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NSYSU
1.
Jian, Shu-fang.
LKB1 binds to APC and modulates Wnt signaling pathway in lung cancer cells.
Degree: Master, Institute of Biomedical Sciences, 2013, NSYSU
URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0204113-120134
► STK11/LKB1, a serine/threonine protein kinase, is a key upstream kinase of adenine monophosphate-activated protein kinase (AMPK), a necessary kinase in the control of cell polarity…
(more)
▼ STK11/LKB1, a serine/threonine protein kinase, is a key upstream kinase of adenine monophosphate-activated protein kinase (AMPK), a necessary kinase in the control of cell polarity and maintains cellular energy homeostasis. Although it has become clear that LKB1 is mutated in a significant number of PeutzâJeghers syndrome (PJS) and sporadic cancers, most frequently in adenocarcinoma of the lung. Little is known about how the LKB1 involves in lung cancer progression process. Here, we employed
Immunoprecipitation-HPLC-Mass Spectrometry (IP-LC-MS) to identify the novel proteins interacting with Lkb1 in lung cancer cells. We found that Lkb1 interacts with Apc, under normal cell conditions, and this physical interaction between Lkb1 and Apc was further confirmed by reverse-
immunoprecipitation assays. Our findings here provide the first evidence that Lkb1 interacts with Apc to suppress WNT pathway, which involves in the regulation of cell proliferation and migration in lung cancer cells, and LKB1 downstream gene analyses lead to the identification of several Wnt regulated genes, CD44, COX-2 and SURVIVIN, whose expression levels are altered in vitro. Altogether, our results indicate that LKB1 regulates Wnt pathway to suppress tumorigenic/metastatic potential of human lung cancer cells.
Advisors/Committee Members: LONG-SEN CHANG (chair), Kuang-Hung Cheng (committee member), Chang-Chun Hsiao (chair).
Subjects/Keywords: lung cancer; immunoprecipitation assays; mutate; proliferation; migration
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APA (6th Edition):
Jian, S. (2013). LKB1 binds to APC and modulates Wnt signaling pathway in lung cancer cells. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0204113-120134
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Jian, Shu-fang. “LKB1 binds to APC and modulates Wnt signaling pathway in lung cancer cells.” 2013. Thesis, NSYSU. Accessed March 04, 2021.
http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0204113-120134.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Jian, Shu-fang. “LKB1 binds to APC and modulates Wnt signaling pathway in lung cancer cells.” 2013. Web. 04 Mar 2021.
Vancouver:
Jian S. LKB1 binds to APC and modulates Wnt signaling pathway in lung cancer cells. [Internet] [Thesis]. NSYSU; 2013. [cited 2021 Mar 04].
Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0204113-120134.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Jian S. LKB1 binds to APC and modulates Wnt signaling pathway in lung cancer cells. [Thesis]. NSYSU; 2013. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0204113-120134
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
2.
Kalantari, Roya.
Building the Human Argonaute 2 Interaction Network.
Degree: 2015, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/1737
► RNA interference (RNAi) is a system that has been largely studied and defined by its ability to affect gene expression and translation in the cytoplasm.…
(more)
▼ RNA interference (RNAi) is a system that has been largely studied and defined by its ability to affect gene expression and translation in the cytoplasm. However, Argonaute (AGO) proteins, which are the major catalytic component of the RNA-induced silencing complex (RISC), have been found to be involved in nuclear roles outside of the canonical RNAi pathway. Within non-mammalian systems such as yeast and plants, AGOs have been shown to be involved in functions such as DNA methylation and heterochromatin formation.
My laboratory has utilized systems involving small RNAs to target nuclear events such as transcription and splicing in human cells. In the case of transcription, we have shown that small RNAs are capable of targeting long noncoding RNAs (lncRNAs) along both the promoter and past the 3’ end of genes in order to control gene expression. We have also demonstrated that targeting of small RNAs to introns and exons of pre-mRNA can robustly alter the splicing pattern. Within these systems, we have found that AGO proteins are recruited by the small RNAs to the nuclear target. However, the protein-protein interactions and mechanisms involved remain unclear.
Identification and understanding of the interactions of AGO proteins in the nucleus is essential for comprehension of the mechanisms by which these proteins act. I have studied AGO2 interactions through
immunoprecipitation and a novel semi-quantitative mass spectrometry technique known as the Normalized Spectral Index Method (SINQ). Stringent screening of mass spectrometry results identified interactions with the TRNC6 proteins, and AGO3. Most cytoplasmic interacting partners were also partners for AGO2 in the nucleus, however interactions with the loading complex was impaired although it is present in nuclei. These data demonstrate that the core RNAi machinery is largely conserved between cytoplasm and nucleus. This work opens new avenues for the utilization of small RNAs in gene regulation both in the laboratory and in the clinic.
Advisors/Committee Members: Mendelson, Carole R., Corey, David R., Liu, Qinghua, Olson, Eric N., Yu, Hongtao.
Subjects/Keywords: Argonaute Proteins; Immunoprecipitation; RNA-Induced Silencing Complex
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Chicago ·
MLA ·
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CSE |
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APA (6th Edition):
Kalantari, R. (2015). Building the Human Argonaute 2 Interaction Network. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/1737
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Kalantari, Roya. “Building the Human Argonaute 2 Interaction Network.” 2015. Thesis, University of Texas Southwestern Medical Center. Accessed March 04, 2021.
http://hdl.handle.net/2152.5/1737.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Kalantari, Roya. “Building the Human Argonaute 2 Interaction Network.” 2015. Web. 04 Mar 2021.
Vancouver:
Kalantari R. Building the Human Argonaute 2 Interaction Network. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2015. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/2152.5/1737.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Kalantari R. Building the Human Argonaute 2 Interaction Network. [Thesis]. University of Texas Southwestern Medical Center; 2015. Available from: http://hdl.handle.net/2152.5/1737
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University
3.
Gibbons, Hunter Ramsdell.
T-Helper Polarization: Regulation by Noncoding RNA and Super-Enhancers.
Degree: PhD, Microbiology and Immunology, 2019, Vanderbilt University
URL: http://hdl.handle.net/1803/14264
► Naïve CD4+ T cells polarize into many varied CD4+ T-helper (TH) cell subsets depending on the cytokine milieu present during T cell receptor stimulation. Each…
(more)
▼ Naïve CD4+ T cells polarize into many varied CD4+ T-helper (TH) cell subsets depending on the cytokine milieu present during T cell receptor stimulation. Each T cell subset produces a unique cytokine profile to defend against varied pathogens. The polarization of each T cell subset is regulated by unique transcription factors and noncoding elements to induce cytokine expression. The research detailed identifies a noncoding RNA, GATA3-AS1, which is necessary for the expression of GATA3 and TH2 cell polarization. Furthermore, we describe the repression of IFN-γ by super-enhancer disruption via bromodomain inhibitor JQ1. Our results lend novel insight into the regulation of hallmark genes by noncoding elements in T-helper cell polarization.
Advisors/Committee Members: Oliver McDonald (committee member), Gregor Neuert (committee member), James W Thomas (committee member), Thomas Aune (committee member), Amy Major (Committee Chair).
Subjects/Keywords: T-Helper; Noncoding RNA; Super-enhancer; cytokine; transcription; Immunoprecipitation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Gibbons, H. R. (2019). T-Helper Polarization: Regulation by Noncoding RNA and Super-Enhancers. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14264
Chicago Manual of Style (16th Edition):
Gibbons, Hunter Ramsdell. “T-Helper Polarization: Regulation by Noncoding RNA and Super-Enhancers.” 2019. Doctoral Dissertation, Vanderbilt University. Accessed March 04, 2021.
http://hdl.handle.net/1803/14264.
MLA Handbook (7th Edition):
Gibbons, Hunter Ramsdell. “T-Helper Polarization: Regulation by Noncoding RNA and Super-Enhancers.” 2019. Web. 04 Mar 2021.
Vancouver:
Gibbons HR. T-Helper Polarization: Regulation by Noncoding RNA and Super-Enhancers. [Internet] [Doctoral dissertation]. Vanderbilt University; 2019. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/1803/14264.
Council of Science Editors:
Gibbons HR. T-Helper Polarization: Regulation by Noncoding RNA and Super-Enhancers. [Doctoral Dissertation]. Vanderbilt University; 2019. Available from: http://hdl.handle.net/1803/14264

Texas A&M University
4.
Wang, Bo.
Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors.
Degree: MS, Chemical Engineering, 2011, Texas A&M University
URL: http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847
► Mesenchymal stem cells are more and more widely used in tissue engineering due to their pluripotency and no relative ethical problems. Traditional characterization techniques to…
(more)
▼ Mesenchymal stem cells are more and more widely used in tissue engineering due to their pluripotency and no relative ethical problems. Traditional characterization techniques to detect mesenchymal stem cell states include flow cytometry, gene expressing profiling and immunohistochemistry. However, these methods can only provide transient and low level information from current RNA or protein levels about mesenchymal stem cells, which may cause problems when predicting the possible downstream lineages they will commit into.
We have developed chromatin
immunoprecipitation (ChIP)-based epigenetic technique to detect mesenchymal stem cell states. For the systems we tested, this epigenetic assessor successfully characterized cell state changes and gave similar results obtained from gene expression profiling or protein expression assay. This epigenetic technique can provide information about mesenchymal stem cells states from a more fundamental chromatin level, which is promising for predicting future lineages from current states.
Advisors/Committee Members: Hahn, Mariah (advisor), Jayaraman, Arul (committee member), Grunlan, Melissa (committee member).
Subjects/Keywords: mesenchymal stem cells; epigenetics; chromatin immunoprecipitation; external stimuli; cell responses
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Wang, B. (2011). Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847
Chicago Manual of Style (16th Edition):
Wang, Bo. “Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors.” 2011. Masters Thesis, Texas A&M University. Accessed March 04, 2021.
http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847.
MLA Handbook (7th Edition):
Wang, Bo. “Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors.” 2011. Web. 04 Mar 2021.
Vancouver:
Wang B. Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors. [Internet] [Masters thesis]. Texas A&M University; 2011. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847.
Council of Science Editors:
Wang B. Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors. [Masters Thesis]. Texas A&M University; 2011. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847

University of Texas Southwestern Medical Center
5.
Nalley, Kip A.
Ubiquitin, the Proteasome, and Dynamics at the Protein/DNA Interface.
Degree: 2006, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/474
► Recently it has been discovered that a mutant species of Gal4, that contains a three amino acid change in a surface loop of the DNA…
(more)
▼ Recently it has been discovered that a mutant species of Gal4, that contains a three amino acid change in a surface loop of the DNA binding domain, does not occupy the GAL 1/10 promoter under Gal4 inducing conditions as measured by Chromatin
Immunoprecipitation (ChIP) assays. However, this protein, Gap71, occupies the promoter similarly to Gal4 under non-inducing (poised) conditions. Additionally this protein was found to be poorly ubiquitylated in vitro under conditions where Gal4 is ubiquitylated. In order to determine the mechanisms involved in the protein destabilization I have examined the properties of the individual mutations that comprise Gap71. These experiments have revealed that serine 22 is a site of phosphorylation of the Gal4 DBD and that lysine 23 is essential for S22 phosphorylation, possibly acting as part of the kinase recognition site. Mutation of either residue blocks Gal4 DBD phosphorylation, its subsequent ubiquitylation and compromises the ability of the activator to bind promoter DNA in vivo. These data represent the first report of an essential phosphorylation event for this paradigmatic transcription factor.
In addition, experiments were done to directly measure the dynamics of the Gal4 /DNA complex. To measure the dynamics I have exploited the system developed by Dr. D. Picard and others using the Gal4 DNA binding domain fused to the estrogen receptor ligand binding domain. Each of these constructs has been shown to be inactive until the addition of estradiol, when they are released and bind the Gal4 UAS. These constructs allow me to temporally control the appearance of a large quantity protein that is able to compete with the endogenous Gal4 for the UAS sites in the genome. Under non-inducing conditions, the results are consistent with a rapidly exchanging complex. However, upon induction, the Gal4-promoter complexes "lock in" and exhibit long half-lives of one hour or more. Furthermore, pharmacological inhibition of proteasome-mediated proteolysis had little or no effect of Gal4-mediated gene expression. These studies show that proteasome-mediated turnover is not a general requirement for transactivator function and, when considered in the context of previous studies, that different transactivator-promoter complexes can have widely different lifetimes.
