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

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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Jian S. LKB1 binds to APC and modulates Wnt signaling pathway in lung cancer cells. [Internet] [Thesis]. NSYSU; 2013. [cited 2019 Oct 22]. 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. 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 (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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Schwartz JC. Small RNAs Regulate Transcription by Interacting with Noncoding RNA Transcripts. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2010. [cited 2019 Oct 22]. 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 Texas Southwestern Medical Center

3. 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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Kalantari R. Building the Human Argonaute 2 Interaction Network. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2015. [cited 2019 Oct 22]. 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

University of Georgia

4. Stephens, Christoher B. Identification of putative interacting proteins with cTHY28.

Degree: MS, Poultry Science, 2011, University of Georgia

URL: http://purl.galileo.usg.edu/uga_etd/stephens_christoher_b_201112_ms

► 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 (6^th Edition):

Stephens, C. B. (2011). Identification of putative interacting proteins with cTHY28. (Masters Thesis). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/stephens_christoher_b_201112_ms

Chicago Manual of Style (16^th Edition):

Stephens, Christoher B. “Identification of putative interacting proteins with cTHY28.” 2011. Masters Thesis, University of Georgia. Accessed October 22, 2019. http://purl.galileo.usg.edu/uga_etd/stephens_christoher_b_201112_ms.

MLA Handbook (7^th Edition):

Stephens, Christoher B. “Identification of putative interacting proteins with cTHY28.” 2011. Web. 22 Oct 2019.

Vancouver:

Stephens CB. Identification of putative interacting proteins with cTHY28. [Internet] [Masters thesis]. University of Georgia; 2011. [cited 2019 Oct 22]. Available from: http://purl.galileo.usg.edu/uga_etd/stephens_christoher_b_201112_ms.

Council of Science Editors:

Stephens CB. Identification of putative interacting proteins with cTHY28. [Masters Thesis]. University of Georgia; 2011. Available from: http://purl.galileo.usg.edu/uga_etd/stephens_christoher_b_201112_ms

University of Georgia

5. Stephens, Christopher Brad. Analysis of protein-protein interactions with cTHY28.

Degree: PhD, Poultry Science, 2015, University of Georgia

URL: http://purl.galileo.usg.edu/uga_etd/stephens_christopher_b_201512_phd

► 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. (2015). Analysis of protein-protein interactions with cTHY28. (Doctoral Dissertation). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/stephens_christopher_b_201512_phd

Chicago Manual of Style (16^th Edition):

Stephens, Christopher Brad. “Analysis of protein-protein interactions with cTHY28.” 2015. Doctoral Dissertation, University of Georgia. Accessed October 22, 2019. http://purl.galileo.usg.edu/uga_etd/stephens_christopher_b_201512_phd.

MLA Handbook (7^th Edition):

Stephens, Christopher Brad. “Analysis of protein-protein interactions with cTHY28.” 2015. Web. 22 Oct 2019.

Vancouver:

Stephens CB. Analysis of protein-protein interactions with cTHY28. [Internet] [Doctoral dissertation]. University of Georgia; 2015. [cited 2019 Oct 22]. Available from: http://purl.galileo.usg.edu/uga_etd/stephens_christopher_b_201512_phd.

Council of Science Editors:

Stephens CB. Analysis of protein-protein interactions with cTHY28. [Doctoral Dissertation]. University of Georgia; 2015. Available from: http://purl.galileo.usg.edu/uga_etd/stephens_christopher_b_201512_phd

Texas A&M University

6. Wang, Bo. Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors.

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

APA (6^th Edition):

Wang, B. (2011). Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors. (Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847

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, Bo. “Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors.” 2011. Thesis, Texas A&M University. Accessed October 22, 2019. http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847.

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, Bo. “Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors.” 2011. Web. 22 Oct 2019.

Vancouver:

Wang B. Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors. [Internet] [Thesis]. Texas A&M University; 2011. [cited 2019 Oct 22]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847.

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

Council of Science Editors:

Wang B. Generating a Consistent Framework for Evaluating Cell Response to External Stimuli through Epigenetic Assessors. [Thesis]. Texas A&M University; 2011. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-05-8847

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

University of Edinburgh

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: histones; bivalent; a-globin; chromatin immunoprecipitation; ChIP studies; gene editing

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

APA (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 October 22, 2019. 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. 22 Oct 2019.

