subject:(transcription factor)

Oregon State University

1. Kyrylkova, Kateryna. The role of the transcriptional regulatory protein BCL11B in dental and craniofacial development.

Degree: PhD, Pharmacy, 2014, Oregon State University

URL: http://hdl.handle.net/1957/45238

► BCL11B is a transcriptional regulatory protein that plays essential roles during mouse embryonic development. BCL11B is expressed and functions in the immune and nervous systems… (more)

▼ BCL11B is a transcriptional regulatory protein that plays essential roles during mouse embryonic development. BCL11B is expressed and functions in the immune and nervous systems as well as within ectodermal organs. Multiple studies have characterized the roles of BCL11B in T cells, brain, and skin. However, very little is known about the mechanistic role of BCL11B during tooth development, and data are not available on the function of BCL11B in the craniofacial skeleton. BCL11B is expressed widely within the oral cavity during development, and mice lacking BCL11B exhibit a spectrum of tooth developmental defects. The most striking feature of the Bcl11b[superscript -/-] dental phenotype is a defect in development of enamel-secreting cells, known as ameloblasts, in the mouse incisor. Ameloblasts are localized exclusively on the labial aspect of the mouse incisor in wild-type mice. In contrast, Bcl11b[superscript -/-] mice exhibit defective ameloblasts on the labial and develop ectopic, ameloblast-like cells on the lingual aspect of the tooth. BCL11B regulates asymmetric ameloblast formation by regulating the development of epithelial stem cell niches in the posterior part of the incisor. Specifically, BCL11B induces proliferation and differentiation of epithelial stem cells into ameloblasts in the labial cervical loop, whereas BCL11B suppresses these processes within the lingual epithelium. Such bidirectional actions of BCL11B are mediated by spatio-specific regulation of a large gene network comprised of genes that encode members of fibroblast growth factor (FGF) and transforming growth factor β (TGFβ) superfamilies, Sprouty proteins, and sonic hedgehog (SHH). In addition, my data integrate BCL11B into FGF and SHH signaling pathways revealing the molecular mechanisms that suppress development of ectopic ameloblast-like cells in the lingual epithelium. In the second half of this dissertation, I show that BCL11B is expressed in the osteogenic mesenchyme of developing craniofacial skeleton, and loss of BCL11B in these tissues has striking effects on craniofacial development. Bcl11b[superscript -/-] mice exhibit accelerated mineralization of the skull during embryonic development and synostosis of facial and coronal sutures. My results demonstrate that BCL11B normally functions to suppress proliferation and premature differentiation of osteoblasts in the craniofacial complex. I suggest that the principal mechanistic basis of these actions of BCL11B is the repression of Fgfr2c expression within the osteogenic mesenchyme. Taken together, my data demonstrate that BCL11B plays an important role in proliferation and differentiation of ameloblast and osteoblast lineages. In addition, my work implicates BCL11B in regulation of FGF and TGFβ signaling pathways. Therefore, these studies contribute to a better understanding of the molecular and cellular functions of BCL11B in vivo. Advisors/Committee Members: Leid, Mark (advisor), Kioussi, Chrissa (committee member).

Subjects/Keywords: Transcription factor; Transcription factors

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APA (6^th Edition):

Kyrylkova, K. (2014). The role of the transcriptional regulatory protein BCL11B in dental and craniofacial development. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/45238

Chicago Manual of Style (16^th Edition):

Kyrylkova, Kateryna. “The role of the transcriptional regulatory protein BCL11B in dental and craniofacial development.” 2014. Doctoral Dissertation, Oregon State University. Accessed September 18, 2019. http://hdl.handle.net/1957/45238.

MLA Handbook (7^th Edition):

Kyrylkova, Kateryna. “The role of the transcriptional regulatory protein BCL11B in dental and craniofacial development.” 2014. Web. 18 Sep 2019.

Vancouver:

Kyrylkova K. The role of the transcriptional regulatory protein BCL11B in dental and craniofacial development. [Internet] [Doctoral dissertation]. Oregon State University; 2014. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/1957/45238.

Council of Science Editors:

Kyrylkova K. The role of the transcriptional regulatory protein BCL11B in dental and craniofacial development. [Doctoral Dissertation]. Oregon State University; 2014. Available from: http://hdl.handle.net/1957/45238

Penn State University

2. Tajiri, Momoko. Roles of Archaeal general transcription factors TFB1 and TFB2 in Thermococus Kodakarensis during heat stress response.

Degree: PhD, Integrative Biosciences, 2008, Penn State University

URL: https://etda.libraries.psu.edu/catalog/8925

► This dissertation summarizes two projects concerning roles for homologues of a general transcription factor (GTF), called transcription factor B (TFB) during transcription regulation in Archaea.… (more)

▼ This dissertation summarizes two projects concerning roles for homologues of a general transcription factor (GTF), called transcription factor B (TFB) during transcription regulation in Archaea. Since the discovery of the third domain of life, Archaea, numerous efforts have been made to understand life cycle of multiple archaeal species. The discovery of archaea with multiple homologues of GTFs in their genomes lead to the hypothesis that these archaea may use the multiplicity to control gene expression. However, in what extent the roles of these factors differ has not been fully investigated. First part of the dissertation research uses both biochemical and genetic approaches to investigate roles of two TFB homologues from hyperthermophilic archaeon Thermococcus kodakarensis. The overall goal of this study is to provide insights into how the multiple TFB homologues are involved in transcription regulation. T. kodakarensis was chosen as a study model because of the the availability of well-established genetic systems, which is not true for many other archaea. T. kodakarensis also possess two homologues of TFB (annotated as TFB1 and TFB2) with one TBP, providing simplied system for investigation. Present study provided evidence that each TFB homologues has different characteristics in DNA binding and abortive transcription activities. TFB1 appeared to have stronger association with DNA-TBP complex than TFB2. It was also found that TFB1-containing pre-initiation complex produced more abortive products than TFB2 suggesting the former spend more time for abortive transcription prior to promoter escape than the latter. Because both TFB homologues are transcribed at the same level in an optimum condition, more promoters possibly associate with TFB1 than TFB2 under that condition. Under heat stress, I found that transcription of tfb2 is induced more than tfb1. The population increase will potentially overcome less affinity of TFB2 to DNA and more promoter may be recognized by TFB2 than TFB1 under heat stress. Since TFB2 spend less time and resources for abortive transcription, it may be an ideal TFB homologue to be used to express stress response proteins. Possibly, T. kodakarensis manipulate population of the two TFB homologues in the cell to adjust for transcription activity. I did not observe clear differences in gene expression patterns between tfb1 or tfb2 disrupted strains under heat stress. However,for multiple genes, larger fold changes in tfb1 disrupted strain were observed than tfb2 disrupted strain, suggesting these genes could be transcribed efficiently by TFB2 under heat stress. Over-all, observations suggest that a unique mechanism to utilize the two TFB homologues for fine adjustment of intracellular gene expression may exist in T. kodakarensis. Second part of the research is the development of a new genetic methodologies to control gene expression in the cells. Using the inducible promoters from a T. kodakarensis enzyme, 1,6 bis-phosphatase, conditional gene expression system was established. This is the…

Subjects/Keywords: general transcription factor; archaea; TFB

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APA (6^th Edition):

Tajiri, M. (2008). Roles of Archaeal general transcription factors TFB1 and TFB2 in Thermococus Kodakarensis during heat stress response. (Doctoral Dissertation). Penn State University. Retrieved from https://etda.libraries.psu.edu/catalog/8925

Chicago Manual of Style (16^th Edition):

Tajiri, Momoko. “Roles of Archaeal general transcription factors TFB1 and TFB2 in Thermococus Kodakarensis during heat stress response.” 2008. Doctoral Dissertation, Penn State University. Accessed September 18, 2019. https://etda.libraries.psu.edu/catalog/8925.

MLA Handbook (7^th Edition):

Tajiri, Momoko. “Roles of Archaeal general transcription factors TFB1 and TFB2 in Thermococus Kodakarensis during heat stress response.” 2008. Web. 18 Sep 2019.

Vancouver:

Tajiri M. Roles of Archaeal general transcription factors TFB1 and TFB2 in Thermococus Kodakarensis during heat stress response. [Internet] [Doctoral dissertation]. Penn State University; 2008. [cited 2019 Sep 18]. Available from: https://etda.libraries.psu.edu/catalog/8925.

Council of Science Editors:

Tajiri M. Roles of Archaeal general transcription factors TFB1 and TFB2 in Thermococus Kodakarensis during heat stress response. [Doctoral Dissertation]. Penn State University; 2008. Available from: https://etda.libraries.psu.edu/catalog/8925

University of Southern California

3. Skylar, Anna Maria. Genetic control of meristematic proliferation in Arabidopsis thaliana.

Degree: PhD, Molecular Biology, 2014, University of Southern California

URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/458438/rec/2996

► When a dormant seed of flowering plants receives environmental cues to begin germination, a remarkable series of transformation takes place. The seed coat cracks open,… (more)

Subjects/Keywords: meristems; Arabidopsis; transcription factor binding

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APA (6^th Edition):

Skylar, A. M. (2014). Genetic control of meristematic proliferation in Arabidopsis thaliana. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/458438/rec/2996

Chicago Manual of Style (16^th Edition):

Skylar, Anna Maria. “Genetic control of meristematic proliferation in Arabidopsis thaliana.” 2014. Doctoral Dissertation, University of Southern California. Accessed September 18, 2019. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/458438/rec/2996.

MLA Handbook (7^th Edition):

Skylar, Anna Maria. “Genetic control of meristematic proliferation in Arabidopsis thaliana.” 2014. Web. 18 Sep 2019.

Vancouver:

Skylar AM. Genetic control of meristematic proliferation in Arabidopsis thaliana. [Internet] [Doctoral dissertation]. University of Southern California; 2014. [cited 2019 Sep 18]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/458438/rec/2996.

Council of Science Editors:

Skylar AM. Genetic control of meristematic proliferation in Arabidopsis thaliana. [Doctoral Dissertation]. University of Southern California; 2014. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/458438/rec/2996

University of Manchester

4. Webber, Aaron. Transcriptional co-regulation of microRNAs and protein-coding genes.

Degree: 2013, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:214196

► This thesis was presented by Aaron Webber on the 4th December 2013 for the degree of Doctor of Philosophy from the University of Manchester. The… (more)

▼ This thesis was presented by Aaron Webber on the 4th December 2013 for the degree of Doctor of Philosophy from the University of Manchester. The title of this thesis is ‘Transcriptional co-regulation of microRNAs and protein-coding genes’. The thesis relates to gene expression regulation within humans and closely related primate species. We have investigated the binding site distributions from publically available ChIP-seq data of 117 transcription regulatory factors (TRFs) within the human genome. These were mapped to cis-regulatory regions of two major classes of genes,  20,000 genes encoding proteins and  1500 genes encoding microRNAs. MicroRNAs are short 20 - 24 nt noncoding RNAs which bind complementary regions within target mRNAs to repress translation. The complete collection of ChIP-seq binding site data is related to genomic associations between protein-coding and microRNA genes, and to the expression patterns and functions of both gene types across human tissues. We show that microRNA genes are associated with highly regulated protein-coding gene regions, and show rigorously that transcriptional regulation is greater than expected, given properties of these protein-coding genes. We find enrichment in developmental proteins among protein-coding genes hosting microRNA sequences. Novel subclasses of microRNAs are identified that lie outside of protein-coding genes yet may still be expressed from a shared promoter region with their protein-coding neighbours. We show that such microRNAs are more likely to form regulatory feedback loops with the transcriptional regulators lying in the upstream protein-coding promoter region.We show that when a microRNA and a TRF regulate one another, the TRF is more likely to sometimes function as a repressor. As in many studies, the data show that microRNAs lying downstream of particular TRFs target significantly many genes in common with these TRFs. We then demonstrate that the prevalence of such TRF/microRNA regulatory partnerships relates directly to the variation in mRNA expression across human tissues, with the least variable mRNAs having the most significant enrichment in such partnerships. This result is connected to theory describing the buffering of gene expression variation by microRNAs. Taken together, our study has demonstrated significant novel linkages between the transcriptional TRF and post-transcriptional microRNA-mediated regulatory layers.We finally consider transcriptional regulators alone, by mapping these to genes clustered on the basis of their expression patterns through time, within the context of CD4+ T cells from African green monkeys and Rhesus macaques infected with Simian immunodeficiency virus (SIV). African green monkeys maintain a functioning immune system despite never clearing the virus, while in rhesus macaques, the immune system becomes chronically stimulated leading to pathogenesis. Gene expression clusters were identified characterizing the natural and pathogenic host systems. We map transcriptional regulators to these expression clusters… Advisors/Committee Members: ROBERTSON, DAVID DL, Robertson, David, Griffiths-Jones, Samuel.