Advisors/Committee Members: Kodadek, Thomas J..
Subjects/Keywords: Chromatin Immunoprecipitation; Transcription Factors; Ubiquitin
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Nalley, K. A. (2006). Ubiquitin, the Proteasome, and Dynamics at the Protein/DNA Interface. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/474
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Nalley, Kip A. “Ubiquitin, the Proteasome, and Dynamics at the Protein/DNA Interface.” 2006. Thesis, University of Texas Southwestern Medical Center. Accessed March 04, 2021.
http://hdl.handle.net/2152.5/474.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Nalley, Kip A. “Ubiquitin, the Proteasome, and Dynamics at the Protein/DNA Interface.” 2006. Web. 04 Mar 2021.
Vancouver:
Nalley KA. Ubiquitin, the Proteasome, and Dynamics at the Protein/DNA Interface. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2006. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/2152.5/474.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Nalley KA. Ubiquitin, the Proteasome, and Dynamics at the Protein/DNA Interface. [Thesis]. University of Texas Southwestern Medical Center; 2006. Available from: http://hdl.handle.net/2152.5/474
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Wayne State University
6.
Wang, Haihui.
Ribonomic Control During Global Brain Ischemia And Reperfusion.
Degree: PhD, Physiology, 2014, Wayne State University
URL: https://digitalcommons.wayne.edu/oa_dissertations/1059
► Abstract RIBONOMIC CONTROL DURING GLOBAL BRAIN ISCHEMIA AND REPERFUSION by HAIHUI WANG August 2014 Advisor: Donald J. DeGracia, Ph.D. Major: Physiology Degree: Doctor of…
(more)
▼ Abstract
RIBONOMIC CONTROL DURING GLOBAL BRAIN ISCHEMIA AND REPERFUSION
by HAIHUI WANG
August 2014
Advisor: Donald J. DeGracia, Ph.D.
Major: Physiology
Degree: Doctor of Philosophy
The study presented here used "omic" technology to look at the mechanism behind the selective delayed death of hippocampus CA1 neurons after transient global brain ischemia. The main findings are summarized:
1. The main form of ELAV protein family member detected in CA1/CA3 in Hu protein
immunoprecipitation and polysomes was HuB (Rel-N1). HuB is present in control CA3, 8 hr reperfused CA3, and 8 hr reperfused CA1, but absent from control CA1. AUF-1, hnRNP K, hnRNP M were also absent from control CA1 following Hu protein
immunoprecipitation and Western blot, suggesting that HuB bound AUF-1, hnRNP K, hnRNP M in all experimental groups except control CA1.
2. mRNA populations were different between sucrose pad preparation and sucrose gradient preparations of polysomes, although both were enriched with ARE-mRNA. This suggests different RNA binding complexes were isolated by the two methods.
3. Polysomes fractionation on sucrose pad and Hu protein immunoprecipitations using post-mitochondrial supernatants from homogenized brain regions were shown by 316 liquid chromatography mass spectroscopy to be over 75% contaminated by neuron debris, cytoskeleton and internal membrane structures, in spite of showing no
contamination by Western blots of organelle markers. This suggests proteomics should become the accepted standard for validating purity of reactions derived from homogenized tissues.
To summarize the results, I have worked up a consistent method of isolating polysomes from whole animal model, which has less contamination than the sucrose density gradient method. Both results from Hu IP and polysomes experiments show that control CA1 is in a different state compared with control CA3. My results suggest that
the selective vulnerability of CA1 after ischemia reperfusion injury may be due, in part, to the fact that CA1 is "weaker" from the beginning. This finding is significant as it shifts the focus of research from studying the difference of ischemia reperfusion injury to the different initial states of CA1 and CA3 neurons. This study has also reformed our general
idea as revealed by the high resolution of proteomics, which is superior to Western blotting for detecting contamination of samples. It is shown here that contaminationmakes up a large proportion of subcellular fractionations. This result suggests proteomics should be the new standard for quantifying contaminants, particularly in fractions obtained from whole tissues in animal experimental models.
Advisors/Committee Members: Donald J. DeGracia.
Subjects/Keywords: ARE-mRNA; HuB; Hu immunoprecipitation; microarray; polysomes; proteomics; Physiology
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Wang, H. (2014). Ribonomic Control During Global Brain Ischemia And Reperfusion. (Doctoral Dissertation). Wayne State University. Retrieved from https://digitalcommons.wayne.edu/oa_dissertations/1059
Chicago Manual of Style (16th Edition):
Wang, Haihui. “Ribonomic Control During Global Brain Ischemia And Reperfusion.” 2014. Doctoral Dissertation, Wayne State University. Accessed March 04, 2021.
https://digitalcommons.wayne.edu/oa_dissertations/1059.
MLA Handbook (7th Edition):
Wang, Haihui. “Ribonomic Control During Global Brain Ischemia And Reperfusion.” 2014. Web. 04 Mar 2021.
Vancouver:
Wang H. Ribonomic Control During Global Brain Ischemia And Reperfusion. [Internet] [Doctoral dissertation]. Wayne State University; 2014. [cited 2021 Mar 04].
Available from: https://digitalcommons.wayne.edu/oa_dissertations/1059.
Council of Science Editors:
Wang H. Ribonomic Control During Global Brain Ischemia And Reperfusion. [Doctoral Dissertation]. Wayne State University; 2014. Available from: https://digitalcommons.wayne.edu/oa_dissertations/1059
7.
Brazel, Ailbhe Jane.
A genetic and epigenetic editing approach to characterise the nature and function of bivalent histone modifications.
Degree: PhD, 2018, University of Edinburgh
URL: http://hdl.handle.net/1842/29603
► In eukaryotes, DNA is wrapped around a group of proteins termed histones that are required to precisely control gene expression during development. The amino acids…
(more)
▼ In eukaryotes, DNA is wrapped around a group of proteins termed histones that are required to precisely control gene expression during development. The amino acids of both the globular domains and unstructured tails of these histones can be modified by chemical moieties, such as methylation, acetylation and ubiquitination. The ‘histone code’ hypothesis proposes that specific combinations of these and other histone modifications contain transcriptional information, which guides the cell machinery to activate or repress gene expression in individual cell types. Chromatin immunoprecipitation (ChIP) experiments using undifferentiated stem cell populations have identified the genomic co-localisation of histone modifications reported to have opposing effects on transcription, which is known as bivalency. The human α-globin promoter, a well-established model for the study of transcriptional regulation, is bivalent in embryonic stem (ES) cells and this bivalency is resolved once the ES cells terminally differentiate (i.e. only activating or repressing marks remain). In a humanised mouse model, the deletion of a bone fide enhancer within the human α-globin locus results in heterogeneous expression patterns in primary erythroid cells. Notably, this correlates with an unresolved bivalent state at this promoter in terminally differentiated cells. Using this mouse model it is not feasible to ascertain whether the transcriptional heterogeneity observed in the cells lacking an α-globin enhancer is reflective of epigenetic heterogeneity (i.e. a mixed population of cells) rather than co-localisation of bivalent histone modifications within the same cells. Furthermore, the functional contribution of bivalency to development has yet to be described. To address these difficulties, I aimed to generate a fluorescent reporter system for human α-globin to facilitate the separation of transcriptionally heterogeneous erythroid cells. This model will provide material for ChIP studies on transcriptionally active and inactive populations to determine whether the epigenetic bivalency is reflective of a mixed cell population or true bivalency. In addition, I aimed to produce epigenetic editing tools to target bivalent promoters, which in combination with in vitro differentiation assays would provide an interesting framework to test the function of bivalency during development. In this study, I extensively tested gene-editing strategies for generating a fluorescent reporter knock-in in humanised mouse ES cells. I validated the suitability of humanised mouse ES cell lines for gene targeting studies and optimised a robust in vitro differentiation protocol for studying erythropoiesis. I utilised both recombineering and CRISPR/Cas9 gene editing tools in tandem with PiggyBac transposon technology, to knock-in the reporter gene. I made significant steps in gene targeting and successfully inserted the reporter downstream of the α-globin gene. I also generated a cloning system to express site-specific DNA-binding domains (TALEs) fused to epigenetic…
Subjects/Keywords: 572; histones; bivalent; a-globin; chromatin immunoprecipitation; ChIP studies; gene editing
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Brazel, A. J. (2018). A genetic and epigenetic editing approach to characterise the nature and function of bivalent histone modifications. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/29603
Chicago Manual of Style (16th Edition):
Brazel, Ailbhe Jane. “A genetic and epigenetic editing approach to characterise the nature and function of bivalent histone modifications.” 2018. Doctoral Dissertation, University of Edinburgh. Accessed March 04, 2021.
http://hdl.handle.net/1842/29603.
MLA Handbook (7th Edition):
Brazel, Ailbhe Jane. “A genetic and epigenetic editing approach to characterise the nature and function of bivalent histone modifications.” 2018. Web. 04 Mar 2021.
Vancouver:
Brazel AJ. A genetic and epigenetic editing approach to characterise the nature and function of bivalent histone modifications. [Internet] [Doctoral dissertation]. University of Edinburgh; 2018. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/1842/29603.
Council of Science Editors:
Brazel AJ. A genetic and epigenetic editing approach to characterise the nature and function of bivalent histone modifications. [Doctoral Dissertation]. University of Edinburgh; 2018. Available from: http://hdl.handle.net/1842/29603

University of Toronto
8.
Strauss, Maximilian Walter Ernst.
Identification of Protein Interactors of a Pathological TDP-43 C-Terminal Fragment Using Quantitative Mass Spectrometry.
Degree: 2019, University of Toronto
URL: http://hdl.handle.net/1807/98400
► Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons (MN) in the brain and spinal cord. ALS is pathologically classified by cytoplasmic inclusions…
(more)
▼ Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons (MN) in the brain and spinal cord. ALS is pathologically classified by cytoplasmic inclusions of the normally nuclear TAR-DNA binding protein 43 kDa (TDP-43) in patient MNs. TDP-43 a DNA/RNA binding protein that is recruited to stress granules (SG) to sequester mRNA non-essential to survival. We have discovered a splice variant of TDP-43 with a mass of 35 kDa (TDP-35) that is toxic to MNs and is recruited to SGs upon expression in cultured cells. Here, I used affinity purification mass spectrometry (AP-MS) method to identify the protein interactors of TDP-35 in SGs. The failure of BioID fusion tags to replicate our TDP-35 SGs led me to confirm the validity of our EGFP tagged TDP-35 behaviour. As well, the AP-MS protocol I developed serves to guide future investigation into TDP-35 SGs and identified tubulin subunits as potential TDP-35 interactors.
M.Sc.
Advisors/Committee Members: Robertson, Janice, Laboratory Medicine and Pathobiology.
Subjects/Keywords: ALS; HEK293T; Immunoprecipitation; Mass Spectrometry; TDP-35; TDP-43; 0571
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Strauss, M. W. E. (2019). Identification of Protein Interactors of a Pathological TDP-43 C-Terminal Fragment Using Quantitative Mass Spectrometry. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/98400
Chicago Manual of Style (16th Edition):
Strauss, Maximilian Walter Ernst. “Identification of Protein Interactors of a Pathological TDP-43 C-Terminal Fragment Using Quantitative Mass Spectrometry.” 2019. Masters Thesis, University of Toronto. Accessed March 04, 2021.
http://hdl.handle.net/1807/98400.
MLA Handbook (7th Edition):
Strauss, Maximilian Walter Ernst. “Identification of Protein Interactors of a Pathological TDP-43 C-Terminal Fragment Using Quantitative Mass Spectrometry.” 2019. Web. 04 Mar 2021.
Vancouver:
Strauss MWE. Identification of Protein Interactors of a Pathological TDP-43 C-Terminal Fragment Using Quantitative Mass Spectrometry. [Internet] [Masters thesis]. University of Toronto; 2019. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/1807/98400.
Council of Science Editors:
Strauss MWE. Identification of Protein Interactors of a Pathological TDP-43 C-Terminal Fragment Using Quantitative Mass Spectrometry. [Masters Thesis]. University of Toronto; 2019. Available from: http://hdl.handle.net/1807/98400

Eastern Michigan University
9.
McDonough, Kelli.
Reproducibility and reliability of chromatin immunoprecipitation in clinical research.
