subject:(gene gene interactions)

University of Utah

1. Abo, Ryan P. Bioinformatic tools for genetic epidemiology: application to candidate gene analysis in breast cancer.

Degree: PhD, Biomedical Informatics;, 2010, University of Utah

URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/247/rec/156

► This dissertation describes the development, implementation, and application of bioinformatic methods and tools. The objective was to provide enhanced methods for the identification of genetic… (more)

Subjects/Keywords: Bioinformatics; Gene-gene interactions; Genetic epidemiology; Haplotypes

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APA (6^th Edition):

Abo, R. P. (2010). Bioinformatic tools for genetic epidemiology: application to candidate gene analysis in breast cancer. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/247/rec/156

Chicago Manual of Style (16^th Edition):

Abo, Ryan P. “Bioinformatic tools for genetic epidemiology: application to candidate gene analysis in breast cancer.” 2010. Doctoral Dissertation, University of Utah. Accessed April 10, 2021. http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/247/rec/156.

MLA Handbook (7^th Edition):

Abo, Ryan P. “Bioinformatic tools for genetic epidemiology: application to candidate gene analysis in breast cancer.” 2010. Web. 10 Apr 2021.

Vancouver:

Abo RP. Bioinformatic tools for genetic epidemiology: application to candidate gene analysis in breast cancer. [Internet] [Doctoral dissertation]. University of Utah; 2010. [cited 2021 Apr 10]. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/247/rec/156.

Council of Science Editors:

Abo RP. Bioinformatic tools for genetic epidemiology: application to candidate gene analysis in breast cancer. [Doctoral Dissertation]. University of Utah; 2010. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/247/rec/156

University of Alberta

2. Sapkota, Shraddha. Longitudinal Associations of Genetic Polymorphisms and Personality Traits: Independent and Interactive Effects on Neurocognitive Performance in Older Adults.

Degree: MS, Centre for Neuroscience, 2013, University of Alberta

URL: https://era.library.ualberta.ca/files/c534fp52q

► Research has linked multifaceted neurocognitive phenotypes to genetic polymorphisms and environmental factors. This study examines associations of personality traits and single nucleotide polymorphisms (SNPs) on… (more)

Subjects/Keywords: gene x gene interactions; personality traits; neurocognition

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APA (6^th Edition):

Sapkota, S. (2013). Longitudinal Associations of Genetic Polymorphisms and Personality Traits: Independent and Interactive Effects on Neurocognitive Performance in Older Adults. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/c534fp52q

Chicago Manual of Style (16^th Edition):

Sapkota, Shraddha. “Longitudinal Associations of Genetic Polymorphisms and Personality Traits: Independent and Interactive Effects on Neurocognitive Performance in Older Adults.” 2013. Masters Thesis, University of Alberta. Accessed April 10, 2021. https://era.library.ualberta.ca/files/c534fp52q.

MLA Handbook (7^th Edition):

Sapkota, Shraddha. “Longitudinal Associations of Genetic Polymorphisms and Personality Traits: Independent and Interactive Effects on Neurocognitive Performance in Older Adults.” 2013. Web. 10 Apr 2021.

Vancouver:

Sapkota S. Longitudinal Associations of Genetic Polymorphisms and Personality Traits: Independent and Interactive Effects on Neurocognitive Performance in Older Adults. [Internet] [Masters thesis]. University of Alberta; 2013. [cited 2021 Apr 10]. Available from: https://era.library.ualberta.ca/files/c534fp52q.

Council of Science Editors:

Sapkota S. Longitudinal Associations of Genetic Polymorphisms and Personality Traits: Independent and Interactive Effects on Neurocognitive Performance in Older Adults. [Masters Thesis]. University of Alberta; 2013. Available from: https://era.library.ualberta.ca/files/c534fp52q

University of New Mexico

3. Baca, Michael. Gene-environment interactions affect long-term depression (LTD) through changes in dopamine D2 receptor affinity in Snap25 haplodeficient mice.

Degree: Biomedical Sciences Graduate Program, 2013, University of New Mexico

URL: https://digitalrepository.unm.edu/biom_etds/111

► Genes and environmental conditions interact in the development of cognitive capacities and each plays an important role in neuropsychiatric disorders such as attention deficit/hyperactivity disorder… (more)

▼ Genes and environmental conditions interact in the development of cognitive capacities and each plays an important role in neuropsychiatric disorders such as attention deficit/hyperactivity disorder (ADHD) and schizophrenia. Multiple studies have indicated that the gene for the SNARE protein, SNAP-25 is a candidate susceptibility gene for ADHD, as well as schizophrenia, while maternal smoking is a candidate environmental risk factor for ADHD. In this study, mice heterozygous for a Snap25 allele and deficient in SNAP-25 expression were utilized to model genetic effects in combination with prenatal exposure to nicotine to explore genetic and environmental (G x E) factors and interactions. Striatal long-term depression (LTD) is a form of synaptic plasticity in which there is a reduction in the glutamate released by cortical afferents onto striatal medium spiny neurons (MSNs). The glutamatergic inputs activate ionotropic and group I metabotropic glutamate receptors while dopaminergic inputs from the substantia nigra pars compacta activate type-2 dopamine receptors (D2Rs), which collectively lead to post-synaptic production of endocannabinoids that diffuse in a retrograde manner to activate pre-synaptic type-1 cannabinoid (CB1) receptors on to pre-synaptic terminals. The CB1 receptors initiate signaling cascades that lead to the long-term decrease in glutamate release in pre-synaptic glutamate terminals. Using a high frequency stimulus (HFS) electrophysiological paradigm for LTD induction in striatal MSNs, I first characterized synaptic depression in four G x E groups representing mice prenatal nicotine exposed or not or having Snap25 deficiency or not, that showed responses which could be divided by cluster analysis into populations expressing LTD and short-term depression (STD). STD is characterized by an initial decrease in amplitude in the response to the HFS followed by near full recovery of the response within 30 minutes, while LTD occurs when the initial decrease remains attenuated for at least 30 minutes. I found that prenatal exposure to nicotine in Snap25 heterozygote mice produced a less robust LTD population and less return to baseline in the STD population. Using receptor antagonists in the same HFS electrophysiological paradigm I next examined the roles of dopaminergic D2Rs and cannabinoid CB1Rs, both critical for LTD induction in the striatum. I found that prenatal exposure to nicotine in Snap25 heterozygote mice produced a deficit in the D2R-dependent induction of LTD, although the CB1R involvement in plasticity was not impaired. From these results I developed the hypothesis that the impaired induction of LTD due to prenatal exposure to nicotine in Snap25 heterozygote mice, could be related to changes in D2R affinity and/or changes in the number of D2R receptors. This was initially tested using a [35S]-GTPγS binding assay to measure the agonist-stimulated response of G-protein-coupled D2R receptors. Indeed, the agonist-stimulated response was found to be reduced in Snap25 heterozygote mice… Advisors/Committee Members: Partridge, L. Donald, Wilson, Michael, Allan, Andrea, James, Conrad.

Subjects/Keywords: Neuroscience; Gene-environment interactions; Electrophysiology

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APA (6^th Edition):

Baca, M. (2013). Gene-environment interactions affect long-term depression (LTD) through changes in dopamine D2 receptor affinity in Snap25 haplodeficient mice. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biom_etds/111

Chicago Manual of Style (16^th Edition):

Baca, Michael. “Gene-environment interactions affect long-term depression (LTD) through changes in dopamine D2 receptor affinity in Snap25 haplodeficient mice.” 2013. Doctoral Dissertation, University of New Mexico. Accessed April 10, 2021. https://digitalrepository.unm.edu/biom_etds/111.

MLA Handbook (7^th Edition):

Baca, Michael. “Gene-environment interactions affect long-term depression (LTD) through changes in dopamine D2 receptor affinity in Snap25 haplodeficient mice.” 2013. Web. 10 Apr 2021.

Vancouver:

Baca M. Gene-environment interactions affect long-term depression (LTD) through changes in dopamine D2 receptor affinity in Snap25 haplodeficient mice. [Internet] [Doctoral dissertation]. University of New Mexico; 2013. [cited 2021 Apr 10]. Available from: https://digitalrepository.unm.edu/biom_etds/111.

Council of Science Editors:

Baca M. Gene-environment interactions affect long-term depression (LTD) through changes in dopamine D2 receptor affinity in Snap25 haplodeficient mice. [Doctoral Dissertation]. University of New Mexico; 2013. Available from: https://digitalrepository.unm.edu/biom_etds/111

University of Miami

4. Ayala-Haedo, Juan A. Understanding the Role of Novel Gene-Environmental and Gene-Gene Interactions in the Pathogenesis of Age Related Macular Degeneration.

Degree: PhD, Molecular Cell and Developmental Biology (Medicine), 2010, University of Miami

URL: https://scholarlyrepository.miami.edu/oa_dissertations/944

► The purpose of the study was to assess single nucleotide polymorphisms (SNPs) in NOS2 A, ESR1, ESR2 and MMP-2 genes that may affect the… (more)

▼ The purpose of the study was to assess single nucleotide polymorphisms (SNPs) in NOS2 A, ESR1, ESR2 and MMP-2 genes that may affect the risk for age-related macular degeneration (AMD) and may interact with environmental factors such as estrogen exposure and smoking, thereby modifying their effect on AMD. AMD is an ocular degenerative disease with known genetic and environmental factors. However, the disease risk genes identified so far account only for part of the genetic attributable risk and the role of new disease risk genes remain to be evaluated. For non-genetic risk factors, the most extensively analyzed are smoking and estrogen exposure. Smoking increases the risk for development of AMD and estrogen exposure has a protective effect. Both of these factors have been linked to oxidative pathway activation and extracellular matrix homeostasis (ECM) through interactions with the NOS2A and metallomatrix proteinase (MMP) genes, respectively. In addition, estrogen exerts its activity through the estrogen receptors ER alpha and ER beta. We examined a Caucasian cohort of AMD cases and controls. Nine hundred and ninety-eight individuals (males and females) for the NOS2A gene and 777 females for both the ESR1/2 and MMP-2 genes were assessed. We genotyped TagSNPs within these selected candidate gene regions using HapMap phase II or III. Multivariable logistic regression or generalized estimating equation (GEE) models containing SNP genotypes, age, sex, environmental factor and genotype/environmental interaction were constructed. In addition, because we previously reported interactions between the ARMS2 locus and estrogen exposure and smoking, we also analyzed interactions within ARMS2 locus. We found that SNPs in NOS2A are associated with increased risk for AMD and might modulate the smoking effect on AMD. The synergistic interaction between NOS2A and smoking is independent of the ARMS2 locus. No SNP in the MMP-2 gene was significantly associated with increased risk for AMD. We also detected no significant interactions with estrogen exposure or with the ARMS2 locus. SNPs within the ESR1 gene are associated with an increased risk for developing AMD and the inverse association of AMD and HRT is dependent on SNP genotypes in ESR1 and ESR2 and independent of the ARMS2 locus. Advisors/Committee Members: Vinata B. Lokeshwar, Richard K. Lee, John R. Gilbert, Margaret A. Pericak-Vance.