Subjects/Keywords: MicroRNA; Transcription factor; Regulatory network

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APA (6^th Edition):

Webber, A. (2013). Transcriptional co-regulation of microRNAs and protein-coding genes. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:214196

Chicago Manual of Style (16^th Edition):

Webber, Aaron. “Transcriptional co-regulation of microRNAs and protein-coding genes.” 2013. Doctoral Dissertation, University of Manchester. Accessed September 18, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:214196.

MLA Handbook (7^th Edition):

Webber, Aaron. “Transcriptional co-regulation of microRNAs and protein-coding genes.” 2013. Web. 18 Sep 2019.

Vancouver:

Webber A. Transcriptional co-regulation of microRNAs and protein-coding genes. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2019 Sep 18]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:214196.

Council of Science Editors:

Webber A. Transcriptional co-regulation of microRNAs and protein-coding genes. [Doctoral Dissertation]. University of Manchester; 2013. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:214196

5. Tamura, Taizo. High-resolution analysis of DNA binding property of VND7, the master transcription factor for vessel cell differentiation : 道管分化マスター転写因子VND7のDNA結合特性に関する高解像度解析; ドウカンブンカマスターテンシャインシ VND7 ノ DNA ケツゴウトクセイニカンスルコウカイゾウドカイセキ.

Degree: 博士(バイオサイエンス), 2017, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学

URL: http://hdl.handle.net/10061/11517

Subjects/Keywords: Transcription factor

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APA (6^th Edition):

Tamura, T. (2017). High-resolution analysis of DNA binding property of VND7, the master transcription factor for vessel cell differentiation : 道管分化マスター転写因子VND7のDNA結合特性に関する高解像度解析; ドウカンブンカマスターテンシャインシ VND7 ノ DNA ケツゴウトクセイニカンスルコウカイゾウドカイセキ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/11517

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):

Tamura, Taizo. “High-resolution analysis of DNA binding property of VND7, the master transcription factor for vessel cell differentiation : 道管分化マスター転写因子VND7のDNA結合特性に関する高解像度解析; ドウカンブンカマスターテンシャインシ VND7 ノ DNA ケツゴウトクセイニカンスルコウカイゾウドカイセキ.” 2017. Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed September 18, 2019. http://hdl.handle.net/10061/11517.

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

MLA Handbook (7^th Edition):

Tamura, Taizo. “High-resolution analysis of DNA binding property of VND7, the master transcription factor for vessel cell differentiation : 道管分化マスター転写因子VND7のDNA結合特性に関する高解像度解析; ドウカンブンカマスターテンシャインシ VND7 ノ DNA ケツゴウトクセイニカンスルコウカイゾウドカイセキ.” 2017. Web. 18 Sep 2019.

Vancouver:

Tamura T. High-resolution analysis of DNA binding property of VND7, the master transcription factor for vessel cell differentiation : 道管分化マスター転写因子VND7のDNA結合特性に関する高解像度解析; ドウカンブンカマスターテンシャインシ VND7 ノ DNA ケツゴウトクセイニカンスルコウカイゾウドカイセキ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; 2017. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/10061/11517.

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

Council of Science Editors:

Tamura T. High-resolution analysis of DNA binding property of VND7, the master transcription factor for vessel cell differentiation : 道管分化マスター転写因子VND7のDNA結合特性に関する高解像度解析; ドウカンブンカマスターテンシャインシ VND7 ノ DNA ケツゴウトクセイニカンスルコウカイゾウドカイセキ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; 2017. Available from: http://hdl.handle.net/10061/11517

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

6. Schneider, Andrew. Investigating the Role of the VAL1 Transcription Factor in Arabidopsis thaliana Embryo Development.

Degree: PhD, Plant Pathology, Physiology, and Weed Science, 2015, Virginia Tech

URL: http://hdl.handle.net/10919/56694

► Developing oilseeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated at the transcriptional… (more)

Subjects/Keywords: Arabidopsis; seeds; transcription factor; epigenetic

11 more images…

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APA (6^th Edition):

Schneider, A. (2015). Investigating the Role of the VAL1 Transcription Factor in Arabidopsis thaliana Embryo Development. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/56694

Chicago Manual of Style (16^th Edition):

Schneider, Andrew. “Investigating the Role of the VAL1 Transcription Factor in Arabidopsis thaliana Embryo Development.” 2015. Doctoral Dissertation, Virginia Tech. Accessed September 18, 2019. http://hdl.handle.net/10919/56694.

MLA Handbook (7^th Edition):

Schneider, Andrew. “Investigating the Role of the VAL1 Transcription Factor in Arabidopsis thaliana Embryo Development.” 2015. Web. 18 Sep 2019.

Vancouver:

Schneider A. Investigating the Role of the VAL1 Transcription Factor in Arabidopsis thaliana Embryo Development. [Internet] [Doctoral dissertation]. Virginia Tech; 2015. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/10919/56694.

Council of Science Editors:

Schneider A. Investigating the Role of the VAL1 Transcription Factor in Arabidopsis thaliana Embryo Development. [Doctoral Dissertation]. Virginia Tech; 2015. Available from: http://hdl.handle.net/10919/56694

University of Ottawa

7. Sarvan, Sabina. Structural and Functional Characterization of Campylobacter Jejuni Ferric Uptake Regulator (CjFur) .

Degree: 2018, University of Ottawa

URL: http://hdl.handle.net/10393/37202

► Transition metals are crucial components of several metabolic pathways and are critical for DNA, RNA and protein synthesis. However, when found in excess, these metal… (more)

▼ Transition metals are crucial components of several metabolic pathways and are critical for DNA, RNA and protein synthesis. However, when found in excess, these metal ions are toxic. To maintain the physiological concentration of metal ions at non-toxic concentration, bacteria rely on members of the Ferric uptake regulator (Fur) family of metalloregulators. Intriguingly, despite being coined as “metalloregulator”, specific members of the Fur family activate and repress gene expression in presence or absence of regulatory metals. Based on these observations, we hypothesized that the ability of these transcription factors to adopt different structural conformations underlies their ability to display different functions in presence and absence of metal ions. To address this important question, we solved the crystal structure of apo-Fur protein from Campylobacter jejuni. Structural analysis revealed that the protein adopts a V-shaped conformation harboring an evolutionary conserved cluster of positively charged residues on the surface. Using an extensive library of mutants and electrophoretic mobility shift analysis, we found that substituting residues forming the positively charged surface is detrimental for Fur interaction with DNA. Furthermore, our in vivo studies suggest that these positively charged residues are important for the regulation of CjFur target genes and that different mechanisms modulate the activity of Fur family of metalloregulators depending on the number of occupied metal binding sites. We showed that the disruption of metal binding sites of CjFur significantly reduces DNA binding in vitro and is deleterious for the repression of Fur target genes and gut colonization by C. jejuni. Finally, based on initial findings that adding a tag at the N-terminus of CjFur significantly reduces its ability to incorporate regulatory metal ions and bind DNA, we developed a new protocol for the purification of a highly active untagged CjFur protein. Overall, our studies shed new lights on the mechanistic basis controlling Fur gene regulatory activity in C. jejuni.

Subjects/Keywords: X-ray crystallography; Transcription factor

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APA (6^th Edition):

Sarvan, S. (2018). Structural and Functional Characterization of Campylobacter Jejuni Ferric Uptake Regulator (CjFur) . (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/37202

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):

Sarvan, Sabina. “Structural and Functional Characterization of Campylobacter Jejuni Ferric Uptake Regulator (CjFur) .” 2018. Thesis, University of Ottawa. Accessed September 18, 2019. http://hdl.handle.net/10393/37202.

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

MLA Handbook (7^th Edition):

Sarvan, Sabina. “Structural and Functional Characterization of Campylobacter Jejuni Ferric Uptake Regulator (CjFur) .” 2018. Web. 18 Sep 2019.

Vancouver:

Sarvan S. Structural and Functional Characterization of Campylobacter Jejuni Ferric Uptake Regulator (CjFur) . [Internet] [Thesis]. University of Ottawa; 2018. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/10393/37202.

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

Council of Science Editors:

Sarvan S. Structural and Functional Characterization of Campylobacter Jejuni Ferric Uptake Regulator (CjFur) . [Thesis]. University of Ottawa; 2018. Available from: http://hdl.handle.net/10393/37202

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

North Carolina State University

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

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

URL: http://www.lib.ncsu.edu/resolver/1840.16/3628

► 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… (more)

▼ 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 (6^th 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 (16^th Edition):

Wang, Tianyuan. “Identifying Transcription Factor Targets and Studying Human Complex Disease Genes.” 2009. Doctoral Dissertation, North Carolina State University. Accessed September 18, 2019. http://www.lib.ncsu.edu/resolver/1840.16/3628.

MLA Handbook (7^th Edition):

Wang, Tianyuan. “Identifying Transcription Factor Targets and Studying Human Complex Disease Genes.” 2009. Web. 18 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 18]. 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

9. Yin, Haifeng. Expression and developmental requirement for transcription factor Sp2.

Degree: PhD, Functional Genomics, 2009, North Carolina State University

URL: http://www.lib.ncsu.edu/resolver/1840.16/4630

► The Sp-family of DNA-binding proteins is comprised by nine members, and controls the expression of many mammalian genes. Most Sp-family members have been well studied… (more)

▼ The Sp-family of DNA-binding proteins is comprised by nine members, and controls the expression of many mammalian genes. Most Sp-family members have been well studied with respect to their patterns of expression as well as requirement for mammalian development. However, little information regarding the expression and function of Sp2 was available. Our laboratory has reported that Sp2 is widely expressed in murine and human cell lines, Sp2 DNA-binding activity and trans-activation are negatively regulated in vitro, and that the vast majority of Sp2 localizes to sub-nuclear foci associated with the nuclear matrix. To extend these studies, expression of the mouse Sp2 locus was analyzed in detail and the requirement for Sp2 for mouse development was evaluated via the creation of a conditional "knock-out" mouse strain. To initiate the analysis of Sp2 I first identified transcriptional start sites using a PCR-assisted (5'RACE) strategy. Sequencing of 5Ã¢â‚¬â„¢RACE clones showed that transcriptional start sites clustered within three regions of the Sp2 locus producing three types of transcripts: Exon 2A (type I), Exon 4 (type II) and Exon 5 (type III). Synthesis of type I transcripts was shown to be directed by a promoter that contains sequences encoding at least four discrete enhancer and inhibitory elements. Additional promoters were not identified within the Sp2 locus. Using RT-PCR and RNA in situ hybridization assays, Sp2 was shown to be widely expressed at embryonic and post-natal stages and it's expression was noted to be particularly concentrated in brain sub-regions. Sp2 conditional "knock-out" mice were generated via the insertion of loxP sites flanking the first two Sp2 coding exons. The developmental consequences of loss of Sp2 function were evaluated following matings with three Cre recombinase-carrying strains that express Cre in a widespread (CMV-Cre) or tissue-restricted fashion (Keratin 14-Cre and Keratin14-Cre/Estrogen receptor fusion). Sp2 hemizygous animals are indistinguishable from wild-type animals, whereas nullizygous animals perish early in gestation. These data indicate that Sp2 is an essential gene at the organismal level, yet we have also shown that Sp2 nullizygous cells are viable in adult, mosaic animals. Constitutive (Keratin 14-Cre) or induced (Keratin 14-Cre/Esr) expression of the Cre recombinase in basal keratinocytes resulted in a dramatic increase in stem cell proliferation and the loss of Keratin 5 and Keratin 15 expression in these cells. Taken together, we conclude that Sp2 is required for early embryogenesis and regulates the proliferation and differentiation of adult progenitor cells. Advisors/Committee Members: Jonathan M. Horowitz, Committee Chair (advisor).

