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You searched for +publisher:"North Carolina State University" +contributor:("David McK. Bird, Committee Member"). Showing records 1 – 3 of 3 total matches.

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North Carolina State University

1. Wang, Tianyuan. Identifying Transcription Factor Targets and Studying Human Complex Disease Genes.

Degree: PhD, Bioinformatics, 2009, North Carolina State University

Transcription factors (TFs) have been characterized as mediators of human complex disease processes. The target genes of TFs also may be associated with disease. Identification of potential TF targets could further our understanding of gene-gene interactions underlying complex disease. We focused on two TFs, USF1 and ZNF217, because of their biological importance, especially their known genetic association with coronary artery disease (CAD), and the availability of chromatin immunoprecipitation microarray (ChIP-chip) results. First, we used USF1 ChIP-chip data as a training dataset to develop and evaluate several kernel logistic regression prediction models. Our most accurate predictor significantly outperformed standard PWM-based prediction methods. This novel prediction method enables a more accurate and efficient genome-scale identification of USF1 binding and associated target genes. Second, the results from independent linkage and gene expression studies suggest that ZNF217 also may be a candidate gene for CAD. We further investigated the role of ZNF217 for CAD in three independent CAD samples with different phenotypes. Our association studies of ZNF217 identified three SNPs having consistent association with CAD in three samples. Aorta expression profiling indicated that the proportion of the aorta with raised lesions was also positively correlated to ZNF217 expression. The combined evidence suggests that ZNF217 is a novel susceptibility gene for CAD. Finally, we applied our previously developed TF binding site (TFBS) prediction method to ZNF217. The performance of the prediction models of ZNF217 and USF1 are very similar. We demonstrated that our TFBS prediction method can be extended to other TFs. In summary, the results of this dissertation research are (1) evaluation of two TFs, USF1 and ZNF217, as susceptibility factors for CAD; (2) development of a generalized method for TFBS prediction; (3) prediction of TFBSs and target genes of two TFs, and identification of SNPs within TFBSs. This research allows for the development of study design to access TF based interactions in genetic susceptibility to human complex disease. Advisors/Committee Members: Elizabeth R. Hauser, Committee Co-Chair (advisor), Jonathan M. Horowitz, Committee Member (advisor), David McK. Bird, Committee Member (advisor), Steffen Heber, Committee Co-Chair (advisor), Jeffrey L. Thorne, Committee Member (advisor).

Subjects/Keywords: binding site; prediction; transcription factor

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APA (6th Edition):

Wang, T. (2009). Identifying Transcription Factor Targets and Studying Human Complex Disease Genes. (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/3628

Chicago Manual of Style (16th Edition):

Wang, Tianyuan. “Identifying Transcription Factor Targets and Studying Human Complex Disease Genes.” 2009. Doctoral Dissertation, North Carolina State University. Accessed September 19, 2019. http://www.lib.ncsu.edu/resolver/1840.16/3628.

MLA Handbook (7th Edition):

Wang, Tianyuan. “Identifying Transcription Factor Targets and Studying Human Complex Disease Genes.” 2009. Web. 19 Sep 2019.

Vancouver:

Wang T. Identifying Transcription Factor Targets and Studying Human Complex Disease Genes. [Internet] [Doctoral dissertation]. North Carolina State University; 2009. [cited 2019 Sep 19]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/3628.

Council of Science Editors:

Wang T. Identifying Transcription Factor Targets and Studying Human Complex Disease Genes. [Doctoral Dissertation]. North Carolina State University; 2009. Available from: http://www.lib.ncsu.edu/resolver/1840.16/3628


North Carolina State University

2. Oh, Yeon Yee. Genome Wide Transcription Studies on Infection Structure Formation and Function in Magnaporthe grisea.

Degree: PhD, Plant Pathology, 2008, North Carolina State University

Rice blast caused by the filamentous ascomycete fungi, Magnaporthe grisea (anamorph Pyricularia oryzae) is the most destructive disease of rice through out the world. To gain access to its host, M. grisea develops a specialized infection structure called an appressorium. To understand the mechanisms regulating formation and function of this structure, we performed microarray experiments using the M. grisea whole genome oligonucleotide array containing M. grisea and rice elements. The most dramatic change in gene expression occurred during spore germination where 21% showed differential expression with the vast majority being up-regulated. Approximately 3 % of the predicted genes were differentially expressed during appressorium formation in response to both a hydrophobic surface signal and exogenous cyclic AMP. Our data shows that germination stimulates a major transcriptional response characterized by a dramatic transcription of genes involved in metabolism and biosynthesis. In contrast, induction of appressorium formation triggered a significant decrease in this suite of genes, including the translational apparatus, with a coordinate increase in the expression of genes involved in protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation. Significantly, the set of upregulated genes was enriched for those encoding predicted secreted proteins. We identified 42 transcriptionally regulated transcription factors during appressorium formation, the majority of whose putative functions are regulation of secondary metabolism, nutrient assimilation and cell development. Functional characterization of differentially expressed genes using targeted gene disruption revealed novel pathogenicity factors, a subtilisin protease SPM1 and a NAD specific glutamate dehydrogenase Mgd1 in M. grisea. Our finding shows that protein turnover and amino acid metabolism are essential for proper appressorium formation and the infection process. Further, we found many differentially expressed genes, which included highly conserved transcription factors, were not required for appressorium formation and function. This may suggest that M. grisea employs a number of failsafe and backup systems, such as functional redundancy and compensatory processes in order to protect appressorium formation and to ensure the fungus can successfully invade its host. Genome wide transcriptional profiles followed by comprehensive functional studies provided broad and in depth insight into infection structure development in M. grisea. Our data will directly benefit efforts to find novel fungal pathogenecity factors and further to develop disease management systems. Advisors/Committee Members: Dr. Ralph A. Dean, Committee Member (advisor), Dr. Gary A. Payne, Committee Member (advisor), Dr. David McK. Bird, Committee Member (advisor), Dr. Gregory C. Gibson, Committee Member (advisor).

