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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Kyrylkova K. The role of the transcriptional regulatory protein BCL11B in dental and craniofacial development. [Internet] [Doctoral dissertation]. Oregon State University; 2014. [cited 2021 Jan 17]. 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

University of Central Florida

2. Zhang, Xiaolei. Discovery and Optimization of Novel Small-molecular Inhibitors Suppressing Stat3-dependent Tumor Process.

Degree: 2011, University of Central Florida

URL: https://stars.library.ucf.edu/etd/6681

► With the critical role of aberrantly active Signal Transducer and Activator of Transcription (Stat) 3 protein in many human cancers, selective small-molecule inhibitors targeting… (more)

▼ With the critical role of aberrantly active Signal Transducer and Activator of Transcription (Stat) 3 protein in many human cancers, selective small-molecule inhibitors targeting the dimerization event which is required for stat3 activation, would be valuable as therapeutic agents. And the inhibitors will be useful chemical probes to clarify the complex biological functions of Stat3. By computational and structural analyses of the interaction between Stat3 and the lead dimerization disruptor, S3I-201, we have designed a diverse set of analogs. One of the most active analogs, S3I-201.1066 is derived to contain a cyclo-hexyl benzyl moiety on the amide nitrogen, which increases the binding to the Stat3 SH2 domain. Evidence is presented from in vitro biochemical and biophysical studies that S3I-201.1066 directly interacts with Stat3 or the SH2 domain, with an affinity (K[subscript D]) of 2.74 [micrometer], and disrupts the binding of Stat3 to the cognate pTyr-peptide, GpYLPQTV-NH2, with an IC₅₀ of 23 [micrometer]. Moreover, S3I-201.1066 selectively blocks the association of Stat3 with the epidermal growth factor receptor (EGFR), and inhibits Stat3 tyrosine phosphorylation and nuclear translocation in EGF-stimulated mouse fibroblasts. In cancer cells that harbor aberrant Stat3 activity, S3I-201.1066 inhibits constitutive Stat3 DNA-binding and transcriptional activities. By contrast, S3I-201.1066 has no effect on Src activation or the EGFR-mediated activation of the Erk1/2MAPK pathway. S3I-201.1066 selectively suppresses the viability, survival, and malignant transformation of the human breast and pancreatic cancer lines and the v-Src-transformed mouse fibroblasts harboring persistently active Stat3. Treatment with S3I-201.1066 on malignant cells harboring aberrantly active Stat3 down regulated the expression of c-Myc, Bcl-xL, Survivin, matrix metalloproteinase 9, and VEGF, which are known Stat3-regulated genes important in diverse tumor processes. The in vivo administration of S3I-201.1066 induced significant anti-tumor response in mouse models of human breast cancer, which correlates with the inhibition of constitutively active Stat3 and the suppression of known Stat3-regulated genes. Further computer-aided lead optimization derives higher-affinity (K[subscript D], 504 nM), orally bioavailable Stat3 SH2 domain-binding ligand, BP-1-102 as a structural analog of S3I-201.1066. The most significant modification is the pentafluorobenzene sulfonamide component of BP-1-102, which permits accessibility of a third sub-pocket of the Stat3 SH2 domain surface. BP-1-102-mediated inhibition of aberrantly-active Stat3 in human pancreatic cancer, Panc-1, breast cancer, MDA-MB-231, and prostate (DU145) cancer cells and in the mouse transformed fibroblasts harboring aberrantly-active Stat3. It also disrupts Stat3-NF[kappa]B cross-talk and suppresses the release of granulocyte colony-stimulating factor, soluble intercellular adhesion molecule-1, macrophage-migration-inhibitory factor/glycosylation-inhibiting factor,… Advisors/Committee Members: Turkson, James.

Subjects/Keywords: Transcription factors; STAT3 Transcription Factor; Medical Sciences

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APA (6^th Edition):

Zhang, X. (2011). Discovery and Optimization of Novel Small-molecular Inhibitors Suppressing Stat3-dependent Tumor Process. (Doctoral Dissertation). University of Central Florida. Retrieved from https://stars.library.ucf.edu/etd/6681

Chicago Manual of Style (16^th Edition):

Zhang, Xiaolei. “Discovery and Optimization of Novel Small-molecular Inhibitors Suppressing Stat3-dependent Tumor Process.” 2011. Doctoral Dissertation, University of Central Florida. Accessed January 17, 2021. https://stars.library.ucf.edu/etd/6681.

MLA Handbook (7^th Edition):

Zhang, Xiaolei. “Discovery and Optimization of Novel Small-molecular Inhibitors Suppressing Stat3-dependent Tumor Process.” 2011. Web. 17 Jan 2021.

Vancouver:

Zhang X. Discovery and Optimization of Novel Small-molecular Inhibitors Suppressing Stat3-dependent Tumor Process. [Internet] [Doctoral dissertation]. University of Central Florida; 2011. [cited 2021 Jan 17]. Available from: https://stars.library.ucf.edu/etd/6681.

