Early childhood gut microbiomes show strong geographic differences among subjects at high risk for type 1 diabetes.

Objective: Gut microbiome dysbiosis is associated with numerous diseases, including type 1 diabetes. This pilot study determines how geographical location affects the microbiome of infants at high risk for type 1 diabetes in a population of homogenous HLA class II genotypes.

Research Design And Methods: High-throughput 16S rRNA sequencing was performed on stool samples collected from 90 high-risk, nonautoimmune infants participating in The Environmental Determinants of Diabetes in the Young (TEDDY) study in the U.

Pyrokinin β-neuropeptide affects necrophoretic behavior in fire ants (S. invicta), and expression of β-NP in a mycoinsecticide increases its virulence.

Fire ants are one of the world's most damaging invasive pests, with few means for their effective control. Although ecologically friendly alternatives to chemical pesticides such as the insecticidal fungus Beauveria bassiana have been suggested for the control of fire ant populations, their use has been limited due to the low virulence of the fungus and the length of time it takes to kill its target. We present a means of increasing the virulence of the fungal agent by expressing a fire ant neuropeptide.

Objective Bayes model selection in probit models.

We describe a new variable selection procedure for categorical responses where the candidate models are all probit regression models. The procedure uses objective intrinsic priors for the model parameters, which do not depend on tuning parameters, and ranks the models for the different subsets of covariates according to their model posterior probabilities. When the number of covariates is moderate or large, the number of potential models can be very large, and for those cases, we derive a new stochastic search algorithm that explores the potential sets of models driven by their model posterior probabilities.

Generalized shrinkage F-like statistics for testing an interaction term in gene expression analysis in the presence of heteroscedasticity.

Background: Many analyses of gene expression data involve hypothesis tests of an interaction term between two fixed effects, typically tested using a residual variance. In expression studies, the issue of variance heteroscedasticity has received much attention, and previous work has focused on either between-gene or within-gene heteroscedasticity. However, in a single experiment, heteroscedasticity may exist both within and between genes.

Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes.

Recent studies have suggested a bacterial role in the development of autoimmune disorders including type 1 diabetes (T1D). Over 30 billion nucleotide bases of Illumina shotgun metagenomic data were analyzed from stool samples collected from four pairs of matched T1D case-control subjects collected at the time of the development of T1D associated autoimmunity (i.e.

Interval estimation in two-stage, drop-the-losers clinical trials with flexible treatment selection.

In a two-stage, drop-the-losers clinical trial, researchers choose the 'best' among a number of treatments at an interim analysis after the first stage. The selected treatment continues to the second stage for confirmation of efficacy, and the remaining treatments (the 'losers') are dropped from the study. Wu et al.

A regionalised strategy for improving motor vehicle-related highway driver deaths using a weighted averages method.

Objective: The state of Florida has some of the most dangerous highways in the USA. In 2006, Florida averaged 1.65 fatalities per 100 million vehicle miles travelled (VMT) compared with the national average of 1.

Fecal microbiota in premature infants prior to necrotizing enterocolitis.

Intestinal luminal microbiota likely contribute to the etiology of necrotizing enterocolitis (NEC), a common disease in preterm infants. Microbiota development, a cascade of initial colonization events leading to the establishment of a diverse commensal microbiota, can now be studied in preterm infants using powerful molecular tools. Starting with the first stool and continuing until discharge, weekly stool specimens were collected prospectively from infants with gestational ages ≤32 completed weeks or birth weights≤1250 g.

The potential influence of common viral infections diagnosed during hospitalization among critically ill patients in the United States.

Viruses are the most common source of infection among immunocompetent individuals, yet they are not considered a clinically meaningful risk factor among the critically ill. This work examines the association of viral infections diagnosed during the hospital stay or not documented as present on admission to the outcomes of ICU patients with no evidence of immunosuppression on admission. This is a population-based retrospective cohort study of University HealthSystem Consortium (UHC) academic centers in the U.

Epistasis: obstacle or advantage for mapping complex traits?

Identification of genetic loci in complex traits has focused largely on one-dimensional genome scans to search for associations between single markers and the phenotype. There is mounting evidence that locus interactions, or epistasis, are a crucial component of the genetic architecture of biologically relevant traits. However, epistasis is often viewed as a nuisance factor that reduces power for locus detection.

Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.).

Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants. Whereas resistance is often quantitative, there is limited information on the genes that underpin quantitative variation in disease resistance. We used a population genomic approach to identify genes in loblolly pine (Pinus taeda) that are associated with resistance to pitch canker, a disease incited by the necrotrophic pathogen Fusarium circinatum.

Toward defining the autoimmune microbiome for type 1 diabetes.