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 2019 Oct 22]. 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

Eastern Michigan University

8. McDonough, Kelli. Reproducibility and reliability of chromatin immunoprecipitation in clinical research.

Degree: Health Sciences, 2016, Eastern Michigan University

URL: http://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 http://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 October 22, 2019. http://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. 22 Oct 2019.

Vancouver:

McDonough K. Reproducibility and reliability of chromatin immunoprecipitation in clinical research. [Internet] [Thesis]. Eastern Michigan University; 2016. [cited 2019 Oct 22]. Available from: http://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: http://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 Edinburgh

9. 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 October 22, 2019. http://hdl.handle.net/1842/22970.

MLA Handbook (7^th Edition):

Sharma, Nidhi. “Characterising the role of TLE1 in Crohn's disease.” 2016. Web. 22 Oct 2019.

Vancouver:

Sharma N. Characterising the role of TLE1 in Crohn's disease. [Internet] [Doctoral dissertation]. University of Edinburgh; 2016. [cited 2019 Oct 22]. 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

Wayne State University

10. Wang, Haihui. Ribonomic Control During Global Brain Ischemia And Reperfusion.

Degree: PhD, Physiology, 2014, Wayne State University

URL: https://digitalcommons.wayne.edu/oa_dissertations/1059

► Abstract RIBONOMIC CONTROL DURING GLOBAL BRAIN ISCHEMIA AND REPERFUSION by HAIHUI WANG August 2014 Advisor: Donald J. DeGracia, Ph.D. Major: Physiology Degree: Doctor of… (more)

▼ Abstract RIBONOMIC CONTROL DURING GLOBAL BRAIN ISCHEMIA AND REPERFUSION by HAIHUI WANG August 2014 Advisor: Donald J. DeGracia, Ph.D. Major: Physiology Degree: Doctor of Philosophy The study presented here used "omic" technology to look at the mechanism behind the selective delayed death of hippocampus CA1 neurons after transient global brain ischemia. The main findings are summarized: 1. The main form of ELAV protein family member detected in CA1/CA3 in Hu protein immunoprecipitation and polysomes was HuB (Rel-N1). HuB is present in control CA3, 8 hr reperfused CA3, and 8 hr reperfused CA1, but absent from control CA1. AUF-1, hnRNP K, hnRNP M were also absent from control CA1 following Hu protein immunoprecipitation and Western blot, suggesting that HuB bound AUF-1, hnRNP K, hnRNP M in all experimental groups except control CA1. 2. mRNA populations were different between sucrose pad preparation and sucrose gradient preparations of polysomes, although both were enriched with ARE-mRNA. This suggests different RNA binding complexes were isolated by the two methods. 3. Polysomes fractionation on sucrose pad and Hu protein immunoprecipitations using post-mitochondrial supernatants from homogenized brain regions were shown by 316 liquid chromatography mass spectroscopy to be over 75% contaminated by neuron debris, cytoskeleton and internal membrane structures, in spite of showing no contamination by Western blots of organelle markers. This suggests proteomics should become the accepted standard for validating purity of reactions derived from homogenized tissues. To summarize the results, I have worked up a consistent method of isolating polysomes from whole animal model, which has less contamination than the sucrose density gradient method. Both results from Hu IP and polysomes experiments show that control CA1 is in a different state compared with control CA3. My results suggest that the selective vulnerability of CA1 after ischemia reperfusion injury may be due, in part, to the fact that CA1 is "weaker" from the beginning. This finding is significant as it shifts the focus of research from studying the difference of ischemia reperfusion injury to the different initial states of CA1 and CA3 neurons. This study has also reformed our general idea as revealed by the high resolution of proteomics, which is superior to Western blotting for detecting contamination of samples. It is shown here that contaminationmakes up a large proportion of subcellular fractionations. This result suggests proteomics should be the new standard for quantifying contaminants, particularly in fractions obtained from whole tissues in animal experimental models. Advisors/Committee Members: Donald J. DeGracia.

Subjects/Keywords: ARE-mRNA; HuB; Hu immunoprecipitation; microarray; polysomes; proteomics; Physiology

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

APA (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 October 22, 2019. https://digitalcommons.wayne.edu/oa_dissertations/1059.