Council of Science Editors:

Zhang X. Discovery and Optimization of Novel Small-molecular Inhibitors Suppressing Stat3-dependent Tumor Process. [Doctoral Dissertation]. University of Central Florida; 2011. Available from: https://stars.library.ucf.edu/etd/6681

University of Manchester

3. 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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Webber A. Transcriptional co-regulation of microRNAs and protein-coding genes. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2021 Jan 17]. 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

North Carolina State University

4. 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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Wang T. Identifying Transcription Factor Targets and Studying Human Complex Disease Genes. [Internet] [Doctoral dissertation]. North Carolina State University; 2009. [cited 2021 Jan 17]. 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

5. 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 (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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Yin H. Expression and developmental requirement for transcription factor Sp2. [Internet] [Doctoral dissertation]. North Carolina State University; 2009. [cited 2021 Jan 17]. 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

6. 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 January 17, 2021. 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. 17 Jan 2021.

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 2021 Jan 17]. 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

University of Toronto

7. Cox, Michael John. The Design and Use of a High throughput Microscopy Screen to Monitor Transcription Factor Localization in Saccharomyces cerevisiae.

Degree: PhD, 2014, University of Toronto

URL: http://hdl.handle.net/1807/74802

►

Cellular signalling networks control gene expression by modulating the activities of transcription factors through regulatory mechanisms that affect their transactivation or transrepression potential, DNA-binding affinity,… (more)

▼

Cellular signalling networks control gene expression by modulating the activities of transcription factors through regulatory mechanisms that affect their transactivation or transrepression potential, DNA-binding affinity, localization, or abundance. This regulation often requires the site-specific phosphorylation of the transcription factor by a kinase. I have developed a high throughput microscopy screen and used it to monitor the nucleo-cytoplasmic distribution and abundance of 122 different GFP-tagged transcription factors in 84 different Saccharomyces cerevisae kinase mutant backgrounds and in wild type cells after exposure to eight different environmental stress conditions that modulate kinase signalling pathways. Thirty one GFP-tagged transcription factors exhibited changes in localization or abundance, mostly in response to an acute exposure to environmental stress rather than to the chronic loss of a non-essential kinase. These screens revealed that the Yero88c transcriptional repressor, which was not previously known to undergo changes in localization, translocates from the cytoplasm to the nucleus in response to multiple environmental stresses; its paralog, Yblo54w, displayed similar behavior. Yero88c and Yblo54w are known to repress the transcription of ribosome biogenesis (Ribi) genes in response to environmental stress and the downregulation of the TORC1 or PKA signalling pathways (Lippman Broach, 2009). I show that the nuclear accumulation of Yero88c and Yblo54w is inhibited by TORC1 and PKA signalling. Further analysis implicates the kinase Sch9 and the Tap42-associated phosphatase complexes in the regulation of Yero88c localization by TORC1. Serine-to-alanine substitutions at six putative PKA/Sch9 consensus phosphoacceptor sites in its sequence causes Yero88c to localize to the nucleus constitutively. These data suggest that under optimal growth conditions PKA and Sch9 phosphorylate Yero88c causing it to localize to the cytosol, whereas the activation of TORC1-regulated phosphatases in response to stress induces the dephosphorylation and nuclear accumulation of Yero88c resulting in the repression of Ribi genes and the attenuation of cell growth.

2016-11-30 00:00:00

Advisors/Committee Members: Andrews, Brenda J, Molecular and Medical Genetics.

Subjects/Keywords: cerevisiae; kinase; transcription factor; 0379

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APA (6^th Edition):

Cox, M. J. (2014). The Design and Use of a High throughput Microscopy Screen to Monitor Transcription Factor Localization in Saccharomyces cerevisiae. (Doctoral Dissertation). University of Toronto. Retrieved from http://hdl.handle.net/1807/74802

Chicago Manual of Style (16^th Edition):

Cox, Michael John. “The Design and Use of a High throughput Microscopy Screen to Monitor Transcription Factor Localization in Saccharomyces cerevisiae.” 2014. Doctoral Dissertation, University of Toronto. Accessed January 17, 2021. http://hdl.handle.net/1807/74802.

MLA Handbook (7^th Edition):

Cox, Michael John. “The Design and Use of a High throughput Microscopy Screen to Monitor Transcription Factor Localization in Saccharomyces cerevisiae.” 2014. Web. 17 Jan 2021.

Vancouver:

Cox MJ. The Design and Use of a High throughput Microscopy Screen to Monitor Transcription Factor Localization in Saccharomyces cerevisiae. [Internet] [Doctoral dissertation]. University of Toronto; 2014. [cited 2021 Jan 17]. Available from: http://hdl.handle.net/1807/74802.

Council of Science Editors:

Cox MJ. The Design and Use of a High throughput Microscopy Screen to Monitor Transcription Factor Localization in Saccharomyces cerevisiae. [Doctoral Dissertation]. University of Toronto; 2014. Available from: http://hdl.handle.net/1807/74802

University of Southern California

8. 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/3001

► 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/3001

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 January 17, 2021. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/458438/rec/3001.

MLA Handbook (7^th Edition):

Skylar, Anna Maria. “Genetic control of meristematic proliferation in Arabidopsis thaliana.” 2014. Web. 17 Jan 2021.

Vancouver:

Skylar AM. Genetic control of meristematic proliferation in Arabidopsis thaliana. [Internet] [Doctoral dissertation]. University of Southern California; 2014. [cited 2021 Jan 17]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/458438/rec/3001.