Several studies have shown that gut bacteria have a role in diabetes in murine models. Specific bacteria have been correlated with the onset of diabetes in a rat model. However, it is unknown whether human intestinal microbes have a role in the development of autoimmunity that often leads to type 1 diabetes (T1D), an autoimmune disorder in which insulin-secreting pancreatic islet cells are destroyed.

PANGEA: pipeline for analysis of next generation amplicons.

High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching and classification, have been compiled into a pipeline called PANGEA.

Testing for the existence of clusters.

Detecting and determining clusters present in a certain sample has been an important concern, among researchers from different fields, for a long time. In particular, assessing whether the clusters are statistically significant, is a question that has been asked by a number of experimenters. Recently, this question arose again in a study in maize genetics, where determining the significance of clusters is crucial as a primary step in the identification of a genome-wide collection of mutants that may affect the kernel composition.

Influence of fecal sample storage on bacterial community diversity.

Previous studies have identified a correlation, either positive or negative, between specific stool bacteria strains and certain autoimmune diseases. These conflicting data may relate to sample collection. The aim of this work was to evaluate the influence of the collection parameters of time and temperature on bacterial community composition.

Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model.

Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these samples and the 16S rRNA gene was amplified using universal primer sets.

Score statistics for mapping quantitative trait loci.

We propose a method to detect the existence of quantitative trait loci (QTL) in a backcross population using a score test. Since the score test only uses the MLEs of parameters under the null hypothesis, it is computationally simpler than the likelihood ratio test (LRT). Moreover, because the location parameter of the QTL is unidentifiable under the null hypothesis, the distribution of the maximum of the LRT statistics, typically the statistic of choice for testing H0: no QTL, does not have the standard chi-square distribution asymptotically under the null hypothesis.

A preliminary gene expression profile of acute graft-versus-host disease.

Allogeneic hematopoietic stem cell transplantation (HSCT) is the treatment of choice for high-risk hematological malignancies, yet a major complication associated with this therapy is acute graft-versus-host disease (GVHD). Despite a well-defined pathophysiological mechanism, there are no definitive markers for predicting acute GVHD development or progression to advanced stages. In the current study, we enrolled four acute GVHD and four acute GVHD-free recipients of allogeneic HSCT and collected peripheral blood just prior to onset of clinical acute GVHD for analysis on Affymetrix GeneChip Human Genome U133 Plus 2.

Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms.

Sequencing of the Populus trichocarpa genome creates an opportunity to describe the transcriptome of a woody perennial species and establish an atlas of gene expression. A comparison with the transcriptomes of other species can also define genes that are conserved or diverging in plant species. Here, the transcriptome in vegetative organs of the P.

Estimating a weighted average of stratum-specific parameters.

This article investigates estimators of a weighted average of stratum-specific univariate parameters and compares them in terms of a design-based estimate of mean-squared error (MSE). The research is motivated by a stratified survey sample of Florida Medicaid beneficiaries, in which the parameters are population stratum means and the weights are known and determined by the population sampling frame. Assuming heterogeneous parameters, it is common to estimate the weighted average with the weighted sum of sample stratum means; under homogeneity, one ignores the known weights in favor of precision weighting.

Nonparametric functional mapping of quantitative trait loci.

Functional mapping is a useful tool for mapping quantitative trait loci (QTL) that control dynamic traits. It incorporates mathematical aspects of biological processes into the mixture model-based likelihood setting for QTL mapping, thus increasing the power of QTL detection and the precision of parameter estimation. However, in many situations there is no obvious functional form and, in such cases, this strategy will not be optimal.

Model-based Bayesian clustering (MBBC).

Motivation: The program MBBC 2.0 clusters time-course microarray data using a Bayesian product partition model.

Results: The Bayesian product partition model in Booth et al.

Pyrosequencing enumerates and contrasts soil microbial diversity.

Estimates of the number of species of bacteria per gram of soil vary between 2000 and 8.3 million (Gans et al., 2005; Schloss and Handelsman, 2006).

Hematopoietic stem cell mobilization with G-CSF induces innate inflammation yet suppresses adaptive immune gene expression as revealed by microarray analysis.

Objective: Granulocyte colony-stimulating factor (G-CSF) is used to boost granulocyte counts in immunocompromised patients, but its effects on the immune system may be counterproductive. We tested the hypothesis that G-CSF-mobilized peripheral blood stem cell (PBSC) products are immunologically downregulated based on gene microarray analysis.

Methods: Ten peripheral blood samples from normal donors for allogeneic PBSC transplantation were obtained before and after administration of G-CSF and tested on Affymetrix Human U133 Plus 2.