Subjects/Keywords: transcription factor Sp2; development

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

APA (6^th Edition):

Yin, H. (2009). Expression and developmental requirement for transcription factor Sp2. (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/4630

Chicago Manual of Style (16^th Edition):

Yin, Haifeng. “Expression and developmental requirement for transcription factor Sp2.” 2009. Doctoral Dissertation, North Carolina State University. Accessed September 18, 2019. http://www.lib.ncsu.edu/resolver/1840.16/4630.

MLA Handbook (7^th Edition):

Yin, Haifeng. “Expression and developmental requirement for transcription factor Sp2.” 2009. Web. 18 Sep 2019.

Vancouver:

Yin H. Expression and developmental requirement for transcription factor Sp2. [Internet] [Doctoral dissertation]. North Carolina State University; 2009. [cited 2019 Sep 18]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/4630.

Council of Science Editors:

Yin H. Expression and developmental requirement for transcription factor Sp2. [Doctoral Dissertation]. North Carolina State University; 2009. Available from: http://www.lib.ncsu.edu/resolver/1840.16/4630

University of Rochester

10. Ding, Qian. The Role of BARHL2 in the Neurogenesis of Mouse Retina and Spinal Cord.

Degree: PhD, 2010, University of Rochester

URL: http://hdl.handle.net/1802/9737

► The evolutionary conserved BarH family of homeodomain transcription factors plays essential roles in cell fate specification, cell differentiation, migration and survival by either activation or… (more)

▼ The evolutionary conserved BarH family of homeodomain transcription factors plays essential roles in cell fate specification, cell differentiation, migration and survival by either activation or repression mechanisms. Barhl2, a member of the Barh gene family, is expressed restrictively in the central nervous system. In the retina, Barhl2 is expressed in developing and mature retinal ganglion cells (RGCs), amacrine cells (ACs) and horizontal cells. Here, to investigate the role of Barhl2 in retinal development, Barhl2 deficient mice were generated. Analysis of AC subtypes in Barhl2 deficient retinas suggests that Barhl2 plays a critical role in AC subtype determination. A significant reduction of glycinergic and GABAergic ACs with a substantial increase in the number of cholinergic ACs was observed in Barhl2-null retinas. Barhl2 is also critical for the development of a normal complement of RGCs. Barhl2 deficiency resulted in the approximate 35% apoptotic RGCs during development. Genetic analysis revealed that Barhl2 functions downstream of the Atoh7-Pou4f2 regulatory pathway and regulates the maturation and/or survival of RGCs. Thus, BARHL2 appears to have numerous roles in retinal development, including regulating neuronal subtype specification, differentiation, and survival. In the spinal cord part, we present evidence showing that BARHL2 is required for the development of dI1 interneurons. Targeted deletion of Barhl2 resulted in a significant reduction in a subset of dI1 interneurons, dI1i, that project the axons ipsilaterally. Utilizing genetic axonal tracing and retrograde tracing method, we found that Barhl2-null dI1i interneurons adopted a dI1c-like contralateral axonal projection and ectopically expressed Lhx2, indicating the dI1i interneurons were transfated to a dI1c identity. Moreover, BARHL2 binds to conserved motifs in Lhx2, suggesting that BARHL2 directly regulates the expression of Lhx2. These results demonstrate the requirement for BARHL2 in the acquisition of dI1 subtype identities and also reveal a genetic hierarchy between progenitors and post-mitotic neurons that drives dI1 interneuron differentiation. This study provides insights into the problem of how the identities of distinct classes of neurons at different positions are controlled within the nervous systems. Our results contribute to a better understanding of transcriptional programs that define neuronal subtype identities and molecular mechanisms that guide distinctive aspects of their subtype-specific properties.

Subjects/Keywords: Transcription Factor; Subtype; Neuron

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

APA (6^th Edition):

Ding, Q. (2010). The Role of BARHL2 in the Neurogenesis of Mouse Retina and Spinal Cord. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/9737

Chicago Manual of Style (16^th Edition):

Ding, Qian. “The Role of BARHL2 in the Neurogenesis of Mouse Retina and Spinal Cord.” 2010. Doctoral Dissertation, University of Rochester. Accessed September 18, 2019. http://hdl.handle.net/1802/9737.

MLA Handbook (7^th Edition):

Ding, Qian. “The Role of BARHL2 in the Neurogenesis of Mouse Retina and Spinal Cord.” 2010. Web. 18 Sep 2019.

Vancouver:

Ding Q. The Role of BARHL2 in the Neurogenesis of Mouse Retina and Spinal Cord. [Internet] [Doctoral dissertation]. University of Rochester; 2010. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/1802/9737.

Council of Science Editors:

Ding Q. The Role of BARHL2 in the Neurogenesis of Mouse Retina and Spinal Cord. [Doctoral Dissertation]. University of Rochester; 2010. Available from: http://hdl.handle.net/1802/9737

University of New South Wales

11. Chavalit, Tanit. WDR5 is a novel partner of KLF3 and this interaction is important for KLF3 genomic localisation.

Degree: Biotechnology & Biomolecular Sciences, 2018, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/60070

► Krüppel-like Factor 3 (KLF3) is a member of the Krüppel-like factor family and is a potent transcriptional repressor. KLF3 is comprised of two domains: a… (more)

▼ Krüppel-like Factor 3 (KLF3) is a member of the Krüppel-like factor family and is a potent transcriptional repressor. KLF3 is comprised of two domains: a functional domain (FD) at the N-terminus and a DNA binding domain (DBD) at the C-terminus. We have recently demonstrated using chromatin immunoprecipitation combined with massively parallel DNA sequencing (ChIP-seq) that in addition to the DNA-binding domain, somewhat surprisingly, the functional domain of KLF3 is also involved in the in vivo genomic localisation of this transcription factor. Using loss-of-function experiments, we showed that DBD alone goes to far fewer genomic locations than full-length KLF3. Gain-of-function experiments support our hypothesis that the functional domain is also important – when the KLF3 functional domain is fused to an unrelated artificial DNA-binding domain the functional domain takes the artificial DNA-binding domain to new places in the genome, a significant portion of which are KLF3 target sites. We are interested in determining how the non-DNA binding functional domain contributes to genomic localisation and hypothesised that this occurs through binding to a novel KLF3-FD partner protein. The aim of this project was to identify this KLF3-FD partner protein. We made use of HEK293 cells stably expressing KLF3-FD-V5 (that is the KLF3 functional domain tagged with a V5 epitope tag). V5-KLF3 was immunoprecipitated from these cells by virtue of the V5 tag using an anti-V5 antibody and partner candidates were identified by mass spectrometry. Interestingly, WDR5 was identified as a novel candidate KLF3-FD partner protein. We mapped the WDR5 binding interface to KLF3 residues 251 to 260. We generated a mutation at arginine 254 that disrupted the interaction between KLF3 and WDR5 in vivo. This mutation allowed us to examine the functional importance of the interaction in KLF3-FD mediated genomic localisation. The role of WDR5 in KLF3 genomic localisation was examined by stably overexpressing KLF3-FD constructs containing this mutation in HEK293 cells. Target genes where KLF3-FD had been shown to mediate genomic localisation and where WDR5 had also been shown to bind were chosen. Interestingly, our data suggests that KLF3-FD failed to localise to a number of the FD-specific target genes when WDR5 binding was impaired. This suggests that binding to WDR5 plays a crucial role in KLF3-FD genomic localisation. We propose that binding to WDR5 allows the KLF3-FD to specify target gene selection. Advisors/Committee Members: Crossley, Merlin, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW, Quinlan, Kate, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW.

Subjects/Keywords: Transcription factor; KLF3; WDR5

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

APA (6^th Edition):

Chavalit, T. (2018). WDR5 is a novel partner of KLF3 and this interaction is important for KLF3 genomic localisation. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/60070

Chicago Manual of Style (16^th Edition):

Chavalit, Tanit. “WDR5 is a novel partner of KLF3 and this interaction is important for KLF3 genomic localisation.” 2018. Doctoral Dissertation, University of New South Wales. Accessed September 18, 2019. http://handle.unsw.edu.au/1959.4/60070.

MLA Handbook (7^th Edition):

Chavalit, Tanit. “WDR5 is a novel partner of KLF3 and this interaction is important for KLF3 genomic localisation.” 2018. Web. 18 Sep 2019.

Vancouver:

Chavalit T. WDR5 is a novel partner of KLF3 and this interaction is important for KLF3 genomic localisation. [Internet] [Doctoral dissertation]. University of New South Wales; 2018. [cited 2019 Sep 18]. Available from: http://handle.unsw.edu.au/1959.4/60070.

Council of Science Editors:

Chavalit T. WDR5 is a novel partner of KLF3 and this interaction is important for KLF3 genomic localisation. [Doctoral Dissertation]. University of New South Wales; 2018. Available from: http://handle.unsw.edu.au/1959.4/60070

Queens University

12. Ferrant, Harriet Ann. Homo and hetero-dimerization studies of two Zn(II)2Cys6 transcription factors in fission yeast .

Degree: Biology, 2012, Queens University

URL: http://hdl.handle.net/1974/7313

► This thesis presents a strategy designed to determine how Thi1 and Thi5 may differentially regulate thiamine production and the vegetative and sexual life cycles in… (more)

Subjects/Keywords: Thi1; Thi5; Transcription factor; Thiamine

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APA (6^th Edition):

Ferrant, H. A. (2012). Homo and hetero-dimerization studies of two Zn(II)2Cys6 transcription factors in fission yeast . (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/7313

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):

Ferrant, Harriet Ann. “Homo and hetero-dimerization studies of two Zn(II)2Cys6 transcription factors in fission yeast .” 2012. Thesis, Queens University. Accessed September 18, 2019. http://hdl.handle.net/1974/7313.

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

MLA Handbook (7^th Edition):

Ferrant, Harriet Ann. “Homo and hetero-dimerization studies of two Zn(II)2Cys6 transcription factors in fission yeast .” 2012. Web. 18 Sep 2019.

Vancouver:

Ferrant HA. Homo and hetero-dimerization studies of two Zn(II)2Cys6 transcription factors in fission yeast . [Internet] [Thesis]. Queens University; 2012. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/1974/7313.

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

Council of Science Editors:

Ferrant HA. Homo and hetero-dimerization studies of two Zn(II)2Cys6 transcription factors in fission yeast . [Thesis]. Queens University; 2012. Available from: http://hdl.handle.net/1974/7313

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

13. Ramachandran, Vasagi. Studies on molecular functions of Arabidopsis DOF transcription factors regulating vascular cell differentiation : 維管束細胞分化を制御するシロイヌナズナDOF転写因子の分子機能に関する研究; イカンソクサイボウブンカオセイギョスルシロイヌナズナ DOF テンシャインシノブンシキノウニカンスルケンキュウ.

Degree: 博士(バイオサイエンス), 2017, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学

URL: http://hdl.handle.net/10061/12180

Subjects/Keywords: Dof transcription factor

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APA (6^th Edition):

Ramachandran, V. (2017). Studies on molecular functions of Arabidopsis DOF transcription factors regulating vascular cell differentiation : 維管束細胞分化を制御するシロイヌナズナDOF転写因子の分子機能に関する研究; イカンソクサイボウブンカオセイギョスルシロイヌナズナ DOF テンシャインシノブンシキノウニカンスルケンキュウ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/12180

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):

Ramachandran, Vasagi. “Studies on molecular functions of Arabidopsis DOF transcription factors regulating vascular cell differentiation : 維管束細胞分化を制御するシロイヌナズナDOF転写因子の分子機能に関する研究; イカンソクサイボウブンカオセイギョスルシロイヌナズナ DOF テンシャインシノブンシキノウニカンスルケンキュウ.” 2017. Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed September 18, 2019. http://hdl.handle.net/10061/12180.

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

MLA Handbook (7^th Edition):

Ramachandran, Vasagi. “Studies on molecular functions of Arabidopsis DOF transcription factors regulating vascular cell differentiation : 維管束細胞分化を制御するシロイヌナズナDOF転写因子の分子機能に関する研究; イカンソクサイボウブンカオセイギョスルシロイヌナズナ DOF テンシャインシノブンシキノウニカンスルケンキュウ.” 2017. Web. 18 Sep 2019.