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/3001

Queens University

9. 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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Ferrant HA. Homo and hetero-dimerization studies of two Zn(II)2Cys6 transcription factors in fission yeast . [Internet] [Thesis]. Queens University; 2012. [cited 2021 Jan 17]. 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

10. 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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Schneider A. Investigating the Role of the VAL1 Transcription Factor in Arabidopsis thaliana Embryo Development. [Internet] [Doctoral dissertation]. Virginia Tech; 2015. [cited 2021 Jan 17]. 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 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 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51325/SOURCE02?view=true

► 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 (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 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51325/SOURCE02?view=true

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 January 17, 2021. http://handle.unsw.edu.au/1959.4/60070 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51325/SOURCE02?view=true.

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. 17 Jan 2021.

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 2021 Jan 17]. Available from: http://handle.unsw.edu.au/1959.4/60070 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51325/SOURCE02?view=true.

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 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51325/SOURCE02?view=true

University of Pennsylvania

12. Fernandez Garcia, Meilin Mary. Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors.

Degree: 2019, University of Pennsylvania

URL: https://repository.upenn.edu/edissertations/3624

► Transcription factors (TFs) forage the genome to instruct cell plasticity, identity, and differentiation. These developmental processes are elicited through TF engagement with chromatin. Yet, how… (more)

▼ Transcription factors (TFs) forage the genome to instruct cell plasticity, identity, and differentiation. These developmental processes are elicited through TF engagement with chromatin. Yet, how and which TFs can engage with chromatin and thus, nucleosomes, remains largely unexplored. Pioneer TFs are TF that display a high affinity for nucleosomes. Extensive genetic and biochemical studies on the pioneer TF FOXA, a driver of fibroblast to hepatocyte reprogramming, revealed its nucleosome binding ability and chromatin targeting lead to chromatin accessibility and subsequent cooperative binding of TFs. Similarly, a number of reprogramming TFs have been suggested to have pioneering activity due to their ability to target compact chromatin and increase accessibility and enhancer formation in vivo. But whether these factors directly interact with nucleosomes remains to be assessed. Here we test the nucleosome binding ability of the cell reprogramming TFs, Oct4, Sox2, Klf4 and cMyc, that are required for the generation of induced pluripotent stem cells. In addition, we also test neuronal and macrophage reprogramming TFs. Our study shows that reprogramming TFs bind nucleosomes with a range of nucleosome binding affinities, indicating that although specific cocktails of TFs are required for reprogramming, mechanistically these TFs show differential nucleosome interacting behaviors. These results allowed us to assess differential features between TFs nucleosome binding ability and to correlate their binding with reprogramming potential. To determine how general is nucleosome binding we extended our analysis to screen 593 of the 2,000 predicted human TFs in the genome for potential nucleosome binding and validated their binding in solution. Based on 3D structural analysis, we proposed that strong nucleosome binders anchor DNA through short -helixes and have a flexible and adaptable DNA binding domain while weak nucleosome binders use -sheets or unstructured regions and have a higher rigidity within their DNA binding domain. Through the experiments presented in this dissertation we present the first study revealing the shared structural features contributing to nucleosome binding potential of pioneer TFs and thus allow for predication of novel pioneer TFs with cell reprogramming potential.

Subjects/Keywords: Pioneer Transcription Factor; Biochemistry; Biophysics

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APA (6^th Edition):

Fernandez Garcia, M. M. (2019). Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors. (Thesis). University of Pennsylvania. Retrieved from https://repository.upenn.edu/edissertations/3624

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):

Fernandez Garcia, Meilin Mary. “Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors.” 2019. Thesis, University of Pennsylvania. Accessed January 17, 2021. https://repository.upenn.edu/edissertations/3624.

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

MLA Handbook (7^th Edition):

Fernandez Garcia, Meilin Mary. “Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors.” 2019. Web. 17 Jan 2021.

Vancouver:

Fernandez Garcia MM. Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors. [Internet] [Thesis]. University of Pennsylvania; 2019. [cited 2021 Jan 17]. Available from: https://repository.upenn.edu/edissertations/3624.

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

Council of Science Editors:

Fernandez Garcia MM. Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors. [Thesis]. University of Pennsylvania; 2019. Available from: https://repository.upenn.edu/edissertations/3624

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 January 17, 2021. 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. 17 Jan 2021.

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 2021 Jan 17]. 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

14. 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 January 17, 2021. 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. 17 Jan 2021.

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 2021 Jan 17]. 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 Texas Southwestern Medical Center

15. Aloisio, Gina. Pax7 Expression Defines Germline Stem Cells in the Adult Testis.

Degree: 2015, University of Texas Southwestern Medical Center

URL: http://hdl.handle.net/2152.5/6591

►

The file named "ALOISIO-DISSERTATION-2017.pdf" is the primary dissertation file. Four (4) supplemental files are also available and may be viewed individually.

Spermatogenesis is a complex,… (more)

Subjects/Keywords: PAX7 Transcription Factor; Stem Cells; Testis

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APA (6^th Edition):

Aloisio, G. (2015). Pax7 Expression Defines Germline Stem Cells in the Adult Testis. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/6591

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):

Aloisio, Gina. “Pax7 Expression Defines Germline Stem Cells in the Adult Testis.” 2015. Thesis, University of Texas Southwestern Medical Center. Accessed January 17, 2021. http://hdl.handle.net/2152.5/6591.