Degree: Health Sciences, 2016, Eastern Michigan University
URL: https://commons.emich.edu/theses/682
► Association between histones and DNA is crucial for many cellular functions such as gene transcription and epigenetic silencing. Changes to chromatin structure influence gene…
(more)
▼ Association between histones and DNA is crucial for many cellular functions such as gene transcription and epigenetic silencing. Changes to chromatin structure influence gene expression via histone modifications. Chromatin
immunoprecipitation (ChIP) is an experimental technique used to investigate the interactions between histones and DNA. ChIP determines the specific location in the genome that histone modifications are associated with, indicating the target of the histone modifiers. Despite the appeal of ChIP as an in vitro technique, there are limitations to its use. There is variability from one preparation to the next, given the many steps and reagents used throughout the technique. No one has been able to demonstrate consistent results in a clinical population using white blood cells. It was established, for the first time, the normal variability of ChIP results in THP-1 cells, Jurkat cells, TF-1a, and human male circulating leukocytes over time for histone modifications H3k4me3 and H3k9Ac.
Advisors/Committee Members: Irwin Martin, Ph.D., Timothy Cornell, M.D., Thomas Shanley, M.D..
Subjects/Keywords: Chromatin Immunoprecipitation; Clinical Research; Epigenetics; Health and Medical Administration
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
McDonough, K. (2016). Reproducibility and reliability of chromatin immunoprecipitation in clinical research. (Thesis). Eastern Michigan University. Retrieved from https://commons.emich.edu/theses/682
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
McDonough, Kelli. “Reproducibility and reliability of chromatin immunoprecipitation in clinical research.” 2016. Thesis, Eastern Michigan University. Accessed March 04, 2021.
https://commons.emich.edu/theses/682.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
McDonough, Kelli. “Reproducibility and reliability of chromatin immunoprecipitation in clinical research.” 2016. Web. 04 Mar 2021.
Vancouver:
McDonough K. Reproducibility and reliability of chromatin immunoprecipitation in clinical research. [Internet] [Thesis]. Eastern Michigan University; 2016. [cited 2021 Mar 04].
Available from: https://commons.emich.edu/theses/682.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
McDonough K. Reproducibility and reliability of chromatin immunoprecipitation in clinical research. [Thesis]. Eastern Michigan University; 2016. Available from: https://commons.emich.edu/theses/682
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Manitoba
10.
Ilic, Aleksandar.
Role of UCHL1 in regulating gene expression in prostate cancer cells.
Degree: Biochemistry and Medical Genetics, 2014, University of Manitoba
URL: http://hdl.handle.net/1993/23912
► Ubiquitin C-terminal hydrolase L1 (UCHL1) is a multifunctional protein primarily expressed in neuronal cells and involved in numerous cellular processes. UCHL1 has been linked with…
(more)
▼ Ubiquitin C-terminal hydrolase L1 (UCHL1) is a multifunctional protein primarily expressed in neuronal cells and involved in numerous cellular processes. UCHL1 has been linked with neurodegenerative diseases and a wide range of cancers but its specific role remains unknown. Previous UCHL1 knockdown studies have shown that UCHL1 controls the expression of pro- and anti-apoptotic genes as well as genes involved in cell cycle regulation but it is unknown how UCHL1 regulates these genes.
We have shown that UCHL1 is cross-linked to DNA in DU145 but not in LNCaP or PC3 prostate cancer cells. Therefore, we hypothesized that UCHL1 regulates the expression of pro- or anti-apoptotic genes as well as the genes involved in the cell cycle through its interaction with DNA. By utilizing ChIP and ChIP-seq analyses it is possible to determine the UCHL1 target sequences on the genomic DNA.
It was shown that UCHL1 is only expressed in DU145 but not in LNCaP, PC3 or C4-2 prostate cancer cell lines. Additionally, UCHL1 is expressed and cross-linked to DNA in HEK293T cells. It is believed that UCHL1 is silenced by upstream promoter methylation when it is not expressed. However, treatment with the epigenetic drugs 5-aza-2′-deoxycytidine and trichostatin A (TSA) did not result in induction of UCHL1 expression in LNCaP, PC3 or C4-2 prostate cancer cell lines.
UCHL1 is also associated with p53. However, ChIP assay results have shown that UCHL1 and p53 do not bind to genomic DNA of upstream promoter regions CDKN1A and BAX genes. Additionally, through UCHL1 ChIP-seq analyses in DU145 and HEK293T cells, we discovered that UCHL1 co-localizes to the DNA with the shelterin complex shedding light on a new role of UCHL1 that has never been described before.
Advisors/Committee Members: Davie, Jim (Biochemistry and Medical Genetics) (supervisor), McManus, Kirk (Biochemistry and Medical Genetics) Rastegar, Mojgan (Biochemistry and Medical Genetics) Myal, Yvonne (Pathology) (examiningcommittee).
Subjects/Keywords: UCHL1; Prostate cancer; Next-generation sequencing; Chromatin immunoprecipitation; Epigenetic drugs
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ilic, A. (2014). Role of UCHL1 in regulating gene expression in prostate cancer cells. (Masters Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/23912
Chicago Manual of Style (16th Edition):
Ilic, Aleksandar. “Role of UCHL1 in regulating gene expression in prostate cancer cells.” 2014. Masters Thesis, University of Manitoba. Accessed March 04, 2021.
http://hdl.handle.net/1993/23912.
MLA Handbook (7th Edition):
Ilic, Aleksandar. “Role of UCHL1 in regulating gene expression in prostate cancer cells.” 2014. Web. 04 Mar 2021.
Vancouver:
Ilic A. Role of UCHL1 in regulating gene expression in prostate cancer cells. [Internet] [Masters thesis]. University of Manitoba; 2014. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/1993/23912.
Council of Science Editors:
Ilic A. Role of UCHL1 in regulating gene expression in prostate cancer cells. [Masters Thesis]. University of Manitoba; 2014. Available from: http://hdl.handle.net/1993/23912

University of Southern California
11.
Huang, Fangjin.
Identify Werner protein molecular partners in S phase alt
cell.
Degree: MS, Molecular Microbiology and Immunology, 2012, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/21674/rec/3330
► The Werner protein (WRN) is encoded by the WRN gene. Mutations in this gene are the causal factor for the outset of an autosomal recessive…
(more)
▼ The Werner protein (WRN) is encoded by the WRN gene.
Mutations in this gene are the causal factor for the outset of an
autosomal recessive progerid disorder known as Werner Syndrome. WRN
has been proposed to function in ALT, a pathway that maintains
telomere length independent of telomerase and involves high level
of recombination processes observed in about 15% of cancer cells.
These functions are probably accomplished by the interactions
between WRN and many other proteins. Thus I studied the WRN complex
formation in ALT cells to further investigate the potential role of
WRN in ALT pathway. In this study, I used CCL75.1 cell as a
representative for ALT cell lines and synchronized CCL75.1 cells to
S phase using optimized double thymidine block. I found out that
the optimal condition for harvesting S phase CCL75.1 cells was as
follows: cells were blocked with media containing 4 mM thymidine
for 18 hours, released in regular media for 9 hours, blocked again
in 4 mM thymidine media for 19 hours and harvested after regular
media incubation for 3 hours. Protein extracts from asynchronous
and S phase CCL75.1 and Hela cells were subjected to
immunoprecipitation of WRN protein followed by Western Blot
analysis to determine the interaction between WRN and Ku70, PARP1
and TRF2. In both Hela and CCL75.1 cell lines, the interactions of
WRN with Ku70 and PARP1 can be detected in asynchronous cells, but
the association with TRF2 can only be detected during S phase. My
results suggest that WRN complex in CCL75.1 cell is similar to that
of Hela cell during S phase, indicating that the cell cycle related
regulation of WRN complex is not different in ALT cells and that
the difference between telomerase positive cell and ALT cell is
probably not due to the variation of WRN complex composition in S
phase. It is likely that WRN influences the activity of ALT cells
in other ways.
Advisors/Committee Members: Comai, Lucio (Committee Chair), Reddy, Sita (Committee Member), Schönthal, Axel H. (Committee Member), Schonthal, Axel H. (Committee Member).
Subjects/Keywords: alternative lengthening of telomere; cell cycle synchronization; immunoprecipitation; Werner protein
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Huang, F. (2012). Identify Werner protein molecular partners in S phase alt
cell. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/21674/rec/3330
Chicago Manual of Style (16th Edition):
Huang, Fangjin. “Identify Werner protein molecular partners in S phase alt
cell.” 2012. Masters Thesis, University of Southern California. Accessed March 04, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/21674/rec/3330.
MLA Handbook (7th Edition):
Huang, Fangjin. “Identify Werner protein molecular partners in S phase alt
cell.” 2012. Web. 04 Mar 2021.
Vancouver:
Huang F. Identify Werner protein molecular partners in S phase alt
cell. [Internet] [Masters thesis]. University of Southern California; 2012. [cited 2021 Mar 04].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/21674/rec/3330.
Council of Science Editors:
Huang F. Identify Werner protein molecular partners in S phase alt
cell. [Masters Thesis]. University of Southern California; 2012. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/21674/rec/3330

University of Edinburgh
12.
Sharma, Nidhi.
Characterising the role of TLE1 in Crohn's disease.
Degree: PhD, 2016, University of Edinburgh
URL: http://hdl.handle.net/1842/22970
► The inflammatory bowel diseases (IBD) are chronic, relapsing and remitting diseases of the gastrointestinal tract. There are two main types of IBD: Crohn’s disease (CD)…
(more)
▼ The inflammatory bowel diseases (IBD) are chronic, relapsing and remitting diseases of the gastrointestinal tract. There are two main types of IBD: Crohn’s disease (CD) and ulcerative colitis (UC). The prevalence of IBD is highest in the western world, approximately 100-200 people per 100,000 are affected. In recent years there has been a marked increase in the incidence of CD and UC, in both adults and children (Henderson et al., 2012; Molodecky et al., 2012). This is particularly relevant in Scotland where recent research shows that there has been a 79% increase in the number of cases of paediatric IBD since the 1990’s (Henderson et al., 2012). A yeast 2 hybrid screen identified TLE1as an interacting partner of the known CD susceptibility gene; Nucleotide- binding oligomerisation protein 2 (Nod2). An initial genome wide association study (GWAS) also found an association between the rs6559629 SNP, located in Tle1 and ileal CD (p =3.1 x 10-5) and showed that carriage of the Tle1 risk allele increases the effects of Nod2 mutations in CD. TLE1 functions as a transcriptional co repressor in a variety of different cellular and developmental pathways The work presented in this thesis investigates the potential role of TLE1 in CD. This has been approached using four different strategies: sequencing TLE1 in CD patients and controls, analysing the effects of knocking down TLE1 on genome wide expression, investigating whether the known IBD susceptibility protein XBP1 binds to a predicted binding site in TLE1 and investigating TLE1 levels and localisation in human intestinal samples from CD patients and controls Sequencing TLE1 exons and introns 15/16 and 16/17 in a Scottish cohort of 24 CD patients and healthy controls identified a number of potentially pathogenic exonic and intronic SNPs. Two exonic SNPs and thirteen intronic SNPs were identified and these were further investigated in larger Scottish (203 CD cases, 190 HC) and European cohorts (6,333 CD cases and 15,056 HC) but were not present at statistically significantly different frequencies. Secondly, the effects of TLE1 knock down on genome wide expression were analysed using an Illumina HT12 expression chip. The results showed that TLE1 knock down significantly altered expression of 19 loci (Bonferroni) and 526 loci (FDR). Four of the 19 Bonferroni significant loci are potentially involved in CD: RIOK1 (p=4.3×10-3), SGPL1 (p=4.3×10-3), TUSC3 (p=1.8×10-2) and CCND1 (p=2.7×10-3). Furthermore, expression of SGPL1 and RIOK1 were shown to be differentially expressed at the mRNA level between inflamed patients and controls. The third approach investigates a predicted binding site for the known IBD susceptibility gene, XBP1 in TLE1 which was identified using the Haploreg program. This work shows, using chromatin immunoprecipitation, that exogenous XBP1 does not appear to bind to this predicted binding site. Finally, TLE1 expression was analysed in human intestinal resection samples from patients of known NOD2 status. This work shows that TLE1 and NOD2 are expressed in…
Subjects/Keywords: 616.3; Crohn’s disease; TLE1; chromatin immunoprecipitation; NOD2; IBD pathogenesis
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Sharma, N. (2016). Characterising the role of TLE1 in Crohn's disease. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/22970
Chicago Manual of Style (16th Edition):
Sharma, Nidhi. “Characterising the role of TLE1 in Crohn's disease.” 2016. Doctoral Dissertation, University of Edinburgh. Accessed March 04, 2021.
http://hdl.handle.net/1842/22970.
