subject:(immunoprecipitation)

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)

Subjects/Keywords: lung cancer; immunoprecipitation assays; mutate; proliferation; migration

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APA (6^th 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 (16^th 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 (7^th 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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APA (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: T-Helper; Noncoding RNA; Super-enhancer; cytokine; transcription; Immunoprecipitation

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APA (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: mesenchymal stem cells; epigenetics; chromatin immunoprecipitation; external stimuli; cell responses

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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

12 more images…

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APA (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: ALS; HEK293T; Immunoprecipitation; Mass Spectrometry; TDP-35; TDP-43; 0571

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APA (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Chromatin Immunoprecipitation; Clinical Research; Epigenetics; Health and Medical Administration

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

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 (6^th 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 (16^th 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 (7^th 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)

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 (6^th 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 (16^th 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 (7^th 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)

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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Microfluidics; Chromatin immunoprecipitation; next generation sequencing; histone modifications

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

APA (6^th 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 (16^th 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 (7^th 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 Manager

APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

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 (6^th 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 (16^th 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 (7^th 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)

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 (6^th 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 (16^th 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 (7^th 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

10 more images…

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APA (6^th 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 (16^th 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 (7^th 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 · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th 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 (16^th 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 (7^th 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

Open Access Theses and Dissertations