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

MLA Handbook (7^th Edition):

Aloisio, Gina. “Pax7 Expression Defines Germline Stem Cells in the Adult Testis.” 2015. Web. 17 Jan 2021.

Vancouver:

Aloisio G. Pax7 Expression Defines Germline Stem Cells in the Adult Testis. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2015. [cited 2021 Jan 17]. Available from: http://hdl.handle.net/2152.5/6591.

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

Council of Science Editors:

Aloisio G. Pax7 Expression Defines Germline Stem Cells in the Adult Testis. [Thesis]. University of Texas Southwestern Medical Center; 2015. Available from: http://hdl.handle.net/2152.5/6591

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

Boston University

16. 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 (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 January 17, 2021. http://hdl.handle.net/2144/16744.

MLA Handbook (7^th Edition):

Abraham, Elizabeth June. “Genetic varients leading to atrial fibrillation.” 2016. Web. 17 Jan 2021.

Vancouver:

Abraham EJ. Genetic varients leading to atrial fibrillation. [Internet] [Masters thesis]. Boston University; 2016. [cited 2021 Jan 17]. 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 Toronto

17. Higgs, Gemma Victoria. CREB Induces Structural Changes in LA Neurons making them more Advantageous for Inclusion into the Fear Memory Trace.

Degree: 2012, University of Toronto

URL: http://hdl.handle.net/1807/42888

►

The current study aimed to determine the selective advantage of lateral amygdala (LA) neurons overexpressing the transcription factor CREB that enables their preferential incorporation into… (more)

Subjects/Keywords: Transcription factor; Dendritic spines; Fear memory; 0317

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APA (6^th Edition):

Higgs, G. V. (2012). CREB Induces Structural Changes in LA Neurons making them more Advantageous for Inclusion into the Fear Memory Trace. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/42888

Chicago Manual of Style (16^th Edition):

Higgs, Gemma Victoria. “CREB Induces Structural Changes in LA Neurons making them more Advantageous for Inclusion into the Fear Memory Trace.” 2012. Masters Thesis, University of Toronto. Accessed January 17, 2021. http://hdl.handle.net/1807/42888.

MLA Handbook (7^th Edition):

Higgs, Gemma Victoria. “CREB Induces Structural Changes in LA Neurons making them more Advantageous for Inclusion into the Fear Memory Trace.” 2012. Web. 17 Jan 2021.

Vancouver:

Higgs GV. CREB Induces Structural Changes in LA Neurons making them more Advantageous for Inclusion into the Fear Memory Trace. [Internet] [Masters thesis]. University of Toronto; 2012. [cited 2021 Jan 17]. Available from: http://hdl.handle.net/1807/42888.

Council of Science Editors:

Higgs GV. CREB Induces Structural Changes in LA Neurons making them more Advantageous for Inclusion into the Fear Memory Trace. [Masters Thesis]. University of Toronto; 2012. Available from: http://hdl.handle.net/1807/42888

University of Connecticut

18. Quader, Saad A. Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites.

Degree: MS, Computer Science and Engineering, 2013, University of Connecticut

URL: https://opencommons.uconn.edu/gs_theses/448

► Background: Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites are not well suited to the variability in the lengths… (more)

▼ Background: Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites are not well suited to the variability in the lengths of binding sites. Besides, many methods discard known binding sites while building the model. Moreover, the impact of Information Content (IC) and the positional dependence of nucleotides within an aligned set of TFBSs has not been well researched for modeling variable-length binding sites. In this paper, we propose ML-Consensus, a consensus model for variable-length binding sites which does not exclude any input binding sites. We consider Pairwise Score (PS) as a measure of positional dependence of nucleotides within an alignment of binding sites. We investigate how the prediction accuracy of ML-Consensus is affected by using IC, PS, and any particular binding site alignment strategy. We perform leave-one-out cross-validations on datasets of six species from the TRANSFAC public database, and analyze the results using ROC curves and Wilcoxon matched-pair signed-ranks test. Results: We observed that the incorporation of IC and PS in ML-Consensus results in statistically significant improvement in the prediction accuracy. Moreover, any two positions in the multiple sequence alignment of the binding sites were found to be interdependent only when they the distance between them was below a certain value. Lastly, configurations with state-of-the-art alignment strategies did not perform significantly better than configurations with a naive alignment strategy. Conclusions: There exists a core region within a set of known binding sites, ix and positions in that core region are interdependent. Additionally, it is possible to improve the existing state-of-the-art multiple sequence alignment algorithms by using such information as mentioned above about the core region among the binding sites. Availability: All source codes (C#), results, supporting evidence, supplementary data and figures are available from <a href="http://biogrid.engr.uconn.edu/mlconsensus/">http://biogrid.engr.uconn.edu/mlconsensus/</a> . Advisors/Committee Members: Sanguthevar Rajasekaran, Daniel Schwartz, Chun-Hsi Huang.