MLA Handbook (7th Edition):
Sharma, Nidhi. “Characterising the role of TLE1 in Crohn's disease.” 2016. Web. 04 Mar 2021.
Vancouver:
Sharma N. Characterising the role of TLE1 in Crohn's disease. [Internet] [Doctoral dissertation]. University of Edinburgh; 2016. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/1842/22970.
Council of Science Editors:
Sharma N. Characterising the role of TLE1 in Crohn's disease. [Doctoral Dissertation]. University of Edinburgh; 2016. Available from: http://hdl.handle.net/1842/22970

University of Georgia
13.
Stephens, Christopher Brad.
Analysis of protein-protein interactions with cTHY28.
Degree: 2016, University of Georgia
URL: http://hdl.handle.net/10724/35464"
► cTHY28 is a nuclear localized phosphoprotein that was previously isloated from chicken lymphocytes during a screening procedure for apoptotic genes; however, the function of this…
(more)
▼ cTHY28 is a nuclear localized phosphoprotein that was previously isloated from chicken lymphocytes during a screening procedure for apoptotic genes; however, the function of this gene product is not well understood. In order to elucidate the
cellular function of cTHY28, an immunoprecipitation assay was developed. Using this assay, preliminary data indicated that there was a protein-protein interaction between cTHY28, nucleolin and DNA topoisomerase I (topoI). To further analyze this
protein-protein interaction in order to futher characterize cTHY28’s function, a reciprocal co-immunoprecipitation assay was developed. In order to accomplish this goal, the chicken nucleolin and topoI genes were isolated and ligated into a pET28b
bacterial overexpression vector. Using this vector system, sufficent quantites of nucleolin and topoI, as well as cTHY28, were generated and served as an antigen source to immunize rabbits for production of anti-cTHY28, anti-nucleolin and anti-topoI
antisera. These antisera were characterized using an ELISA (Enzyme Linked Immunosorbent Assay) and western immunoblot analysis. Antibodies isolated from these antisera were used to develop a reciprocal co-immunoprecipitation assay. However, experiments
using this assay procedure failed to confirm a cTHY28/nucleolin/topoI protein interaction, although it did demonstrate a protein-protein interaction between nucleolin and topoI.
Subjects/Keywords: cTHY28; nucleolin; DNA topoisomerase I; Protein-Protein Interactions; Co-Immunoprecipitation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Stephens, C. B. (2016). Analysis of protein-protein interactions with cTHY28. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/35464"
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Stephens, Christopher Brad. “Analysis of protein-protein interactions with cTHY28.” 2016. Thesis, University of Georgia. Accessed March 04, 2021.
http://hdl.handle.net/10724/35464".
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Stephens, Christopher Brad. “Analysis of protein-protein interactions with cTHY28.” 2016. Web. 04 Mar 2021.
Vancouver:
Stephens CB. Analysis of protein-protein interactions with cTHY28. [Internet] [Thesis]. University of Georgia; 2016. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/10724/35464".
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Stephens CB. Analysis of protein-protein interactions with cTHY28. [Thesis]. University of Georgia; 2016. Available from: http://hdl.handle.net/10724/35464"
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Virginia Tech
14.
Murphy, Travis Wilson.
Microfluidic tools for molecular analysis and engineering.
Degree: PhD, Chemical Engineering, 2019, Virginia Tech
URL: http://hdl.handle.net/10919/90793
► Technical advances in the healthcare industry have made a range of new data available to physicians and patients. Home use DNA testing kits have made…
(more)
▼ Technical advances in the healthcare industry have made a range of new data available to physicians and patients. Home use DNA testing kits have made it possible to examine one’s predisposition to certain genetic diseases. Using these advanced methods, we are able to gain insights into a patient’s disease state where we were previously unable. Unfortunately, some of these new analyses currently require large amounts of patient sample, which make the examinations largely impractical to perform. In order to overcome the sample requirements, which make these analyses impractical, we develop microscale reactor systems capable of reducing the amount of material required for these new analyses. Here I demonstrate our developed technologies to automate 3 different processes aimed at enabling the study of protein-DNA interactions and produce therapeutics at the point of care. First, we developed an analytical system to study protein-DNA interactions (which are important to understanding patient responses to treatment), that allow for parallel analyses which can be done with sample from less than one needle biopsy, where existing methods would require dozens or more (50 vs 10,000,000 cells.) Next, we developed automated system for preparing DNA sequencing libraries using as little as 10 pg DNA (~2 cells of DNA). The device run multiple reactions simultaneously while reducing batch to batch variation and operator hands-on time. Finally, we developed a v Therapeutics-On-a-Chip platform that produces clinically relevant therapeutic proteins in clinically relevant dosages using a cell-free approach, while saving the trouble and cost associated with protein storage and transportation.
Advisors/Committee Members: Lu, Chang (committeechair), Davis, Richey M. (committee member), Goldstein, Aaron S. (committee member), Ducker, William A. (committee member).
Subjects/Keywords: Microfluidics; Epigenomics; Precision Medicine; Therapeutics; Chromatin Immunoprecipitation; Next Generation Sequencing; NGS
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Murphy, T. W. (2019). Microfluidic tools for molecular analysis and engineering. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/90793
Chicago Manual of Style (16th Edition):
Murphy, Travis Wilson. “Microfluidic tools for molecular analysis and engineering.” 2019. Doctoral Dissertation, Virginia Tech. Accessed March 04, 2021.
http://hdl.handle.net/10919/90793.
MLA Handbook (7th Edition):
Murphy, Travis Wilson. “Microfluidic tools for molecular analysis and engineering.” 2019. Web. 04 Mar 2021.
Vancouver:
Murphy TW. Microfluidic tools for molecular analysis and engineering. [Internet] [Doctoral dissertation]. Virginia Tech; 2019. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/10919/90793.
Council of Science Editors:
Murphy TW. Microfluidic tools for molecular analysis and engineering. [Doctoral Dissertation]. Virginia Tech; 2019. Available from: http://hdl.handle.net/10919/90793

University of Georgia
15.
Stephens, Christoher B.
Identification of putative interacting proteins with cTHY28.
Degree: 2014, University of Georgia
URL: http://hdl.handle.net/10724/27827
► cTHY28 is a highly conserved, nuclear protein that was identified in a screen of cellular proteins that mediate apoptosis in avian lymphocytes. To determine the…
(more)
▼ cTHY28 is a highly conserved, nuclear protein that was identified in a screen of cellular proteins that mediate apoptosis in avian lymphocytes. To determine the cellular function of cTHY28, a co-immunoprecipitation assay was developed to
identify proteins that interact with cTHY28. Mass spectrometric analysis of co-immunoprecipitated material from DT-40 lymphocytes revealed three putative interacting proteins: nucleolin, DNA topoisomerase I and elongation factor-2. From a functional
perspective, nucleolin is associated with pre-rRNA processing, DNA topoisomerase I relaxes supercoiled DNA, and elongation factor-2 is involved in protein translation. Since these proteins have a direct, protein-protein interaction with cTHY28, it is
hypothesized that cTHY28 may augment their cellular function.
Subjects/Keywords: cTHY28; Nucleolin; DNA Topoisomerase I; Co-Immunoprecipitation; Protein-Protein Interactions
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Stephens, C. B. (2014). Identification of putative interacting proteins with cTHY28. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/27827
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Stephens, Christoher B. “Identification of putative interacting proteins with cTHY28.” 2014. Thesis, University of Georgia. Accessed March 04, 2021.
http://hdl.handle.net/10724/27827.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Stephens, Christoher B. “Identification of putative interacting proteins with cTHY28.” 2014. Web. 04 Mar 2021.
Vancouver:
Stephens CB. Identification of putative interacting proteins with cTHY28. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/10724/27827.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Stephens CB. Identification of putative interacting proteins with cTHY28. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/27827
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
16.
Lan, Qing.
Transcriptional Regulation of Intestinal Stem Cell Lineage in Drosophila.
Degree: 2017, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/7091
► The general metadata – e.g., title, author, abstract, subject headings, etc. – is publicly available, but access to the submitted files is restricted to UT…
(more)
▼ The general metadata – e.g., title, author, abstract, subject headings, etc. – is publicly available, but access to the submitted files is restricted to UT Southwestern campus access and/or authorized UT Southwestern users.
The question of how somatic stem cells respond to tissue needs is always intriguing, since aberrant somatic stem cell behaviors may lead to adult tissue degeneration or tumorigenesis. Here, this thesis focuses on the transcriptional regulation of a somatic stem cell lineage: the intestinal stem cell in Drosophila adult gut. The Drosophila adult gut is a dynamic organ. It is maintained by hundreds of somatic gut stem cell evenly distributed throughout the gut epithelium. These multi-potent somatic stem cells undergo self-renewal and differentiation to replenish two mature gut cell types: the absorptive enterocytes and secretory entero-endocrine cells. Through an RNAi screen targeting transcription factors required for stem cell-mediated acute gut regeneration, two novel transcription factors, the FoxA family Fork head (Fkh) and SoxE family sox100b (dSox9), were uncovered and functionally characterized in this thesis. During gut regeneration, transcription factor Fkh and dSox9 are required for stem cell proliferation. During gut homeostasis, Fkh maintains stemness and prevents progenitor from precocious differentiation; dSox9 controls lineage differentiation through Jak-Stat pathway. To further probe mechanisms underlying gut stem cell physiology, ChIP-Seq technique was applied to map chromatin binding sites of gut stem cell regulators (HA tagged) in stem/progenitor cells of dissected fly guts, including transcription factors (FoxA family/Fkh, SoxE family/dSox9, bHLH family/Da), niche pathway downstream factors (Jak-Stat pathway/Stat92E, BMP pathway/Mad, Notch pathway/Su(H), JNK pathway/Kay), and transcriptional regulators (Mediator/Med20, p300/Nej). A set of shared ChIP-Seq peak regions likely functions as enhancers to drive gene expression in gut stem/progenitor cells. This thesis leads to the speculation of a transcriptional network that maintains gut stem/progenitor cell normal physiology in adult Drosophila.
Advisors/Committee Members: Jiang, Jin, Kraus, W. Lee, Sadek, Hesham A., Jiang, Huaqi.
Subjects/Keywords: Chromatin Immunoprecipitation; Drosophila; Forkhead Transcription Factors; Intestines; Stem Cells
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lan, Q. (2017). Transcriptional Regulation of Intestinal Stem Cell Lineage in Drosophila. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/7091
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lan, Qing. “Transcriptional Regulation of Intestinal Stem Cell Lineage in Drosophila.” 2017. Thesis, University of Texas Southwestern Medical Center. Accessed March 04, 2021.
http://hdl.handle.net/2152.5/7091.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lan, Qing. “Transcriptional Regulation of Intestinal Stem Cell Lineage in Drosophila.” 2017. Web. 04 Mar 2021.
Vancouver:
Lan Q. Transcriptional Regulation of Intestinal Stem Cell Lineage in Drosophila. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2017. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/2152.5/7091.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lan Q. Transcriptional Regulation of Intestinal Stem Cell Lineage in Drosophila. [Thesis]. University of Texas Southwestern Medical Center; 2017. Available from: http://hdl.handle.net/2152.5/7091
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Virginia Tech
17.
Deng, Chengyu.
Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience.
Degree: PhD, Chemical Engineering, 2021, Virginia Tech
URL: http://hdl.handle.net/10919/101765
► Epigenetic is the study of alternations in organisms not caused by alternation of the genetic codes. Epigenetic information plays pivotal role during growth, aging and…
(more)
▼ Epigenetic is the study of alternations in organisms not caused by alternation of the genetic codes. Epigenetic information plays pivotal role during growth, aging and disease. Epigenetic information is dynamic and modifiable, and thus serves as an ideal target for various diagnostic and therapeutic strategies of human diseases. Microfluidics is a technology that manipulates liquids with extremely small volumes in miniaturized devices. Microfluidics has improved the sensitivity and resolution of epigenetic analysis. In this thesis, I report three projects focusing on low-input, cell-type-specific and spatially resolved histone modification profiling on microfluidic platforms. Histone modification is one type of epigenetic information and regulates gene expression. First, we studied the influence of culture condition and bacterium infection on histone modification profile of brain tumor cells. Second, we introduced mu-CM, combining a low-input microfluidic device with indexed ChIPmentation and is capable of performing 8 assays in parallel using as few as 20 cells. Last, we investigated spatial variations in the epigenome and transcriptome across adult mouse neocortex, the outer layer of brain involving in higher-order function, such as cognition. I identified distinct spatial patterns responsible for central nervous system development using machine learning algorithm. Our method is well suited for studying scarce samples, such as cells populations isolated from patients in the context of precision medicine.