Vancouver:

Ramachandran V. Studies on molecular functions of Arabidopsis DOF transcription factors regulating vascular cell differentiation : 維管束細胞分化を制御するシロイヌナズナDOF転写因子の分子機能に関する研究; イカンソクサイボウブンカオセイギョスルシロイヌナズナ DOF テンシャインシノブンシキノウニカンスルケンキュウ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; 2017. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/10061/12180.

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

Council of Science Editors:

Ramachandran V. Studies on molecular functions of Arabidopsis DOF transcription factors regulating vascular cell differentiation : 維管束細胞分化を制御するシロイヌナズナDOF転写因子の分子機能に関する研究; イカンソクサイボウブンカオセイギョスルシロイヌナズナ DOF テンシャインシノブンシキノウニカンスルケンキュウ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; 2017. Available from: http://hdl.handle.net/10061/12180

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

Texas A&M University

14. Hur, Jung-Im. Functional genomics analysis of the arabidopsis ABI5 bZIP transcription factor.

Degree: 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2552

► During embryogenesis, the architecture of the plant and the food reserves for seed germination are established. Abscisic acid (ABA) regulates seed development and dormancy. It… (more)

▼ During embryogenesis, the architecture of the plant and the food reserves for seed germination are established. Abscisic acid (ABA) regulates seed development and dormancy. It controls genes involved in stress responses. ABA-responsive basic leucine zipper (bZIP) transcription factors are identified by interaction with ABA responsive cis-regulatory elements. The transcription factor ABI5 is one of these. It regulates gene expression during embryogenesis and in response to ABA. An ABA-insensitive mutant, abi5-6, exhibits no gross morphological defects other than the effect on seed germination in the presence of ABA. Thus, microarray analysis was employed to search for molecular phenotypes. We used cDNA microarrays to analyze ABA regulated gene expression and the role of ABI5 in seedlings. 310 genes were identified as ABI5/ABA regulated genes. 161 of these genes were regulated by ABI5, and 134 of ABI5-regulated genes were co-regulated by ABA. Only a small number of genes altered expression in both Pro35S:ABI5 and abi5-6 genetic backgrounds indicating the preferential binding of the bZIP protein dimers to specific promoter sequences. To determine the optimal platform for identifying ABI5-regulated genes in seeds, a cDNA microarray, the Agilent Arabidopsis Oligo microarray, and the Affymetrix ATH1 arrays were tested. Cross platform comparisons utilized 4,518 genes present on all three platforms. The best correlation was between the Agilent and the Affymetrix results. Furthermore, the Affymetrix results correlated best with qRT-PCR validation data for selected genes. A small number of genes including AtCOR413 pm-1 showed a consistent expression pattern across the three platforms. A robust ABRE cis-regulatory element was identified in the promoter of AtCOR413 pm-1. Further studies showed binding of ABI5 to the promoter of AtCOR413 pm-1 by Electrophoretic Mobility Shift Assays (EMSA) and validated the expression of ABI5 and AtCOR413 pm-1 in abi5-6 seeds by qRT-PCR and RNA gel blot analysis. Transactivation assays using AtCOR413 pm-1 promoter:GUS fusions in Arabidopsis dry seed and seedlings revealed ABI5 acts as a negative regulator for AtCOR413 pm-1 in dry seeds, while other proteins may play major roles in regulating responses to ABA and low temperature (LT) in seedlings. Advisors/Committee Members: Thomas, Terry L (advisor), McKnight, Thomas D. (committee member), Morgan, Page W. (committee member), Pepper, Alan E. (committee member).

Subjects/Keywords: ABI5 bZIP transcription factor; Genomics analysis

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

APA (6^th Edition):

Hur, J. (2009). Functional genomics analysis of the arabidopsis ABI5 bZIP transcription factor. (Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2552

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):

Hur, Jung-Im. “Functional genomics analysis of the arabidopsis ABI5 bZIP transcription factor.” 2009. Thesis, Texas A&M University. Accessed September 18, 2019. http://hdl.handle.net/1969.1/ETD-TAMU-2552.

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

MLA Handbook (7^th Edition):

Hur, Jung-Im. “Functional genomics analysis of the arabidopsis ABI5 bZIP transcription factor.” 2009. Web. 18 Sep 2019.

Vancouver:

Hur J. Functional genomics analysis of the arabidopsis ABI5 bZIP transcription factor. [Internet] [Thesis]. Texas A&M University; 2009. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2552.

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

Council of Science Editors:

Hur J. Functional genomics analysis of the arabidopsis ABI5 bZIP transcription factor. [Thesis]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2552

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

15. 能登, 舞. 脊椎動物の初期発生においてSox13相同分子種の発現は保存されている : Conserved expression of Sox13 orthologs in early vertebrate development.

Degree: 博士（医学）, 2017, Akita University / 秋田大学

URL: http://hdl.handle.net/10295/2332

► The skin and nervous tissue is derived from the ectoderm1, 2). In Xenopus, ectodermal explants (animal caps) from blastula embryos show high tissue plasticity and… (more)

Subjects/Keywords: Sox transcription factor family; Sox13; neural development

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APA (6^th Edition):

能登, �. (2017). 脊椎動物の初期発生においてSox13相同分子種の発現は保存されている : Conserved expression of Sox13 orthologs in early vertebrate development. (Thesis). Akita University / 秋田大学. Retrieved from http://hdl.handle.net/10295/2332

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):

能登, 舞. “脊椎動物の初期発生においてSox13相同分子種の発現は保存されている : Conserved expression of Sox13 orthologs in early vertebrate development.” 2017. Thesis, Akita University / 秋田大学. Accessed September 18, 2019. http://hdl.handle.net/10295/2332.

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

MLA Handbook (7^th Edition):

能登, 舞. “脊椎動物の初期発生においてSox13相同分子種の発現は保存されている : Conserved expression of Sox13 orthologs in early vertebrate development.” 2017. Web. 18 Sep 2019.

Vancouver:

能登 �. 脊椎動物の初期発生においてSox13相同分子種の発現は保存されている : Conserved expression of Sox13 orthologs in early vertebrate development. [Internet] [Thesis]. Akita University / 秋田大学; 2017. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/10295/2332.

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

Council of Science Editors:

能登 �. 脊椎動物の初期発生においてSox13相同分子種の発現は保存されている : Conserved expression of Sox13 orthologs in early vertebrate development. [Thesis]. Akita University / 秋田大学; 2017. Available from: http://hdl.handle.net/10295/2332

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

University of Edinburgh

16. Lin, Chia-Yi. Characterizing the function of transcription factor 15 (Tcf15) in pluripotent cells.

Degree: PhD, 2015, University of Edinburgh

URL: http://hdl.handle.net/1842/10503

► Pluripotent embryonic stem (ES) cells are heterogeneous mixtures of naïve and lineage-primed states defined by distinct transcription factor expression profiles. However, the events that prime… (more)

▼ Pluripotent embryonic stem (ES) cells are heterogeneous mixtures of naïve and lineage-primed states defined by distinct transcription factor expression profiles. However, the events that prime pluripotent cells for differentiation are not well understood. Id proteins, which are inhibitors of basic helix-loop-helix (bHLH) transcription factors, contribute to pluripotency by blocking differentiation. Using Yeast-Two-Hybrid screening, our lab identified Tcf15 as an Id-regulated transcription factor. In this study, I first examined the expression of Tcf15 during differentiation in vitro and during early development in vivo in the mouse. Tcf15 expression is higher in primed pluripotent embryonic stem (ES) cells than in naïve ES cells or epiblast stem cells (EpiSCs). In addition, Tcf15 is expressed heterogeneously in ES cells and is also detected in the inner cell mass (ICM) of E4.5 mouse embryos. Expression of Tcf15 was upregulated during early stages of differentiation and downregulated before cells committed to any specific lineage. Using Tcf15-Venus reporter cells, I found that expression of Tcf15 is specifically associated with a novel subpopulation of ES cells primed for somatic lineages. Gain of function and loss of function studies were then performed to perturb Tcf15 expression in ES cells in order to assess the function of Tcf15 in self-renewal and during differentiation. An inducible Id-resistant form of Tcf15 accelerates somatic lineage commitment by maturating naïve pluripotent ES cells transit toward primed epiblast and later on epiblastderived somatic lineages whilst suppressing differentiation towards extraembryonic endoderm. Preliminary loss of function studies also suggest that down-regulation of Tcf15 may promote a naïve state within pluripotent cells. I investigated the mechanism by which Tcf15 expression becomes associated with the epiblast-primed state by identifying the upstream regulators and downstream targets of Tcf15. Tcf15 expression is dependent on FGF signalling. Microarray analysis identified that Tcf15 downregulates the naïve pluripotency determinant Nanog and upregulates the epiblast determinant Otx2. Taken together, our results suggest that Tcf15 acts in opposition to the pluripotency network to prime pluripotent cells towards differentiation.

Subjects/Keywords: 616.02; stem cells; Tcf15; pluripotent; transcription factor

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APA (6^th Edition):

Lin, C. (2015). Characterizing the function of transcription factor 15 (Tcf15) in pluripotent cells. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/10503

Chicago Manual of Style (16^th Edition):

Lin, Chia-Yi. “Characterizing the function of transcription factor 15 (Tcf15) in pluripotent cells.” 2015. Doctoral Dissertation, University of Edinburgh. Accessed September 18, 2019. http://hdl.handle.net/1842/10503.

MLA Handbook (7^th Edition):

Lin, Chia-Yi. “Characterizing the function of transcription factor 15 (Tcf15) in pluripotent cells.” 2015. Web. 18 Sep 2019.

Vancouver:

Lin C. Characterizing the function of transcription factor 15 (Tcf15) in pluripotent cells. [Internet] [Doctoral dissertation]. University of Edinburgh; 2015. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/1842/10503.

Council of Science Editors:

Lin C. Characterizing the function of transcription factor 15 (Tcf15) in pluripotent cells. [Doctoral Dissertation]. University of Edinburgh; 2015. Available from: http://hdl.handle.net/1842/10503

University of Hong Kong

17. Chen, Wei. A factor analysis approach to transcription regulatory network reconstruction using gene expression data.

Degree: PhD, 2012, University of Hong Kong

URL: Chen, W. [陈玮]. (2012). A factor analysis approach to transcription regulatory network reconstruction using gene expression data. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4961778 ; http://dx.doi.org/10.5353/th_b4961778 ; http://hdl.handle.net/10722/180958

► Reconstruction of Transcription Regulatory Network (TRN) and Transcription Factor Activity (TFA) from gene expression data is an important problem in systems biology. Currently, there exist… (more)

▼ Reconstruction of Transcription Regulatory Network (TRN) and Transcription Factor Activity (TFA) from gene expression data is an important problem in systems biology. Currently, there exist various factor analysis methods for TRN reconstruction, but most approaches have specific assumptions not satisfied by real biological data. Network Component Analysis (NCA) can handle such limitations and is considered to be one of the most effective methods. The prerequisite for NCA is knowledge of the structure of TRN. Such structure can be obtained from ChIP-chip or ChIP-seq experiments, which however have quite limited applications. In order to cope with the difficulty, we resort to heuristic optimization algorithm such as Particle Swarm Optimization (PSO), in order to explore the possible structures of TRN and choose the most plausible one. Regarding the structure estimation problem, we extend classical PSO and propose a novel Probabilistic binary PSO. Furthermore, an improved NCA called FastNCA is adopted to compute the objective function accurately and fast, which enables PSO to run efficiently. Since heuristic optimization cannot guarantee global convergence, we run PSO multiple times and integrate the results. Then GCV-LASSO (Generalized Cross Validation - Least Absolute Shrinkage and Selection Operator) is performed to estimate TRN. We apply our approach and other factor analysis methods on the synthetic data. The results indicate that the proposed PSOFastNCA-GCV-LASSO algorithm gives better estimation. In order to incorporate more prior information on TRN structure and gene expression dynamics in the linear factor analysis model for improved estimation of TRN and TFAs, a linear Bayesian framework is adopted. Under the unified Bayesian framework, Bayesian Linear Sparse Factor Analysis Model (BLSFM) and Bayesian Linear State Space Model (BLSSM) are developed for instantaneous and dynamic TRN, respectively. Various approaches to incorporate partial and ambiguous prior network structure information in the Bayesian framework are proposed to improve performance in practical applications. Furthermore, we propose a novel mechanism for estimating the hyper-parameters of the distribution priors in our BLSFM and BLSSM models, which can significantly improve the estimation compared to traditional ways of hyper-parameter setting. With this development, reasonably good estimation of TFAs and TRN can be obtained even without use of any structure prior of TRN. Extensive numerical experiments are performed to investigate our developed methods under various settings, with comparison to some existing alternative approaches. It is demonstrated that our hyper-parameter estimation method improves the estimation of TFA and TRN in most settings and has superior performance, and that structure priors in general leads to improved estimation performance. Regarding application to real biological data, we execute the PSO-FastNCAGCV-LASSO algorithm developed in the thesis using E. Coli microarray data and obtain sensible estimation of TFAs and… Advisors/Committee Members: Hung, YS, Chang, C.