Subjects/Keywords: Transcription Factor Binding Sites; DNA motif

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APA (6^th Edition):

Quader, S. A. (2013). Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites. (Masters Thesis). University of Connecticut. Retrieved from https://opencommons.uconn.edu/gs_theses/448

Chicago Manual of Style (16^th Edition):

Quader, Saad A. “Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites.” 2013. Masters Thesis, University of Connecticut. Accessed January 17, 2021. https://opencommons.uconn.edu/gs_theses/448.

MLA Handbook (7^th Edition):

Quader, Saad A. “Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites.” 2013. Web. 17 Jan 2021.

Vancouver:

Quader SA. Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites. [Internet] [Masters thesis]. University of Connecticut; 2013. [cited 2021 Jan 17]. Available from: https://opencommons.uconn.edu/gs_theses/448.

Council of Science Editors:

Quader SA. Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites. [Masters Thesis]. University of Connecticut; 2013. Available from: https://opencommons.uconn.edu/gs_theses/448

University of Adelaide

19. 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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Chiasson DM. Characterization of GmSAT1 and related proteins from legume nodules. [Internet] [Thesis]. University of Adelaide; 2012. [cited 2021 Jan 17]. 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

20. 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 January 17, 2021. 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. 17 Jan 2021.

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 2021 Jan 17]. 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

21. 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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Mazurkiewicz D. Characterisation of a novel family of eukaryotic ammonium transport proteins. [Internet] [Thesis]. University of Adelaide; 2014. [cited 2021 Jan 17]. 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

University of Ottawa

22. 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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Ryan T. Molecular Mechanisms of Myogenesis in Stem Cells . [Internet] [Thesis]. University of Ottawa; 2011. [cited 2021 Jan 17]. 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

University of Newcastle

23. Li, Jun. Identification of regulatory genes controlling cell wall invertase expression in Arabidopsis reproductive organs.

Degree: PhD, 2018, University of Newcastle

URL: http://hdl.handle.net/1959.13/1392706

►

Research Doctorate - Doctor of Philosophy (PhD)

In higher plants, sucrose (Suc) is synthesised in source leaves for translocation through phloem to non-photosynthetic organs (sinks).… (more)

▼

Research Doctorate - Doctor of Philosophy (PhD)

In higher plants, sucrose (Suc) is synthesised in source leaves for translocation through phloem to non-photosynthetic organs (sinks). Upon reaching sink cells, Suc is often hydrolysed by cell wall invertase (CWIN) into glucose (Glc) and fructose (Fru), as building blocks, energy source and signalling molecules for growth and development. Despite the central roles of CWIN in assimilate partitioning, the upstream molecular machineries that control CWIN expression remain largely unknown. This PhD project therefore aims to identify the ‘master’ regulatory genes controlling CWIN expression in reproductive organs using Arabidopsis as a model. We hypothesised that CWIN gene expression is possibly regulated by some transcription factors (TFs) and small RNAs (sRNAs). As the first step, a suite of bioinformatics tools was employed to search for candidate genes controlling the expression of CWIN2 and CWIN4, which are predominantly expressed in Arabidopsis reproductive organs. The analyses identify 18 TF genes and one microRNA (miRNA) as putative regulators of CWIN2 or CWIN4. Among them, MYB21, ARF6, ARF8, AP3 and CRC were confirmed to be regulators for CWIN gene expression based on the finding that their mutants exhibited reduced mRNA level of CWIN2 or CWIN4. One miRNA, miR3932, displayed an inverse expression pattern and an imperfect sequence match with CWIN2, indicating its possible involvement in degrading CWIN2 RNA. Due to time constraint, further studies were focused on examining the roles of candidate TFs in modulating the expression of the CWIN genes. Measurement of GUS signal in the mutants of the confirmed TF genes transformed with ProCWIN2/4:GUS revealed that MYB21, ARF6 and ARF8 mainly control CWIN2 expression in anthers/pollen, whereas MYB21, ARF6, ARF8, AP3 and CRC appear to regulate CWIN4 expression in nectaries and/or petals. Indeed, over-expression of AP3 increased CWIN2 and CWIN4 expression in the inflorescence, Furthermore, increasing the expression of CWIN4 driven by ARF8, promoter partially recovered arf8-3 short silique phenotype. Finally, transient expression of ARF6 and CRC induced CWIN2 and CWIN4 transcript levels, respectively, in Arabidopsis leaf protoplasts. Based on the results obtained, we proposed a model on the molecular network controlling CWIN2 and CWIN4 expression by MYB21, ARF6, ARF8, AP3, CRC and possible hormone pathways. Understanding the regulatory mechanisms controlling CWIN gene expression fills a major knowledge gap in the area. It also provides an opportunity to genetically modify the expression of CWIN2 and/or CWIN4 or related genes in reproductive organs by manipulating their regulatory genes. This approach has the potential to significantly improve the partitioning of assimilates towards plant reproductive organs for…

Advisors/Committee Members: University of Newcastle. Faculty of Science, School of Environmental and Life Sciences.

