Hormonal and genetic regulation of Helicobacter hepaticus-induced intestinal inflammation

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.Title from PDF of title page (University of Missouri--Columbia, viewed on March 11, 2011).Vita.Thesis advisor: Craig L. Franklin."December 2010"Ph. D. University of Missouri-Columbia 2010.Inflammatory Bowel Diseases (IBDs) affect millions of people worldwide and are characterized by a chronic intestinal inflammation resulting from a dysregulated immune response to environmental stimuli in genetically susceptible individuals. Utilizing a mouse model of IBD, the studies presented herein investigated 1) the role for estrogen and estrogen receptors in disease development 2) genetic factors contributing to differential disease susceptibility 3) differences in bacterial flora between susceptible and resistant mice. Infection of the A/J mouse strain with the bacterium Helicobacter hepaticus results in acute over-expression of proinflammatory cytokines followed 2-3 months later by chronic cecal inflammation that is more severe in females than in males. Studies in these mice investigating the role for estrogen and estrogen receptors have revealed that selective signaling through estrogen receptor [beta] is immunomodulatory and decreases intestinal inflammation. Helicobacter hepaticus infected A/J mice develop intestinal inflammation, but infected C57BL/6 mice do not. Our investigations into the genetic factors responsible for Helicobacter hepaticus-induced intestinal inflammation have identified two major quantitative trait loci (QTL) on chromosome 3 and 17 associated with disease susceptibility. We also show that the microbial flora between these two mouse strains differs and can impact disease susceptibility. Together the work presented herein a further understanding into the role of hormones in controlling inflammation and insight into the genetic and bacterial factors associated with disease susceptibility.Includes bibliographical references

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome.

The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology

Site-specific and mRNA-specific control of accurate mRNA editing by a helicase complex in trypanosomes

Trypanosome U-insertion/deletion RNA editing in mitochondrial mRNAs involves guide RNAs (gRNAs) and the auxiliary RNA editing substrate binding complex (RESC) and RNA editing helicase 2 complex (REH2C). RESC and REH2C stably copurify with editing mRNAs but the functional interplay between these complexes remains unclear. Most steady-state mRNAs are partially edited and include misedited “junction” regions that match neither pre-mRNA nor fully edited transcripts. Editing specificity is central to mitochondrial RNA maturation and function, but its basic control mechanisms remain unclear. Here we applied a novel nucleotide-resolution RNA-seq approach to examine ribosomal protein subunit 12 (RPS12) and ATPase subunit 6 (A6) mRNA transcripts. We directly compared transcripts associated with RESC and REH2C to those found in total mitochondrial RNA. RESC-associated transcripts exhibited site-preferential enrichments in total and accurate edits. REH2C loss-of-function induced similar substrate-specific and site-specific editing effects in total and RESC-associated RNA. It decreased total editing primarily at RPS12 5′ positions but increased total editing at examined A6 3′ positions. REH2C loss-of-function caused site-preferential loss of accurate editing in both transcripts. However, changes in total or accurate edits did not necessarily involve common sites. A few 5′ nucleotides of the initiating gRNA (gRNA-1) directed accurate editing in both transcripts. However, in RPS12, two conserved 3′-terminal adenines in gRNA-1 could direct a noncanonical 2U-insertion that causes major pausing in 3′–5′ progression. In A6, a noncanonical sequence element that depends on REH2C in a region normally targeted by the 3′ half of gRNA-1 may hinder early editing progression. Overall, we defined transcript-specific effects of REH2C loss

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome.

The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology

Comparative FISH-Mapping of MC1R, ASIP, and TYRP1 in New and Old World Camelids and Association Analysis With Coat Color Phenotypes in the Dromedary (Camelus dromedarius)

Melanocortin 1 receptor (MC1R), the agouti signaling protein (ASIP), and tyrosinase related protein 1 (TYRP1) are among the major regulators of pigmentation in mammals. Recently, MC1R and ASIP sequence variants were associated with white and black/dark brown coat colors, respectively, in the dromedary. Here we confirmed this association by independent sequencing and mutation discovery of MC1R and ASIP coding regions and by TaqMan genotyping in 188 dromedaries from Saudi Arabia and United States, including 38 black, 53 white, and 97 beige/brown/red animals. We showed that heterozygosity for a missense mutation c.901C > T in MC1R is sufficient for the white coat color suggesting a possible dominant negative effect. Likewise, we confirmed that the majority of black dromedaries were homozygous for a frameshift mutation in ASIP exon 2, except for 4 animals, which were heterozygous. In search for additional mutations underlying the black color, we identified another frameshift mutation in ASIP exon 4 and 6 new variants in MC1R including a significantly associated SNP in 3′UTR. In pursuit of sequence variants that may modify dromedary wild-type color from dark-reddish brown to light beige, we identified 4 SNPs and one insertion in TYRP1 non-coding regions. However, none of these were associated with variations in wild-type colors. Finally, the three genes were cytogenetically mapped in New World (alpaca) and Old World (dromedary and Bactrian camel) camelids. The MC1R was assigned to chr21, ASIP to chr19 and TYRP1 to chr4 in all 3 species confirming extensive conservation of camelid karyotypes. Notably, while the locations of ASIP and TYRP1 were in agreement with human-camelid comparative map, mapping MC1R identified a new evolutionary conserved synteny segment between camelid chromosome 21 and HSA16. The findings contribute to coat color genomics and the development of molecular tests in camelids and toward the chromosome level reference assemblies of camelid genomes