Subjects/Keywords: Genetic transcription - Regulation - Statistical methods.; Factor analysis.

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APA (6^th Edition):

Chen, W. (2012). A factor analysis approach to transcription regulatory network reconstruction using gene expression data. (Doctoral Dissertation). University of Hong Kong. Retrieved from Chen, W. [陈玮]. (2012). A factor analysis approach to transcription regulatory network reconstruction using gene expression data. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4961778 ; http://dx.doi.org/10.5353/th_b4961778 ; http://hdl.handle.net/10722/180958

Chicago Manual of Style (16^th Edition):

Chen, Wei. “A factor analysis approach to transcription regulatory network reconstruction using gene expression data.” 2012. Doctoral Dissertation, University of Hong Kong. Accessed September 18, 2019. Chen, W. [陈玮]. (2012). A factor analysis approach to transcription regulatory network reconstruction using gene expression data. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4961778 ; http://dx.doi.org/10.5353/th_b4961778 ; http://hdl.handle.net/10722/180958.

MLA Handbook (7^th Edition):

Chen, Wei. “A factor analysis approach to transcription regulatory network reconstruction using gene expression data.” 2012. Web. 18 Sep 2019.

Vancouver:

Chen W. A factor analysis approach to transcription regulatory network reconstruction using gene expression data. [Internet] [Doctoral dissertation]. University of Hong Kong; 2012. [cited 2019 Sep 18]. Available from: Chen, W. [陈玮]. (2012). A factor analysis approach to transcription regulatory network reconstruction using gene expression data. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4961778 ; http://dx.doi.org/10.5353/th_b4961778 ; http://hdl.handle.net/10722/180958.

Council of Science Editors:

Chen W. A factor analysis approach to transcription regulatory network reconstruction using gene expression data. [Doctoral Dissertation]. University of Hong Kong; 2012. Available from: Chen, W. [陈玮]. (2012). A factor analysis approach to transcription regulatory network reconstruction using gene expression data. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4961778 ; http://dx.doi.org/10.5353/th_b4961778 ; http://hdl.handle.net/10722/180958

Penn State University

18. Shuman, Laurie Ann. Interaction of Metastatic Breast Cancer Cells with Osteoblasts.

Degree: PhD, Immunology and Infectious Diseases, 2009, Penn State University

URL: https://etda.libraries.psu.edu/catalog/9358

► A majority of cancer deaths (90%) are a result of the dissemination of tumor cells from the primary site to a secondary site, not due… (more)

▼ A majority of cancer deaths (90%) are a result of the dissemination of tumor cells from the primary site to a secondary site, not due to the primary tumor itself. Therefore, it is necessary to investigate mechanisms utilized by tumor cells to promote growth in and destruction of the secondary sites. Advances in microarray technology allow for rapid screening and identification of potential genetic targets involved in host response to cancers, however there is a need for high-throughput screening of the identified targets to determine their efficacy. In vitro systems that more accurately represent in vivo microenvironments would be a useful tool to screen potential genetic targets as treatment of diseases. Here we examined the interaction of breast cancer cells with osteoblasts in a specialized culture device (bioreactor). Breast cancer preferentially metastasizes to the bone resulting in the formation of osteolytic lesions. While administration of osteoclast-inhibiting drugs, such as bisphosphonates, slow further lesion formation, existing lesions do not heal. Therefore, osteoblasts appear functionally disabled in the presence of metastatic breast cancer cells. Previous studies in this laboratory have shown that breast cancer cells alter osteoblast adhesion and morphology, increase osteoblast apoptosis, and decrease the expression of osteoblast differentiation genes when exposed to metastatic breast cancer cell conditioned medium for extended periods (5 – 35 days). In order to examine the interaction of metastatic breast cancer cells with osteoblasts apart from osteoclasts, a specialized bioreactor culture system was utilized. In this culture device, osteoblasts grew and differentiated into a multiple-cell-layer, three-dimensional mineralizing tissue. Co-culture of metastatic breast cancer cells with osteoblasts in a bioreactor were compared to co-culture in conventional cell culture. The breast cancer cells not only attached and grew on the osteoblast tissue in the bioreactor culture system, but also formed distinct colonies that aligned in the same axis as the osteoblasts, similar to “Indian filing” seen in authentic pathological tissue. Moreover, in this culture system, the breast cancer cells penetrated the osteoblast tissue, a phenomenon not apparent with conventional cell culture methods. Metastatic breast cancer cells also interfered with the differentiation of osteoblasts as evidenced by a decrease in production of proteins, such as osteocalcin and collagen. In addition, co-culture of the metastatic breast cancer cells with osteoblasts resulted in increased production of the inflammatory cytokine, IL-6, a known activator of osteoclasts. The bioreactor culture system is advantageous over conventional cell culture systems in emulating the bone microenvironment and for studying the interaction of metastatic breast cancer cells with osteoblasts. Additionally, in this report, transcription factor targets within MC3T3-E1 cells treated with MDA-MB-231 human metastatic breast cancer cell conditioned medium were…

Subjects/Keywords: transcription factor; cytokine; metastasis; osteoblast; Breast cancer

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APA (6^th Edition):

Shuman, L. A. (2009). Interaction of Metastatic Breast Cancer Cells with Osteoblasts. (Doctoral Dissertation). Penn State University. Retrieved from https://etda.libraries.psu.edu/catalog/9358

Chicago Manual of Style (16^th Edition):

Shuman, Laurie Ann. “Interaction of Metastatic Breast Cancer Cells with Osteoblasts.” 2009. Doctoral Dissertation, Penn State University. Accessed September 18, 2019. https://etda.libraries.psu.edu/catalog/9358.

MLA Handbook (7^th Edition):

Shuman, Laurie Ann. “Interaction of Metastatic Breast Cancer Cells with Osteoblasts.” 2009. Web. 18 Sep 2019.

Vancouver:

Shuman LA. Interaction of Metastatic Breast Cancer Cells with Osteoblasts. [Internet] [Doctoral dissertation]. Penn State University; 2009. [cited 2019 Sep 18]. Available from: https://etda.libraries.psu.edu/catalog/9358.

Council of Science Editors:

Shuman LA. Interaction of Metastatic Breast Cancer Cells with Osteoblasts. [Doctoral Dissertation]. Penn State University; 2009. Available from: https://etda.libraries.psu.edu/catalog/9358

University of Manchester

19. Webber, Aaron. Transcriptional co-regulation of microRNAs and protein-coding genes.

Degree: PhD, 2013, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/transcriptional-coregulation-of-micrornas-and-proteincoding-genes(f5b601b2-33f3-4608-9ae8-b7d5a0c6beaf).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.677721

► This thesis was presented by Aaron Webber on the 4th December 2013 for the degree of Doctor of Philosophy from the University of Manchester. The… (more)

▼ This thesis was presented by Aaron Webber on the 4th December 2013 for the degree of Doctor of Philosophy from the University of Manchester. The title of this thesis is ‘Transcriptional co-regulation of microRNAs and protein-coding genes’. The thesis relates to gene expression regulation within humans and closely related primate species. We have investigated the binding site distributions from publically available ChIP-seq data of 117 transcription regulatory factors (TRFs) within the human genome. These were mapped to cis-regulatory regions of two major classes of genes,  20,000 genes encoding proteins and  1500 genes encoding microRNAs. MicroRNAs are short 20 - 24 nt noncoding RNAs which bind complementary regions within target mRNAs to repress translation. The complete collection of ChIP-seq binding site data is related to genomic associations between protein-coding and microRNA genes, and to the expression patterns and functions of both gene types across human tissues. We show that microRNA genes are associated with highly regulated protein-coding gene regions, and show rigorously that transcriptional regulation is greater than expected, given properties of these protein-coding genes. We find enrichment in developmental proteins among protein-coding genes hosting microRNA sequences. Novel subclasses of microRNAs are identified that lie outside of protein-coding genes yet may still be expressed from a shared promoter region with their protein-coding neighbours. We show that such microRNAs are more likely to form regulatory feedback loops with the transcriptional regulators lying in the upstream protein-coding promoter region. We show that when a microRNA and a TRF regulate one another, the TRF is more likely to sometimes function as a repressor. As in many studies, the data show that microRNAs lying downstream of particular TRFs target significantly many genes in common with these TRFs. We then demonstrate that the prevalence of such TRF/microRNA regulatory partnerships relates directly to the variation in mRNA expression across human tissues, with the least variable mRNAs having the most significant enrichment in such partnerships. This result is connected to theory describing the buffering of gene expression variation by microRNAs. Taken together, our study has demonstrated significant novel linkages between the transcriptional TRF and post-transcriptional microRNA-mediated regulatory layers. We finally consider transcriptional regulators alone, by mapping these to genes clustered on the basis of their expression patterns through time, within the context of CD4+ T cells from African green monkeys and Rhesus macaques infected with Simian immunodeficiency virus (SIV). African green monkeys maintain a functioning immune system despite never clearing the virus, while in rhesus macaques, the immune system becomes chronically stimulated leading to pathogenesis. Gene expression clusters were identified characterizing the natural and pathogenic host systems. We map transcriptional regulators to these expression…

Subjects/Keywords: 572.8; MicroRNA; Transcription factor; Regulatory network

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APA (6^th Edition):

Webber, A. (2013). Transcriptional co-regulation of microRNAs and protein-coding genes. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/transcriptional-coregulation-of-micrornas-and-proteincoding-genes(f5b601b2-33f3-4608-9ae8-b7d5a0c6beaf).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.677721

Chicago Manual of Style (16^th Edition):

Webber, Aaron. “Transcriptional co-regulation of microRNAs and protein-coding genes.” 2013. Doctoral Dissertation, University of Manchester. Accessed September 18, 2019. https://www.research.manchester.ac.uk/portal/en/theses/transcriptional-coregulation-of-micrornas-and-proteincoding-genes(f5b601b2-33f3-4608-9ae8-b7d5a0c6beaf).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.677721.

MLA Handbook (7^th Edition):

Webber, Aaron. “Transcriptional co-regulation of microRNAs and protein-coding genes.” 2013. Web. 18 Sep 2019.

Vancouver:

Webber A. Transcriptional co-regulation of microRNAs and protein-coding genes. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2019 Sep 18]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/transcriptional-coregulation-of-micrornas-and-proteincoding-genes(f5b601b2-33f3-4608-9ae8-b7d5a0c6beaf).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.677721.

