Atopic asthma is a complex disease process that has a significant social, personal and economic burden across all ages. Leukotriene-receptors are involved in the cascade of inflammation that may result in symptoms of atopy and asthma. Two leukotriene receptors have been identified in the lung. The cysteinyl leukotriene receptor 1 and cysteinyl leukotriene receptor 2 genes (i.e., CYSLTR1 and CYSLTR2) have been sequenced, and a number of single nucleotide polymorphisms (SNPs) within these genes have been identified.The purpose of this study was to: (1) Determine the relationship between CYSLTR1 genotypes, CYSLTR2 genotype, atopy, elevated IgE level, and eosinophilia, (2) Determine the relationship between CYSLTR1 genotypes, CYSLTR2 genotype, asthma, and atopic asthma, and (3) Determine the degree of interaction between CYSLTR2 genetic variation and gender in atopic asthma.Nested within two sub-studies of the Tucson Epidemiological Study of Airway Obstructive Disease (TESAOD) study, a prospective longitudinal cohort, 853 individuals were entered into this study. Study criteria included Non-Hispanic white adults, who consented to genetic testing in the two sub-studies. Tagging SNPs of the CYSLTR1 and CYSLTR2 genes were genotyped. Serum IgE status and eosinophilia were obtained from existing dataset. Questionnaires collected in the parent study were used to obtain demographic and clinical data.SNP rs321006 in the CYSLTR1 gene was associated with atopy among Non-Hispanic white women. Assuming a recessive model, among female Non-Hispanic white adults, the odds of having rs321073 CC genotype was 5.82 times higher among those with atopic asthma than those without atopic asthma. No gene by gender interaction was found between SNP of interest in CYSLTR2 and atopic asthma. Genetic association of SNPs rs321006 with atopy and rs321073 with atopic asthma are novel findings to date.Implications for nurses, clinicians, and scientists include better understanding of associations of these genetic variations with asthma, atopy, and atopic asthma that can generate further inquiry into other mechanisms of atopic asthma. These novel genetic associations with atopy and atopic asthma may have the potential for personalized medicine that might afford patients with appropriate treatment based on their genotype.

Rice is one of the most important crops in the world and is the first whose genome was completely sequenced. This landmark accomplishment placed O. sativa as a leading model in plant biology, especially for cereals. The genus Oryza includes 23 species, two of them independently domesticated in Asia and Africa. Wild species of Oryza contain a reservoir of useful agronomical traits which could be exploited for the benefit of rice agriculture, which is facing global problems as other crops, mainly due to a rampant increase in the human population and progressive deterioration of soils and water supplies. The Oryza Mapping Alignment Project has opened great opportunities to tap the genetic potential encapsulated in these species. Four BAC libraries generated from the African species of Oryza: O. barthii, O. glaberrima (AA genome), O. punctata (BB genome) and O. brachyantha (FF genome) were fully characterized and shown to provide enough coverage to represent their respective genomes. BAC clones from these libraries were fingerprinted and end-sequenced to assemble physical maps that were heavily manually edited using the sequence of O. sativa as a reference genome. The physical maps showed high coverage for all the species across all chromosomes. Both, BAC libraries and physical maps were used to investigate synteny and structural variation. The four species show high colinearity to the reference genome, although synteny perturbations were detected, including contractions, expansions, and putative inversions and translocations, which potential have an important impact in the evolution of these species.