Subjects/Keywords: Gene-gene And Gene-environmental Interactions; Genetics; AMD

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APA (6^th Edition):

Ayala-Haedo, J. A. (2010). Understanding the Role of Novel Gene-Environmental and Gene-Gene Interactions in the Pathogenesis of Age Related Macular Degeneration. (Doctoral Dissertation). University of Miami. Retrieved from https://scholarlyrepository.miami.edu/oa_dissertations/944

Chicago Manual of Style (16^th Edition):

Ayala-Haedo, Juan A. “Understanding the Role of Novel Gene-Environmental and Gene-Gene Interactions in the Pathogenesis of Age Related Macular Degeneration.” 2010. Doctoral Dissertation, University of Miami. Accessed April 10, 2021. https://scholarlyrepository.miami.edu/oa_dissertations/944.

MLA Handbook (7^th Edition):

Ayala-Haedo, Juan A. “Understanding the Role of Novel Gene-Environmental and Gene-Gene Interactions in the Pathogenesis of Age Related Macular Degeneration.” 2010. Web. 10 Apr 2021.

Vancouver:

Ayala-Haedo JA. Understanding the Role of Novel Gene-Environmental and Gene-Gene Interactions in the Pathogenesis of Age Related Macular Degeneration. [Internet] [Doctoral dissertation]. University of Miami; 2010. [cited 2021 Apr 10]. Available from: https://scholarlyrepository.miami.edu/oa_dissertations/944.

Council of Science Editors:

Ayala-Haedo JA. Understanding the Role of Novel Gene-Environmental and Gene-Gene Interactions in the Pathogenesis of Age Related Macular Degeneration. [Doctoral Dissertation]. University of Miami; 2010. Available from: https://scholarlyrepository.miami.edu/oa_dissertations/944

Penn State University

5. Hall, Molly Ann. Beyond genome-wide association studies (GWAS): Emerging methods for investigating complex associations for common traits.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/26751

► Genome-wide association studies (GWAS) have identified numerous loci associated with human phenotypes. This approach, however, does not consider the richly diverse and complex environment with… (more)

▼ Genome-wide association studies (GWAS) have identified numerous loci associated with human phenotypes. This approach, however, does not consider the richly diverse and complex environment with which humans interact throughout the life course, nor does it allow for interrelationships among genetic loci and across traits. Methods that embrace pleiotropy (the effect of one locus on more than one trait), gene-environment (GxE) and gene-gene (GxG) interactions will further unveil the impact of alterations in biological pathways and identify genes that are only involved with disease in the context of the environment. This valuable information can be used to assess personal risk and choose the most appropriate medical interventions based on an individual’s genotype and environment. Additionally, a richer picture of the genetic and environmental aspects that impact complex disease will inform environmental regulations to protect vulnerable populations. Three key limitations of GWAS lead to an inability to robustly model trait prediction in a manner that reflects biological complexity: 1) GWAS explore traits in isolation, one phenotype at a time, preventing investigators from uncovering relationships that exist among multiple traits; 2) GWAS do not account for the exposome; rather, they simply explore the effect of genetic loci on an outcome; and 3) GWAS do not allow for interactions between genetic loci, despite the complexity that exists in biology. The aims described in this dissertation address these limitations. Methods employed in each aim have the potential to: uncover genetic interactions, unveil complex biology behind phenotype networks, inform public policy decisions concerning environmental exposures, and ultimately assess individual disease-risk. Advisors/Committee Members: Marylyn Deriggi Ritchie, Dissertation Advisor/Co-Advisor, Marylyn Deriggi Ritchie, Committee Chair/Co-Chair, Santhosh Girirajan, Committee Chair/Co-Chair, Scott Brian Selleck, Committee Member, Ross Cameron Hardison, Committee Member, George H Perry, Committee Member, Catherine Mc Carty, Special Member.

Subjects/Keywords: gene-gene interactions; epistasis; PheWAS; phenome; EWAS; exposome; gene-environment interactions; complex traits

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APA (6^th Edition):

Hall, M. A. (2015). Beyond genome-wide association studies (GWAS): Emerging methods for investigating complex associations for common traits. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/26751

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hall, Molly Ann. “Beyond genome-wide association studies (GWAS): Emerging methods for investigating complex associations for common traits.” 2015. Thesis, Penn State University. Accessed April 10, 2021. https://submit-etda.libraries.psu.edu/catalog/26751.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hall, Molly Ann. “Beyond genome-wide association studies (GWAS): Emerging methods for investigating complex associations for common traits.” 2015. Web. 10 Apr 2021.

Vancouver:

Hall MA. Beyond genome-wide association studies (GWAS): Emerging methods for investigating complex associations for common traits. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Apr 10]. Available from: https://submit-etda.libraries.psu.edu/catalog/26751.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hall MA. Beyond genome-wide association studies (GWAS): Emerging methods for investigating complex associations for common traits. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/26751

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Edinburgh

6. Williamson, Luke Jonathan. Characterising gene-gene and gene-environment interactions within the fitness landscape of a snoRNA.

Degree: PhD, 2019, University of Edinburgh

URL: http://hdl.handle.net/1842/35823

► Empirical fitness landscapes allow a previously hypothetical concept describing the genotype-phenotype relationship to be visualised and dissected. The fitness landscapes of entire molecules have only… (more)

Subjects/Keywords: gene mutations; temperature variations; U3 small nucleolar RNA; snoRNA; gene-gene interactions; changing environment

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APA (6^th Edition):

Williamson, L. J. (2019). Characterising gene-gene and gene-environment interactions within the fitness landscape of a snoRNA. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/35823

Chicago Manual of Style (16^th Edition):

Williamson, Luke Jonathan. “Characterising gene-gene and gene-environment interactions within the fitness landscape of a snoRNA.” 2019. Doctoral Dissertation, University of Edinburgh. Accessed April 10, 2021. http://hdl.handle.net/1842/35823.

MLA Handbook (7^th Edition):

Williamson, Luke Jonathan. “Characterising gene-gene and gene-environment interactions within the fitness landscape of a snoRNA.” 2019. Web. 10 Apr 2021.

Vancouver:

Williamson LJ. Characterising gene-gene and gene-environment interactions within the fitness landscape of a snoRNA. [Internet] [Doctoral dissertation]. University of Edinburgh; 2019. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/1842/35823.

Council of Science Editors:

Williamson LJ. Characterising gene-gene and gene-environment interactions within the fitness landscape of a snoRNA. [Doctoral Dissertation]. University of Edinburgh; 2019. Available from: http://hdl.handle.net/1842/35823

7. Han, Bing. DETECTING CANCER-RELATED GENES AND GENE-GENE INTERACTIONS BY MACHINE LEARNING METHODS.

Degree: PhD, Electrical Engineering & Computer Science, 2011, University of Kansas

URL: http://hdl.handle.net/1808/8781

► To understand the underlying molecular mechanisms of cancer and therefore to improve pathogenesis, prevention, diagnosis and treatment of cancer, it is necessary to explore the… (more)

Subjects/Keywords: Computer science; Bioinformatics; Cancer; Differential gene relations; Gene-gene interactions; Machine learning; System biology

12 more images…

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APA (6^th Edition):

Han, B. (2011). DETECTING CANCER-RELATED GENES AND GENE-GENE INTERACTIONS BY MACHINE LEARNING METHODS. (Doctoral Dissertation). University of Kansas. Retrieved from http://hdl.handle.net/1808/8781

Chicago Manual of Style (16^th Edition):

Han, Bing. “DETECTING CANCER-RELATED GENES AND GENE-GENE INTERACTIONS BY MACHINE LEARNING METHODS.” 2011. Doctoral Dissertation, University of Kansas. Accessed April 10, 2021. http://hdl.handle.net/1808/8781.

MLA Handbook (7^th Edition):

Han, Bing. “DETECTING CANCER-RELATED GENES AND GENE-GENE INTERACTIONS BY MACHINE LEARNING METHODS.” 2011. Web. 10 Apr 2021.

Vancouver:

Han B. DETECTING CANCER-RELATED GENES AND GENE-GENE INTERACTIONS BY MACHINE LEARNING METHODS. [Internet] [Doctoral dissertation]. University of Kansas; 2011. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/1808/8781.

Council of Science Editors:

Han B. DETECTING CANCER-RELATED GENES AND GENE-GENE INTERACTIONS BY MACHINE LEARNING METHODS. [Doctoral Dissertation]. University of Kansas; 2011. Available from: http://hdl.handle.net/1808/8781

Texas A&M University

8. Satpathy, Sitanshu. Probabilistic Analysis of Pair Wise Gene Interactions Using Support Vector Clustering.

Degree: MS, Electrical Engineering, 2017, Texas A&M University

URL: http://hdl.handle.net/1969.1/173093

► The most difficult challenge in genetic epidemiology is to characterize the gene interactions that affect a complex disease. DNA microarray has made it easier for… (more)

Subjects/Keywords: Gene Interactions; Support Vector Clustering; Gaussian Kernel

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APA (6^th Edition):

Satpathy, S. (2017). Probabilistic Analysis of Pair Wise Gene Interactions Using Support Vector Clustering. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/173093

Chicago Manual of Style (16^th Edition):

Satpathy, Sitanshu. “Probabilistic Analysis of Pair Wise Gene Interactions Using Support Vector Clustering.” 2017. Masters Thesis, Texas A&M University. Accessed April 10, 2021. http://hdl.handle.net/1969.1/173093.

MLA Handbook (7^th Edition):

Satpathy, Sitanshu. “Probabilistic Analysis of Pair Wise Gene Interactions Using Support Vector Clustering.” 2017. Web. 10 Apr 2021.

Vancouver:

Satpathy S. Probabilistic Analysis of Pair Wise Gene Interactions Using Support Vector Clustering. [Internet] [Masters thesis]. Texas A&M University; 2017. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/1969.1/173093.

Council of Science Editors:

Satpathy S. Probabilistic Analysis of Pair Wise Gene Interactions Using Support Vector Clustering. [Masters Thesis]. Texas A&M University; 2017. Available from: http://hdl.handle.net/1969.1/173093

University of Southern California

9. Li, Rui "Rachel". Joint analysis of two related studies of different data types and different study designs using hierarchical modeling in detecting gene-environment interactions.