Council of Science Editors:

Webber A. Transcriptional co-regulation of microRNAs and protein-coding genes. [Doctoral Dissertation]. University of Manchester; 2013. Available from: https://www.research.manchester.ac.uk/portal/en/theses/transcriptional-coregulation-of-micrornas-and-proteincoding-genes(f5b601b2-33f3-4608-9ae8-b7d5a0c6beaf).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.677721

University of Tennessee – Knoxville

20. Choi, Jinlyung. GlyR3 regulation in Clostridium thermocellum.

Degree: 2015, University of Tennessee – Knoxville

URL: https://trace.tennessee.edu/utk_graddiss/3296

► Bio-ethanol from cellulosic biomass is a promising candidate as a liquid transportation fuel because of its high-energy content and the abundance of cellulose. Consolidated bioprocessing… (more)

▼ Bio-ethanol from cellulosic biomass is a promising candidate as a liquid transportation fuel because of its high-energy content and the abundance of cellulose. Consolidated bioprocessing (CBP) helps to reduce the traditional 2-step process of bio-ethanol production into single-step to improve cost efficiency. A bacterium, Clostridium thermocellum, has a multi-enzyme complex for hydrolyzing cellulase, called the Cellulosome that enables the organism to have high rates of cellulose utilization. However, the ethanol yield of C. thermocellum needs to be improved in order to make consolidated bioprocessing with C. thermocellum commercially viable. It is essential to understand the regulation of carbohydrate-degrading enzyme activity to apply metabolic engineering, synthetic biology, and molecular biology techniques to strain improvement. GlyR3 is a protein that regulates the activity of carbohydrate active proteins in C. thermocellum. Recent studies have described how GlyR3 regulates the celC operon, which includes two carbohydrate-active enzymes (Newcomb, Chen, & Wu, 2007a). In this dissertation I investigate additional regulatory targets of the GlyR3 protein, which is a LacI family protein. First, it will be shown that GlyR3 regulates a gene downstream of celC operon, manB, explaining that GlyR3 not only induces its own expression under presence of laminaribiose, but in the case of manB, repress expression. Bioinformatics tools are then used to find putative GlyR3 binding sites in the whole genome in C. thermocellum. Electrophoretic mobility shift assay (EMSA) can show direct binding between GlyR3 and DNA sequences of interest. Second, we are going to show that GlyR3 regulates genes that are located far from the celC operon. Reverse transcript (RT) –PCR and mRNA sequencing will be used to show in vivo changes in expression of genes in the whole genome resulting from changing levels of GlyR3 expression resulting from the addition of laminaribiose. This research reveals two distinct binding motifs for GlyR3, a celC-type and a manB-type, which are used to identify additional operons potentially regulated by GlyR3 and demonstrates a global regulatory role for GlyR3 in C. thermocellum.

Subjects/Keywords: GlyR3; Clostridium thermocellum; Transcription factor; Motif; Biotechnology

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APA (6^th Edition):

Choi, J. (2015). GlyR3 regulation in Clostridium thermocellum. (Doctoral Dissertation). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_graddiss/3296

Chicago Manual of Style (16^th Edition):

Choi, Jinlyung. “GlyR3 regulation in Clostridium thermocellum.” 2015. Doctoral Dissertation, University of Tennessee – Knoxville. Accessed September 18, 2019. https://trace.tennessee.edu/utk_graddiss/3296.

MLA Handbook (7^th Edition):

Choi, Jinlyung. “GlyR3 regulation in Clostridium thermocellum.” 2015. Web. 18 Sep 2019.

Vancouver:

Choi J. GlyR3 regulation in Clostridium thermocellum. [Internet] [Doctoral dissertation]. University of Tennessee – Knoxville; 2015. [cited 2019 Sep 18]. Available from: https://trace.tennessee.edu/utk_graddiss/3296.

Council of Science Editors:

Choi J. GlyR3 regulation in Clostridium thermocellum. [Doctoral Dissertation]. University of Tennessee – Knoxville; 2015. Available from: https://trace.tennessee.edu/utk_graddiss/3296

University of Sydney

21. Guan, Fiona Hui Xian. Functional Characterisation of ELF2 in Haemopoietic Development .

Degree: 2015, University of Sydney

URL: http://hdl.handle.net/2123/15344

► ELF2 (E74-like factor 2), a member of the Ets family of transcription factors, has been reported to regulate genes important in B cell development, cell… (more)

Subjects/Keywords: ELF2; Haemopoiesis; ELF - Subfamily; ETS Transcription Factor

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APA (6^th Edition):

Guan, F. H. X. (2015). Functional Characterisation of ELF2 in Haemopoietic Development . (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/15344

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):

Guan, Fiona Hui Xian. “Functional Characterisation of ELF2 in Haemopoietic Development .” 2015. Thesis, University of Sydney. Accessed September 18, 2019. http://hdl.handle.net/2123/15344.

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

MLA Handbook (7^th Edition):

Guan, Fiona Hui Xian. “Functional Characterisation of ELF2 in Haemopoietic Development .” 2015. Web. 18 Sep 2019.

Vancouver:

Guan FHX. Functional Characterisation of ELF2 in Haemopoietic Development . [Internet] [Thesis]. University of Sydney; 2015. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/2123/15344.

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

Council of Science Editors:

Guan FHX. Functional Characterisation of ELF2 in Haemopoietic Development . [Thesis]. University of Sydney; 2015. Available from: http://hdl.handle.net/2123/15344

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

Duke University

22. Kabadi, Ami Meda. Engineering Transcription Factors to Program Cell Fate Decisions .

Degree: 2015, Duke University

URL: http://hdl.handle.net/10161/9831

► Technologies for engineering new functions into proteins are advancing biological research, biotechnology, and medicine at an astounding rate. Building on fundamental research of natural… (more)

▼ Technologies for engineering new functions into proteins are advancing biological research, biotechnology, and medicine at an astounding rate. Building on fundamental research of natural protein structure and function, scientists are identifying new protein domains with previously undescribed properties and engineering new proteins with expanded functionalities. Such tools are enabling the precise study of fundamental aspects of cellular behavior and the development of a new class of gene therapies that manipulate the expression of endogenous genes. The applications of these gene regulation technologies include but are not limited to controlling cell fate decisions, reprogramming cell lineage commitment, monitoring cellular states, and stimulating expression of therapeutic factors. While the field has come a long way in the past 20 years, there are still many limitations. Historically, gene therapy and gene replacement therapies have relied on over-expression of natural transcription factors that activate specific endogenous gene networks. However, natural transcription factors are often inadequate for generating efficient, fast, and homogenous cellular responses. Furthermore, most natural transcription factors have complex structures and functions that are difficult to improve or alter by rational design. This thesis presents three novel and widely applicable methods for engineering transcription factors for programming cell fate decisions in primary human cells. MyoD is the master transcription factor defining the myogenic lineage. Expression of MyoD in certain non-myogenic lineages induces a coordinated change in differentiation state. We use MyoD as a model for developing our protein engineering techniques because myogenesis is a well-studied pathway that is characterized by an easily detected change in phenotype from mono-nucleated to multinucleated cells. Furthermore, efficient generation of myocytes in vitro presents an attractive patient-specific method by which to treat muscle-wasting diseases such as muscular dystrophy. We first demonstrate that we can improve the ability of MyoD to convert human dermal fibroblasts and human adipose-derived stem cells into myocyte-like cells. By fusing potent modular activation domains to the MyoD protein, we increased myogenic gene expression, myofiber formation, cell fusion, and global reprogramming of the myogenic gene network. The engineered MyoD transcription factor induced myogenisis in a little as ten days, a process that takes three or more weeks with the natural MyoD protein. While increasing the potency of transcriptional activation is one mechanism by which to improve transcription factor function, there are many other possible routes such as increasing DNA-binding affinity, increasing protein stability, altering interactions with co-factors, or inducing post-translational modifications. Endogenous regulatory pathways are complex, and it is difficult to predict specific amino acid changes that will produce the desired outcome. Therefore, we… Advisors/Committee Members: Gersbach, Charles A (advisor).

Subjects/Keywords: Biomedical engineering; MyoD; Myogenesis; Transcription Factor

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APA (6^th Edition):

Kabadi, A. M. (2015). Engineering Transcription Factors to Program Cell Fate Decisions . (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/9831

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):

Kabadi, Ami Meda. “Engineering Transcription Factors to Program Cell Fate Decisions .” 2015. Thesis, Duke University. Accessed September 18, 2019. http://hdl.handle.net/10161/9831.

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

MLA Handbook (7^th Edition):

Kabadi, Ami Meda. “Engineering Transcription Factors to Program Cell Fate Decisions .” 2015. Web. 18 Sep 2019.

Vancouver:

Kabadi AM. Engineering Transcription Factors to Program Cell Fate Decisions . [Internet] [Thesis]. Duke University; 2015. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/10161/9831.

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

Council of Science Editors:

Kabadi AM. Engineering Transcription Factors to Program Cell Fate Decisions . [Thesis]. Duke University; 2015. Available from: http://hdl.handle.net/10161/9831

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

Washington University in St. Louis

23. Zhao, Yue. Quantitative Analysis Demonstrates Most Transcription Factors Require only Simple Models of Specificity.

Degree: PhD, Biology and Biomedical Sciences: Computational and Systems Biology, 2011, Washington University in St. Louis

URL: https://openscholarship.wustl.edu/etd/675

► Organisms must control their gene expression to properly respond to developmental, stress or other environmental cues. A key part of this process is transcriptional regulation,… (more)

▼ Organisms must control their gene expression to properly respond to developmental, stress or other environmental cues. A key part of this process is transcriptional regulation, which is largely accomplished by a complex network of transcription factor proteins: TFs) interact with their specific binding sites in the genome. Understanding how TFs select correct binding sites out of the vast number of potential binding sites in the genome is a key challenge in molecular biology. Recently, unprecedented amount of quantitative binding data have become available as results of developments in high-throughput experimental techniques. However, interpretation of high-throughput binding data has proved to be controversial, largely due to the lack of physically principled data analysis methods. ii An important question in the analysis of binding data is the complexity of the specificity model needed. This has important implications for both the characterization of specificity and for the prediction of the consequences of mutations. Structurally, TF-DNA interactions are complex with a wide variety of interactions between the protein and DNA making a simple recognition code impossible. Energetically, however, the situation may be much simpler. Detailed studies of a handful of TFs have shown that individual base pairs often contribute independently to the total binding energy. This view of simplicity has been challenged by data from high-throughput binding experiments, although the extent to which the sample model breaks down is uncertain due to lack of rigorous analysis methods. The goal of this thesis is to assess the complexity of model required to accurately represent TF specificity. To this end, I have developed a new statistical analysis method BEEML: Binding Energy Estimation by Maximum Likelihood) that parameterizes models of TF specificity from high-throughput quantitative binding data, using a realistic biophysical model. Employing the BEEML method, I show that the energetics of most TF-DNA interactions are simple, with bases in the binding site contribute approximately independently to the total binding energy. Further, I show that interactions in the binding site occur mostly between adjacent positions. Advisors/Committee Members: Gary Stormo.

Subjects/Keywords: Bioinformatics; Biochemistry; Quantitative Model; Transcription Factor Specificity

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APA (6^th Edition):

Zhao, Y. (2011). Quantitative Analysis Demonstrates Most Transcription Factors Require only Simple Models of Specificity. (Doctoral Dissertation). Washington University in St. Louis. Retrieved from https://openscholarship.wustl.edu/etd/675

Chicago Manual of Style (16^th Edition):

Zhao, Yue. “Quantitative Analysis Demonstrates Most Transcription Factors Require only Simple Models of Specificity.” 2011. Doctoral Dissertation, Washington University in St. Louis. Accessed September 18, 2019. https://openscholarship.wustl.edu/etd/675.

MLA Handbook (7^th Edition):

Zhao, Yue. “Quantitative Analysis Demonstrates Most Transcription Factors Require only Simple Models of Specificity.” 2011. Web. 18 Sep 2019.

Vancouver:

Zhao Y. Quantitative Analysis Demonstrates Most Transcription Factors Require only Simple Models of Specificity. [Internet] [Doctoral dissertation]. Washington University in St. Louis; 2011. [cited 2019 Sep 18]. Available from: https://openscholarship.wustl.edu/etd/675.

Council of Science Editors:

Zhao Y. Quantitative Analysis Demonstrates Most Transcription Factors Require only Simple Models of Specificity. [Doctoral Dissertation]. Washington University in St. Louis; 2011. Available from: https://openscholarship.wustl.edu/etd/675

Princeton University

24. Hannon, Colleen Elizabeth. A Model for a Genome-Wide Molecular Readout of the Bicoid Morphogen Gradient .

Degree: PhD, 2017, Princeton University

URL: http://arks.princeton.edu/ark:/88435/dsp01v118rh15k

► In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis.… (more)

Subjects/Keywords: Bicoid; chromatin; homeodomain; morphogen; transcription factor

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APA (6^th Edition):

Hannon, C. E. (2017). A Model for a Genome-Wide Molecular Readout of the Bicoid Morphogen Gradient . (Doctoral Dissertation). Princeton University. Retrieved from http://arks.princeton.edu/ark:/88435/dsp01v118rh15k

Chicago Manual of Style (16^th Edition):

Hannon, Colleen Elizabeth. “A Model for a Genome-Wide Molecular Readout of the Bicoid Morphogen Gradient .” 2017. Doctoral Dissertation, Princeton University. Accessed September 18, 2019. http://arks.princeton.edu/ark:/88435/dsp01v118rh15k.