Subjects/Keywords: cell wall invertase; transcription factor; Arabidopsis

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

APA (6^th Edition):

Li, J. (2018). Identification of regulatory genes controlling cell wall invertase expression in Arabidopsis reproductive organs. (Doctoral Dissertation). University of Newcastle. Retrieved from http://hdl.handle.net/1959.13/1392706

Chicago Manual of Style (16^th Edition):

Li, Jun. “Identification of regulatory genes controlling cell wall invertase expression in Arabidopsis reproductive organs.” 2018. Doctoral Dissertation, University of Newcastle. Accessed January 17, 2021. http://hdl.handle.net/1959.13/1392706.

MLA Handbook (7^th Edition):

Li, Jun. “Identification of regulatory genes controlling cell wall invertase expression in Arabidopsis reproductive organs.” 2018. Web. 17 Jan 2021.

Vancouver:

Li J. Identification of regulatory genes controlling cell wall invertase expression in Arabidopsis reproductive organs. [Internet] [Doctoral dissertation]. University of Newcastle; 2018. [cited 2021 Jan 17]. Available from: http://hdl.handle.net/1959.13/1392706.

Council of Science Editors:

Li J. Identification of regulatory genes controlling cell wall invertase expression in Arabidopsis reproductive organs. [Doctoral Dissertation]. University of Newcastle; 2018. Available from: http://hdl.handle.net/1959.13/1392706

University of Manchester

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

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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Webber A. Transcriptional co-regulation of microRNAs and protein-coding genes. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2021 Jan 17]. 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

George Mason University

25. Rubaharan, Myurajan. Nejire, a CBP/p300 Family Transcription Factor, Regulates Dendritic Development by Modulating the Localization of the Krüppel-like Transcription Factor Dar1 in Drosophila Sensory Neurons .

Degree: 2014, George Mason University

URL: http://hdl.handle.net/1920/9111

► Dendrite morphogenesis represents a critical process in the establishment, maintenance and modulation of neural connectivity that is the basis of a functional nervous system. Dendrites,… (more)

▼ Dendrite morphogenesis represents a critical process in the establishment, maintenance and modulation of neural connectivity that is the basis of a functional nervous system. Dendrites, as the primary sites of synaptic and/or sensory input largely determine the size and nature of the neuronal receptive field. The Drosophila melanogaster peripheral nervous system (PNS) has emerged as an excellent model system for studying molecular mechanisms underlying class specific dendrite development. Dendritic arborization (da) neurons are grouped into four distinct classes (I- IV) based upon increasing orders of dendritic complexity (Grueber et al., 2002). A recent study has identified dar1, a Krüppel-like transcription factor, as an essential regulator involved in controlling dendrite development and growth via microtubule modulation (Ye et al., 2011). Interestingly, at the embryonic stage Dar1 protein exhibits nuclear localization in all da neuron subclasses, however at the third instar larval stage of development, Dar1 exhibits a subcellular shift towards class-specific differential localization. Specifically, Dar1 is primarily nuclear in the morphologically simple class I neurons, in contrast to largely cytoplasmic localization in the highly complex class IV da neurons. This observation led us to investigate putative protein interaction partners of Dar1 that potentially regulate this class specific differential localization, and the result of perturbing this localization. We conducted a pilot RNAi screen of putative Dar1- interacting proteins to investigate their potential mechanistic role(s) in dendrite development and Dar1 differential localization in class IV da neurons. From this pilot screen, we identified the CBP/p300 homolog nejire (nej) as a novel regulator of dendritic development that also modulates Dar1 subcellular localization. We have conducted detailed structure-function studies using domain-specific deletions of nej that have provided further insights into the specific role of different protein domains in mediating distinct aspects of dendritic growth. Furthermore, we have used these domain-specific deletion constructs to elucidate the interaction between Dar1 and Nej. Collectively, these analyses contribute to our understanding of molecular mechanisms of combinatorial transcription factor activity at a class-specific level and how this regulation contributes to specification of distinct neuronal morphologies that underlie the establishment of complex neural networks. Advisors/Committee Members: Cox, Daniel N (advisor).

Subjects/Keywords: dendrites; neuron; Drosophila; transcription factor; Nejire; Dar1

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

APA (6^th Edition):

Rubaharan, M. (2014). Nejire, a CBP/p300 Family Transcription Factor, Regulates Dendritic Development by Modulating the Localization of the Krüppel-like Transcription Factor Dar1 in Drosophila Sensory Neurons . (Thesis). George Mason University. Retrieved from http://hdl.handle.net/1920/9111

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):

Rubaharan, Myurajan. “Nejire, a CBP/p300 Family Transcription Factor, Regulates Dendritic Development by Modulating the Localization of the Krüppel-like Transcription Factor Dar1 in Drosophila Sensory Neurons .” 2014. Thesis, George Mason University. Accessed January 17, 2021. http://hdl.handle.net/1920/9111.

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

MLA Handbook (7^th Edition):

Rubaharan, Myurajan. “Nejire, a CBP/p300 Family Transcription Factor, Regulates Dendritic Development by Modulating the Localization of the Krüppel-like Transcription Factor Dar1 in Drosophila Sensory Neurons .” 2014. Web. 17 Jan 2021.

Vancouver:

Rubaharan M. Nejire, a CBP/p300 Family Transcription Factor, Regulates Dendritic Development by Modulating the Localization of the Krüppel-like Transcription Factor Dar1 in Drosophila Sensory Neurons . [Internet] [Thesis]. George Mason University; 2014. [cited 2021 Jan 17]. Available from: http://hdl.handle.net/1920/9111.