Degree: PhD, Statistical Genetics and Genetic Epidemiology, 2011, University of Southern California

URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/673621/rec/3693

► Identifying causal susceptibility alleles for asthma poses many challenges. These include the multigenic nature of the disease, the lack of reliable assessment of individual exposures,… (more)

Subjects/Keywords: joint modeling; hierarchical modeling; gene-environment interactions

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APA (6^th Edition):

Li, R. ". (2011). Joint analysis of two related studies of different data types and different study designs using hierarchical modeling in detecting gene-environment interactions. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/673621/rec/3693

Chicago Manual of Style (16^th Edition):

Li, Rui "Rachel". “Joint analysis of two related studies of different data types and different study designs using hierarchical modeling in detecting gene-environment interactions.” 2011. Doctoral Dissertation, University of Southern California. Accessed April 10, 2021. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/673621/rec/3693.

MLA Handbook (7^th Edition):

Li, Rui "Rachel". “Joint analysis of two related studies of different data types and different study designs using hierarchical modeling in detecting gene-environment interactions.” 2011. Web. 10 Apr 2021.

Vancouver:

Li R". Joint analysis of two related studies of different data types and different study designs using hierarchical modeling in detecting gene-environment interactions. [Internet] [Doctoral dissertation]. University of Southern California; 2011. [cited 2021 Apr 10]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/673621/rec/3693.

Council of Science Editors:

Li R". Joint analysis of two related studies of different data types and different study designs using hierarchical modeling in detecting gene-environment interactions. [Doctoral Dissertation]. University of Southern California; 2011. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/673621/rec/3693

University of Toronto

10. Ierullo, Matthew. A New Suite of Pathogenesis-induced Gene Expression Markers in Arabidopsis thaliana.

Degree: 2015, University of Toronto

URL: http://hdl.handle.net/1807/69648

►

Plant immunity comprises of two main branches. In one branch, plants recognize microbial molecules called pathogen-associated molecular patterns (PAMPs); inducing PAMP-triggered immunity (PTI). Successful pathogens… (more)

Subjects/Keywords: Arabidopsis; Gene marker; Interactions database; Interactions network; Pseudomonas psyringae; 0307

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APA (6^th Edition):

Ierullo, M. (2015). A New Suite of Pathogenesis-induced Gene Expression Markers in Arabidopsis thaliana. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/69648

Chicago Manual of Style (16^th Edition):

Ierullo, Matthew. “A New Suite of Pathogenesis-induced Gene Expression Markers in Arabidopsis thaliana.” 2015. Masters Thesis, University of Toronto. Accessed April 10, 2021. http://hdl.handle.net/1807/69648.

MLA Handbook (7^th Edition):

Ierullo, Matthew. “A New Suite of Pathogenesis-induced Gene Expression Markers in Arabidopsis thaliana.” 2015. Web. 10 Apr 2021.

Vancouver:

Ierullo M. A New Suite of Pathogenesis-induced Gene Expression Markers in Arabidopsis thaliana. [Internet] [Masters thesis]. University of Toronto; 2015. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/1807/69648.

Council of Science Editors:

Ierullo M. A New Suite of Pathogenesis-induced Gene Expression Markers in Arabidopsis thaliana. [Masters Thesis]. University of Toronto; 2015. Available from: http://hdl.handle.net/1807/69648

University of Georgia

11. Stephens, Jessica Deene. A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia.

Degree: 2018, University of Georgia

URL: http://hdl.handle.net/10724/37024

► How species interactions influence ecological and evolutionary processes has been a driving interest among biologists. My dissertation research has largely focused on understanding the ecological… (more)

▼ How species interactions influence ecological and evolutionary processes has been a driving interest among biologists. My dissertation research has largely focused on understanding the ecological and evolutionary outcomes of plant interactions with insects and microbes, and how these interactions have potentially lead to the diversification of carnivorous plants. I have focused this work on the genus Sarracenia (pitcher plants). Pitcher plants are found in nutrient poor habitats and have evolved complex trapping structures used in attraction, retention, and digestion of prey. Within these trapping structures are communities of microbes that may be involved in digestion of prey. These plants are highly dependent on insects to obtain nutrients, and prey capture can directly affect seed production. This dependence on prey is predicted to create intense competition among sympatric species leading to strong selection on traits related to prey attraction and capture, as well as selection on the plant microbiome to facilitate the digestion of prey. Insight into the patterns and processes of these interactions requires an explicit understanding of evolutionary relationships of interest. Often species level relationships in groups that exhibit highly convergent traits are the result of recent radiations, which can complicate phylogenetic analyses. Therefore, I used a combination of target enrichment and recently developed coalescent methods to resolve relationships in these ‘difficult’ groups. I have used these techniques to resolve species level relationships in both the genus Sarracenia and also Helianthus. The resulting Sarracenia phylogeny was then used to assess whether this group has evolved suites of trapping traits to attract specific prey types through a common garden approach. Results indicate there are in fact strong correlations among suites of traits and the prey captured for each species across the entire genus of Sarracenia. Together these data support the hypothesis of carnivorous syndromes within the genus Sarracenia. Additionally, these plants rely on their microbiota to digest prey. The diversity and structure of these microbial communities is largely unknown. I sequenced the microbiome across all Sarracenia species in a common garden approach to examine whether host species, season, and/or year structured communities. Results suggest that there are significant differences in microbial communities with the majority of variation explained by pitcher plant species. This suggests that the plant is exerting some selection pressure on the microbiome community. Future work examining the proteome of Sarracenia could elucidate this process. Furthermore, experimental approaches across all these interaction types can further our understanding of the evolutionary of carnivory.

Subjects/Keywords: gene capture; coalescent; phylogenomics; species tree estimation; plant interactions; plant-insect interactions; plant-microbe interactions

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APA (6^th Edition):

Stephens, J. D. (2018). A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/37024

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Stephens, Jessica Deene. “A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia.” 2018. Thesis, University of Georgia. Accessed April 10, 2021. http://hdl.handle.net/10724/37024.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Stephens, Jessica Deene. “A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia.” 2018. Web. 10 Apr 2021.

Vancouver:

Stephens JD. A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia. [Internet] [Thesis]. University of Georgia; 2018. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/10724/37024.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Stephens JD. A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia. [Thesis]. University of Georgia; 2018. Available from: http://hdl.handle.net/10724/37024

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Georgia

12. Stephens, Jessica Deene. A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia.

Degree: 2018, University of Georgia

URL: http://hdl.handle.net/10724/37181

► How species interactions influence ecological and evolutionary processes has been a driving interest among biologists. My dissertation research has largely focused on understanding the ecological… (more)

▼ How species interactions influence ecological and evolutionary processes has been a driving interest among biologists. My dissertation research has largely focused on understanding the ecological and evolutionary outcomes of plant interactions with insects and microbes, and how these interactions have potentially lead to the diversification of carnivorous plants. I have focused this work on the genus Sarracenia (pitcher plants). Pitcher plants are found in nutrient poor habitats and have evolved complex trapping structures used in attraction, retention, and digestion of prey. Within these trapping structures are communities of microbes that may be involved in digestion of prey. These plants are highly dependent on insects to obtain nutrients, and prey capture can directly affect seed production. This dependence on prey is predicted to create intense competition among sympatric species leading to strong selection on traits related to prey attraction and capture, as well as selection on the plant microbiome to facilitate the digestion of prey. Insight into the patterns and processes of these interactions requires an explicit understanding of evolutionary relationships of interest. Often species level relationships in groups that exhibit highly convergent traits are the result of recent radiations, which can complicate phylogenetic analyses. Therefore, I used a combination of target enrichment and recently developed coalescent methods to resolve relationships in these ‘difficult’ groups. I have used these techniques to resolve species level relationships in both the genus Sarracenia and also Helianthus. The resulting Sarracenia phylogeny was then used to assess whether this group has evolved suites of trapping traits to attract specific prey types through a common garden approach. Results indicate there are in fact strong correlations among suites of traits and the prey captured for each species across the entire genus of Sarracenia. Together these data support the hypothesis of carnivorous syndromes within the genus Sarracenia. Additionally, these plants rely on their microbiota to digest prey. The diversity and structure of these microbial communities is largely unknown. I sequenced the microbiome across all Sarracenia species in a common garden approach to examine whether host species, season, and/or year structured communities. Results suggest that there are significant differences in microbial communities with the majority of variation explained by pitcher plant species. This suggests that the plant is exerting some selection pressure on the microbiome community. Future work examining the proteome of Sarracenia could elucidate this process. Furthermore, experimental approaches across all these interaction types can further our understanding of the evolutionary of carnivory.

Subjects/Keywords: gene capture; coalescent; phylogenomics; species tree estimation; plant interactions; plant-insect interactions; plant-microbe interactions

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APA (6^th Edition):

Stephens, J. D. (2018). A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/37181

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Stephens, Jessica Deene. “A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia.” 2018. Thesis, University of Georgia. Accessed April 10, 2021. http://hdl.handle.net/10724/37181.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Stephens, Jessica Deene. “A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia.” 2018. Web. 10 Apr 2021.

Vancouver:

Stephens JD. A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia. [Internet] [Thesis]. University of Georgia; 2018. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/10724/37181.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Stephens JD. A macroevolutionary perspective on species interactions in the carnivorous pitcher plant genus Sarracenia. [Thesis]. University of Georgia; 2018. Available from: http://hdl.handle.net/10724/37181

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

13. Du, Manyu. MECHANISTIC STUDIES OF LONG-DISTANCE GENE REGULATION IN BUDDING YEAST.

Degree: 2019, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/17217mxd451

► Eukaryotic transcription occurs within the nucleus where DNA is packaged into high order chromosome structures. Long-distance chromosomal interactions play very important roles in gene regulation… (more)

▼ Eukaryotic transcription occurs within the nucleus where DNA is packaged into high order chromosome structures. Long-distance chromosomal interactions play very important roles in gene regulation in higher eukaryotic species like human and mouse. In budding yeast, gene expression is traditionally thought to be regulated over short distances because the upstream regulatory sequences (URSs) are usually located close to the core promoters. However, recent chromosome conformation capture experiments have detected numerous long-distance chromosomal interactions in the budding yeast genome. The function of these interactions in gene regulation remains unclear. Here, I developed a medium-throughput assay to screen for long-distance interactions that affect the activity of a reporter gene. I found three regulatory mechanisms that act from a distance: silencing, transcriptional interference, and 3D clustering, which alter expression level of the reporter gene as well as its cell-to-cell variability. These results demonstrate that transcription in budding yeast, similar to transcription in higher eukaryotes, can be regulated over long distances. I anticipate our assay can be used as a general platform to screen for functional long-distance chromosomal interactions that affect gene expression. Additionally, there remains a question to resolve the causal relation between long-distance chromosomal interactions and gene expression. Although there is a huge technical advance in tools for detecting long-distance chromosomal interactions using chromosome conformation capture based assays, tools for perturbing chromosomal interactions are lacking. In this thesis, I will also report a novel synthetic biology method, Chemically Induced Chromosomal Interaction (CICI), which allows us to selectively perturb the chromosomal interactions at targeted loci in a controllable manner. I carried out CICI in both haploid and diploid yeast and showed CICI formation at multiple intra- and inter- chromosomal loci with different Hi-C contact frequencies. Surprisingly, interactions can also form between loci located in two different topologically associating domains (TADs) separated by the nucleolus, however, with a slower rate. I expect CICI to be used as a powerful tool to study chromosome dynamics and the function of long-distance interactions on gene regulation or homology directed DNA repair. Since CICI took advantage of the Fluorescent repressor operator system (FROS), a high-affinity FROS is a prerequisite for CICI to work in the living cell. Escherichia coli lac repressor (LacI) and its recognition site (LacO) is a standard setup in FROS with a measured dissociation constant (Kd) in the sub-picomolar range in vitro. However, when I investigated the binding affinity of Lac repressor (LacI) in living yeast cells, I found the LacI in the standard FROS showed an apparent Kd of ~0.6 μM, which is six orders of magnitude higher than the in vitro value. By genetically altering: i) fusion protein structure, ii) fusion protein stability, iii) binding… Advisors/Committee Members: Lu Bai, Dissertation Advisor/Co-Advisor, Lu Bai, Committee Chair/Co-Chair, Manuel Llinas, Committee Member, Benjamin Franklin Pugh, Committee Member, Qunhua Li, Outside Member, Ken Keiler, Program Head/Chair, David Scott Gilmour, Committee Member.