MLA Handbook (7^th Edition):

Wang, Haihui. “Ribonomic Control During Global Brain Ischemia And Reperfusion.” 2014. Web. 22 Oct 2019.

Vancouver:

Wang H. Ribonomic Control During Global Brain Ischemia And Reperfusion. [Internet] [Doctoral dissertation]. Wayne State University; 2014. [cited 2019 Oct 22]. 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

University of Texas Southwestern Medical Center

11. 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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Nalley KA. Ubiquitin, the Proteasome, and Dynamics at the Protein/DNA Interface. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2006. [cited 2019 Oct 22]. 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

University of Rochester

12. Li, Na. Mechanism and Significance of the Interaction between the Two Subunits of the Organic Solute Transporter, Ostα-Ostβ.

Degree: PhD, 2010, University of Rochester

URL: http://hdl.handle.net/1802/9818

► The heteromeric organic solute and steroid transporter (Ostα-Ostβ) is a major basolateral transporter of bile acids and endogenous and exogenous conjugated steroids in a variety… (more)

▼ The heteromeric organic solute and steroid transporter (Ostα-Ostβ) is a major basolateral transporter of bile acids and endogenous and exogenous conjugated steroids in a variety of tissues, including the small intestine, kidney, adrenal gland, and liver. The functional Ostα-Ostβ transporter requires co-expression of two distinct gene products, a predicted 340 amino acid, seven-transmembrane (TM) domain protein, Ostα, and a 128 amino acid, single TM domain polypeptide, Ostβ. The purpose of this study was to identify the mechanism by which these two gene products interact to generate transport activity. Direct evidence for heterodimerization between Ostα and Ostβ, as well as for homodimerization of Ostα, was provided by studies that utilized co-immunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC) analysis. BiFC analysis and surface immunolabeling of transfected HEK293 cells also indicated that the carboxyl termini of both Ostα and Ostβ are facing towards the intracellular space. The interaction between Ostα and Ostβ was found to be required not only for delivery of the proteins to the plasma membrane, but for maintaining protein stability, as assessed in transfected HEK293 cells and in tissues from Ostα-deficient mice. By characterizing multiple Ostβ mutant constructs, the TM domain of Ostβ was identified as a major site of interaction with Ostα. Of significance, the complex formed between Ostα and a 25-amino acid peptide consisting largely of the TM domain of Ostβ was trapped in the endoplasmic reticulum, suggesting that this peptide or related peptides may be used as inhibitors of the transporter. Additional studies revealed that the cysteine-rich region in Ostα appeared to be required for transport activity, but not for heterodimerization or trafficking. In contrast, mutation of the putative endoplasmic reticulum retrieval sequences (Arg-Arg-Lys and Arg- Asn-Arg) had only small effects on function. Overall, these findings provide important insights into the structure and function of the heterodimeric Ostα-Ostβ transporter, and suggest an approach for inhibiting this transporter. Because Ostα- Ostβ is critical for intestinal bile acid and lipid absorption, these findings have important implications for the regulation of bile acid and lipid levels in humans.

Subjects/Keywords: Ostα; Ostβ; Bile Acid Absorption; Cholesterol; Co-Immunoprecipitation; BiFc; Mutagenesis

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

APA (6^th Edition):

Li, N. (2010). Mechanism and Significance of the Interaction between the Two Subunits of the Organic Solute Transporter, Ostα-Ostβ. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/9818

Chicago Manual of Style (16^th Edition):

Li, Na. “Mechanism and Significance of the Interaction between the Two Subunits of the Organic Solute Transporter, Ostα-Ostβ.” 2010. Doctoral Dissertation, University of Rochester. Accessed October 22, 2019. http://hdl.handle.net/1802/9818.

MLA Handbook (7^th Edition):

Li, Na. “Mechanism and Significance of the Interaction between the Two Subunits of the Organic Solute Transporter, Ostα-Ostβ.” 2010. Web. 22 Oct 2019.

Vancouver:

Li N. Mechanism and Significance of the Interaction between the Two Subunits of the Organic Solute Transporter, Ostα-Ostβ. [Internet] [Doctoral dissertation]. University of Rochester; 2010. [cited 2019 Oct 22]. Available from: http://hdl.handle.net/1802/9818.