Advisors/Committee Members: Lu, Chang (committeechair), Goldstein, Aaron S. (committee member), Davalos, Rafael V. (committee member), Tong, Rong (committee member).
Subjects/Keywords: Microfluidics; Chromatin immunoprecipitation; next generation sequencing; histone modifications
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
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APA (6th Edition):
Deng, C. (2021). Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/101765
Chicago Manual of Style (16th Edition):
Deng, Chengyu. “Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience.” 2021. Doctoral Dissertation, Virginia Tech. Accessed March 04, 2021.
http://hdl.handle.net/10919/101765.
MLA Handbook (7th Edition):
Deng, Chengyu. “Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience.” 2021. Web. 04 Mar 2021.
Vancouver:
Deng C. Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience. [Internet] [Doctoral dissertation]. Virginia Tech; 2021. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/10919/101765.
Council of Science Editors:
Deng C. Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience. [Doctoral Dissertation]. Virginia Tech; 2021. Available from: http://hdl.handle.net/10919/101765
18.
KOH MINGSHI.
Mechanisms of hormonally-induced transcription of LHBeta subunit gene in its chromatin setting.
Degree: 2005, National University of Singapore
URL: http://scholarbank.nus.edu.sg/handle/10635/17080
Subjects/Keywords: Luteinizing hormone; Chromatin immunoprecipitation; estrogen receptor; histone deacetylation; gonadotropin releasing hormone; plasmid immunoprecipitation
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
MINGSHI, K. (2005). Mechanisms of hormonally-induced transcription of LHBeta subunit gene in its chromatin setting. (Thesis). National University of Singapore. Retrieved from http://scholarbank.nus.edu.sg/handle/10635/17080
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
MINGSHI, KOH. “Mechanisms of hormonally-induced transcription of LHBeta subunit gene in its chromatin setting.” 2005. Thesis, National University of Singapore. Accessed March 04, 2021.
http://scholarbank.nus.edu.sg/handle/10635/17080.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
MINGSHI, KOH. “Mechanisms of hormonally-induced transcription of LHBeta subunit gene in its chromatin setting.” 2005. Web. 04 Mar 2021.
Vancouver:
MINGSHI K. Mechanisms of hormonally-induced transcription of LHBeta subunit gene in its chromatin setting. [Internet] [Thesis]. National University of Singapore; 2005. [cited 2021 Mar 04].
Available from: http://scholarbank.nus.edu.sg/handle/10635/17080.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
MINGSHI K. Mechanisms of hormonally-induced transcription of LHBeta subunit gene in its chromatin setting. [Thesis]. National University of Singapore; 2005. Available from: http://scholarbank.nus.edu.sg/handle/10635/17080
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
19.
Ξανθοπούλου, Φωτεινή - Αλεξάνδρα.
Πρωτεωμική προσέγγιση της λειτουργίας του σωματίου ματίσματος σε φυσιολογικές και παθολογικές καταστάσεις - σύνδρομο Down.
Degree: 2013, National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ)
URL: http://hdl.handle.net/10442/hedi/42573
► In this thesis we studied the chorionic villi cultured cells. In the context of studying thesecells we established primary cell cultures from the original trophoblastic…
(more)
▼ In this thesis we studied the chorionic villi cultured cells. In the context of studying thesecells we established primary cell cultures from the original trophoblastic tissue andexamined the presence of mesenchymal cell populations with FACS. The cells ability todifferentiate, into osteogenic and neural lineages in particular, was also verified viadifferentiation experiments.The proteomic profile of chorionic villi cultured cells was studied by 2-dimensionalpolyacrylamide gel electrophoresis. Comparison of normal fetuses-derived chorionic villicultured cells proteomic profile and the proteins expressed in cells derived from fetuseswhere Down syndrome has been previously diagnosed with the use of cytogenetictechniques, revealed several proteins that were differentially expressed and couldtherefore be further examined for their potential use as markers/targets for thisaneuploidy. However, given that the spliceosome, that is located in the nucleus, and itsabberant isoforms, have been previously related to the syndrome’s phenotype,emphasis has been put on proteins expressed in that particular subcellular location.Splicing factor 3a2, found to be localized in the nuclear speckles by confocalmicroscopy, was found to be missing a possibly crucial for the unimpaired function ofthe spliceosome fraction of 5kDa in Down syndrome samples. Immunoprecipitationassays followed by 2DE analysis have not been fully able to reveal the broader pictureof the proteins affected by this abnormality, due to technique limitations; yet as in otherpregnancy-associated pathological conditions, gelsolin seems to be down regulated intrisomic cells.
Σε αυτή τη διατριβή αντικείμενο μελέτης αποτέλεσαν τα καλλιεργημένα κύτταρα χοριακών λαχνών. Στο πλαίσιο της μελέτης αυτών των κυττάρων δημιουργήθηκαν πρωτογενείς καλλιέργειες από τον αρχικό ιστό του τροφοβλάστη και εξετάσθηκε η παρουσία σε αυτά μεσεγχυματικών πληθυσμών με κυτταρομετρία ροής, FACS. Η ικανότητά τους να διαφοροποιούνται, συγκεκριμένα σε οστεογενείς και νευρωνικές γενιές, επαληθεύθηκε με πειράματα διαφοροποίησης.Για τη μελέτη του πρωτεωμικού προφίλ των καλλιεργημένων κυττάρων χοριακών λαχνών χρησιμοποιήθηκε η δισδιάστατη ηλεκτροφόρηση πολυακρυλαμιδίου. Η σύγκριση του πρωτεωμικού προφίλ των κυττάρων που προέρχονται από φυσιολογικές κυήσεις και κυήσεις με έμβρυα στα οποία διαγνώσθηκε σύνδρομο Down με κυτταρογενετικές τεχνικές, αποκάλυψε διάφορες πρωτεΐνες που εκφράζονται διαφορετικά στις δυο αυτές καταστάσεις και οι οποίες θα μπορούσαν να εξετασθούν περαιτέρω για την ενδεχόμενη χρήση τους ως δείκτες/στόχοι για τη συγκεκριμένη ανευπλοειδία. Ωστόσο, δεδομένου ότι το σωμάτιο ματίσματος, το οποίο εντοπίζεται στον πυρήνα, και οι μη φυσιολογικές ισομορφές του, είχαν στο παρελθόν συσχετισθεί με το φαινότυπο του συνδρόμου, δόθηκε έμφαση στις πρωτεΐνες που εκφράζονται σε αυτό το συγκεκριμένο υποκυτταρικό σωματίδιο. Ο παράγοντας ματίσματος 3a2, ο οποίος με ομοεστιακή μικροσκοπία βρέθηκε πως εντοπίζεται στα πυρηνικά στίγματα,βρέθηκε κατατετμημένος κατά ένα, πιθανώς σημαντικό για τη σωστή λειτουργία…
Subjects/Keywords: Σωμάτιο ματίσματος; Σύνδρομο Down; Τροφοβλάστες; Πρωτεωμική; Ανοσοκατακρήμνιση; Spliceosome; Down syndrome; Chorionic villi; Proteomics; Immunoprecipitation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ξανθοπούλου, . . -. . (2013). Πρωτεωμική προσέγγιση της λειτουργίας του σωματίου ματίσματος σε φυσιολογικές και παθολογικές καταστάσεις - σύνδρομο Down. (Thesis). National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ). Retrieved from http://hdl.handle.net/10442/hedi/42573
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Ξανθοπούλου, Φωτεινή - Αλεξάνδρα. “Πρωτεωμική προσέγγιση της λειτουργίας του σωματίου ματίσματος σε φυσιολογικές και παθολογικές καταστάσεις - σύνδρομο Down.” 2013. Thesis, National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ). Accessed March 04, 2021.
http://hdl.handle.net/10442/hedi/42573.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Ξανθοπούλου, Φωτεινή - Αλεξάνδρα. “Πρωτεωμική προσέγγιση της λειτουργίας του σωματίου ματίσματος σε φυσιολογικές και παθολογικές καταστάσεις - σύνδρομο Down.” 2013. Web. 04 Mar 2021.
Vancouver:
Ξανθοπούλου -. Πρωτεωμική προσέγγιση της λειτουργίας του σωματίου ματίσματος σε φυσιολογικές και παθολογικές καταστάσεις - σύνδρομο Down. [Internet] [Thesis]. National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ); 2013. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/10442/hedi/42573.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Ξανθοπούλου -. Πρωτεωμική προσέγγιση της λειτουργίας του σωματίου ματίσματος σε φυσιολογικές και παθολογικές καταστάσεις - σύνδρομο Down. [Thesis]. National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ); 2013. Available from: http://hdl.handle.net/10442/hedi/42573
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Saskatchewan
20.
Akin, Zeynep Nesrin.
Identification and characterization of hoxa2 target genes by ChIP.
Degree: 2004, University of Saskatchewan
URL: http://hdl.handle.net/10388/etd-09282004-100435
► Hox genes are evolutionarily conserved transcription factors which act to control important developmental pathways involved in morphogenesis of the embryo. Hoxa2 is expressed in the…
(more)
▼ Hox genes are evolutionarily conserved transcription factors which act to control important developmental pathways involved in morphogenesis of the embryo. Hoxa2 is expressed in the developing CNS in rhombomeres 2-7 in the presumptive hindbrain. During development Hoxa2 expression extends caudally throughout the spinal cord and persists into adulthood. Although previous analysis of Hoxa2 expression indicates its possible role in neuronal circuit specification and/or dorsal-ventral patterning within the spinal cord, the precise genetic pathways through which Hoxa2 affects spinal cord development have not been characterized. We have used
immunoprecipitation of Hoxa2-target DNA complexes from chromatin preparations of E18 mouse spinal cord and hindbrain tissue to isolate in vivo downstream target genes of Hoxa2. Seven DNA fragments were isolated, sequenced and were shown to exhibit in vitro DNA binding by Hoxa2. A search of sequence databases for the target sequences revealed that of these, two displayed high identity with novel mouse genes: toll-associated serine protease (Tasp) and the murine homolog of the human dual specificity tyrosine phosphorylation regulated kinase 4 (Dyrk4). Also, two of the isolated clones are presumably bacterial sequences containing the canonical homeodomain binding site TAAT, and the remaining three clones have not yet been mapped in the mouse genome. A potential core Hoxa2 binding motif consisting of 5' CCATCA/T 3', which is based on a previously characterized Hoxa2-Pbx consensus sequence (Lampe et al., 2004), has been identified in both the Tasp and Dyrk4 intronic elements. Both Dyrk4 and Tasp mRNA have been detected within the developing mouse from E10-18 and in the adult CNS. Analysis by RT-PCR of Tasp expression in Hoxa2-/- newborn mice hindbrain and spinal cord tissues showed an upregulation of Tasp, and transient transfection experiments indicated that Hoxa2 may act as a transcriptional repressor of Tasp through an intronic regulatory element. Transfection studies using the intronic sequence of Dyrk4 indicated that it may function as an enhancer of transcription of Dyrk4 in the presence of Hoxa2. Both Dyrk4 and Tasp belong to large protein subfamilies whose members play a role in numerous developmental pathways in several organisms. Tasp, also known as HtrA3, interacts with TGFâ signaling molecules which are known to be key regulators of development, dorsoventral patterning and are involved in various neuronal pathways. Although the function of Dyrk4 is not known, many of its family members are involved in the regulation of transcription factors and signaling molecules via phosphorylation that are involved in neuronal pathways also. Hoxa2 may act in specifying neuronal subtypes and dorsoventral patterning in the CNS through down and upregulation of its downstream targets Dyrk4 and Tasp, respectively.
Advisors/Committee Members: Nazarali, Adil J..