Subjects/Keywords: gene expression; 3D genome organization; long-distance chromosomal interactions; 3D gene clustering

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Du, M. (2019). MECHANISTIC STUDIES OF LONG-DISTANCE GENE REGULATION IN BUDDING YEAST. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/17217mxd451

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Du, Manyu. “MECHANISTIC STUDIES OF LONG-DISTANCE GENE REGULATION IN BUDDING YEAST.” 2019. Thesis, Penn State University. Accessed April 10, 2021. https://submit-etda.libraries.psu.edu/catalog/17217mxd451.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Du, Manyu. “MECHANISTIC STUDIES OF LONG-DISTANCE GENE REGULATION IN BUDDING YEAST.” 2019. Web. 10 Apr 2021.

Vancouver:

Du M. MECHANISTIC STUDIES OF LONG-DISTANCE GENE REGULATION IN BUDDING YEAST. [Internet] [Thesis]. Penn State University; 2019. [cited 2021 Apr 10]. Available from: https://submit-etda.libraries.psu.edu/catalog/17217mxd451.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Du M. MECHANISTIC STUDIES OF LONG-DISTANCE GENE REGULATION IN BUDDING YEAST. [Thesis]. Penn State University; 2019. Available from: https://submit-etda.libraries.psu.edu/catalog/17217mxd451

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Louisville

14. Zhang, Jie. Evaluation of methods for analyzing gene-gene interaction data for survival outcomes.

Degree: MS, 2011, University of Louisville

URL: 10.18297/etd/1640 ; https://ir.library.louisville.edu/etd/1640

► In recent years, a number of computational and statistical problems for identifying SNP-SNP interactions in high dimensional survival data have been studied, and several… (more)

Subjects/Keywords: Gene-gene interactions; Elastic net; Survival; Survival MDR; Lasso; Random survival forest

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APA (6^th Edition):

Zhang, J. (2011). Evaluation of methods for analyzing gene-gene interaction data for survival outcomes. (Masters Thesis). University of Louisville. Retrieved from 10.18297/etd/1640 ; https://ir.library.louisville.edu/etd/1640

Chicago Manual of Style (16^th Edition):

Zhang, Jie. “Evaluation of methods for analyzing gene-gene interaction data for survival outcomes.” 2011. Masters Thesis, University of Louisville. Accessed April 10, 2021. 10.18297/etd/1640 ; https://ir.library.louisville.edu/etd/1640.

MLA Handbook (7^th Edition):

Zhang, Jie. “Evaluation of methods for analyzing gene-gene interaction data for survival outcomes.” 2011. Web. 10 Apr 2021.

Vancouver:

Zhang J. Evaluation of methods for analyzing gene-gene interaction data for survival outcomes. [Internet] [Masters thesis]. University of Louisville; 2011. [cited 2021 Apr 10]. Available from: 10.18297/etd/1640 ; https://ir.library.louisville.edu/etd/1640.

Council of Science Editors:

Zhang J. Evaluation of methods for analyzing gene-gene interaction data for survival outcomes. [Masters Thesis]. University of Louisville; 2011. Available from: 10.18297/etd/1640 ; https://ir.library.louisville.edu/etd/1640

15. Sugier, Pierre-Emmanuel. Interactions gène-gène et gène-environnement dans les études génétiques de maladies multifactorielles : application à l’asthme et l’atopie : Gene-gene and gene-environment interactions in genetic studies of multifactorial diseases : application to asthma and atopy.

Degree: Docteur es, Épidémiologie génétique, 2018, Sorbonne université

URL: http://www.theses.fr/2018SORUS519

►

L’asthme résulte de multiples facteurs génétiques et environnementaux et des interactions entre ces facteurs. L’objectif de cette thèse a été de proposer des stratégies d’analyses… (more)

▼

L’asthme résulte de multiples facteurs génétiques et environnementaux et des interactions entre ces facteurs. L’objectif de cette thèse a été de proposer des stratégies d’analyses d’interactions gène-gène et gène-environnement pour identifier de nouveaux gènes associés à l’asthme et l’atopie. Pour identifier de nouveaux gènes dans l’atopie, nous avons proposé une stratégie d’analyse d’interaction gène-gène qui intègre une analyse pan-génomique (GWAS) à laquelle est appliquée un filtrage statistique des résultats, puis un filtrage des gènes susceptibles d’interagir à l’aide d’une méthode de fouille de textes appliquée aux données de la littérature. Les tests d’interactions entre variants génétiques sont appliqués aux paires de gènes sélectionnées. Ces analyses, menées dans trois études familiales (n=3244), ont permis d’identifier une interaction entre deux gènes (ADGRV1 et DNAH5) impliqués dans la mobilité ciliaire, mécanisme émergent dans l’asthme. Notre deuxième objectif était d’identifier de nouveaux gènes et des interactions gène-environnement influençant le délai de survenu de l’asthme. Une méta-analyse de GWAS du délai de survenue de l’asthme, menée dans neuf études (n=19348), a permis d’identifier un nouveau locus (16q12) et d’en confirmer quatre autres. Cinq de ces études comportaient des données sur l’exposition au tabagisme passif pendant la petite enfance (ELTS) (n=8273). Une méta-analyse des cinq études d’interactions gène-ELTS, sur l’ensemble du génome, influençant le délai de survenue de l’asthme, suivie par des annotations fonctionnelles, a permis d’identifier quatre gènes, ayant des fonctions biologiquement pertinentes en lien avec l'exposition au tabac.

Asthma results from multiple genetic and environmental factors and from interactions between these factors. The global aim of this thesis was to propose gene-gene and gene-environment interaction strategies of analysis to identify new genes associated with the risk of asthma and atopy. To identify new genes underlying atopy, we have proposed a gene-gene interaction strategy of analysis. This strategy integrates a genome-wide association study (GWAS) to which a statistical filtering of the results is applied, and then a selection of the genes most likely to interact using a text mining method applied to the scientific literature from PubMed. The tests of interactions between genetic variants are applied to the selected gene pairs. These analyzes, conducted in three family studies (n = 3,244), identified an interaction between two genes (ADGRV1 and DNAH5) involved in ciliary mobility, an emerging mechanism in asthma. Our second goal was to identify new genes and gene-environment interactions that influence time-to-asthma onset. A meta-analysis of GWAS of the time-to-asthma onset, conducted in nine studies (n = 19,348), identified a new locus associated with the risk of asthma (16q12) and confirmed four more. Five of these nine studies included environmental factor data on early-life tobacco smoke (ELTS) exposure. We conducted a genome-environment-wide…

Advisors/Committee Members: Demenais, Florence (thesis director), Bouzigon, Emmanuelle (thesis director).

Subjects/Keywords: Épidémiologie génétique; Études d'associations pangénomiques; Interactions gène-gène; Interactions gène-environnement; Asthme; Atopie; Genetic epidemiology; Genome-wide association studies; Gene-gene interaction; Gene-environment; Asthma; Atopy; 616.2; 614.4; 570

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sugier, P. (2018). Interactions gène-gène et gène-environnement dans les études génétiques de maladies multifactorielles : application à l’asthme et l’atopie : Gene-gene and gene-environment interactions in genetic studies of multifactorial diseases : application to asthma and atopy. (Doctoral Dissertation). Sorbonne université. Retrieved from http://www.theses.fr/2018SORUS519

Chicago Manual of Style (16^th Edition):

Sugier, Pierre-Emmanuel. “Interactions gène-gène et gène-environnement dans les études génétiques de maladies multifactorielles : application à l’asthme et l’atopie : Gene-gene and gene-environment interactions in genetic studies of multifactorial diseases : application to asthma and atopy.” 2018. Doctoral Dissertation, Sorbonne université. Accessed April 10, 2021. http://www.theses.fr/2018SORUS519.

MLA Handbook (7^th Edition):

Sugier, Pierre-Emmanuel. “Interactions gène-gène et gène-environnement dans les études génétiques de maladies multifactorielles : application à l’asthme et l’atopie : Gene-gene and gene-environment interactions in genetic studies of multifactorial diseases : application to asthma and atopy.” 2018. Web. 10 Apr 2021.

Vancouver:

Sugier P. Interactions gène-gène et gène-environnement dans les études génétiques de maladies multifactorielles : application à l’asthme et l’atopie : Gene-gene and gene-environment interactions in genetic studies of multifactorial diseases : application to asthma and atopy. [Internet] [Doctoral dissertation]. Sorbonne université; 2018. [cited 2021 Apr 10]. Available from: http://www.theses.fr/2018SORUS519.

Council of Science Editors:

Sugier P. Interactions gène-gène et gène-environnement dans les études génétiques de maladies multifactorielles : application à l’asthme et l’atopie : Gene-gene and gene-environment interactions in genetic studies of multifactorial diseases : application to asthma and atopy. [Doctoral Dissertation]. Sorbonne université; 2018. Available from: http://www.theses.fr/2018SORUS519

University of Newcastle

16. Biswas, Mohitosh. Assessment of potential drug and gene interactions for cardiovascular and antidepressant drugs from high-throughput genotyping data in a community cohort of older Australians.