A role for gene variants in regulating the pharmacokinetics of systemically available toxicants has not yet been established. A panel of 18 genetically-diverse inbred mouse strains was used to determine the range of total exposure kinetic parameters in blood and bone marrow following a single oral administration of benzene (100 μg/kg) to male and female mice. Large ranges in several pharmacokinetic parameters were found when data from blood and bone marrow were analyzed. AUC and CL_F pharmacokinetic parameters in blood and bone marrow pharmacokinetics were strikingly different as were these parameters in males and females. Final clearance (CL_F) was found to be the most statistically robust pharmacokinetic parameter as it accounted for exposure of the matrix (AUC) and normalized for dose variations among the strains. The CL_F values in blood and bone marrow used for haplotype association mapping showed 331 and 164 quantitative trait loci with statistical significance, respectively (male mice; -logP>4). Two loci were found to be shared between males and females QTL bone marrow data sets and one common locus was found for male blood and bone marrow data. No overlap was found among blood QTL in males and females (or between blood and bone marrow data from females). Protein and mRNA expression data for the primary benzene-metabolizing enzymes CYP2E1 and UGT1A6 showed very little strain-dependent variation. Strain dependent differences in mRNA levels of NQO1 and MPO were small but statistically significant, as were those for GAPDH and β2-microglobulin. These data demonstrated that polymorphisms with the greatest contribution toward overall variations in systemic exposures occurred in genes encoding for non-metabolic proteins. While exposure does not equate to toxicity, identification of the genes regulating distribution and clearance may be useful for investigating host susceptibility to toxic effects following benzene exposure. This research was supported in part by the NIEHS NTP Grant N01ES45529, NIEHS Toxicology and Toxicogenomics Training Grant (5T32ES007091-29), NIEHS/NTP Division of Intramural Research, and Southwest Environmental Science Center Grant P3ES06694.

This is a research paper submitted for LIBR220 (Medical and Health Sciences Librarianship), a graduate course in Library and Information Sciences at San Jose State University. / PURPOSE: To evaluate ways in which hospital librarians can help clinicians keep up with the rapid growth of genetic information and incorporate it into patient care as we enter the era of genomic medicine. SETTING: Hospital medical libraries DESCRIPTION: The fast-growing new field of genomic medicine applies human genetic information to the understanding and treatment of disease. Historically, evidence-based healthcare has been informed by studies on large populations. Breakthroughs in genetic analysis technologies are presenting healthcare providers with new opportunities to diagnose and customize clinical treatment based on the genetic structure of individual patients. In the hospital setting, access to genomic medicine information resources, clinical guidelines, and continuing education will be critical in the near future. This research paper will explore resources and programs that hospital librarians can offer to clinicians, to serve their genomic medicine information needs and help them navigate through unfamiliar territory.

The origin of new coding sequence is a major puzzle in biology. The evolutionary pressures on new sequences are largely unknown, but structural constraints are thought to play a role. Previously, 3' untranslated region (UTR) conversion to open reading frame (ORF) was observed in Saccharomyces. We sought to identify genes that were polymorphic for stop codon position in S. cerevisiae and S. paradoxus. Using strain sequence data from the Saccharomyces Genome Resequencing Project, we found 1336 genes that had evidence of stop codon polymorphism. Of those, we found 62 genes that had evidence of addition to ancestral sequence that represented the conversion of ancestral 3' UTR to derived ORF. Two of these genes, YGL058W and YNL034W-A, are prime candidates for structural studies as they are short proteins with long additions and known structures. In future studies, they will be used to infer any structural constraints on newly evolving proteins.

All cellular processes depend on the coordinate expression of genes and their interactions. Regulatory sequences encoded in the genome stipulate the necessary instructions interpreted by sequence-specific transcription factors (TFs) to control the spatial-temporal output of gene expression. Detection of cis-regulatory signals is challenging, owing to the lack of distinguishing features such as open reading frames and an overwhelming excess of spurious to functional TF binding site matching sequences embedded within the vast non-coding regions of vertebrate genomes. From an evolutionary standpoint, functional alterations in cis-regulatory architecture are thought to be important in diversifying morphology and physiology in the evolution of vertebrates, which share a similar body plan and complement of genes. Correspondingly, recent studies have highlighted the plasticity of cis-regulatory architecture organization over evolutionary time, finding associations with examples of both diverged and conserved patterns of gene expression. These observations underscore the gap in our collective knowledge with respect to the rules by which TFs recognize and bind their targets in vivo, as well as how this process evolves in vertebrates, and serve as a motivating basis for this thesis work. To begin, I probed the extent of conservation and divergence of sequence and expression profiles across tissues of diverse vertebrate species, identifying thousands of candidate genes with conserved expression by microarray analysis. However, corresponding conservation of non-exonic and potentially regulatory sequence was lacking, suggestive of binding site turnover over evolutionary time. Next, I analyzed the sequence specificity of a wide array of mouse and yeast TFs, finding great diversity and complexity in their binding preferences, with many factors recognizing multiple distinct motifs. Furthermore, comparative analysis of orthologous TFs suggest well conserved binding specificities. I also demonstrate the likely biological relevance of sequences highly preferred by these TFs by revealing distinctive signatures in their distribution and organization within putative regulatory regions in each genome. Lastly, I have begun to explore the organization of cis-regulatory sequences active in vertebrate tissues by high-throughput sequencing of open chromatin. Together, these data help illuminate the organization and evolution of vertebrate regulatory architectures, providing a useful toolkit for the testing of new models and hypotheses.