Subjects/Keywords: immunoprecipitation; CNS development; Hox; target gene
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Akin, Z. N. (2004). Identification and characterization of hoxa2 target genes by ChIP. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/etd-09282004-100435
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Akin, Zeynep Nesrin. “Identification and characterization of hoxa2 target genes by ChIP.” 2004. Thesis, University of Saskatchewan. Accessed March 04, 2021.
http://hdl.handle.net/10388/etd-09282004-100435.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Akin, Zeynep Nesrin. “Identification and characterization of hoxa2 target genes by ChIP.” 2004. Web. 04 Mar 2021.
Vancouver:
Akin ZN. Identification and characterization of hoxa2 target genes by ChIP. [Internet] [Thesis]. University of Saskatchewan; 2004. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/10388/etd-09282004-100435.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Akin ZN. Identification and characterization of hoxa2 target genes by ChIP. [Thesis]. University of Saskatchewan; 2004. Available from: http://hdl.handle.net/10388/etd-09282004-100435
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University
21.
Ebersole, Brittany Anne.
Investigating the role of palmitoylation in the function of the dopamine D2 receptor.
Degree: 2015, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/24760
► The dopamine D2 receptor (D2R) is a G protein-coupled receptor (GPCR) that is crucial for regulation of processes such as mood, reward, and motor control.…
(more)
▼ The dopamine D2 receptor (D2R) is a G protein-coupled receptor (GPCR) that is crucial for regulation of processes such as mood, reward, and motor control. Abnormalities in D2R expression and/or neurotransmission are associated with a variety of human disorders, including schizophrenia, Parkinson’s disease, bipolar disorder, depression, and drug abuse. Palmitoylation, the thioester attachment of palmitate to cysteine residues, has become a topic of interest for GPCRs as it has been shown to modulate signaling, trafficking, and stability of these receptors.
In this dissertation, an optimized version of bioorthogonal click chemistry (BCC) was developed with the ultimate goal of studying D2R palmitoylation. With this technique, proteins are labeled with the chemical probe 15-hexadecynoic acid (15-HDYA) at sites of palmitoylation. Proteins of interest are then isolated by
immunoprecipitation with magnetic beads and analyzed for 15-HDYA incorporation. The utility of this approach was demonstrated by verifying the palmitoylation of the μ-opioid receptor (MOR), a GPCR responsible for mediating the analgesic and addictive properties of most clinically relevant opioid agonist drug. The MOR has been reported to be palmitoylated using two other palmitoylation assays, but not BCC. Additionally, our optimized BCC protocol was able to measure changes in palmitoylation upon overexpression of two palmitoyl acyltransferases (PATs). This was the first demonstration that specific PATs are capable of affecting levels of palmitoylated MOR.
While previous experiments in insect cells have shown that the D2R is palmitoylated, nothing was known about the site, function, or enzymes responsible. Here, the palmitoylation of the D2R was analyzed using our modified BCC protocol in a mammalian cell system. Analysis of a series of D2R mutations revealed that palmitoylation of the D2R occurs on the C-terminal cysteine residue (C443) of the polypeptide. Deletion of C443 led to an almost complete absence of D2R palmitoylation and significantly inhibited trafficking of the receptor to the plasma membrane. Rather, the C443 deletion mutant accumulated in the Golgi, indicating that palmitoylation of the D2R is important for cell surface expression of the receptor.
Using the full-length D2R as bait in a membrane yeast two-hybrid (MYTH) screen, the palmitoyl acyltransferase (PAT) zDHHC4 was identified as a D2R interacting protein. Co-
immunoprecipitation analysis revealed that several other PATs, including zDHHC3 (GODZ) and zDHHC8, also interacted with the D2R and that each of the three PATs was capable of affecting the palmitoylation status of the D2R. Finally, biochemical analysis of the D2R mutants indicates that palmitoylation of the receptor plays a critical role in stability but not the signaling capacity of the D2R.¬
Advisors/Committee Members: Robert G Levenson, Dissertation Advisor/Co-Advisor, Faoud T Ishmael, Committee Member, Patricia Sue Grigson, Committee Member, Thomas E Spratt, Committee Member.
Subjects/Keywords: palmitoylation; dopamine D2 receptor; GPCR; click chemistry; immunoprecipitation; yeast two-hybrid; palmitoyl acyltransferases
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ebersole, B. A. (2015). Investigating the role of palmitoylation in the function of the dopamine D2 receptor. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/24760
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Ebersole, Brittany Anne. “Investigating the role of palmitoylation in the function of the dopamine D2 receptor.” 2015. Thesis, Penn State University. Accessed March 04, 2021.
https://submit-etda.libraries.psu.edu/catalog/24760.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Ebersole, Brittany Anne. “Investigating the role of palmitoylation in the function of the dopamine D2 receptor.” 2015. Web. 04 Mar 2021.
Vancouver:
Ebersole BA. Investigating the role of palmitoylation in the function of the dopamine D2 receptor. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Mar 04].
Available from: https://submit-etda.libraries.psu.edu/catalog/24760.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Ebersole BA. Investigating the role of palmitoylation in the function of the dopamine D2 receptor. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/24760
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University
22.
Li, Shu.
BIOCHEMICAL AND FUNCTIONAL STUDIES OF S-RNASE-BASED SELF-INCOMPATIBILITY IN PETUNIA INFLATA.
Degree: 2016, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/13440swl5324
► Self-incompatibility (SI) is an intraspecific reproductive barrier that is widely adopted by flowering plants to prevent inbreeding and promote outcrossing. Studies on SI in five…
(more)
▼ Self-incompatibility (SI) is an intraspecific reproductive barrier that is widely adopted by flowering plants to prevent inbreeding and promote outcrossing. Studies on SI in five families during the past three decades have revealed three distinct mechanisms, and our lab focuses on the SI system employed by the Solanaceae family, using Petunia inflata as a model. In Solanaceae SI, self/non-self recognition between pollen and pistil is regulated by a highly polymorphic locus, the S-locus, which houses a single S-RNase gene regulating pistil specificity and, in S2-haplotype and S3-haplotype, 17 S-locus F-box (SLF) genes collectively regulating pollen specificity in SI. According to the collaborative non-self recognition model, for a given S-haplotype: (i) each SLF functions as the F-box protein component of an SCF (Skp1-Cullin1-F-box protein) complex, which mediates uniquitination of S-RNase(s), with which the SLF interacts, and its (their) subsequent degradation by the 26S proteasome; (ii) each SLF only interacts with a subset of its non-self S-RNases, and a complete suite of SLFs are collectively required to detoxify all non-self S-RNases to allow cross-compatible pollination; (iii) none of the SLF proteins interact with their self-S-RNase, allowing it to degrade RNAs in the cytosol of the self pollen tube to result in incompatible pollination.
The overall goal of my dissertation research is to assess several predictions of the collaborative non-self recognition model to better understand the molecular and biochemical basis of Solanaecae type SI. In Chapter 2, I describe the use of Co-
Immunoprecipitation (Co-IP) followed by Mass Spectrometry (MS) to identify the components of the SLF-containing complex. Our lab previously showed that PiSSK1 (a pollen-specific Skp1-like protein), PiCUL1-P (a pollen-specific Cullin1), and PiRBX1 (a Petunia conventional Rbx1) co-immunoprecipitated with S¬2-SLF1:GFP (GFP-fused SLF1 of S2-haplotype) expressed in transgenic pollen. Using PiSSK1:FLAG:GFP expressed in transgenic plants as bait, I confirmed the presence of PiCUL1-P and PiRBX1 in the S2-SLF1-containing complex, and further identified two additional SLF proteins, SLF4 and SLF13, as the F-box protein component of similar SCF complexes. To address the question of whether all 17 SLF proteins of S2-haplotype and S3-haplotype are assembled into similar SCF complexes, I modified the Co-IP/MS procedure, including addition of style extracts of four different S-genotypes to pollen extracts containing PiSSK1:FLAG:GFP. The results, described in Chapter 3, showed that all 17 SLF proteins were assembled into similar SCF complexes, suggesting that these SCFSLF complexes have evolved specifically to function in SI. Interestingly, an SLF-like protein and four of the 179 non-SLF F-box proteins predicted to be expressed in pollen, also co-immunoprecipitated with PiSSK1:FLAG:GFP. Sequence comparison revealed a 6-amino acid motif conserved among all the F-box proteins that interacted with PiSSK1.
Our lab initiated a lab-wide effort to…
Advisors/Committee Members: Teh-Hui Kao, Dissertation Advisor/Co-Advisor, Teh-Hui Kao, Committee Chair/Co-Chair, Gabriele Brigitte Monshausen, Committee Member, Dawn S Luthe, Committee Member, Michael Axtell, Outside Member.
Subjects/Keywords: Self-incompatibility; S-Locus F-box proteins; SCF complexes; Mass Spectrometry; Co-immunoprecipitation; Petunia inflata
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Li, S. (2016). BIOCHEMICAL AND FUNCTIONAL STUDIES OF S-RNASE-BASED SELF-INCOMPATIBILITY IN PETUNIA INFLATA. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/13440swl5324
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Li, Shu. “BIOCHEMICAL AND FUNCTIONAL STUDIES OF S-RNASE-BASED SELF-INCOMPATIBILITY IN PETUNIA INFLATA.” 2016. Thesis, Penn State University. Accessed March 04, 2021.
https://submit-etda.libraries.psu.edu/catalog/13440swl5324.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Li, Shu. “BIOCHEMICAL AND FUNCTIONAL STUDIES OF S-RNASE-BASED SELF-INCOMPATIBILITY IN PETUNIA INFLATA.” 2016. Web. 04 Mar 2021.
Vancouver:
Li S. BIOCHEMICAL AND FUNCTIONAL STUDIES OF S-RNASE-BASED SELF-INCOMPATIBILITY IN PETUNIA INFLATA. [Internet] [Thesis]. Penn State University; 2016. [cited 2021 Mar 04].
Available from: https://submit-etda.libraries.psu.edu/catalog/13440swl5324.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Li S. BIOCHEMICAL AND FUNCTIONAL STUDIES OF S-RNASE-BASED SELF-INCOMPATIBILITY IN PETUNIA INFLATA. [Thesis]. Penn State University; 2016. Available from: https://submit-etda.libraries.psu.edu/catalog/13440swl5324
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University
23.
Samorodnitsky, Eric.
Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms Using Chromatin Immunoprecipitation Data
.
Degree: 2011, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/11601
► Eukaryotic genes are regulated by hundreds of proteins that assemble into a preinitation complex (PIC), which functions to initiate transcription. PIC mechanisms of assembly and…
(more)
▼ Eukaryotic genes are regulated by hundreds of proteins that assemble into a preinitation complex (PIC), which functions to initiate transcription. PIC mechanisms of assembly and disassembly in vivo are largely unknown. To address this issue, in Chapter 2, I wrote the computational tool, PathCom (short for PATHway COMpatibility). PathCom takes, as input, an assumed PIC assembly pathway and genome-wide occupancy data. Assuming that occupancy data can be treated as binding duration and explicitly defined assembly/disassembly steps, PathCom outputs plausible PIC disassembly pathways. I exemplify this process by modeling ChIP-chip data of the general transcription factors (TBP, TFIIB, TFIIE, TFIIF, TFIIH, and RNA polymerase II), sequence-specific regulators, and chromatin remodelers of budding yeast Saccharomyces cerevisiae. My modeling found that TBP, sequence-specific regulator, and chromatin remodeler occupancy to be transient compared with the other general transcription factors, given the assumptions inherent in the system. Furthermore, I used PathCom to model the disassembly of GTF’s under heat shock conditions and found TBP occupancy to still be transient under heat shock conditions. PathCom can be used to model any assembly/disassembly process, given all species form a complex together. The reliability of the output modeling of PathCom relies on the accuracy of the assumptions inherent in the modeling and on the quality of the input occupancy data.
To improve the quality of ChIP data, ChIP-chip is being replaced by ChIP-seq. This new technology offers higher resolution and lower background for transcription factor binding site identification. Therefore, in Chapter 3, I wrote a four-step algorithm to infer true transcription factor binding sites from ChIP-seq data. This algorithm accounts for peak representation on both DNA strands, reproducibility of peaks, and the presence of a motif. This algorithm was written for the genomic toolkit Galaxy. Steps in the algorithm, when possible, were written using preexisting tools on Galaxy. When not possible, certain steps were written in Python. This algorithm is freely available at http://dancluster.g2.bx.psu.edu.