Degree: PhD, 2018, University of Newcastle

URL: http://hdl.handle.net/1959.13/1393461

►

Research Doctorate - Doctor of Philosophy (PhD)

The safety and efficacy of drugs may be affected by drug-drug interactions (DDIs), drug-gene interactions (DGIs) and multifactorial… (more)

▼

Research Doctorate - Doctor of Philosophy (PhD)

The safety and efficacy of drugs may be affected by drug-drug interactions (DDIs), drug-gene interactions (DGIs) and multifactorial combinations involving both kinds of interactions. This PhD thesis hypothesises that older people, who are often exposed to polypharmacy, may be at risk of drug and gene interactions that have clinically significant consequences for medication safety and efficacy. This hypothesis was tested by investigating the prevalence of predicted drug and gene interactions for cardiovascular drugs of interest (clopidogrel, statins or warfarin) in a community cohort of older Australians from the Hunter Community Study. These drugs were chosen because they are widely used by older people in the community and because both adverse effects and therapeutic failure of these drugs can be life-threatening. To investigate whether the findings also applied to other drug classes, the prevalence of predicted drug and gene interactions for antidepressant drugs of interest (TCAs or SSRIs) was also determined. The project used self-reported medication data of 2,642 study participants (55 years of age or greater), predominantly of European ancestry. Potential interacting medications were identified from a composite list derived from the Monthly Index of Medical Specialties (MIMS) list of evidence-based clinically significant interactions and relevant clinical tables of CYP and OATP1B1 inhibitors, inducers or substrates from the U.S. Food and Drug Administration (FDA) and elsewhere. To determine the prevalence of potential clinically significant DDIs, co-prescribed drugs potentially interacting with the cardiovascular or antidepressant drugs of interest were identified from this composite list and the prevalence of study participants exposed to the interacting drugs determined. To determine the prevalence of potential clinically significant DGIs, genotype data were obtained from Affymetrix Kaiser Axiom human microarrays and imputed data from the 1000 Genomes and HapMap Phase II European reference panels. Clinically significant pharmacogenotypes were identified using the Clinical Pharmacogenetics Implementation Consortium (CPIC) pharmacogenomics based dosing guidelines. Participants were considered at risk of simple DGIs if they had a clinically significant genotype potentially affecting the safety or efficacy of the main drug under investigation but were not taking any interacting drugs. Participants were considered to be at risk of multifactorial DGIs if they had one or more clinically significant genotypes for the main drug under investigation and were also taking other interacting drugs potentially affecting medication safety or efficacy. Of the 1062 participants on cardiovascular drugs of interest (clopidogrel, statins or warfarin), 351 participants (33.1%; 95% CI 30%-36%) were at risk of clinically significant DDIs, with a mean of 1.8±1.2 possible interactions per participant. Relevant genotype data were available for 307 participants taking clopidogrel,…

Advisors/Committee Members: University of Newcastle. Faculty of Health & Medicine, School of Biomedical Sciences and Pharmacy.

Subjects/Keywords: DDIs; DGIs; gene interactions; drug interactions; Hunter Community Study; clopidogrel; warfarin; statins

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APA (6^th Edition):

Biswas, M. (2018). Assessment of potential drug and gene interactions for cardiovascular and antidepressant drugs from high-throughput genotyping data in a community cohort of older Australians. (Doctoral Dissertation). University of Newcastle. Retrieved from http://hdl.handle.net/1959.13/1393461

Chicago Manual of Style (16^th Edition):

Biswas, Mohitosh. “Assessment of potential drug and gene interactions for cardiovascular and antidepressant drugs from high-throughput genotyping data in a community cohort of older Australians.” 2018. Doctoral Dissertation, University of Newcastle. Accessed April 10, 2021. http://hdl.handle.net/1959.13/1393461.

MLA Handbook (7^th Edition):

Biswas, Mohitosh. “Assessment of potential drug and gene interactions for cardiovascular and antidepressant drugs from high-throughput genotyping data in a community cohort of older Australians.” 2018. Web. 10 Apr 2021.

Vancouver:

Biswas M. Assessment of potential drug and gene interactions for cardiovascular and antidepressant drugs from high-throughput genotyping data in a community cohort of older Australians. [Internet] [Doctoral dissertation]. University of Newcastle; 2018. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/1959.13/1393461.

Council of Science Editors:

Biswas M. Assessment of potential drug and gene interactions for cardiovascular and antidepressant drugs from high-throughput genotyping data in a community cohort of older Australians. [Doctoral Dissertation]. University of Newcastle; 2018. Available from: http://hdl.handle.net/1959.13/1393461

17. Abou-Khater, Charbel. Caractérisation de nouveaux gènes et polymorphismes potentiellement impliqués dans les interactions hôtes-pathogènes : Finding novel gene candidates and polymorphisms involved in host-pathogen interactions.

Degree: Docteur es, Biologie. Microbiologie, 2017, Aix Marseille Université

URL: http://www.theses.fr/2017AIXM0196

►

La coévolution ainsi que les différentes interactions entre hôte et pathogène contribuent à former la diversité génétique de ces deux organismes. Dans le cadre de… (more)

▼

La coévolution ainsi que les différentes interactions entre hôte et pathogène contribuent à former la diversité génétique de ces deux organismes. Dans le cadre de cette thèse, nous nous sommes intéressés à l’étude de la variabilité génétique de 1760 gènes immunitaires choisis suivant des critères définis, pour essayer d’expliquer pourquoi il existe une variation individuelle face aux infections. L’objectif principal de ce projet était alors de caractériser et d'analyser de nouveaux gènes et polymorphismes immunitaires pouvant expliquer le contrôle ou la susceptibilité à certaines infections. Deux études pilotes nous ont permis de développer le pipeline de détection de polymorphismes. Pour la première, le polymorphisme des 3 gènes CD28, CTLA4, et ICOS a été caractérisé. Dans la deuxième, nous avons caractérisé le polymorphisme de 10 gènes impliqués dans la réponse immunitaire contre M. tuberculosis. Ces gènes ne sont pas très polymorphes et trois d’entre eux sont très conservés. Ces deux études nous ont aidés à préparer l’analyse à grande échelle avec les mises au point et l’amélioration du pipeline. Nous avons sélectionné 1760 gènes en se basant sur des critères définis. La variabilité génétique a été étudiée dans les populations humaines par une analyse minutieuse in silico de données de séquençage d’exomes générées par différents projets et consortiums pour plus de 700 individus représentant 20 populations à travers le monde. 30 gènes les plus polymorphes ont été ainsi identifiés. Ces gènes pourront être entièrement caractérisés et les données produites pourraient être comparées avec des données de résistance/sensibilité de certaines maladies infectieuses.

Host-pathogen co-evolution and interactions contribute in shaping the genetic diversity of both organisms. The objective of this thesis is to define the genetic basis of variability in disease resistance/susceptibility through the development of large-scale in silico screens to identify novel gene candidates implicated in host-pathogen interactions (such as tuberculosis).A pilot study was conducted on CD28, CTLA4, and ICOS to investigate their polymorphism. As a first step in our study based on data available in the literature, we selected a set of ten genes relevant for the immune response against M. tuberculosis. Seven of these genes were moderately polymorphic, while three of them were highly conserved. This analysis was used to prepare and setup the large scale analysis using the same developed pipeline for polymorphism detection and allele reconstruction. For our in silico, we used sequence data from several projects and consortiums to isolate most polymorphic human genes amongst a list of over 1760 candidates selected based on already established relevance for infections and on evolutionary considerations. A first screen of 64 individuals from eight different populations from several regions of the world was performed and most variable genes were selected for further extensive analyses on a larger panel (715 individuals). 30 most polymorphic genes were…

Advisors/Committee Members: Olive, Daniel (thesis director), Abi-Rached, Laurent (thesis director).

Subjects/Keywords: Polymorphisme; Gènes candidats; Snp; Interactions hôtes-Pathogènes; Polymorphisms; Gene candidates; Snp; Host-Pathogen interactions

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APA (6^th Edition):

Abou-Khater, C. (2017). Caractérisation de nouveaux gènes et polymorphismes potentiellement impliqués dans les interactions hôtes-pathogènes : Finding novel gene candidates and polymorphisms involved in host-pathogen interactions. (Doctoral Dissertation). Aix Marseille Université. Retrieved from http://www.theses.fr/2017AIXM0196

Chicago Manual of Style (16^th Edition):

Abou-Khater, Charbel. “Caractérisation de nouveaux gènes et polymorphismes potentiellement impliqués dans les interactions hôtes-pathogènes : Finding novel gene candidates and polymorphisms involved in host-pathogen interactions.” 2017. Doctoral Dissertation, Aix Marseille Université. Accessed April 10, 2021. http://www.theses.fr/2017AIXM0196.

MLA Handbook (7^th Edition):

Abou-Khater, Charbel. “Caractérisation de nouveaux gènes et polymorphismes potentiellement impliqués dans les interactions hôtes-pathogènes : Finding novel gene candidates and polymorphisms involved in host-pathogen interactions.” 2017. Web. 10 Apr 2021.

Vancouver:

Abou-Khater C. Caractérisation de nouveaux gènes et polymorphismes potentiellement impliqués dans les interactions hôtes-pathogènes : Finding novel gene candidates and polymorphisms involved in host-pathogen interactions. [Internet] [Doctoral dissertation]. Aix Marseille Université 2017. [cited 2021 Apr 10]. Available from: http://www.theses.fr/2017AIXM0196.

Council of Science Editors:

Abou-Khater C. Caractérisation de nouveaux gènes et polymorphismes potentiellement impliqués dans les interactions hôtes-pathogènes : Finding novel gene candidates and polymorphisms involved in host-pathogen interactions. [Doctoral Dissertation]. Aix Marseille Université 2017. Available from: http://www.theses.fr/2017AIXM0196

18. Duncombe, Jillian L. 1990-. AN EVALUATION OF GENE INTERACTIONS AFFECTING CARCASS YIELD AND MARBLING IN BEEF CATTLE.

Degree: 2016, University of Saskatchewan

URL: http://hdl.handle.net/10388/7369

► Genotype-specific management of beef cattle in feedlots has the potential to improve carcass uniformity. Gene variants affecting marbling include LEPc.73C>T, ADH1Cc.-64T>C, TG5, and GALR2c.-199T>G while… (more)