Council of Science Editors:

Li N. Mechanism and Significance of the Interaction between the Two Subunits of the Organic Solute Transporter, Ostα-Ostβ. [Doctoral Dissertation]. University of Rochester; 2010. Available from: http://hdl.handle.net/1802/9818

University of Florida

13. Mathew, Reshmi. Bardet- Biedl Syndrome 5 and Arrestin1 in photoreceptor outer segments with additional proteins of larger macromolecular complex.

Degree: 2015, University of Florida

URL: http://ufdc.ufl.edu/AA00037428

► Bardet-Biedl Syndrome 5 gene (BBS5) encodes a protein that has been directly linked to the autosomal recessive disorder called Bardet-Biedl syndrome. Previous studies in our… (more)

Subjects/Keywords: Antibodies; Bead welding; Cilia; Flasks; Gels; Immunoprecipitation; Photoreceptors; Plasmids; Retina; Transfection

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APA (6^th Edition):

Mathew, R. (2015). Bardet- Biedl Syndrome 5 and Arrestin1 in photoreceptor outer segments with additional proteins of larger macromolecular complex. (Thesis). University of Florida. Retrieved from http://ufdc.ufl.edu/AA00037428

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):

Mathew, Reshmi. “Bardet- Biedl Syndrome 5 and Arrestin1 in photoreceptor outer segments with additional proteins of larger macromolecular complex.” 2015. Thesis, University of Florida. Accessed October 22, 2019. http://ufdc.ufl.edu/AA00037428.

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

MLA Handbook (7^th Edition):

Mathew, Reshmi. “Bardet- Biedl Syndrome 5 and Arrestin1 in photoreceptor outer segments with additional proteins of larger macromolecular complex.” 2015. Web. 22 Oct 2019.

Vancouver:

Mathew R. Bardet- Biedl Syndrome 5 and Arrestin1 in photoreceptor outer segments with additional proteins of larger macromolecular complex. [Internet] [Thesis]. University of Florida; 2015. [cited 2019 Oct 22]. Available from: http://ufdc.ufl.edu/AA00037428.

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

Council of Science Editors:

Mathew R. Bardet- Biedl Syndrome 5 and Arrestin1 in photoreceptor outer segments with additional proteins of larger macromolecular complex. [Thesis]. University of Florida; 2015. Available from: http://ufdc.ufl.edu/AA00037428

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

University of Southern California

14. 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/3324

► 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 (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/3324

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 October 22, 2019. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/21674/rec/3324.

MLA Handbook (7^th Edition):

Huang, Fangjin. “Identify Werner protein molecular partners in S phase alt cell.” 2012. Web. 22 Oct 2019.

Vancouver:

Huang F. Identify Werner protein molecular partners in S phase alt cell. [Internet] [Masters thesis]. University of Southern California; 2012. [cited 2019 Oct 22]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/21674/rec/3324.

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/3324

University of Manitoba

15. 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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Ilic A. Role of UCHL1 in regulating gene expression in prostate cancer cells. [Internet] [Masters thesis]. University of Manitoba; 2014. [cited 2019 Oct 22]. 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 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

►

Note: The general metadata – e.g., title, author, abstract, subject headings, etc. – is publicly available, but access to the submitted files is restricted to… (more)

▼

Note: 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 only.

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 (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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Lan Q. Transcriptional Regulation of Intestinal Stem Cell Lineage in Drosophila. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2017. [cited 2019 Oct 22]. 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

Texas A&M University

17. Zhou, Jian. Characterizing the Function of Clockwork Orange in the Circadian Feedback Loops in Drosophila melanogaster.