MLA Handbook (7^th Edition):

Hannon, Colleen Elizabeth. “A Model for a Genome-Wide Molecular Readout of the Bicoid Morphogen Gradient .” 2017. Web. 18 Sep 2019.

Vancouver:

Hannon CE. A Model for a Genome-Wide Molecular Readout of the Bicoid Morphogen Gradient . [Internet] [Doctoral dissertation]. Princeton University; 2017. [cited 2019 Sep 18]. Available from: http://arks.princeton.edu/ark:/88435/dsp01v118rh15k.

Council of Science Editors:

Hannon CE. A Model for a Genome-Wide Molecular Readout of the Bicoid Morphogen Gradient . [Doctoral Dissertation]. Princeton University; 2017. Available from: http://arks.princeton.edu/ark:/88435/dsp01v118rh15k

Boston University

25. Abraham, Elizabeth June. Genetic varients leading to atrial fibrillation.

Degree: MS, Medical Sciences, 2016, Boston University

URL: http://hdl.handle.net/2144/16744

► BACKGROUND: Atrial Fibrillation (AF) is the most common cardiac arrhythmia, affecting over 3 million Americans. Many people who suffer from AF have pre-disposing factors such… (more)

▼ BACKGROUND: Atrial Fibrillation (AF) is the most common cardiac arrhythmia, affecting over 3 million Americans. Many people who suffer from AF have pre-disposing factors such as hypertension, ischemia, and structural heart disease, but recent research has also demonstrated the importance of genetic factors that can contribute to AF. In the present study, we sought to determine the causative mutation in a family with AF, atrial septal, and ventricular septal defects. METHODS: We evaluated a pedigree with 16 family members, one of whom had an ASD, one a VSD, and three had AF. Exome sequencing was performed on three of the five affected family members followed by confirmation with Sanger sequencing in all family members. A separate cohort from the MGH AF Study with early-onset AF (age at onset 47.1 ± 10.9 years, 79.3% male) was also screened for mutations using a combination of Sanger sequencing and high resolution melting. Variants were then functionally characterized using reporter assays in a mammalian cell line using wild-type and mutant constructs driving NPPA, αMHC and NPPB promoter reporters. RESULTS: Exome sequencing of the three affected individuals in the family identified a highly conserved mutation, R585L, in the transcription factor gene, GATA6. We also identified three additional GATA6 variants (P91S, A177T, and A543G) in the cases with early-onset AF from the MGH AF Study. We found that three of the four variants had a marked upregulation of luciferase activity (R585L; 4.1 fold, p<0.0001; P91S; 2.5 fold, p=0.0002; A177T; 1.7 fold, p=0.03). Additionally, when co-overexpressed with GATA4 and MEF2C, all GATA6 variants exhibited upregulation of the αMHC and NPPA activity compared to control. CONCLUSION: Overall, we found gain-of-function mutations in GATA6 in both a family with early-onset AF and atrioventricular septal defects as well as in patients with sporadic, early-onset AF. This evidence suggests that specific gain of function mutations in GATA6 contribute to the development of AF.

Subjects/Keywords: Genetics; Transcription factor; Atrial fibrillation; Genes

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

APA (6^th Edition):

Abraham, E. J. (2016). Genetic varients leading to atrial fibrillation. (Masters Thesis). Boston University. Retrieved from http://hdl.handle.net/2144/16744

Chicago Manual of Style (16^th Edition):

Abraham, Elizabeth June. “Genetic varients leading to atrial fibrillation.” 2016. Masters Thesis, Boston University. Accessed September 18, 2019. http://hdl.handle.net/2144/16744.

MLA Handbook (7^th Edition):

Abraham, Elizabeth June. “Genetic varients leading to atrial fibrillation.” 2016. Web. 18 Sep 2019.

Vancouver:

Abraham EJ. Genetic varients leading to atrial fibrillation. [Internet] [Masters thesis]. Boston University; 2016. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/2144/16744.

Council of Science Editors:

Abraham EJ. Genetic varients leading to atrial fibrillation. [Masters Thesis]. Boston University; 2016. Available from: http://hdl.handle.net/2144/16744

University of Adelaide

26. Chiasson, David Michael. Characterization of GmSAT1 and related proteins from legume nodules.

Degree: 2012, University of Adelaide

URL: http://hdl.handle.net/2440/80104

► Nitrogen is an essential nutrient for plant growth and is normally obtained from the soil medium. Legumes are a unique group of plants that acquired… (more)

▼ Nitrogen is an essential nutrient for plant growth and is normally obtained from the soil medium. Legumes are a unique group of plants that acquired the ability to form a symbiosis with nitrogen-fixing bacteria, called rhizobia, enabling growth in nitrogen-poor soils. GmSAT1, a predicted bHLH transcription factor from soybean, is essential for nitrogen fixation; however the role of this protein remains elusive (Kaiser et al., 1998; Loughlin, 2007). In this work, a further functional characterization of GmSAT1 was undertaken. Using the promoters of known upregulated genes in yeast upon expression of GmSAT1, it was found that purified GmSAT1 directly interacts with DNA. Further, GFP-fusion analysis in onion epidermal cells, found that GmSAT1 localizes to the nucleus, as well as peripheral vesicles, demonstrating that GmSAT1 is a likely a transcription factor. Residues from both the N- and C-termini required for GmSAT1 activity were also identified by exchanging domains with GmSAT2, a protein that arose during the relatively recent whole-genome duplication in soybean. Recently, GmSAT1 was shown to be essential for proper nodule development in soybean (Loughlin, 2007). Therefore, a DNA microarray analysis was conducted to identify transcripts that are differentially expressed after silencing of GmSAT1 by RNA interference (RNAi) in soybean nodules. Of the ninety-five genes downregulated, twelve were associated with the circadian clock, potentially explaining the GmSAT1 RNAi phenotype. Investigations were also initiated in the model legume Medicago truncatula to identify and characterize GmSAT1 orthologues. Two genes, MtSAT1 and MtSAT2 were cloned and analyzed. MtSAT1 and MtSAT2 are expressed in roots and the inner cortex of nodules, similar to GmSAT1. By in planta GFP-fusion analysis, both MtSAT1 and MtSAT2 were found to associate with vesicles and the nucleus. Insertional mutations in either gene alone did not render a phenotype, however downregulating both genes by RNAi disrupted nodule formation. Using the sequence of a newly discovered ammonium channel protein from yeast (ScAMF1), which is activated by GmSAT1, a novel subfamily of major facilitator transporter proteins (MFSs) from plants was identified. Interestingly, members of the MFS gene family are found linked with GmSAT1 loci in soybean, as well as M. truncatula and many sequenced dicots. GmMFS1.3, a representative from soybean, was cloned and characterized. GmMFS1.3 expression was localized to the root stele and the inner cortex of nodules. Further, expression of GmMFS1.3 in yeast induced the uptake of methylammonium. Interestingly, GmMFS1.5 was found to be downregulated in GmSAT1 RNAi nodules. The link between GmSAT1 and the MFS transporters in planta will be the focus of future experiments. A novel receptor-like kinase protein was also characterized from soybean nodules. GmCaMK1 was identified in a protein interaction screen using conserved calmodulin as bait. The calmodulin-binding domain overlaps the GmCaMK1 kinase subdomain XI, however it was found that… Advisors/Committee Members: Kaiser, Brent Norman (advisor), School of Agriculture, Food and Wine (school).

Subjects/Keywords: legume; nitrogen fixation; nodule; transcription factor; transporter

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

APA (6^th Edition):

Chiasson, D. M. (2012). Characterization of GmSAT1 and related proteins from legume nodules. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/80104

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):

Chiasson, David Michael. “Characterization of GmSAT1 and related proteins from legume nodules.” 2012. Thesis, University of Adelaide. Accessed September 18, 2019. http://hdl.handle.net/2440/80104.

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

MLA Handbook (7^th Edition):

Chiasson, David Michael. “Characterization of GmSAT1 and related proteins from legume nodules.” 2012. Web. 18 Sep 2019.

Vancouver:

Chiasson DM. Characterization of GmSAT1 and related proteins from legume nodules. [Internet] [Thesis]. University of Adelaide; 2012. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/2440/80104.

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

Council of Science Editors:

Chiasson DM. Characterization of GmSAT1 and related proteins from legume nodules. [Thesis]. University of Adelaide; 2012. Available from: http://hdl.handle.net/2440/80104

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

University of Adelaide

27. Harris, John Creighton. The role of homeodomain-leucine zipper class I transcription factors in the drought response of wheat.

Degree: 2014, University of Adelaide

URL: http://hdl.handle.net/2440/92045

► Traditional breeding for increased yield under water limiting conditions has been hampered by the complexity of the polygenic plant response and the unpredictability of seasonal… (more)

▼ Traditional breeding for increased yield under water limiting conditions has been hampered by the complexity of the polygenic plant response and the unpredictability of seasonal conditions. This has made it difficult to observe the hereditability of a selected trait. Given these difficulties, breeders have been selecting for yield improvement under water deficit by phenotyping methods rather than by genetic association. Hence, an improvement in yield under water limited conditions is often seen under well-watered conditions and so selection has been for yield increase and not “drought tolerance”. Understanding the plant drought response at the molecular level will aid efforts to increase yield under water limited conditions. An approach to reveal the molecular mechanisms of the plant drought response is to study the role of transcription factors which act as global regulators of gene expression. Members of the homeodomain-leucine zipper class I (HD-Zip I) γ-clade TFs show drought and ABA inducible expression and are believed to act in plant adaptation to abiotic stress. It was therefore considered that, HD-Zip I γ-clade TFs pose good candidates for studying a part of the drought response mechanism. To this end three wheat γ-clade HD-Zip I TFs were isolated, TaHDZipI-3, TaHDZipI-4 and TaHDZipI-5, and studies of their function were performed. Studies were performed to confirm the relationship of the isolated γ-clade TFs with homologues. The three wheat γ-clade HD-Zip I TFs show patterns of induction by abiotic stresses and interaction with the putative HD-Zip I cis element that suggests differences exist between dicot and monocot homologues. Transgenic wheat and barley plants constitutively over-expressing wheat γ-clade HD-Zip I TFs have been produced. Investigations were made to analyse any role of HD Zip I TFs in stem development and the regulation of lignin deposition in anther development. Wheat constitutively over-expressing TaHDZipI-4 displayed no differences in stem length contrary to other reported observations made on γ-clade HD-Zip I TFs. However, a stem developmental series showed that there is an increase in endogenous expression correlating with internode maturity and a developmentally specific spike in expression in the entire stem. Analysis of lignin deposition was performed using barley expressing TaHDZipI-3, TaHDZipI-4, and ZmHDZip1 under the 35S promoter. Results suggest that no differences in anther lignin deposition have occurred. Transgenic wheat was grown under two different drought scenarios, sustained water deficit or cyclic drought, to assess the effect of γ-clade HD-Zip I TFs under the regulation of a strong drought inducible promoter. No improvement in yield under water deficit was observed. It appears that wheat HD-Zip I γ-clade TFs have diversified from known dicot homologues in their expression characters and role as transcription factors. Hence, the mechanisms of action of these TFs in monocots may be different from that in Arabidopsis. Despite the efforts and analyses presented here as… Advisors/Committee Members: Eliby, Serik (advisor), School of Agriculture, Food and Wine (school).

Subjects/Keywords: abiotic stress; HD-Zip; transcription factor; wheat

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

APA (6^th Edition):

Harris, J. C. (2014). The role of homeodomain-leucine zipper class I transcription factors in the drought response of wheat. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/92045

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):

Harris, John Creighton. “The role of homeodomain-leucine zipper class I transcription factors in the drought response of wheat.” 2014. Thesis, University of Adelaide. Accessed September 18, 2019. http://hdl.handle.net/2440/92045.

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

MLA Handbook (7^th Edition):

Harris, John Creighton. “The role of homeodomain-leucine zipper class I transcription factors in the drought response of wheat.” 2014. Web. 18 Sep 2019.

Vancouver:

Harris JC. The role of homeodomain-leucine zipper class I transcription factors in the drought response of wheat. [Internet] [Thesis]. University of Adelaide; 2014. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/2440/92045.