▼ Genotype-specific management of beef cattle in feedlots has the potential to improve carcass uniformity. Gene variants affecting marbling include LEPc.73C>T, ADH1Cc.-64T>C, TG5, and GALR2c.-199T>G while those in CRHc.22C>G, POMCc.288C>T, MC4Rc.856C>G and IGF2c.-292C>T influence lean yield. The purpose of the current study was to assess combinations of marbling gene variants with those associated with lean yield and to investigate the effects of a gene variant in serotonin receptor 1B (HTR1B) on beef carcass traits. Gene variants were initially genotyped in 386 crossbred steers and evaluated for associations with carcass traits (hot carcass weight, average fat, grade fat and rib-eye area). The goal was to select a subset of variants to genotype in 2000 steers (1000 with hormone implants and 1000 without implants) with camera graded carcass data (Vision USDA yield grade, Vision grade marbling, rib-eye area and fat thickness). Seven gene variants were selected to proceed with (TG was discontinued) as they either had an association or were involved in gene interactions affecting a trait. In the implanted steers GALR2 affected rib-eye area (P=0.002) where it exhibited an additive effect (TT=83.74 cm2, TG= 84.32 cm2 and GG=86.90 cm2) however there was a dominant effect of the T allele for marbling (P=0.0001; TT/TG = 397.83 and GG=378.27) and fat (P=0.001; TT/TG=8.38 mm and GG=7.31). This same association with marbling (P<0.0001; TG/TT 463.52 mm and GG=430.90) and fat (P=0.006; TT/TG = 10.23 mm and GG=9.14 mm) was also observed in the non-implanted steers where again the T allele showed dominance. Gene-gene interactions affecting a trait were only observed in the non-implanted steers with the multivariate analysis: LEPc.73C>T and IGF2c.-292C>T with fat (P=0.05) and a trend with marbling (P=0.07); MC4Rc.856C>G and POMCc.288C>T with marbling (P=0.05); and GALR2c.-199T>G and POMCc.288C>T with rib-eye area (P=0.03). Associations between gene variants with traits were made simpler due to the fact that some genotypes could be collapsed, as least square means (LSM) were not significantly different, indicating a dominant effect of one allele. The ability to pool genotypes not only simplified the interactions, it resulted in a larger number of animals with combined genotypes. The gene SNP networks generated using EPISNP support the mode of action between gene variants. For example, the gene interaction that was a 3 by 2 was also determined to be Additive-Dominance. Significant associations were also identified between HTRIB c.205G>T SNP with carcass average fat (P=0.001), grade fat (P=0.007) and cutability (P=0.001) and a trend was observed with carcass REA (P=0.061). Although finding significance with several economically important carcass traits in crossbred beef breeds is novel, validating the effects of the HTRIB c.205G>T SNP in a larger cattle population would be beneficial. Advisors/Committee Members: Buchanan, Fiona C, Schmutz, Sheila M, McKinnon, John, Mutsvangwa, Timothy, Shand, Phyllis.

Subjects/Keywords: beef cattle; gene interactions

…study of gene interactions, it may be possible to determine the mechanisms that impact complex… …Gene function can also be variable due to factors such as imprinting, interactions with other… …for livestock confirms that further assessment and analysis of gene interactions is… …x29;. This thesis investigates the effect of gene interactions on carcass traits in beef… …gene function changes with growth hormone interactions, and challenges the industry to adapt…

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APA (6^th Edition):

Duncombe, J. L. 1. (2016). AN EVALUATION OF GENE INTERACTIONS AFFECTING CARCASS YIELD AND MARBLING IN BEEF CATTLE. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/7369

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Duncombe, Jillian L 1990-. “AN EVALUATION OF GENE INTERACTIONS AFFECTING CARCASS YIELD AND MARBLING IN BEEF CATTLE.” 2016. Thesis, University of Saskatchewan. Accessed April 10, 2021. http://hdl.handle.net/10388/7369.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Duncombe, Jillian L 1990-. “AN EVALUATION OF GENE INTERACTIONS AFFECTING CARCASS YIELD AND MARBLING IN BEEF CATTLE.” 2016. Web. 10 Apr 2021.

Vancouver:

Duncombe JL1. AN EVALUATION OF GENE INTERACTIONS AFFECTING CARCASS YIELD AND MARBLING IN BEEF CATTLE. [Internet] [Thesis]. University of Saskatchewan; 2016. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/10388/7369.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Duncombe JL1. AN EVALUATION OF GENE INTERACTIONS AFFECTING CARCASS YIELD AND MARBLING IN BEEF CATTLE. [Thesis]. University of Saskatchewan; 2016. Available from: http://hdl.handle.net/10388/7369

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Queensland University of Technology

19. Chua, Xin-Yi. Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach.

Degree: 2012, Queensland University of Technology

URL: https://eprints.qut.edu.au/55249/

► Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become… (more)

▼ Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests…

Subjects/Keywords: transcriptional regulatory interactions; bacteria; genomics approach; gene regulation; transcriptional regulatory network

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APA (6^th Edition):

Chua, X. (2012). Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach. (Thesis). Queensland University of Technology. Retrieved from https://eprints.qut.edu.au/55249/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chua, Xin-Yi. “Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach.” 2012. Thesis, Queensland University of Technology. Accessed April 10, 2021. https://eprints.qut.edu.au/55249/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chua, Xin-Yi. “Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach.” 2012. Web. 10 Apr 2021.

Vancouver:

Chua X. Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach. [Internet] [Thesis]. Queensland University of Technology; 2012. [cited 2021 Apr 10]. Available from: https://eprints.qut.edu.au/55249/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chua X. Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach. [Thesis]. Queensland University of Technology; 2012. Available from: https://eprints.qut.edu.au/55249/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Univerzitet u Beogradu

20. Đurović, Jelena Ž., 1984-. Analiza polimorfizama gena za receptor za vitamin D i gena asociranih sa trombofilijom kod žena sa idiopatskim infertilitetom.

Degree: Biološki fakultet, 2017, Univerzitet u Beogradu

URL: https://fedorabg.bg.ac.rs/fedora/get/o:16798/bdef:Content/get

►

Biologija - Genetika / Biology - Genetics

Uvod. Genetičke analize mogu ukazati na uzrok infertiliteta kod ţena kod kojih klinički testovi nisu uspeli da utvrde… (more)

Subjects/Keywords: idiopathic infertility; genes associated with thrombophilia; VDR gene; multilocus interactions

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APA (6^th Edition):

Đurović, Jelena Ž., 1. (2017). Analiza polimorfizama gena za receptor za vitamin D i gena asociranih sa trombofilijom kod žena sa idiopatskim infertilitetom. (Thesis). Univerzitet u Beogradu. Retrieved from https://fedorabg.bg.ac.rs/fedora/get/o:16798/bdef:Content/get

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Đurović, Jelena Ž., 1984-. “Analiza polimorfizama gena za receptor za vitamin D i gena asociranih sa trombofilijom kod žena sa idiopatskim infertilitetom.” 2017. Thesis, Univerzitet u Beogradu. Accessed April 10, 2021. https://fedorabg.bg.ac.rs/fedora/get/o:16798/bdef:Content/get.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Đurović, Jelena Ž., 1984-. “Analiza polimorfizama gena za receptor za vitamin D i gena asociranih sa trombofilijom kod žena sa idiopatskim infertilitetom.” 2017. Web. 10 Apr 2021.

Vancouver:

Đurović, Jelena Ž. 1. Analiza polimorfizama gena za receptor za vitamin D i gena asociranih sa trombofilijom kod žena sa idiopatskim infertilitetom. [Internet] [Thesis]. Univerzitet u Beogradu; 2017. [cited 2021 Apr 10]. Available from: https://fedorabg.bg.ac.rs/fedora/get/o:16798/bdef:Content/get.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Đurović, Jelena Ž. 1. Analiza polimorfizama gena za receptor za vitamin D i gena asociranih sa trombofilijom kod žena sa idiopatskim infertilitetom. [Thesis]. Univerzitet u Beogradu; 2017. Available from: https://fedorabg.bg.ac.rs/fedora/get/o:16798/bdef:Content/get

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Illinois – Chicago

21. Parinandi, Gurunadh. Computational Prediction of Pharmacodynamic Drug Interactions Using Public Gene Expression Data.

Degree: 2014, University of Illinois – Chicago

URL: http://hdl.handle.net/10027/11283

► Advances in pharmacogenomics has presently shown that SNPs are associated with drug toxicity and resistance. It has also been shown that SNPs are defined in… (more)

Subjects/Keywords: Pharmacodynamics; Drug Interactions; Connectivity Map; Gene Set Enrichment Analysis

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APA (6^th Edition):

Parinandi, G. (2014). Computational Prediction of Pharmacodynamic Drug Interactions Using Public Gene Expression Data. (Thesis). University of Illinois – Chicago. Retrieved from http://hdl.handle.net/10027/11283

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Parinandi, Gurunadh. “Computational Prediction of Pharmacodynamic Drug Interactions Using Public Gene Expression Data.” 2014. Thesis, University of Illinois – Chicago. Accessed April 10, 2021. http://hdl.handle.net/10027/11283.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Parinandi, Gurunadh. “Computational Prediction of Pharmacodynamic Drug Interactions Using Public Gene Expression Data.” 2014. Web. 10 Apr 2021.

Vancouver:

Parinandi G. Computational Prediction of Pharmacodynamic Drug Interactions Using Public Gene Expression Data. [Internet] [Thesis]. University of Illinois – Chicago; 2014. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/10027/11283.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Parinandi G. Computational Prediction of Pharmacodynamic Drug Interactions Using Public Gene Expression Data. [Thesis]. University of Illinois – Chicago; 2014. Available from: http://hdl.handle.net/10027/11283

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

National University of Ireland – Galway

22. Naughton, Carol. Development and characterisation of novel gene-environment interaction rat models of Parkinson's disease .

Degree: 2016, National University of Ireland – Galway

URL: http://hdl.handle.net/10379/5984

► Despite its discovery almost 60 years ago, levodopa remains the most effective therapy for the treatment of the motor symptoms associated with Parkinson’s disease. However,… (more)

▼ Despite its discovery almost 60 years ago, levodopa remains the most effective therapy for the treatment of the motor symptoms associated with Parkinson’s disease. However, chronic use of levodopa is associated with serious side effects such as the emergence of dyskinesias, on-off effects and is also limited by the fact that it is purely symptomatic and does not slow progression of the disease. One of the reasons suggested for the paucity of disease-modifying therapies for Parkinson’s disease is the lack of relevant animal models which reliably recapitulate the features of the human disease. To date, Parkinson’s disease has been modelled extensively in preclinical animals using selective catecholaminergic neurotoxins such as 6-hydroxydopamine and MPTP, and is typically induced using a single insult. Unfortunately, these models bear little etiological resemblance to the human condition as Parkinson’s disease is thought to arise as a result of complex interactions between underlying genetics and exposure to environmental factors. Therefore, the overarching aim of this project was to develop a novel model of Parkinson’s disease incorporating both genetic and environmental exposures. Not only would this shed further light on relevant gene-environments interactions in the context of the etiology of Parkinson’s disease, but would also provide a novel gene-environment model for testing potential neuroprotective and disease-modifying therapies for this condition. In order to facilitate development of a novel gene-environment model, we first characterised the motor and neuropathological impairments induced by the Parkinson’s disease-associated pesticide, rotenone, and the bacterial inflammagen, Lipopolysaccharide (LPS) and compared them directly to those induced by the ‘gold standard’ catecholamine neurotoxin, 6-OHDA. We then went on to assess the impact of dual exposure of rats to overexpression of the Parkinson’s disease-associated protein, -synuclein, and bacterial-like neuroinflammation and neurodegeneration driven by LPS. Finally, we investigated the impact of -synuclein overexpression in combination with the agritoxin-driven Parkinsonism induced by rotenone. With the single lesion models induced by 6-OHDA, rotenone and LPS, we found that despite similar levels of neurodegeneration, the neurotoxic, environmental and bacterial triggers induced distinctly different patterns of motor dysfunction. With the dual exposure gene-environment studies, we found that exposing rats to both AAV--synuclein and LPS did not exacerbate the Parkinsonism caused by either toxin alone. In contrast, dual exposure to AAV--synuclein and rotenone significantly exacerbated the level of motor dysfunction and neurodegeneration caused by the genetic or environmental factor alone. Overall, this research has shown that different Parkinson’s disease-related neurotoxins can induce different patterns of motor dysfunction indicating the importance of the choice of lesioning agent in preclinical Parkinson’s disease studies. We have also shown… Advisors/Committee Members: Dowd, Eilís (advisor).