It is a microbial world we live in: microbes outnumber other organisms by several orders of magnitude, and they have great importance for the environment. However, environmental microbes are notoriously difficult to grow in the laboratory, and using culture independent techniques is necessary to expand our view. In this thesis, I apply metagenomics and single-cell genomics to environmental samples from ancient human remains and lakes. First, I used metagenomics to learn about bacteria from a Neanderthal’s bone and the gut of Ötzi, a frozen natural mummy. Both were exploratory studies where the main question was what kind of bacteria are present. I found out that Streptomyces dominated this particular Neanderthal fossil, and the DNA lacked the damage that is often seen in ancient samples. Ötzi's gut sample was dominated by Clostridia and fungi belonging to Basidiomycota. Second, ten single-cell amplified genomes of freshwater Alphaproteobacterium LD12 and three metagenomes from Swedish lakes were sequenced. Comparative metagenomics allowed hypothesizing about which functions are important for microbe proliferation in freshwater, pointing to osmoregulation and transport proteins and, possibly, to different strategies of metabolizing sugars. I also focused on SAR11 sister-groups in oceans and lakes. Phylogenies and sequence evolutionary distance estimates indicated the existence of microclusters within LD12, showing variation in abundance between lakes. The most striking difference was the relative amount of recombination compared to mutation, the estimated r/m ratio. SAR11 marine and their freshwater cousins are found at the opposite extremes of the r/m range, lowest and highest, respectively. The genetic background or sequence diversity did not explain the observed dramatic difference, so it is possibly connected to environmental adaptation or population dynamics. In addition, I have spent a substantial amount of effort benchmarking available metagenomic methods, for example fragment recruitment of metagenomes to reference genomes. In conclusion, my exploratory metagenomic studies have shed some light on the bacteria present in ancient human remains; comparative metagenomics has suggested the importance of substrate preference on functional differences between lakes and oceans; finally, single-cell genomes have allowed some insight into molecular evolutionary processes taking place in the freshwater LD12 bacterium.

Activation-tagging is a functional genomics technique where strong enhancers are inserted randomly into target genomes to over-activate endogenous genes. Phenotypes of interest can be selected for investigation of genetic factors contributing to the mutant phenotype. From initial screens of a population of activation-tagged potato, a mutant with chocolate-coloured tuber skin has been identified. In this thesis, a novel sequence capture method for identifying T-DNA loci in activation tagged potato was used to characterize chocolate’s single T-DNA insertion locus. Transcriptome analysis of tuber periderm tissue was used to identify major processes occurring in the chocolate mutant. Our data suggest activation of a chitin-binding receptor-like kinase located 65 kb from T-DNA insert may cause activation of immune signaling pathways in chocolate. The present work explores a putative model of transcriptional and cellular responses involved in gain-of-function immune receptor activation. Selectively, these findings illustrate the periderm tissue as an important area of defense charged against biotic and abiotic stresses. Periderm development and anatomy are highly important for tuber storage. Further characterization of potato tuber periderm may contribute knowledge to model periderm systems and have implications for molecular breeding strategies to improve tuber storage quality. / Thesis (Master, Biology) -- Queen's University, 2012-09-27 11:45:16.478