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

Council of Science Editors:

Rubaharan M. Nejire, a CBP/p300 Family Transcription Factor, Regulates Dendritic Development by Modulating the Localization of the Krüppel-like Transcription Factor Dar1 in Drosophila Sensory Neurons . [Thesis]. George Mason University; 2014. Available from: http://hdl.handle.net/1920/9111

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

Boston University

26. Baer, R. Cooper. Discovery, characterization, and ligand specificity engineering of a novel bacterial transcription factor inducible by progesterone.

Degree: PhD, Microbiology, 2020, Boston University

URL: http://hdl.handle.net/2144/41109

► Having evolved longer than any other group of organisms, bacteria have been perfecting mechanisms of sensing their environments for billions of years. Recent advances in… (more)

▼ Having evolved longer than any other group of organisms, bacteria have been perfecting mechanisms of sensing their environments for billions of years. Recent advances in the field of biosensing have enabled miniaturization of existing biosensors, but the number of characterized biosensor elements remains limited. Sensing parts derived from bacteria make promising targets for integration into biosensor devices and could expand the repertoire of easily detectable compounds. Here, RNA sequencing screening was used to identify a novel TetR family 3-ketosteroid inducible transcription factor called SRTF1 (Steroid Responsive Transcription Factor 1) from the Gram-positive soil bacterium Pimelobacter simplex. This is the first transcription factor confirmed to be inducible by these steroids in-vitro. A potential regulon was identified using in-vitro chromatin immunoprecipitation sequencing, revealing a conserved 20 base pair long palindrome within several promoters in a region of the P. simplex genome highly differentially expressed on exposure to steroids. Biolayer interferometry and intrinsic tryptophan fluorescence were used to quantitatively characterize the transcription factor’s DNA binding strength and hormone induction specificity. Circular dichroism study of SRTF1 revealed it is primarily alpha-helical like almost all other TetR family transcription factors. Bases in a core GCCG repeat within the palindrome were identified as important for SRTF1 binding and a disrupted palindrome was generated that greatly increased a quantum-dot based SRTF1 biosensor’s sensitivity for progesterone. As the transcription factor displays cross reactivity to cortisol and aldosterone that is undesirable in a diagnostic device, a fluorescent reporter assay based on the transcription factor was constructed. This reporter assay showed a similar steroid induction profiles as purified SRTF1, and was used to select for mutant SRTF1 variants generated using error-prone polymerase chain reaction with reduced inducibility by these 11-hydroxy steroids. This pipeline for identifying novel transcription factors, characterizing their DNA and ligand binding profiles, and altering them through mutation of DNA and protein sequences could allow for an expanded number of biosensor parts. Advisors/Committee Members: Galagan, James (advisor), Fearns, Rachel (advisor).

Subjects/Keywords: Microbiology; Biosensor; Pimelobacter simplex; Progesterone; Transcription factor

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

APA (6^th Edition):

Baer, R. C. (2020). Discovery, characterization, and ligand specificity engineering of a novel bacterial transcription factor inducible by progesterone. (Doctoral Dissertation). Boston University. Retrieved from http://hdl.handle.net/2144/41109

Chicago Manual of Style (16^th Edition):

Baer, R Cooper. “Discovery, characterization, and ligand specificity engineering of a novel bacterial transcription factor inducible by progesterone.” 2020. Doctoral Dissertation, Boston University. Accessed January 17, 2021. http://hdl.handle.net/2144/41109.

MLA Handbook (7^th Edition):

Baer, R Cooper. “Discovery, characterization, and ligand specificity engineering of a novel bacterial transcription factor inducible by progesterone.” 2020. Web. 17 Jan 2021.

Vancouver:

Baer RC. Discovery, characterization, and ligand specificity engineering of a novel bacterial transcription factor inducible by progesterone. [Internet] [Doctoral dissertation]. Boston University; 2020. [cited 2021 Jan 17]. Available from: http://hdl.handle.net/2144/41109.

Council of Science Editors:

Baer RC. Discovery, characterization, and ligand specificity engineering of a novel bacterial transcription factor inducible by progesterone. [Doctoral Dissertation]. Boston University; 2020. Available from: http://hdl.handle.net/2144/41109

Princeton University

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

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 January 17, 2021. 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. 17 Jan 2021.

Vancouver:

Hannon CE. A Model for a Genome-Wide Molecular Readout of the Bicoid Morphogen Gradient . [Internet] [Doctoral dissertation]. Princeton University; 2017. [cited 2021 Jan 17]. 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

University of Illinois – Urbana-Champaign

28. Jeong, Hyeon Soo. Transcriptiome analysis of a migraine model.

Degree: MS, Animal Sciences, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/98230

► Migraine is a serious episodic headaches affecting more than 15% of the human population with a detrimental influence on the patients’ life and socioeconomic functioning.… (more)

Subjects/Keywords: Migraine; Transcriptome; Hyperalgesia; Neuropeptides; Transcription factor

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

APA (6^th Edition):

Jeong, H. S. (2017). Transcriptiome analysis of a migraine model. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98230

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):

Jeong, Hyeon Soo. “Transcriptiome analysis of a migraine model.” 2017. Thesis, University of Illinois – Urbana-Champaign. Accessed January 17, 2021. http://hdl.handle.net/2142/98230.