Subjects/Keywords: Parkinson's Disease; Gene-environment interactions; Animal models; Pharmacology and Therapeutics

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APA (6^th Edition):

Naughton, C. (2016). Development and characterisation of novel gene-environment interaction rat models of Parkinson's disease . (Thesis). National University of Ireland – Galway. Retrieved from http://hdl.handle.net/10379/5984

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Naughton, Carol. “Development and characterisation of novel gene-environment interaction rat models of Parkinson's disease .” 2016. Thesis, National University of Ireland – Galway. Accessed April 10, 2021. http://hdl.handle.net/10379/5984.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Naughton, Carol. “Development and characterisation of novel gene-environment interaction rat models of Parkinson's disease .” 2016. Web. 10 Apr 2021.

Vancouver:

Naughton C. Development and characterisation of novel gene-environment interaction rat models of Parkinson's disease . [Internet] [Thesis]. National University of Ireland – Galway; 2016. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/10379/5984.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Naughton C. Development and characterisation of novel gene-environment interaction rat models of Parkinson's disease . [Thesis]. National University of Ireland – Galway; 2016. Available from: http://hdl.handle.net/10379/5984

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

23. Valbuena-Gonzalo, Carlos. Identifying Genetic Causes of Hybrid Necrosis in Arrabidopsis lyrata.

Degree: Ecology and Environmental Sciences, 2019, Umeå University

URL: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-163444

► Deleterious gene interactions due to accumulation of individual genetic variations between different lineages are a cause of population diversification by creating reproductive barriers that… (more)

Subjects/Keywords: ACD6; deleterious gene interactions; DM9; dwarfism; microsatellites; Evolutionary Biology; Evolutionsbiologi

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APA (6^th Edition):

Valbuena-Gonzalo, C. (2019). Identifying Genetic Causes of Hybrid Necrosis in Arrabidopsis lyrata. (Thesis). Umeå University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-163444

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Valbuena-Gonzalo, Carlos. “Identifying Genetic Causes of Hybrid Necrosis in Arrabidopsis lyrata.” 2019. Thesis, Umeå University. Accessed April 10, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-163444.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Valbuena-Gonzalo, Carlos. “Identifying Genetic Causes of Hybrid Necrosis in Arrabidopsis lyrata.” 2019. Web. 10 Apr 2021.

Vancouver:

Valbuena-Gonzalo C. Identifying Genetic Causes of Hybrid Necrosis in Arrabidopsis lyrata. [Internet] [Thesis]. Umeå University; 2019. [cited 2021 Apr 10]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-163444.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Valbuena-Gonzalo C. Identifying Genetic Causes of Hybrid Necrosis in Arrabidopsis lyrata. [Thesis]. Umeå University; 2019. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-163444

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

McMaster University

24. Khan, Mohammad. MonsterLM: A method to estimate the variance explained by genome-wide interactions with environmental factors.

Degree: MSc, 2020, McMaster University

URL: http://hdl.handle.net/11375/25888

►

Estimations of heritability and variance explained due to environmental exposures and interaction effects help in understanding complex diseases. Current methods to detect such interactions rely… (more)

Subjects/Keywords: Statistical Genetics; Linear Model; SNPs; Gene-Environment Interactions

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APA (6^th Edition):

Khan, M. (2020). MonsterLM: A method to estimate the variance explained by genome-wide interactions with environmental factors. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/25888

Chicago Manual of Style (16^th Edition):

Khan, Mohammad. “MonsterLM: A method to estimate the variance explained by genome-wide interactions with environmental factors.” 2020. Masters Thesis, McMaster University. Accessed April 10, 2021. http://hdl.handle.net/11375/25888.

MLA Handbook (7^th Edition):

Khan, Mohammad. “MonsterLM: A method to estimate the variance explained by genome-wide interactions with environmental factors.” 2020. Web. 10 Apr 2021.

Vancouver:

Khan M. MonsterLM: A method to estimate the variance explained by genome-wide interactions with environmental factors. [Internet] [Masters thesis]. McMaster University; 2020. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/11375/25888.

Council of Science Editors:

Khan M. MonsterLM: A method to estimate the variance explained by genome-wide interactions with environmental factors. [Masters Thesis]. McMaster University; 2020. Available from: http://hdl.handle.net/11375/25888

Laurentian University

25. O'Donnell, Patrick. The metabolic enzyme locus Triosephosphate Isomerase (Tpi) in Drosophila melanogaster is sensitive to the pairing- dependent trans interaction transvection .

Degree: 2015, Laurentian University

URL: https://zone.biblio.laurentian.ca/dspace/handle/10219/2501

► Recent advances in our ability to visualize and quantify interactions between chromosomes have made the study of these interactions a key step in advancing our… (more)

Subjects/Keywords: Gene regulation; transvection; trans-interactions; Triose phosphate isomerase

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APA (6^th Edition):

O'Donnell, P. (2015). The metabolic enzyme locus Triosephosphate Isomerase (Tpi) in Drosophila melanogaster is sensitive to the pairing- dependent trans interaction transvection . (Thesis). Laurentian University. Retrieved from https://zone.biblio.laurentian.ca/dspace/handle/10219/2501

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

O'Donnell, Patrick. “The metabolic enzyme locus Triosephosphate Isomerase (Tpi) in Drosophila melanogaster is sensitive to the pairing- dependent trans interaction transvection .” 2015. Thesis, Laurentian University. Accessed April 10, 2021. https://zone.biblio.laurentian.ca/dspace/handle/10219/2501.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

O'Donnell, Patrick. “The metabolic enzyme locus Triosephosphate Isomerase (Tpi) in Drosophila melanogaster is sensitive to the pairing- dependent trans interaction transvection .” 2015. Web. 10 Apr 2021.

Vancouver:

O'Donnell P. The metabolic enzyme locus Triosephosphate Isomerase (Tpi) in Drosophila melanogaster is sensitive to the pairing- dependent trans interaction transvection . [Internet] [Thesis]. Laurentian University; 2015. [cited 2021 Apr 10]. Available from: https://zone.biblio.laurentian.ca/dspace/handle/10219/2501.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

O'Donnell P. The metabolic enzyme locus Triosephosphate Isomerase (Tpi) in Drosophila melanogaster is sensitive to the pairing- dependent trans interaction transvection . [Thesis]. Laurentian University; 2015. Available from: https://zone.biblio.laurentian.ca/dspace/handle/10219/2501

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Georgia

26. Watts, Stephen Jesse. Gene-environment interactions and criminological theory.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/28941

► This dissertation focuses on integrating several popular theories of crime into a biosocial framework that accounts for recent research in the gene-environment interaction (GxE) literature.… (more)

▼ This dissertation focuses on integrating several popular theories of crime into a biosocial framework that accounts for recent research in the gene-environment interaction (GxE) literature. The three theories I specifically focus on are self-control theory, general strain theory (GST), and social learning theory. Regression analyses conducted using data from the National Longitudinal Study of Adolescent Health (Add Health) demonstrate the utility of combining these criminological theories with a GxE modeling approach. These analyses reveal several important findings. First, in the analysis based on self-control theory, MAOA and DAT1 genotype moderate the effect of the parent-child relationship on both low self-control and criminal behavior. Specifically, those in the sample who carry so-called “plasticity alleles” for both MAOA and DAT1 are more vulnerable the negative effects of parenting as it relates to self-control and criminal behavior than are those in the sample who do not carry plasticity alleles for either of these genes, demonstrating a significant a GxE. Secondly, the analyses based on GST reveal that those in the sample that are homozygous for the s-allele of 5-HTTLPR (s/s) are more vulnerable to the negative effects of the attempted or actual suicide of friends and family during adolescence in regards to their levels of depressive symptoms and criminal behavior than are those in the sample that carry other allelic variations for 5-HTTLPR (s/l, l/s, and l/l). Finally, the analysis focusing on social learning theory shows that the effect of affiliations with delinquent peers on one’s own criminal behavior is greater among those individuals who are homozygous for the 10R allele of DAT1 (10R/10R) than among those who carry no 10R DAT1 alleles. These results represent a contribution to the evolving field of biosocial criminology, and call for more theorizing and research of this type. Suggested directions for future research stemming from this project are also discussed.

Subjects/Keywords: gene-environment interactions; criminology; self-control theory; general strain theory

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Watts, S. J. (2014). Gene-environment interactions and criminological theory. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/28941

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Watts, Stephen Jesse. “Gene-environment interactions and criminological theory.” 2014. Thesis, University of Georgia. Accessed April 10, 2021. http://hdl.handle.net/10724/28941.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Watts, Stephen Jesse. “Gene-environment interactions and criminological theory.” 2014. Web. 10 Apr 2021.

Vancouver:

Watts SJ. Gene-environment interactions and criminological theory. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/10724/28941.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Watts SJ. Gene-environment interactions and criminological theory. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/28941

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

27. McCarthy, Ph. D., Neil. Gene-ethanol interactions underlie craniofacial variability in a zebrafish model of FASD.

Degree: PhD, Cell and molecular biology, 2015, University of Texas – Austin

URL: http://hdl.handle.net/2152/32284

► Variation is common in human birth defects and this variability is influenced by genes and the environment. How genes and the environment interact in causing… (more)