The aims of this thesis were to investigate whether characteristics associated with animal welfare are genetically and genomically determined by using quantitative and molecular genetic approaches and to develop strategies indicating how these traits could be used in breeding programmes. Two traits that are closely related to animal welfare and associated with high socio-economic values are piglet survival at birth and aggressive behaviour in pigs. Piglet survival traits were analysed based on quantitative Bayesian approaches using phenotypic and pedigree information only, while aggressive behaviour was analysed based on molecular genetic approaches such as genome-wide association studies and genomic selection using additionally a dense panel of single nucleotide polymorphisms (SNP). The latter approach was validated using behavioural traits related to welfare characteristics in a welldocumented mouse data set. Selection for piglet survival at birth is expected to be effective, because all lines and breeds in this thesis showed considerable variation for this trait and relatively high heritabilities, particularly in lines with low average birth weight. Maternal heritabilities of individual birth weight were mostly at moderate magnitude and thus of great interest for selection. The genetic correlations between piglet survival and birth weight indicated that selection for either individual or average birth weight or variation of birth weight within litter would indirectly increase survival. The genetic associations of piglet survival with economically important (re)production traits are of great importance for breeding organisations. Undesirable genetic correlations between piglet survival and (re)production traits were generally of low magnitude, so that simultaneous improvement of all traits could be achieved. A comparison of five breeds and lines showed that differences in genetic parameters between breeds and lines can be substantial and no single selection strategy would be optimal for all. A unique study of a sire and a dam line originating from one breed but selected for more than 25 years with different breeding goals demonstrated how selection pressure can alter the genetic parameters over years. Breeding organisations should therefore consider selection strategies per breed or line individually to achieve maximum overall improvement. This study gives new insight into the use of genomic selection for traits associated with animal welfare. It is one of the first to present estimates for linkage disequilibrium in the pig using a new 60K SNP panel and the first to evaluate the efficiency of genomic selection against aggressive behaviour in pigs. Genomic selection showed a high predictive ability in comparison to traditional polygenic selection. It was especially advantageous for traits with lower heritabilities. In particular in situations where little family information was available, the performance of polygenic selection was low and genomic selection increased the performance considerably. Reducing the number of SNPs did not significantly change the performance of genomic selection. The consistently high performance across models indicates that low-density SNP panels may be sufficient to ensure a high efficiency of genomic selection, thus reducing the high costs associated with genotyping in pig breeding with its short generation interval. To summarize, this thesis has shown how to optimise quantitative and genomic approaches to improve animal welfare related characteristics efficiently in pig breeding programmes.

The first metazoan to be sequenced was a nematode (Caenorhabditis elegans), and understanding the genome of this model organism has led to many insights about all animals. Although eleven nematode genomes have been published so far and approximately twenty more are under way, the vast majority of the genomes of this incredibly diverse phylum remain unexplored. Next-generation sequencing has made it possible to generate large amounts of genome sequence data in a few days at a fraction of the cost of traditional Sanger-sequencing. However, assembling and annotating these data into genomic resources remains a challenge because of the short reads, the quality issues in these kinds of data, and the presence of contaminants and co-bionts in uncultured samples. In this thesis, I describe the process of creating high quality draft genomes and annotation resources for four nematode species representing three of the five major nematode clades: Caenorhabditis sp. 5, Meloidogyne floridensis, Dirofilaria immitis, and Litomosoides sigmodontis. I describe the new approaches I developed for visualising contamination and co-bionts, and I present the details of the robust workflow I devised to deal with the problems of generating low-cost genomic resources from Illumina short-read sequencing. Results: The draft genome assemblies created using the workflow described in this thesis are comparable to the draft nematode genomes created using Sanger sequencing. Armed with these genomes, I was able to answer two evolutionary genomics questions at very different scales. The first question was whether any non-coding elements were deeply conserved at the level of the whole phylum. Such elements had previously been hypothesised to be responsible for the phylum body plan in vertebrates, insects, and nematodes. I used twenty nematode genomes in several whole-genome alignments and concluded that no such elements were conserved across the whole phylum. The second question addressed the origins of the highly destructive plant-parasitic root-knot nematode Meloidogyne incognita. Comparisons with the newly sequenced Meloidogyne floridensis genome revealed the complex hybrid origins of both species, undermining previous assumptions about the rarity of hybrid speciation in animals. Conclusions: This thesis demonstrates the role of next-generation sequencing in democratising genome sequencing projects. Using the sequencing strategies, workflows, and tools described here, one can rapidly create genomic resources at a very low cost, even for unculturable metazoans. These genomes can be used to understand the evolutionary history of a genus or a phylum, as shown.