Degree: PhD, Biology, 2017, Texas A&M University

URL: http://hdl.handle.net/1969.1/165920

► The Drosophila circadian oscillator controls daily rhythms in physiology, metabolism and behavior via transcriptional feedback loops. CLOCK-CYCLE (CLK-CYC) heterodimers initiate feedback loop function by binding… (more)

▼ The Drosophila circadian oscillator controls daily rhythms in physiology, metabolism and behavior via transcriptional feedback loops. CLOCK-CYCLE (CLK-CYC) heterodimers initiate feedback loop function by binding enhancer box (E-box) elements to activate period (per) and timeless (tim) transcription. PER-TIM heterodimers then accumulate, bind CLK-CYC to inhibit transcription, and are ultimately degraded to enable the next round of transcription. Although tremendous efforts have been made to understand how these feedback loops are regulated, the detailed molecular mechanism of transcriptional repression is still not clear. By using genetic, molecular, and genome-wide bioinformatic analyses, I have characterized the molecular function of the transcription factor CLOCKWORK ORANGE (CWO) for the circadian transcriptional repression, and further identified its downstream targets aiming to understand its function at genome-wide level. The timing of transcriptional events in the circadian feedback loops coincide with, and are controlled by, rhythms in CLK-CYC binding to E-boxes. PER rhythmically binds CLK-CYC to initiate transcriptional repression, and subsequently promotes the removal of CLK-CYC from E-boxes. However, little is known about the mechanism by which CLK-CYC are removed from DNA. Here I show that the transcription repressor CWO rhythmically binds E-boxes upstream of core clock genes in a reciprocal manner to CLK, thereby promoting PER-dependent removal of CLK-CYC from E-boxes, and maintaining repression until PER is degraded and CLK-CYC displaces CWO from E-boxes to initiate transcription. These results suggest a model in which CWO co-represses CLK-CYC transcriptional activity in conjunction with PER by competing for E-box binding once CLK-CYC-PER complexes have formed. Given that CWO orthologs DEC1 and DEC2 also target E-boxes bound by CLOCK-BMAL1, a similar mechanism may operate in the mammalian clock. Furthermore, using ChIP-seq and RNA-seq analyses, I show that CWO directly and indirectly regulates gene expression at genome-wide level. A substantial overlap between CWO and CLK direct target genes suggests that CWO plays a potential role in regulating CLK-mediated transcription globally. Moreover, CWO indirectly regulates a subset of genes encoding kinases and phosphatases at transcriptional level, suggesting its role in the posttranscriptional regulation of CLK during the circadian cycle. Advisors/Committee Members: Hardin, Paul (advisor), Bell-Pedersen, Deborah (committee member), García, Luis René (committee member), Panin, Vladislav (committee member).

Subjects/Keywords: Circadian; Transcription; Feedback loop; Clockwork Orange; Chromatin immunoprecipitation

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

APA (6^th Edition):

Zhou, J. (2017). Characterizing the Function of Clockwork Orange in the Circadian Feedback Loops in Drosophila melanogaster. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/165920

Chicago Manual of Style (16^th Edition):

Zhou, Jian. “Characterizing the Function of Clockwork Orange in the Circadian Feedback Loops in Drosophila melanogaster.” 2017. Doctoral Dissertation, Texas A&M University. Accessed October 22, 2019. http://hdl.handle.net/1969.1/165920.

MLA Handbook (7^th Edition):

Zhou, Jian. “Characterizing the Function of Clockwork Orange in the Circadian Feedback Loops in Drosophila melanogaster.” 2017. Web. 22 Oct 2019.

Vancouver:

Zhou J. Characterizing the Function of Clockwork Orange in the Circadian Feedback Loops in Drosophila melanogaster. [Internet] [Doctoral dissertation]. Texas A&M University; 2017. [cited 2019 Oct 22]. Available from: http://hdl.handle.net/1969.1/165920.

Council of Science Editors:

Zhou J. Characterizing the Function of Clockwork Orange in the Circadian Feedback Loops in Drosophila melanogaster. [Doctoral Dissertation]. Texas A&M University; 2017. Available from: http://hdl.handle.net/1969.1/165920

Virginia Tech

18. Murphy, Travis Wilson. Microfluidic tools for molecular analysis and engineering.

Degree: PhD, Chemical Engineering, 2019, Virginia Tech

URL: http://hdl.handle.net/10919/90793

► The shift of medical technology from a doctor's application of individualized medicine toward precision medicine has been accelerated by the advent of Next Generation Sequencing.… (more)

