Genotypic and Phenotypic comparison of Bacteroides ovatus, B. thetaiotaomicron, and B. xylanisolvens isolates obtained from cow, goat, human, and pig feces

ABSTRACT Gastrointestinal Bacteroides play an important role in the health of their hosts. Do these Bacteroides perform the same functions in hosts that have different diets or gastrointestinal physiology? Do they show any co-evolution with the host environment? Within this study103 isolates of B. ovatus, B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human and pig fecal enrichments with cellulose or xylan/pectin. Isolates were compared using 16S rRNA gene sequencing, repetitive sequence based-PCR (rep-PCR), and phenotypic microarrays. Analysis of 16S rRNA gene sequences revealed high percent sequence identity in these Bacteroides; with distinct phylogenetic groupings by bacterial species, but not host origin. Phenotypic microarray analysis demonstrated these Bacteroides shared the ability to utilize many of the same carbon substrates, without differences due to species or host origin, indicative of their broad carbohydrate fermentation abilities. Limited nitrogen substrates were utilized; in addition to ammonia, guanine and xanthine, purine derivatives, were utilized by most isolates, followed by a few amino sugars. Only rep-PCR analysis demonstrated host specific patterns, indicating that genomic changes due to co-evolution with host did not occur by mutation in the 16S rRNA gene or by a gain or loss of carbohydrate utilization genes within these Bacteroides. In the second part of the study 24 isolates, from the original 103, of B. ovatus, B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human and pig fecal enrichments with cellulose or xylan/pectin. Isolates were compared using whole genome sequencing to determine possible genotypic differences among Bacteroides species and among same species from different host origins. The GC% content and gene numbers of the isolates compared to their type strain were similar but variation in overall genome size was seen in isolates of the same species. A broad analysis of the Clusters of Orthologous groups (COGs) did not show host specificity. A closer look at 4 COG categories (amino acid, carbohydrate, cell wall, and signal transduction) was done. At this level of analysis some differences between species and isolates from differing hosts was evident. Polysaccharide utilization loci (PULs) were compared for homology against the type strains of the isolates. There was variation in the number of homologous and non-homologous PULs and total number of PULs in the isolates. Differences among glycoside hydrolase (GH) families of the isolates of different Bacteroides species were found; comparison of the Bacteroides xylanisolvens isolates demonstrated host related differences for pig isolates compared to other host origins. Differences among homologous capsular polysaccharide (CPS) loci were seen in the downstream gene content of some CPS loci in isolates from different hosts. The results suggest that many of the genetic functions of isolates in this Bacteroides clade are conserved but that there are some differences in genomes by Bacteroides species and mammalian host origin

Impact of a Changing Climate on Fine Particulate Concentrations in Butte, MT

A model was developed to assess the potential change in PM2.5 concentrations in Butte, Montana over the course of the 21st century as the result of climate change and changes in emissions. The EPA AERMOD regulatory model was run using NARCCAP climate data for the years of 2040, 2050, 2060 and 2070, and the results were compared to the NAAQS to determine if there is the potential for future impacts to human health. This model predicted an average annual concentration of 15.84 µg/m3 in the year 2050, which would exceed the primary NAAQS of 12 µg/m3 and is a large increase over the average concentration from 2010 – 2012 of 10.52 µg/m3. The effectiveness of a wood stove change out program was also evaluated to determine its efficacy, and modeled results predicted that by changing out 100% of inefficient stoves with an EPA approved model, concentrations could be reduced below the NAAQS

The Role of ITK and RLK in CD8+ T Cell Development and Function: a Dissertation

Itk and Rlk are members of the Tec kinase family of non-receptor protein tyrosine kinases that are preferentially expressed in T cells. Numerous previous studies have demonstrated that these proteins play an important a role in the regulation of signalling processes downstream of TCR activation in CD4+ T cells, particularly in the phosphorylation of PLCγl. In addition, Itk and Rlk have both been shown to be important for CD4+ T cell development, differentiation, function and homeostasis following TCR activation. In the absence of Itk and Rlk, CD8+ SP thymocytes and T cells develop a memory/previously activated phenotypic profile, however, very little is known about the influence of Itk and Rlk on CD8+ T cell development and function. This study illustrates a previously unappreciated role for Itk and Rlk in the regulation of cytokine signals during CD8+ SP thymocyte maturation, and in the development of the memory CD44hi profile of Itk -/- and Itk -/- Rlk -/- CD8+ SP thymocytes and CD8+ T cells. This study also provides the first detailed study of the role of loss of Itk and particularly both Itk and Rlk in CD8+ signalling and function and shows that these Tec kinase family members play an important role in the maintenance of CD8+ T cell fitness and function, particularly in the ability of CD8+ T cells to accumulate in response to infection. Collectively, my studies demonstrate a critical role for Itk and Rlk in the generation of optimal CD8+ T cell responses. They also raise the novel observation that these proteins may be involved on the regulation of cytokine signals in T cells

Accounting for Indirect Costs in Public Health Cost Analyses

Background. There is a gap in research regarding the resources needed to deliver public health activities, which inhibits informed decision making around investments in public health and the allocation of funds among activities. When conducting cost analyses in public health, it is important to include costs from all cost components, including personnel, non-personnel, and indirect costs. However, defining, identifying, and measuring indirect costs is challenging and can impede studies of this type. Purpose. The purpose of this pilot study is to create a catalog of the methodologies public health researchers have used to account for indirect costs. Methods. We surveyed the final products submitted by the eleven practice-based research networks who received funding from the Robert Wood Johnson Foundation to explore the delivery and cost of public health activities for their indirect cost inclusion method. The primary investigators were contacted to verify their methodology. Ten of the 11 networks (91%) could be reached. Results. Four of the networks used a pre-negotiated rate the health department had with the state agency. Three of the networks used a data collection instrument that had public health administrative staff estimate these costs. Three of the networks did not include indirect costs in their analyses. Implications. Although challenging, it is important to include indirect costs in public health cost analyses as they are a real cost to public health departments and research findings without these costs have limited applicability. This review can assist researchers by reviewing approaches previously used by public health researchers