00001846). This work was supported by the NHLBI Division of Intramural Research (ZIA-HL005102 to M.N.S.), NIH Bench-to-Bedside award (HL-129510-04S1 to M.N.S. and R.T.) and the NIH Office of Dietary Supplements (J.T.), the Spanish Ministry of Science and Innovation (RYC2018-026050-I and PID2019-105665RA-I00 to J.T.), and the UK MRC (MR/P011705/2 and UKDRI-5002 to J.L.G.; MAP UK).Peer reviewedPublisher PD

Constrictive Pericarditis Accompanied by Swine-Origin Influenza A (H1N1) Infection

Swine-origin influenza A (H1N1) is caused by a new strain of the influenza virus. The disease has spread rapidly and was declared a pandemic in April, 2009. So far, however, there is a scarcity of information regarding the complications of swine influenza. A report of the disease in the winter of 2009 in the Southern Hemisphere found that the most common manifestations of influenza A virus infection are upper respiratory tract infection and pneumonia. Although there may be an association between fulminant myocarditis and Swine influenza, cardiovascular complications resulting from swine Influenza A infection are exceedingly rare. We report a case of acute constrictive pericarditis in a healthy subject infected by the swine-origin influenza A (H1N1) virus

Search for Higgs bosons decaying to tautau pairs in ppbar collisions at sqrt(s) = 1.96 TeV

We present a search for the production of neutral Higgs bosons decaying into tautau pairs in ppbar collisions at a center-of-mass energy of 1.96 TeV. The data, corresponding to an integrated luminosity of 5.4 fb-1, were collected by the D0 experiment at the Fermilab Tevatron Collider. We set upper limits at the 95% C.L. on the product of production cross section and branching ratio for a scalar resonance decaying into tautau pairs, and we then interpret these limits as limits on the production of Higgs bosons in the minimal supersymmetric standard model (MSSM) and as constraints in the MSSM parameter space.Comment: 7 pages, 5 figures, submitted to PL

Measurement of the top quark mass using the matrix element technique in dilepton final states

We present a measurement of the top quark mass in pp¯ collisions at a center-of-mass energy of 1.96 TeV at the Fermilab Tevatron collider. The data were collected by the D0 experiment corresponding to an integrated luminosity of 9.7  fb−1. The matrix element technique is applied to tt¯ events in the final state containing leptons (electrons or muons) with high transverse momenta and at least two jets. The calibration of the jet energy scale determined in the lepton+jets final state of tt¯ decays is applied to jet energies. This correction provides a substantial reduction in systematic uncertainties. We obtain a top quark mass of mt=173.93±1.84  GeV