▼ The shift of medical technology from a doctor's application of individualized medicine toward precision medicine has been accelerated by the advent of Next Generation Sequencing. Individualized medicine is where a doctor tries to understand the intricacies of a patient's medical state, where precision medicine uses a wealth of data to understand the individuality of a patient on a biological level to determine treatment course. Next Generation Sequencing allows for the collection of genome wide analyses such as genomic, transcriptomic, and epigenomic sequencing, which provides the backbone of the data driven precision medicine. In order to obtain and use this data, it needs to be produced from minimal amounts of patient tissue, such as the amount from a needle biopsy. In order to perform so many different assays it is paramount that we develop high sensitivity methodologies, such that we can gain an understanding of the patient's physiology without causing much discomfort in gathering large amounts of sample. In pursuit of making more tests, data, and assays available for use in precision medicine, we have developed 3 different microfluidic technologies, which automate and simplify the assays needed for the data collection at a high sensitivity, as well as a versatile platform for therapeutic production. First, we developed a epigenomic assay for chromatin immunoprecipitation, which gives us information on histone modifications across the genome. These histone modifications heavily impact gene expression and how the chromatin is organized, as well promoting or inhibiting transcription of genes. Our technology allowed us to perform multiple parallel assays from as few as 50 cells quickly and reliably using our fluidized bed technology. Next, we developed a library preparation system, which reduces the cost of library preparation by 20x and reduces operator pipetting by 100x. Our system uses a droplet based reactor to quickly and reliably prepare sequencing libraries using the lowest amount of DNA to date, 10 pg. Finally, we designed a therapeutics-on-a-chip platform which is capable of producing clinically relevant proteins on demand from temperature stable components. Using our system, we are capable of producing a number of different therapeutics on demand quickly without rearrangement of the system. Advisors/Committee Members: Lu, Chang (committeechair), Davis, Richey M. (committee member), Goldstein, Aaron S. (committee member), Ducker, William A. (committee member).

Subjects/Keywords: Microfluidics; Epigenomics; Precision Medicine; Therapeutics; Chromatin Immunoprecipitation; Next Generation Sequencing; NGS

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APA (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 October 22, 2019. http://hdl.handle.net/10919/90793.

MLA Handbook (7^th Edition):

Murphy, Travis Wilson. “Microfluidic tools for molecular analysis and engineering.” 2019. Web. 22 Oct 2019.

Vancouver:

Murphy TW. Microfluidic tools for molecular analysis and engineering. [Internet] [Doctoral dissertation]. Virginia Tech; 2019. [cited 2019 Oct 22]. 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

19. 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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

MINGSHI K. Mechanisms of hormonally-induced transcription of LHBeta subunit gene in its chromatin setting. [Internet] [Thesis]. National University of Singapore; 2005. [cited 2019 Oct 22]. 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

Purdue University

20. 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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Wang Y. Protein Affinity Extraction Of Prostate Specific Antigen (PSA) Using Submicron Spheres. [Internet] [Thesis]. Purdue University; 2014. [cited 2019 Oct 22]. 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

Uppsala University

21. 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 (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 October 22, 2019. 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. 22 Oct 2019.

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 2019 Oct 22]. 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

Penn State University

22. Ebersole, Brittany Anne. Investigating the role of palmitoylation in the function of the dopamine D2 receptor.

Degree: PhD, Integrative Biosciences, 2015, Penn State University

URL: https://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.¬

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. (Doctoral Dissertation). Penn State University. Retrieved from https://etda.libraries.psu.edu/catalog/24760

Chicago Manual of Style (16^th Edition):

Ebersole, Brittany Anne. “Investigating the role of palmitoylation in the function of the dopamine D2 receptor.” 2015. Doctoral Dissertation, Penn State University. Accessed October 22, 2019. https://etda.libraries.psu.edu/catalog/24760.

MLA Handbook (7^th Edition):

Ebersole, Brittany Anne. “Investigating the role of palmitoylation in the function of the dopamine D2 receptor.” 2015. Web. 22 Oct 2019.

Vancouver:

Ebersole BA. Investigating the role of palmitoylation in the function of the dopamine D2 receptor. [Internet] [Doctoral dissertation]. Penn State University; 2015. [cited 2019 Oct 22]. Available from: https://etda.libraries.psu.edu/catalog/24760.