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

Council of Science Editors:

Harris JC. The role of homeodomain-leucine zipper class I transcription factors in the drought response of wheat. [Thesis]. University of Adelaide; 2014. Available from: http://hdl.handle.net/2440/92045

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

University of Adelaide

28. Mazurkiewicz, Danielle. Characterisation of a novel family of eukaryotic ammonium transport proteins.

Degree: 2014, University of Adelaide

URL: http://hdl.handle.net/2440/92343

► Species from the family Leguminosae are able to survive in nitrogen (N) limiting conditions via a symbiotic relationship with soil-borne N₂-fixing bacteria collectively known as… (more)

▼ Species from the family Leguminosae are able to survive in nitrogen (N) limiting conditions via a symbiotic relationship with soil-borne N₂-fixing bacteria collectively known as Rhizobium. The symbiosis results in the development of the root nodule where invaded bacteria (bacteroids) reside within a plant derived membrane vesicle(symbiosome) located within the cytoplasm of infected nodule cortical cells. Bacterial nitrogenase activity converts atmospheric N₂ to ammonium (NH₄⁺), which is delivered to the plant in exchange for photosynthetically derived carbon for bacterial consumption. The mechanism regulating the transfer of NH₄⁺ to the plant across the symbiosome membrane is currently unknown. GmSAT1 (Glycine max Symbiotic Ammonium Transporter 1), a symbiosome membrane bound basic Helix-Loop-Helix (bHLH) transcription factor has previously been identified in soybean by its ability to enhance NH₄⁺ and MA transport in the NH₄⁺ transport deficient yeast strain 26972c (Kaiser et al., 1998). In this study, we have revisited microarray analysis of 26972c cells expressing GmSAT1 to identify differentially regulated yeast genes with putative roles in NH₄⁺/MA transport. Central to this study is the identification of ScAMF1 (Saccharomyces cerevisiae Ammonium Major Facilitator 1), a previously uncharacterised major facilitator transport protein, which was upregulated 56.5-fold in response to GmSAT1 activity. ScAMF1 and GmAMF1;3, a representative AMF1 from soybean, were functionally analysed with respect to putative NH₄⁺ transport using a combination of yeast and Xenopus laevis oocyte expression systems. Both AMF1 proteins enhanced ¹⁴C-MA uptake and established a related sensitivity phenotype in 26972c and 31019b, an alternative NH₄⁺ transport mutant strain. In the presence of low (1 mM) NH₄⁺, ScAMF1 overexpression partially rescued growth of 26972c but was unable to establish a similar phenotype in 31019b. The role of ScAMF1 in NH₄⁺ transport was less clear. However, this study reaffirmed endogenous high-affinity NH₄⁺ transporters called MEPs (Methylammonium Permeases) play an important role in GmSAT1-mediated NH₄⁺ complementation. Heterologous expression in X. laevis oocytes suggest that ScAMF1 and GmAMF1;3 behave as non-selective cation channels capable of low-affinity NH₄⁺ transport, revealing NH₄⁺ current activation by Pi or a product of P-metabolism and potential Ca²⁺-gating. This study also provided a preliminary electrophysiological profile of the Arabidopsis AMF1 homologs with respect to NH₄⁺ transport for future studies to explore in detail. Advisors/Committee Members: Kaiser, Brent Norman (advisor), Okamoto, Mamoru (advisor), Tyerman, Stephen Donald (advisor), School of Agriculture, Food and Wine (school).

Subjects/Keywords: legume; nitrogen fixation; ammonium transporter; transcription factor

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

APA (6^th Edition):

Mazurkiewicz, D. (2014). Characterisation of a novel family of eukaryotic ammonium transport proteins. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/92343

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):

Mazurkiewicz, Danielle. “Characterisation of a novel family of eukaryotic ammonium transport proteins.” 2014. Thesis, University of Adelaide. Accessed September 18, 2019. http://hdl.handle.net/2440/92343.

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

MLA Handbook (7^th Edition):

Mazurkiewicz, Danielle. “Characterisation of a novel family of eukaryotic ammonium transport proteins.” 2014. Web. 18 Sep 2019.

Vancouver:

Mazurkiewicz D. Characterisation of a novel family of eukaryotic ammonium transport proteins. [Internet] [Thesis]. University of Adelaide; 2014. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/2440/92343.

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

Council of Science Editors:

Mazurkiewicz D. Characterisation of a novel family of eukaryotic ammonium transport proteins. [Thesis]. University of Adelaide; 2014. Available from: http://hdl.handle.net/2440/92343

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

Cornell University

29. Yan, Jiapei. A Novel Regulator Of Copper Homeostasis, Ccit1, And Spl7 Connect Copper Homeostasis With Pollen Fertility, Jasmonic Acid Biosynthesis And Cadmium Resistance In Arabidopsis Thaliana .

Degree: 2016, Cornell University

URL: http://hdl.handle.net/1813/43646

► The transition metal copper (Cu) is among the most important mineral nutrients and is essential for plant growth, development and fertility. However, Cu is toxic… (more)

▼ The transition metal copper (Cu) is among the most important mineral nutrients and is essential for plant growth, development and fertility. However, Cu is toxic if it is accumulated in cells in excess. To maintain Cu homeostasis, plants have evolved transcriptional regulation of genes involved in Cu uptake, trafficking, tissue partitioning and reallocation among Cu requiring enzymes. SPL7 has been shown to play a central role in this transcriptional regulatory network and is the only transcription factor with a documented role in Cu homeostasis. We have found recently that a member of the bHLH family of TFs, that we designated CCIT1, is transcriptionally regulated by Cu availability, is essential for Cu acquisition and is required for plant growth under low Cu condition. Previous transcriptome analyses have identified CCIT1 among the downstream targets of SPL7. However, the ccit1spl7 double mutant exhibited infertility phenotype due to altered flower morphology, substantiallty reduced pollen production and viability. These results suggest that CCIT1 does not simply act downstream of SPL7, and this interactive regulatory pathway is rather more complex. Y1H and RNA-seq studies identified components of this pathway and the hierarchy of interactions which provide essential molecular evidences of the connection between Cu homeostasis, jasmonic acid biosynthesis and male fertility. On the other hand, cadmium (Cd) is a non-essential, toxic metal that causes plant growth retardation, disrupts micronutrient homeostasis and interferes with photosynthesis and redox balance. The components of the molecular machinery mediating the crosstalk between Cd and essential elements, however, are unknown. We have found recently that the central regulator of Cu homeostasis, SPL7, is important for basal Cd tolerance. Here we show that CCIT1 is induced by Cd toxicity. Loss of CCIT1 function results in hypersensitivity to Cd, and compromised Cu accumulation which is essential for basal Cd tolerance. Transcript abundance comparison between wild-type and ccit1 mutant identified two high-affinity Cu transporters among the targets of CCIT1. Together, the results herein expand the understanding of the interaction between the essential heavy metal Cu and the toxic heavy metal Cd, and might provide novel avenues for biofortification strategies to improve mineral nutrition while avoid toxic metal entry into the food crops. Advisors/Committee Members: Harrison,Maria J (committeeMember), Setter,Timothy Lloyd (committeeMember).

Subjects/Keywords: Cu homeostasis; Cd resistance; Transcription factor

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

APA (6^th Edition):

Yan, J. (2016). A Novel Regulator Of Copper Homeostasis, Ccit1, And Spl7 Connect Copper Homeostasis With Pollen Fertility, Jasmonic Acid Biosynthesis And Cadmium Resistance In Arabidopsis Thaliana . (Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/43646

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):

Yan, Jiapei. “A Novel Regulator Of Copper Homeostasis, Ccit1, And Spl7 Connect Copper Homeostasis With Pollen Fertility, Jasmonic Acid Biosynthesis And Cadmium Resistance In Arabidopsis Thaliana .” 2016. Thesis, Cornell University. Accessed September 18, 2019. http://hdl.handle.net/1813/43646.

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

MLA Handbook (7^th Edition):

Yan, Jiapei. “A Novel Regulator Of Copper Homeostasis, Ccit1, And Spl7 Connect Copper Homeostasis With Pollen Fertility, Jasmonic Acid Biosynthesis And Cadmium Resistance In Arabidopsis Thaliana .” 2016. Web. 18 Sep 2019.

Vancouver:

Yan J. A Novel Regulator Of Copper Homeostasis, Ccit1, And Spl7 Connect Copper Homeostasis With Pollen Fertility, Jasmonic Acid Biosynthesis And Cadmium Resistance In Arabidopsis Thaliana . [Internet] [Thesis]. Cornell University; 2016. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/1813/43646.

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

Council of Science Editors:

Yan J. A Novel Regulator Of Copper Homeostasis, Ccit1, And Spl7 Connect Copper Homeostasis With Pollen Fertility, Jasmonic Acid Biosynthesis And Cadmium Resistance In Arabidopsis Thaliana . [Thesis]. Cornell University; 2016. Available from: http://hdl.handle.net/1813/43646

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

University of Ottawa

30. Ryan, Tammy. Molecular Mechanisms of Myogenesis in Stem Cells .

Degree: 2011, University of Ottawa

URL: http://hdl.handle.net/10393/20150

► Embryonic stem cells (ESCs) represent a promising source of cells for cell replacement therapy in the context of muscle diseases; however, before ESC-based cell therapy… (more)

▼ Embryonic stem cells (ESCs) represent a promising source of cells for cell replacement therapy in the context of muscle diseases; however, before ESC-based cell therapy can be translated to the clinic, we must learn to modulate cell-fate decisions in order to maximize the yield of myocytes from this systems. In order to gain a better understanding of the myogenic cell fate, we sought to define the molecular mechanisms underlying the specification and differentiation of ESCs into cardiac and skeletal muscle. More specifically, the central hypothesis of the thesis is that myogenic signalling cascades modulate cell fate via regulation of transcription factors. Retinoic acid (RA) is known to promote skeletal myogenesis, however the molecular basis for this remains unknown. We showed that RA expands the premyogenic progenitor population in mouse stem cells by directly activating pro-myogenic transcription factors such as Pax3 and Meox1. RA also acts indirectly by activating the pro-myogenic Wnt signalling cascade while simultaneously inhibiting the anti-myogenic influence of BMP4. This ultimately resulted in a significant enhancement of skeletal myogenesis. Furthermore, we showed that this effect was conserved in human embryonic stem cells, with implications for directed differentiation and cell therapy. The regulation of cardiomyogenesis by the Wnt pathway was also investigated. We identified a novel interaction between the cardiomyogenic transcription factor Nkx2.5 and the myosin phosphatase (MP) enzyme complex. Interaction with MP resulted in exclusion of Nkx2.5 from the nucleus and inhibition of its transcriptional activity. Finally, we showed that this interaction was modulated by phosphorylation of the Mypt1 subunit of MP by ROCK, downstream of Wnt3a. Treatment of differentiating mouse ESCs with Wnt3a resulted in exclusion of Nkx2.5 from the nucleus and a subsequent failure to undergo terminal differentiation into cardiomyocytes. This likely represents part of the molecular basis for Wnt-mediated inhibition of terminal differentiation of cardiomyocytes. Taken together, our results provide novel insight into the relationship between myogenic signalling cascades and downstream transcription factors and into how they function together to orchestrate the myogenic cell fate in stem cells.

Subjects/Keywords: embryonic stem cells; myogenesis; transcription factor

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

APA (6^th Edition):

Ryan, T. (2011). Molecular Mechanisms of Myogenesis in Stem Cells . (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/20150

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):

Ryan, Tammy. “Molecular Mechanisms of Myogenesis in Stem Cells .” 2011. Thesis, University of Ottawa. Accessed September 18, 2019. http://hdl.handle.net/10393/20150.

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

MLA Handbook (7^th Edition):

Ryan, Tammy. “Molecular Mechanisms of Myogenesis in Stem Cells .” 2011. Web. 18 Sep 2019.

Vancouver:

Ryan T. Molecular Mechanisms of Myogenesis in Stem Cells . [Internet] [Thesis]. University of Ottawa; 2011. [cited 2019 Sep 18]. Available from: http://hdl.handle.net/10393/20150.

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

Council of Science Editors:

Ryan T. Molecular Mechanisms of Myogenesis in Stem Cells . [Thesis]. University of Ottawa; 2011. Available from: http://hdl.handle.net/10393/20150

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

Open Access Theses and Dissertations