▼ Variation is common in human birth defects and this variability is influenced by genes and the environment. How genes and the environment interact in causing birth defect variability is a fundamental question in biology. I sought to investigate these interactions using a zebrafish model of fetal alcohol spectrum disorder. Fetal alcohol spectrum disorder (FASD) is an umbrella term that describes all ethanol-induced fetal defects. It is highly variable and also highly prevalent, with an estimated 1% of the population being affected. FASD can cause variable defects, including those affecting the craniofacial skeleton, a neural crest- and mesoderm-derived structure. Although both timing and dosage can influence FASD variability, genetics is an underlying factor. Little is known of the genes that cause susceptibility to FASD, and so I sought to uncover these genes and the mechanism of their interaction with ethanol. Using a novel zebrafish genetic screen to uncover gene-ethanol interactions, we found a synergistic interaction between platelet-derived growth factor receptor alpha (pdgfra) and ethanol. Pdgfra is a receptor tyrosine kinase involved in cell migration, proliferation, and survival. Untreated pdgfra mutants display cleft palate. In a percentage of ethanol in which wildtype zebrafish are unaffected, pdgfra mutants display exacerbated loss of the entire palatal skeleton. Furthermore, pdgfra heterozygotes display variable craniofacial defects, uncovering latent haploinsufficiency. Genetic analysis of a group of children with and without FASD suggests that this interaction is highly conserved. In zebrafish, further analysis of the mechanism of this pdgfra-ethanol interaction revealed a protective role of pdgfra to ethanol-induced neural crest cell death. Analysis of the Pdgfra downstream pathway PI3K/AKT/mTOR revealed an inhibitory effect of ethanol at the level of mTOR. Together, these data suggest that genes functioning in growth factor signaling could predispose to ethanol-induced defects. Analysis of another growth factor signaling gene, fgf8a, supported this hypothesis. Ethanol interacts with fgf8a to cause posterior mesoderm-derived craniofacial defects. This phenotype can be recapitulated by blocking both fgf8a and fgf3, suggesting ethanol broadly attenuates growth factor signaling. Analysis of the fgf8a;fgf3 phenotype suggests that Fgf signaling is required for proper specification, via hyaluronan synthetase 2, of the mesoderm-derived posterior craniofacial skeleton. To test whether ethanol may also broadly attenuate Pdgf signaling, we analyzed pdgfra;pdgfrb mutant phenotypes and saw a recapitulation of the pdgfra-ethanol interaction. The synergistic pdgfra;pdgfrb phenotype may be due to a similar increase in neural crest cell death observed in the pdgfra-ethanol interaction. Together, these data reveal genes involved in growth factor signaling may act to protect against ethanol-induced craniofacial defects. Advisors/Committee Members: Eberhart, Johann K. (advisor), Gross, Jeffrey M. (committee member), Harris, R. Adron (committee member), Vokes, Steven A. (committee member), Wallingford, John B. (committee member).

Subjects/Keywords: Gene-environment interactions; Craniofacial development; Fetal alcohol spectrum disorder

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

McCarthy, Ph. D., N. (2015). Gene-ethanol interactions underlie craniofacial variability in a zebrafish model of FASD. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/32284

Chicago Manual of Style (16^th Edition):

McCarthy, Ph. D., Neil. “Gene-ethanol interactions underlie craniofacial variability in a zebrafish model of FASD.” 2015. Doctoral Dissertation, University of Texas – Austin. Accessed April 10, 2021. http://hdl.handle.net/2152/32284.

MLA Handbook (7^th Edition):

McCarthy, Ph. D., Neil. “Gene-ethanol interactions underlie craniofacial variability in a zebrafish model of FASD.” 2015. Web. 10 Apr 2021.

Vancouver:

McCarthy, Ph. D. N. Gene-ethanol interactions underlie craniofacial variability in a zebrafish model of FASD. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2015. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/2152/32284.

Council of Science Editors:

McCarthy, Ph. D. N. Gene-ethanol interactions underlie craniofacial variability in a zebrafish model of FASD. [Doctoral Dissertation]. University of Texas – Austin; 2015. Available from: http://hdl.handle.net/2152/32284

University of Missouri – Columbia

28. Kuang, Xingyan. Studying macromolecular interactions on the large scale : a bioinformatics approach.

Degree: 2014, University of Missouri – Columbia

URL: http://hdl.handle.net/10355/48214

► [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Characterization of macromolecular interactions is not only critical for understanding how macromolecules perform their biological… (more)

▼ [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Characterization of macromolecular interactions is not only critical for understanding how macromolecules perform their biological functions, such as promoting chemical reactions and acting as antibodies, but is also important for finding out molecular mechanisms behind the human diseases. Furthermore, the information of macromolecular binding is pivotal for elucidating metabolic, signal transduction, and other networks. Finally, our knowledge about macromolecular interactions may be critical in studying how complex genetic variations and alternative splicing affect the development and course of diseases such as cancer. Researchers are trying to understand the evolution and physics of macromolecular interactions by collecting and analyzing the interaction data, developing predictive models for characterization of macromolecular structure and function, and, applying the developed techniques to study specific biological systems or particular diseases. Some research methods like machine learning, statistical modeling and data mining based of the macromolecular interaction data derived from experimentally determined structures of macromolecule complexes are frequently used to discover the principle of interactions. Our work incorporates data mining, machine learning and statistical modeling methodology together into the location of macromolecular binding and establishes a comprehensive relational macromolecular database. Additionally, a sequence-based protein binding site prediction method was built using machine learning method and statistic model. This predictor intelligently integrates the information derived from the protein?s sequence and its homology model so that it can offer accurate predictions irrespective of the varying quality of comparative models. Our methods to analyze the mutations have been applied to studying the role of these interactions in diseases, like cancer. Advisors/Committee Members: Korkin, Dmitry (advisor).

Subjects/Keywords: Macromolecules – Analysis; Nucleic acids; DNA-protein interactions; Gene mapping

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kuang, X. (2014). Studying macromolecular interactions on the large scale : a bioinformatics approach. (Thesis). University of Missouri – Columbia. Retrieved from http://hdl.handle.net/10355/48214

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kuang, Xingyan. “Studying macromolecular interactions on the large scale : a bioinformatics approach.” 2014. Thesis, University of Missouri – Columbia. Accessed April 10, 2021. http://hdl.handle.net/10355/48214.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kuang, Xingyan. “Studying macromolecular interactions on the large scale : a bioinformatics approach.” 2014. Web. 10 Apr 2021.

Vancouver:

Kuang X. Studying macromolecular interactions on the large scale : a bioinformatics approach. [Internet] [Thesis]. University of Missouri – Columbia; 2014. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/10355/48214.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kuang X. Studying macromolecular interactions on the large scale : a bioinformatics approach. [Thesis]. University of Missouri – Columbia; 2014. Available from: http://hdl.handle.net/10355/48214

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Sydney

29. Sana, Maryam. Molecular analysis of human gene regulation .

Degree: 2020, University of Sydney

URL: http://hdl.handle.net/2123/23404

► The data presented in this Thesis work towards understanding the heterogeneity of the nucleosome remodelling and deacetylase (NuRD) complex, a multi-subunit complex with deacetylase and… (more)

Subjects/Keywords: NuRD; PWWP2A; ZMYND8; CASZ1b; gene regulation; protein-protein interactions

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sana, M. (2020). Molecular analysis of human gene regulation . (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/23404

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sana, Maryam. “Molecular analysis of human gene regulation .” 2020. Thesis, University of Sydney. Accessed April 10, 2021. http://hdl.handle.net/2123/23404.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sana, Maryam. “Molecular analysis of human gene regulation .” 2020. Web. 10 Apr 2021.

Vancouver:

Sana M. Molecular analysis of human gene regulation . [Internet] [Thesis]. University of Sydney; 2020. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/2123/23404.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sana M. Molecular analysis of human gene regulation . [Thesis]. University of Sydney; 2020. Available from: http://hdl.handle.net/2123/23404

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Cornell University

30. Read, Andrew Charles. DEFENSE AND COUNTER-DEFENSE IN THE RICE-XANTHOMONAS PATHOSYSTEM.

Degree: PhD, Plant Pathology and Plant-Microbe Biology, 2020, Cornell University

URL: http://hdl.handle.net/1813/102892

► Plants have multi-layered immune systems that survey for and respond to pathogens. Successful pathogens subvert these defenses. This defense and counter-defense dynamic leads to a… (more)

▼ Plants have multi-layered immune systems that survey for and respond to pathogens. Successful pathogens subvert these defenses. This defense and counter-defense dynamic leads to a molecular arms race characterized by rapid evolution of plant immunity and pathogen virulence proteins. Pathogens from the bacterial genus Xanthomonas deploy virulence proteins called transcription activator-like (TAL) effectors. TAL effectors comprise DNA binding and gene activation modules and are able to activate specific host genes. Characterized strains of rice-infecting Xanthomonas oryzae encode as many as 26 TAL effectors, with distinct specificities. Hijacking host transcription is a powerful virulence mechanism, however bacterial proteins delivered into the plant cell are at risk of being detected by host defense proteins. Carolina Gold Select rice has an immunity gene, Xo1, that recognizes TAL effectors and prevents disease. Interestingly, this variety is susceptible to some strains of Xanthomonas oryzae, suggesting a second, unidentified counter-defense pathogen protein. Here, I identify and study a class of Xanthomonas counter-defense proteins encoded by genes originally overlooked as TAL effector pseudogenes due to deletions in the N- and C-terminal coding regions. In fact, these truncated TAL effectors (truncTALEs) are non-DNA-binding virulence factors that suppress Xo1-mediated plant immunity. Further, using long-read sequencing a high-quality genome assembly of Carolina Gold Select was generated. Fourteen nucleotide binding and leucine-rich repeat (NLR) defense protein genes were identified at the Xo1 locus. Seven of these Fourteen are expressed in the presence of the pathogen, and one was a strong Xo1 candidate based on structural similarity to the functionally similar Xa1 gene. A broad comparison of NLRs revealed the presence of Xa1-like genes in diverse Oryzae species. Next, by expressing the Xo1 candidate as a transgene in a susceptible variety and observing resistance, we confirmed it to be Xo1. We showed that, like TAL effectors and truncTALEs, the Xo1 protein localizes to the nucleus. Xo1 co-immunoprecipitates with a tagged truncTALE, suggesting that suppression of Xo1-mediated defense is due to interaction of the two proteins. Advisors/Committee Members: Bogdanove, Adam Joseph (chair), Roeder, Adrienne H.K. (committee member), Collmer, Alan (committee member).

Subjects/Keywords: plant immunity; plant-microbe interactions; resistance gene; rice; TAL effector; Xanthomonas

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Read, A. C. (2020). DEFENSE AND COUNTER-DEFENSE IN THE RICE-XANTHOMONAS PATHOSYSTEM. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/102892

Chicago Manual of Style (16^th Edition):

Read, Andrew Charles. “DEFENSE AND COUNTER-DEFENSE IN THE RICE-XANTHOMONAS PATHOSYSTEM.” 2020. Doctoral Dissertation, Cornell University. Accessed April 10, 2021. http://hdl.handle.net/1813/102892.

MLA Handbook (7^th Edition):

Read, Andrew Charles. “DEFENSE AND COUNTER-DEFENSE IN THE RICE-XANTHOMONAS PATHOSYSTEM.” 2020. Web. 10 Apr 2021.

Vancouver:

Read AC. DEFENSE AND COUNTER-DEFENSE IN THE RICE-XANTHOMONAS PATHOSYSTEM. [Internet] [Doctoral dissertation]. Cornell University; 2020. [cited 2021 Apr 10]. Available from: http://hdl.handle.net/1813/102892.

Council of Science Editors:

Read AC. DEFENSE AND COUNTER-DEFENSE IN THE RICE-XANTHOMONAS PATHOSYSTEM. [Doctoral Dissertation]. Cornell University; 2020. Available from: http://hdl.handle.net/1813/102892

Open Access Theses and Dissertations