Advisors/Committee Members: Benjamin Franklin Pugh, Dissertation Advisor/Co-Advisor, Benjamin Franklin Pugh, Committee Chair/Co-Chair, Istvan Albert, Committee Member, Stephen Wade Schaeffer, Committee Member, Claude Walker Depamphilis, Committee Member.
Subjects/Keywords: workflow; modeling; chemical kinetics; Chromatin Immunoprecipitation; preinitation complex assembly and disassembly; binding sites
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Samorodnitsky, E. (2011). Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms Using Chromatin Immunoprecipitation Data
. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11601
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Samorodnitsky, Eric. “Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms Using Chromatin Immunoprecipitation Data
.” 2011. Thesis, Penn State University. Accessed March 04, 2021.
https://submit-etda.libraries.psu.edu/catalog/11601.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Samorodnitsky, Eric. “Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms Using Chromatin Immunoprecipitation Data
.” 2011. Web. 04 Mar 2021.
Vancouver:
Samorodnitsky E. Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms Using Chromatin Immunoprecipitation Data
. [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Mar 04].
Available from: https://submit-etda.libraries.psu.edu/catalog/11601.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Samorodnitsky E. Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms Using Chromatin Immunoprecipitation Data
. [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11601
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Purdue University
24.
Wang, Yao.
Protein Affinity Extraction Of Prostate Specific Antigen (PSA) Using Submicron Spheres.
Degree: MS, Chemistry, 2014, Purdue University
URL: http://docs.lib.purdue.edu/open_access_theses/280
► PSA has been used as a biomarker for prostate cancer for a long time. To characterize different glycoforms of PSA using techniques like UHPLC…
(more)
▼ PSA has been used as a biomarker for prostate cancer for a long time. To characterize different glycoforms of PSA using techniques like UHPLC and cIEF, concentration and purification of PSA from complex samples becomes necessary. Our group has developed submicron silica spheres based affinity beads to extract PSA through
immunoprecipitation. This study focuses on measuring the bead performance when antibody type/amount was varied and PSA concentration was lowered for clinical use. To better satisfy the requirement of large-scale extraction, several attempts were made to increase the bead capacity. The results will be presented and future directions of the project will be discussed.
Advisors/Committee Members: Mary J. Wirth, Chengde Mao, Hilkka I. Kenttamaa.
Subjects/Keywords: Pure sciences; Affinity beads; Immunoprecipitation; Polyacrylamide; Prostate specific antigen; Protein g; Silica modification; Analytical Chemistry
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Wang, Y. (2014). Protein Affinity Extraction Of Prostate Specific Antigen (PSA) Using Submicron Spheres. (Thesis). Purdue University. Retrieved from http://docs.lib.purdue.edu/open_access_theses/280
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Yao. “Protein Affinity Extraction Of Prostate Specific Antigen (PSA) Using Submicron Spheres.” 2014. Thesis, Purdue University. Accessed March 04, 2021.
http://docs.lib.purdue.edu/open_access_theses/280.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Yao. “Protein Affinity Extraction Of Prostate Specific Antigen (PSA) Using Submicron Spheres.” 2014. Web. 04 Mar 2021.
Vancouver:
Wang Y. Protein Affinity Extraction Of Prostate Specific Antigen (PSA) Using Submicron Spheres. [Internet] [Thesis]. Purdue University; 2014. [cited 2021 Mar 04].
Available from: http://docs.lib.purdue.edu/open_access_theses/280.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang Y. Protein Affinity Extraction Of Prostate Specific Antigen (PSA) Using Submicron Spheres. [Thesis]. Purdue University; 2014. Available from: http://docs.lib.purdue.edu/open_access_theses/280
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
25.
Schwartz, Jacob C.
Small RNAs Regulate Transcription by Interacting with Noncoding RNA Transcripts.
Degree: 2010, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/742
► General methods for controlling gene expression have long been appreciated as an attractive target in drug design. Recently, the Corey lab has demonstrated that short…
(more)
▼ General methods for controlling gene expression have long been appreciated as an attractive target in drug design. Recently, the Corey lab has demonstrated that short RNA duplexes designed to target the promoter region for human genes can inhibit or activate gene expression in a sequence dependent manner. The mechanism by which RNAs achieve promoter recognition has remained unclear. Sequence specific recognition could be achieved by (1) RNA hybridization to genomic DNA, or (2) RNA recognition of some uncharacterized RNA species. Promoter targeted duplex RNA has been shown to recruit argonaute proteins to the promoter DNA and these proteins are necessary for duplex RNAs to regulate transcription. Argonaute proteins are known to recognize RNA:RNA interactions. However, genes targeted with duplex RNAs have no characterized transcripts in their promoters. I tested the hypothesis that promoter RNA transcripts exist and serve as a substrate for short duplex RNAs to hybridize to and regulate gene expression of adjacent genes.
I found previously undiscovered RNA transcripts expressed from the promoter of progesterone receptor (PR) using RT-PCR. Quantitative RT-PCR of the promoter RNA of PR reveals expression levels between 10 and 1000 fold lower than PR in T47D and MCF7 breast cancer cells. I have cloned three transcripts overlapping the promoter of PR from two cell lines – T47D and MCF7, each with unique splicing and transcription start sites. All of these transcripts initiate within the protein coding region of PR and run antisense to the gene PR. I have been able to show that the promoter transcripts can be immunoprecipitated with antibodies against the argonaute proteins in cells transfected with duplex RNAs targeting the promoter of PR but not in cells transfected with mismatched duplex RNAs. Also, biotinylated RNAs bind to and pull down these noncoding RNAs. Finally, knockdown of the antisense transcript with an antisense oligonucleotide prevent gene activation by duplex RNAs.
Following this study, our lab uncovered that duplex RNAs can target beyond the 3' terminus of genes and silence or activate transcription. I further showed that this transcription regulation is mediated by argonaute binding to noncoding RNAs overlapping the 3' terminus of the genes, PR and BRCA1. The signal is transmitted from the 3' terminus to the gene promoter because the 5' and 3' ends of these genes are held in a chromatin loop, which I validated using a chromatin conformation capture assay. This brings the ends of the gene in close proximity to each other. Due to this interaction, short RNAs that bind a noncoding RNA at the 3' end of the gene also physically interacts with noncoding RNAs that associate with the gene promoter. This is confirmed by RNA
immunoprecipitation of both transcripts with duplex RNAs targeting either the 5' or 3' ends of the gene.
More than 20 years ago, it was found that proteins recognizing DNA at the 5’ end of genes could regulate transcription. This study presents a paradigm shift implicating noncoding RNAs at the…
Advisors/Committee Members: Corey, David R..
Subjects/Keywords: RNA Interference; Immunoprecipitation; RNA, Double-Stranded
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Schwartz, J. C. (2010). Small RNAs Regulate Transcription by Interacting with Noncoding RNA Transcripts. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/742
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Schwartz, Jacob C. “Small RNAs Regulate Transcription by Interacting with Noncoding RNA Transcripts.” 2010. Thesis, University of Texas Southwestern Medical Center. Accessed March 04, 2021.
http://hdl.handle.net/2152.5/742.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Schwartz, Jacob C. “Small RNAs Regulate Transcription by Interacting with Noncoding RNA Transcripts.” 2010. Web. 04 Mar 2021.
Vancouver:
Schwartz JC. Small RNAs Regulate Transcription by Interacting with Noncoding RNA Transcripts. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2010. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/2152.5/742.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Schwartz JC. Small RNAs Regulate Transcription by Interacting with Noncoding RNA Transcripts. [Thesis]. University of Texas Southwestern Medical Center; 2010. Available from: http://hdl.handle.net/2152.5/742
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Illinois – Chicago
26.
McMurray, Erin N.
Identification of Imprinting Regulators at the Meg3 Differentially Methylated Region.
Degree: 2013, University of Illinois – Chicago
URL: http://hdl.handle.net/10027/9774
► Identification of Imprinting Regulators as the Meg3 Differentially Methylated Region Erin Nichole McMurray, PhD Department of Biological Sciences University of Illinois at Chicago Chicago, Illinois…
(more)
▼ Identification of Imprinting Regulators as the Meg3 Differentially Methylated Region
Erin Nichole McMurray, PhD
Department of Biological Sciences
University of Illinois at Chicago
Chicago, Illinois (2012)
Dissertation Chairperson: Dr. Teresa Orenic, PhD
Genomic imprinting is the differential expression of two alleles of a gene based on the parent of origin. The imprinted Dlk1-Meg3 locus is located on distal mouse chromosome 12, and contains the paternally expressed Dlk1 and the maternally expressed Meg3 genes. Three differentially methylated regions (DMRs) are present at the Dlk1-Meg3 locus, and they are the Dlk1 DMR, the intergenic DMR, and the Meg3 DMR. Several studies have indicated that the Meg3 DMR plays a role in the expression and imprinting of genes at the Dlk1-Meg3 locus.
The goal of this work was to determine the factors present at the Meg3 DMR that may prove necessary for proper imprinting of the Dlk1-Meg3 locus. Chromatin
immunoprecipitation (ChIP) was used to analyze histone modifications and trans-acting DNA binding proteins at the Meg3 DMR during imprinting establishment and maintenance. In embryonic stem (ES) cells, where imprints are being established, Meg3 is biallelically expressed, and the DMR shows variable DNA methylation, with biallelic methylation at one region but paternal allele-specific methylation at another. All histone modifications detected at the Meg3 DMR of ES cells were biallelic. In embryonic day 12.5 (e12.5) embryos, where imprints are already established and are maintained in an allele-specific manner, Meg3 is maternally expressed, the paternal Meg3 DMR is methylated, and activating histone modifications are specific to the maternal DMR. Also in this study, DNA binding proteins that represent potential regulatory factors were identified in both ES cells and e12.5 embryos.
In addition, a combination of methods including electrophoretic mobility shift assays, DNA affinity chromatography, and mass spectrometry were used to determine the presence of novel trans-acting DNA binding proteins at the Meg3 DMR that may prove to be necessary for imprinting regulation of the Dlk1-Meg3 locus. Using these methods, the protein PARP1 was detected at the Meg3 DMR of e12.5 embryos. PARP1 binding of the Meg3 DMR was confirmed in vitro using supershift analysis and in vivo using ChIP. The histone modifications and trans-acting DNA binding proteins detected at the Meg3 DMR in these studies provide a more complete picture of how imprinting is regulated at the Dlk1-Meg3 locus.
Advisors/Committee Members: Orenic, Teresa (advisor), Schmidt, Jennifer (committee member), Okkema, Pete (committee member), Wang, Tian (committee member), Merrill, Brad (committee member).
Subjects/Keywords: Dlk1; Meg3; genomic imprinting; histone modifications' epigenetics; differentially methylated region; chromatin immunoprecipitation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
McMurray, E. N. (2013). Identification of Imprinting Regulators at the Meg3 Differentially Methylated Region. (Thesis). University of Illinois – Chicago. Retrieved from http://hdl.handle.net/10027/9774
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
McMurray, Erin N. “Identification of Imprinting Regulators at the Meg3 Differentially Methylated Region.” 2013. Thesis, University of Illinois – Chicago. Accessed March 04, 2021.
http://hdl.handle.net/10027/9774.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
McMurray, Erin N. “Identification of Imprinting Regulators at the Meg3 Differentially Methylated Region.” 2013. Web. 04 Mar 2021.
Vancouver:
McMurray EN. Identification of Imprinting Regulators at the Meg3 Differentially Methylated Region. [Internet] [Thesis]. University of Illinois – Chicago; 2013. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/10027/9774.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
McMurray EN. Identification of Imprinting Regulators at the Meg3 Differentially Methylated Region. [Thesis]. University of Illinois – Chicago; 2013. Available from: http://hdl.handle.net/10027/9774
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Uppsala University
27.
Gkanatsiou, Eleni.
Development of an assay to monitor the role of Serum Amyloid P-component in Alzheimer's Disease.