A Gnotobiotic Mouse Model Demonstrates That Dietary Fiber Protects against Colorectal Tumorigenesis in a Microbiota- and Butyrate-Dependent Manner

It is controversial whether dietary fiber protects against colorectal cancer because of conflicting results from human epidemiologic studies. However, these studies and mouse models of colorectal cancer have not controlled the composition of gut microbiota, which ferment fiber into short-chain fatty acids such as butyrate. Butyrate is noteworthy because it has energetic and epigenetic functions in colonocytes and tumorsuppressive properties in colorectal-cancer cell lines. We utilized gnotobiotic mouse models colonized with wild-type or mutant strains of a butyrate-producing bacterium to demonstrate that fiber does have a potent tumor-suppressive effect but in a microbiota- and butyrate-dependent manner. Furthermore, due to the Warburg effect, butyrate was metabolized less in tumors where it accumulated and functioned as an HDAC inhibitor to stimulate histone acetylation and affect apoptosis and cell proliferation. To support the relevance of this mechanism in human cancer, we demonstrate that butyrate and histone-acetylation levels are elevated in colorectal adenocarcinomas compared to normal colonic tissues

Touring as Social Practice: Transnational Festivals, Personalized Networks, and New Folk Music Sensibilities

The aim of this dissertation is to contribute to an understanding of the changing relationship between collectivist ideals and individualism within dispersed, transnational, and heterogeneous cultural spaces. I focus on musicians working in professional folk music, a field that has strong, historic associations with collectivism. This field consists of folk festivals, music camps, and other venues at which musicians from a range of countries, affiliated with broad labels such as ‘Celtic,’ ‘Nordic,’ ‘bluegrass,’ or ‘fiddle music,’ interact. Various collaborative connections emerge from such encounters, creating socio-musical networks that cross boundaries of genre, region, and nation. These interactions create a social space that has received little attention in ethnomusicology. While there is an emerging body of literature devoted to specific folk festivals in the context of globalization, few studies have examined the relationship between the transnational character of this circuit and the changing sensibilities, music, and social networks of particular musicians who make a living on it. To this end, I examine the career trajectories of three interrelated musicians who have worked in folk music: the late Canadian fiddler Oliver Schroer (1956-2008), the Irish flute player Nuala Kennedy, and the Italian organetto player Filippo Gambetta. These musicians are all notable for their taste for transnational collaboration and their reputations as mavericks and boundary-pushers. Through case studies of their projects, relationships, and collaborative networks, I explore transformations in the collectivist folk ideal by focussing on how these musicians are implicated in three phenomena: transnational festivals, new folk music sensibilities, and touring as social practice. This research is based on multi-dimensional, multi-sited fieldwork undertaken in Toronto, Genoa, Edinburgh, and at various festivals in Europe and North America between 2007-2013. I conclude that Schroer, Kennedy, and Gambetta experience transnational folk music space as a field of intersecting transnationalisms that are imaginaries and collectivities of varying size and scope. While festivals in this space increasingly celebrate a transcultural ideal and foster the formation of transnational networks, stable, heterogeneous transnational relationships are proving more difficult to attain. I argue that touring on this circuit generates a desire for community continuity that becomes part of the poetics of new instrumental folk music.Ph

Tradition and innovation in Irish instrumental folk music

In the late twentieth century, many new melodies were composed in the genre of traditional Irish instrumental music. In the oral tradition of this music, these new tunes go through a selection process, ultimately decided on by a large, transnational, and loosely connected community of musicians, before entering the common-practice repertoire. This thesis examines a representative group of tunes that are being accepted into the commonpractice repertoire, and through analysis of motivic structure, harmony, mode and other elements, identifies the shifting boundaries of traditional music. Through an identification of these boundaries, observations can be made on the changing tastes of the people playing Irish music today. Chapter One both establishes the historical and contemporary context for the study of Irish traditional music, and reviews literature on the melodic analysis of Irish traditional music, particularly regarding the concept of "tune-families". Chapter Two offers an analysis of traditional tunes in the common-practice repertoire, in order to establish an analytical means for identifying traditional tune structure. Chapter Three is an analysis of five tunes that have entered the common-practice repertoire since 1980. This analysis utilizes the techniques introduced in Chapter Two, and discusses the idea of the melodic "hook", the memorable element that is necessary for a tune to become popular. Through structural analysis, observations are made on the boundaries of tradition and innovation.Arts, Faculty ofMusic, School ofGraduat

Composition Control and Formation Pathway of CZTS and CZTGS Nanocrystal Inks for Kesterite Solar Cells

The ability to reproducibly synthesize nanocrystal (NC) inks with precisely controlled compositions is essential for making efficient kesterite solar cells from NCs. Here we present the results of a study on Cu–Zn–Sn–S NCs in which different particle size fractions were collected over a range of reaction times from various starting reagents. From this we have determined the temporal evolution of the NC ink and identified at least two distinct particle populations that form following injection: large particles containing primarily Cu and Zn, and small particles of Cu and Sn. For short reaction times, the extreme compositional heterogeneity between these size fractions makes the average ink composition highly sensitive to changes in reaction time and precipitation procedure. Longer synthesis times produce more consistent inks, with higher yield, and compositions closer to that of the starting reagents. The choice of metal precursor was found to have a minor impact on the composition of the resulting ink compared to the changes with time, even when substituting Ge precursors for Sn precursors. Using this understanding, we demonstrate the ability to produce inks with targeted off-stoichiometric compositions