Subjects/Keywords: Magnaporthe grisea;

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

APA (6th Edition):

Oh, Y. Y. (2008). Genome Wide Transcription Studies on Infection Structure Formation and Function in Magnaporthe grisea. (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/3602

Chicago Manual of Style (16th Edition):

Oh, Yeon Yee. “Genome Wide Transcription Studies on Infection Structure Formation and Function in Magnaporthe grisea.” 2008. Doctoral Dissertation, North Carolina State University. Accessed September 19, 2019. http://www.lib.ncsu.edu/resolver/1840.16/3602.

MLA Handbook (7th Edition):

Oh, Yeon Yee. “Genome Wide Transcription Studies on Infection Structure Formation and Function in Magnaporthe grisea.” 2008. Web. 19 Sep 2019.

Vancouver:

Oh YY. Genome Wide Transcription Studies on Infection Structure Formation and Function in Magnaporthe grisea. [Internet] [Doctoral dissertation]. North Carolina State University; 2008. [cited 2019 Sep 19]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/3602.

Council of Science Editors:

Oh YY. Genome Wide Transcription Studies on Infection Structure Formation and Function in Magnaporthe grisea. [Doctoral Dissertation]. North Carolina State University; 2008. Available from: http://www.lib.ncsu.edu/resolver/1840.16/3602


North Carolina State University

3. Sumanasinghe, Polwatta Gallage Shantha Ramani. Cytoplasmic Ca2+ Changes in Nematode Treated Lotus japonicus Root Hairs.

Degree: MS, Botany, 2006, North Carolina State University

Nitrogen fixation by Rhizobia and phosphorous extraction by Mycorrhiza, are specific plant microbe interactions that are of paramount economical and ecological importance. Of similar impact to the economy and ecology is the interaction between endoparasitic nematodes and plant roots that leads to major losses in crop production. While Nod factor induced signaling events have been a research focus for many years, the nature of the early responses induced by nematode invasion are just beginning to emerge. Recent reports provide morphological as well as physiological and genetic evidence that symbiotic rhizobia and parasitic nematodes use common signaling pathways in the host plant during induction of feeding sites. One of the earliest physiological responses to Nod factors comprises calcium influx at the tip of the root hair and elevation of cytosolic calcium followed after 10 min by calcium spiking over the nucleus. It was therefore of particular interest to investigate whether similar calcium changes occur after treatment with nematodes. I used the ratiometric cytosolic calcium indicator Indo-1, in conjunction with confocal laser scanning microscopy, to monitor calcium changes in L. japonicus root hairs in space and time before and after treatment with RKN Meloidogyne incognita. The results were compared with those I obtained in parallel experiments after Nod factor application under the same experimental conditions. I showed that treatment with nematodes increases cytoplasmic calcium at the root hair tip by about 263 nM. The response starts about 2 min after RKN were introduced to the chamber and calcium elevation was sustained over a period of at least 20 min. The calcium concentration also increased over the nuclear area by about 183 nM showing a similar time course, however, calcium spiking was not observed. These results indicate that RKN and Nod factors induce a similar elevation of cytoplasmic calcium levels at the root and provide further evidence of the existence of a common signaling pathway between symbiotic rhizobia, mycorrhiza and parasitic nematodes. Advisors/Committee Members: Dr. Wendy F. Boss, Committee Member (advisor), Dr. Nina Stromgren Allen, Committee Chair (advisor), Dr. David McK. Bird, Committee Member (advisor).

Subjects/Keywords: Calcium; Root Knot Nematode; Lotus japonicus

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

APA (6th Edition):

Sumanasinghe, P. G. S. R. (2006). Cytoplasmic Ca2+ Changes in Nematode Treated Lotus japonicus Root Hairs. (Thesis). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/439

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

Chicago Manual of Style (16th Edition):

Sumanasinghe, Polwatta Gallage Shantha Ramani. “Cytoplasmic Ca2+ Changes in Nematode Treated Lotus japonicus Root Hairs.” 2006. Thesis, North Carolina State University. Accessed September 19, 2019. http://www.lib.ncsu.edu/resolver/1840.16/439.

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

MLA Handbook (7th Edition):

Sumanasinghe, Polwatta Gallage Shantha Ramani. “Cytoplasmic Ca2+ Changes in Nematode Treated Lotus japonicus Root Hairs.” 2006. Web. 19 Sep 2019.

Vancouver:

Sumanasinghe PGSR. Cytoplasmic Ca2+ Changes in Nematode Treated Lotus japonicus Root Hairs. [Internet] [Thesis]. North Carolina State University; 2006. [cited 2019 Sep 19]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/439.

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

Council of Science Editors:

Sumanasinghe PGSR. Cytoplasmic Ca2+ Changes in Nematode Treated Lotus japonicus Root Hairs. [Thesis]. North Carolina State University; 2006. Available from: http://www.lib.ncsu.edu/resolver/1840.16/439

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

.