Degree: Biology Education Centre, 2016, Uppsala University
URL: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297654
► Alzheimer’s Disease is the most common form of dementia, affecting 48 million people worldwide. Despite this fact, only 45% of the patients have received…
(more)
▼ Alzheimer’s Disease is the most common form of dementia, affecting 48 million people worldwide. Despite this fact, only 45% of the patients have received the diagnose. The reason behind this is the fact that the cause of the disease is still unclear. Several hypotheses have been suggested, with main focus in the imbalance between the production and the clearance of Αβ in the brain (formation of plaques) or hyperphosphorylation of the tau protein (formation of tangles). In order to have a better understanding of what is actually happening in the brain, more biomarkers need to be developed. Keeping this in mind, we tried to develop a method to monitor the protein levels of SAP in the brain. SAP is a glycoprotein, normally produced by the liver in acute phase immune responses. SAP has been correlated with AD in the 1980s and quite recently it has been shown that SAP is elevated in AD patients, but not in individuals with plaques and no dementia. For this reason, we developed a mass spectrometry based targeted quantification method for monitoring SAP in the brain, as well as C9, a blood contamination reference protein. Our method is robust enough to be further used in large studies, in order to investigate the role of SAP in AD.
Subjects/Keywords: Alzheimer's Disease; Biomarker development; mass spectrometry; quantitative proteomics; Serum Amyloid P-component; immunoprecipitation; Neurosciences; Neurovetenskaper
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Gkanatsiou, E. (2016). Development of an assay to monitor the role of Serum Amyloid P-component in Alzheimer's Disease. (Thesis). Uppsala University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297654
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Gkanatsiou, Eleni. “Development of an assay to monitor the role of Serum Amyloid P-component in Alzheimer's Disease.” 2016. Thesis, Uppsala University. Accessed March 04, 2021.
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297654.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Gkanatsiou, Eleni. “Development of an assay to monitor the role of Serum Amyloid P-component in Alzheimer's Disease.” 2016. Web. 04 Mar 2021.
Vancouver:
Gkanatsiou E. Development of an assay to monitor the role of Serum Amyloid P-component in Alzheimer's Disease. [Internet] [Thesis]. Uppsala University; 2016. [cited 2021 Mar 04].
Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297654.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Gkanatsiou E. Development of an assay to monitor the role of Serum Amyloid P-component in Alzheimer's Disease. [Thesis]. Uppsala University; 2016. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297654
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
28.
Feijóo Buján, Ana.
Comprobación de una interacción física de HMGB1 con su diana
.
Degree: 2017, Universidad da Coruña
URL: http://hdl.handle.net/2183/19992
► [Resumen] En estudios previos, mediante el sistema del doble híbrido en levaduras, se había descrito la interacción física entre la proteína humana HMGB1 y el…
(more)
▼ [Resumen] En estudios previos, mediante el sistema del doble híbrido en levaduras, se había descrito la interacción física entre la proteína humana HMGB1 y el factor transcripcional YY1, ambas relacionadas con procesos cancerígenos. Este método presenta alrededor de un 5% de falsos positivos, por lo que en el presente trabajo se ha intentado confirmar dicha interacción, en la línea celular de próstata tumoral PC-3, mediante la técnica de inmunoprecipitación, utilizando para la inmunoprecipitación anticuerpos anti-HMGB1 y para la detección de la proteína coinmunoprecipitada un anticuerpo anti-YY1. Los resultados obtenidos no fueron positivos, lo que no descarta que ambas proteínas puedan interaccionar en otras condiciones.
Advisors/Committee Members: Cerdán, Maria Esperanza (advisor), Lamas Maceiras, Mónica (advisor).
Subjects/Keywords: HMGB1;
Immunoprecipitation;
YY1;
Prostate cancer;
Biomarker;
Inmunoprecipitación;
Cáncer de próstata;
Biomarcador;
Cancro de próstata
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Feijóo Buján, A. (2017). Comprobación de una interacción física de HMGB1 con su diana
. (Masters Thesis). Universidad da Coruña. Retrieved from http://hdl.handle.net/2183/19992
Chicago Manual of Style (16th Edition):
Feijóo Buján, Ana. “Comprobación de una interacción física de HMGB1 con su diana
.” 2017. Masters Thesis, Universidad da Coruña. Accessed March 04, 2021.
http://hdl.handle.net/2183/19992.
MLA Handbook (7th Edition):
Feijóo Buján, Ana. “Comprobación de una interacción física de HMGB1 con su diana
.” 2017. Web. 04 Mar 2021.
Vancouver:
Feijóo Buján A. Comprobación de una interacción física de HMGB1 con su diana
. [Internet] [Masters thesis]. Universidad da Coruña; 2017. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/2183/19992.
Council of Science Editors:
Feijóo Buján A. Comprobación de una interacción física de HMGB1 con su diana
. [Masters Thesis]. Universidad da Coruña; 2017. Available from: http://hdl.handle.net/2183/19992
29.
Anguraj Vadivel, Arun Kumaran.
GmMYB176 Interactome and Regulation of Isoflavonoid Biosynthesis in Soybean.
Degree: 2017, University of Western Ontario
URL: https://ir.lib.uwo.ca/etd/4639
► MYB transcription factors are one of the largest transcription factor families characterized in plants. They are classified into four types: R1 MYB, R2R3 MYB, R3…
(more)
▼ MYB transcription factors are one of the largest transcription factor families characterized in plants. They are classified into four types: R1 MYB, R2R3 MYB, R3 MYB and R4 MYB. GmMYB176 is an R1MYB transcription factor that regulates Chalcone synthase (CHS8) gene expression and isoflavonoid biosynthesis in soybean. Silencing of GmMYB176 suppressed the expression of the GmCHS8 gene and reduced the accumulation of isoflavonoids in soybean hairy roots. However, overexpression of GmMYB176 does not alter either GmCHS8 gene expression or isoflavonoid levels suggesting that GmMYB176 alone is not sufficient for GmCHS8 gene regulation. I hypothesized that GmMYB176 acts cooperatively with another factor(s) for the regulation of GmCHS8 gene expression and it may also regulate other isoflavonoid biosynthetic genes in soybean. The objective of this research was to identify the GmMYB176 interactome for GmCHS8 gene regulation and elucidate the role of GmMYB176 in isoflavonoid biosynthesis in soybean. GmMYB176 interacting proteins were identified using two translational fusion baits (GmMYB176-YFP and YFP-GmMYB176) by co-immunoprecipitation, followed by liquid chromatography-tandem mass spectrometry. The interaction of selected candidates with GmMYB176 was validated in planta and their DNA binding activities determined. GmMYB176 may form a transcriptional complex with Gm04bZIP and/or Gm05bZIP for the regulation of GmCHS8 gene expression. RNA-seq and metabolomics analyses of soybean hairy roots in which GmMYB176 was either silenced or over-expressed revealed that GmMYB176 regulates multiple genes in the isoflavonoid biosynthesis pathway, affecting the production of metabolites in phenylpropanoid pathway such as phenylalanine, liquiritigenin, daidzin, genistin, glycitein, and glyceollin. The knowledge and information generated on the role of GmMYB176 in the regulation of isoflavonoid biosynthesis will allow genetic manipulation of isoflavonoid level in soybean and/or introduce isoflavonoid pathway in non-legumes.
Subjects/Keywords: Co-immunoprecipitation; MYB; isoflavonoid biosynthesis; transcriptional complex; gene regulation; soybean; Molecular Biology; Plant Biology
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Anguraj Vadivel, A. K. (2017). GmMYB176 Interactome and Regulation of Isoflavonoid Biosynthesis in Soybean. (Thesis). University of Western Ontario. Retrieved from https://ir.lib.uwo.ca/etd/4639
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Anguraj Vadivel, Arun Kumaran. “GmMYB176 Interactome and Regulation of Isoflavonoid Biosynthesis in Soybean.” 2017. Thesis, University of Western Ontario. Accessed March 04, 2021.
https://ir.lib.uwo.ca/etd/4639.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Anguraj Vadivel, Arun Kumaran. “GmMYB176 Interactome and Regulation of Isoflavonoid Biosynthesis in Soybean.” 2017. Web. 04 Mar 2021.
Vancouver:
Anguraj Vadivel AK. GmMYB176 Interactome and Regulation of Isoflavonoid Biosynthesis in Soybean. [Internet] [Thesis]. University of Western Ontario; 2017. [cited 2021 Mar 04].
Available from: https://ir.lib.uwo.ca/etd/4639.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Anguraj Vadivel AK. GmMYB176 Interactome and Regulation of Isoflavonoid Biosynthesis in Soybean. [Thesis]. University of Western Ontario; 2017. Available from: https://ir.lib.uwo.ca/etd/4639
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of the Western Cape
30.
Faro, Andrew.
Investigation of the interactions of retinoblastoma binding protein-6 with transcription factors p53 and Y-Box Binding Protein-1
.
Degree: 2011, University of the Western Cape
URL: http://hdl.handle.net/11394/3638
► Retinoblastoma Binding Protein 6 (RBBP6) is a 250 kDa multi-domain protein that has been implicated in diverse cellular processes including apoptosis, mRNA processing and cell…
(more)
▼ Retinoblastoma Binding Protein 6 (RBBP6) is a 250 kDa multi-domain protein that
has been implicated in diverse cellular processes including apoptosis, mRNA processing and cell cycle regulation. Many of these functions are likely to be related
to its interaction with tumour suppressor proteins p53 and the Retinoblastoma
protein (pRb), and the oncogenic Y-Box Binding Protein-1 (YB-1). RBBP6 inhibits the
binding of p53 to DNA and enhances the HDM2-mediated ubiquitination and
proteasomal degradation of p53. Disruption of RBBP6 leads to an embryonic lethal
phenotype in mice as a result of widespread p53-mediated apoptosis. RBBP6
promotes ubiquitination and degradation of YB-1, leading to its proteasomal
degradation in vivo.The first part of this thesis describes in vitro investigations of the interaction betweenbacterially-expressed human p53 and fragments of human RBBP6 previously identified as interacting with p53, in an attempt to further localise the region of interaction on both proteins. GST-pull down assays and
immunoprecipitation assays confirmed the interaction, and localised it to the core DNA binding domain of p53 and a region corresponding to residues 1422-1668 of RBBP6. However in Nuclear Magnetic Resonance (NMR) chemical shift perturbation assays no evidence was found for the interaction. NMR showed the relevant region of RBBP6 to be unfolded,and no evidence was found for interaction-induced folding. The R273H mutant of the p53 core domain did not abolish the interaction, in contrast to reports that the corresponding murine mutation (R270C) did abolish the interaction.The second part of this thesis describes in vitro investigations of the ubiquitination of YB-1 by RBBP6. A fragment corresponding to the first 335 residues of RBBP6,denoted R3, was expressed in bacteria and found to be soluble. Contrary to expectation, in a fully in vitro assay R3 was not able to ubiquitinate YB-1. However,following addition of human cell lysate, YB-1 was degraded in an R3-dependent and proteasome-dependent manner, indicating that R3 is required for ubiquitination and proteasomal degradation of YB-1. However R3 is not sufficient, with one or more factors being supplied by the cell lysate. In view of the pro-tumourigenic effects of YB-1 in many human cancers, these results lay the foundation for an understanding of the regulatory effect of RBBP6 on YB-1 and its potential role in anti-tumour therapy.
Advisors/Committee Members: Pugh, David J.R (advisor).
Subjects/Keywords: RBBP6;
p53;
YB-1;
Tumour suppressor;
Cancer;
Ubiquitination;
E3 ligase;
Immunoprecipitation;
NMR;
Protein
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APA (6th Edition):
Faro, A. (2011). Investigation of the interactions of retinoblastoma binding protein-6 with transcription factors p53 and Y-Box Binding Protein-1
. (Thesis). University of the Western Cape. Retrieved from http://hdl.handle.net/11394/3638
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Faro, Andrew. “Investigation of the interactions of retinoblastoma binding protein-6 with transcription factors p53 and Y-Box Binding Protein-1
.” 2011. Thesis, University of the Western Cape. Accessed March 04, 2021.
http://hdl.handle.net/11394/3638.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Faro, Andrew. “Investigation of the interactions of retinoblastoma binding protein-6 with transcription factors p53 and Y-Box Binding Protein-1
.” 2011. Web. 04 Mar 2021.
Vancouver:
Faro A. Investigation of the interactions of retinoblastoma binding protein-6 with transcription factors p53 and Y-Box Binding Protein-1
. [Internet] [Thesis]. University of the Western Cape; 2011. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/11394/3638.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Faro A. Investigation of the interactions of retinoblastoma binding protein-6 with transcription factors p53 and Y-Box Binding Protein-1
. [Thesis]. University of the Western Cape; 2011. Available from: http://hdl.handle.net/11394/3638
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
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