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

MLA Handbook (7^th Edition):

Jeong, Hyeon Soo. “Transcriptiome analysis of a migraine model.” 2017. Web. 17 Jan 2021.

Vancouver:

Jeong HS. Transcriptiome analysis of a migraine model. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Jan 17]. Available from: http://hdl.handle.net/2142/98230.

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

Council of Science Editors:

Jeong HS. Transcriptiome analysis of a migraine model. [Thesis]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98230

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

University of Iowa

29. Hsu, Fu-Chiun. Construction of transcriptional regulatory pathways associated with hypoxia in Arabidopsis.

Degree: PhD, Biology, 2011, University of Iowa

URL: https://ir.uiowa.edu/etd/1231

► Transcriptional control plays a major role in regulating hypoxic responses in plants. However, the transcriptional regulatory networks associated with hypoxia remain to be constructed.… (more)

▼ Transcriptional control plays a major role in regulating hypoxic responses in plants. However, the transcriptional regulatory networks associated with hypoxia remain to be constructed. By transcriptomic analysis I show here that a novel systemic transcriptional reprogramming, which is mediated via the interplay of hormones, facilitates the survival of plants under flooding. A feasible strategy for identifying downstream targets of transcription factors (TFs) was developed. The downstream pathways of a hypoxia-responsive TF, WRKY22, were constructed. The results also show that AtERF73/HRE1 (Arabidopsis thaliana Ethylene Response Factor 73/Hypoxia Responsive ERF 1) modulate ethylene-dependent and -independent responses during hypoxia. Transcriptomic analysis of Arabidopsis in both root and shoot tissues during flooding of roots indicates the existence of a systemic communication through transcriptional reprogramming. By functional classification of affected genes, a comprehensive managing program of carbohydrate metabolism was observed. Through transcriptional profiling in ethylene and abscisic acid (ABA) signaling mutants, ein2-5 and abi4-1, an alteration of long-distance hypoxic regulation was uncovered in ein2-5 and abi4-1. Moreover, genes involved in ABA biosynthesis were also found to be differentially regulated between shoots and roots. Many members of the WRKY TF family were highly induced by hypoxia. One of the early-induced WRKYs, WRKY22, which has the highest induced level, was chosen for identifying its downstream targets. Anoxic tolerance was affected in WRKY22 overexpressing (WRKY22-OX) and knock-out (wrky22-ko) lines. Comparison of differential gene expression profiles between the wild-type and WRKY22-OX and between the wild-type and wrky22-ko lines by microarray analysis identified novel hypoxia-responsive genes as WRKY22 targets. Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) and ChIP followed by quantitative PCR (ChIP-qPCR) were utilized to analyze in vivo interactions. To study the role of ethylene during hypoxia, I characterized an AP2/ERF (APETALA2/ethylene response factor) AtERF73/HRE1 that is specifically induced during hypoxia. I showed that the expression of AtERF73/HRE1 can be induced by exogenous 1-aminocyclopropane-1-carboxylic acid (ACC), a precursor of ethylene. Its hypoxic induction was reduced but not completely abolished in ethylene-insensitive mutants and in the presence of inhibitors of ethylene biosynthesis and responses. Increased ethylene sensitivity and exaggerated triple responses were observed in HRE1-RNAi knock-down lines. By comparing expression differences between the wild-type and HRE1-RNAi lines, I found that hypoxic induction of glycolytic and fermentative genes was reduced by the… Advisors/Committee Members: Lin, Jim J.-C. (supervisor).

Subjects/Keywords: Ethylene; Hypoxia; Low Oxygen; Transcription factor; Biology

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

APA (6^th Edition):

Hsu, F. (2011). Construction of transcriptional regulatory pathways associated with hypoxia in Arabidopsis. (Doctoral Dissertation). University of Iowa. Retrieved from https://ir.uiowa.edu/etd/1231

Chicago Manual of Style (16^th Edition):

Hsu, Fu-Chiun. “Construction of transcriptional regulatory pathways associated with hypoxia in Arabidopsis.” 2011. Doctoral Dissertation, University of Iowa. Accessed January 17, 2021. https://ir.uiowa.edu/etd/1231.

MLA Handbook (7^th Edition):

Hsu, Fu-Chiun. “Construction of transcriptional regulatory pathways associated with hypoxia in Arabidopsis.” 2011. Web. 17 Jan 2021.

Vancouver:

Hsu F. Construction of transcriptional regulatory pathways associated with hypoxia in Arabidopsis. [Internet] [Doctoral dissertation]. University of Iowa; 2011. [cited 2021 Jan 17]. Available from: https://ir.uiowa.edu/etd/1231.

Council of Science Editors:

Hsu F. Construction of transcriptional regulatory pathways associated with hypoxia in Arabidopsis. [Doctoral Dissertation]. University of Iowa; 2011. Available from: https://ir.uiowa.edu/etd/1231

Washington University in St. Louis

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

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 January 17, 2021. 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. 17 Jan 2021.

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 2021 Jan 17]. 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

Open Access Theses and Dissertations