Council of Science Editors:

Ebersole BA. Investigating the role of palmitoylation in the function of the dopamine D2 receptor. [Doctoral Dissertation]. Penn State University; 2015. Available from: https://etda.libraries.psu.edu/catalog/24760

University of Saskatchewan

23. 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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Akin ZN. Identification and characterization of hoxa2 target genes by ChIP. [Internet] [Thesis]. University of Saskatchewan; 2004. [cited 2019 Oct 22]. 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

University of Western Ontario

24. Winick-Ng, Warren R. A Non-Canonical Role for Choline Acetyltransferase in Chromatin Organization and the Response to Beta-Amyloid.

Degree: 2016, University of Western Ontario

URL: https://ir.lib.uwo.ca/etd/4215

► The three-dimensional structure of chromatin is essential for context-dependent regulation of gene expression in post-mitotic neurons. Chromosomal rearrangements have been observed in the aging brain,… (more)

▼ The three-dimensional structure of chromatin is essential for context-dependent regulation of gene expression in post-mitotic neurons. Chromosomal rearrangements have been observed in the aging brain, and proteins involved in chromatin organization have altered expression and/or localization in Alzheimer’s disease (AD). A human- and primate-specific transcript of choline acetyltransferase produces an 82-kDa protein (82-kDa ChAT) that is localized to the nucleus of cholinergic neurons, but is found in the cytoplasm in individuals with mild cognitive impairment (MCI) and AD. The function of the 82-kDa ChAT protein is unknown, though recent evidence suggests it has a role in gene expression changes in response to cellular perturbations. In the present study, we explore whether 82-kDa ChAT is involved in global chromatin organization and an epigenetic response to cytotoxic amyloid-β(Aβ) exposure. We show that 82-kDa ChAT associates with chromatin in human SH-SY5Y neural cells using chromatin immunoprecipitation with next-generation sequencing (ChIP-seq), finding that acute exposure of cells to oligomeric Aβ1–42 increases 82-kDa ChAT associations with gene promoters and introns. Following Aβ1–42-exposure, 82-kDa ChAT co-localizes in nuclear aggregates with special AT-rich binding protein 1 (SATB1), which anchors DNA to scaffolding/matrix attachment regions (S/MARs). SATB1 has similar increases in genic associations following Aβ1–42-exposure, and both SATB1 and 82-kDa ChAT associate with synapse-related genes. The 82-kDa ChAT and SATB1 proteins have patterned genomic associations at regions enriched with S/MAR binding motifs, preventing an Aβ1–42-induced increase in an isoform-specific APP mRNA transcript. Finally, we show that 82-kDa ChAT expression during cholinergic differentiation of SH-SY5Y cells increases the steady-state levels of proteins related to synapse formation, resulting in increased neurite complexity. These results demonstrate that 82-kDa ChAT and SATB1 regulate chromatin organization at S/MARs, resulting in context-dependent gene expression changes in cholinergic cells and increased expression of synapse formation-related proteins during cholinergic differentiation. Cholinergic synapse dysfunction and degeneration is observed early in AD progression and 82-kDa ChAT is mislocalized in AD, therefore the loss of both the epigenetic response to Aβ and gene expression changes related to synapse formation and maintenance may have implications for the etiology or progression of MCI and AD.

Subjects/Keywords: Choline acetyltransferase; Chromatin immunoprecipitation; Chromatin organization; Epigenetics; Scaffolding/matrix attachment regions; Super-resolution microscopy; Neurosciences

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

APA (6^th Edition):

Winick-Ng, W. R. (2016). A Non-Canonical Role for Choline Acetyltransferase in Chromatin Organization and the Response to Beta-Amyloid. (Thesis). University of Western Ontario. Retrieved from https://ir.lib.uwo.ca/etd/4215

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):

Winick-Ng, Warren R. “A Non-Canonical Role for Choline Acetyltransferase in Chromatin Organization and the Response to Beta-Amyloid.” 2016. Thesis, University of Western Ontario. Accessed October 22, 2019. https://ir.lib.uwo.ca/etd/4215.

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

MLA Handbook (7^th Edition):

Winick-Ng, Warren R. “A Non-Canonical Role for Choline Acetyltransferase in Chromatin Organization and the Response to Beta-Amyloid.” 2016. Web. 22 Oct 2019.

Vancouver:

Winick-Ng WR. A Non-Canonical Role for Choline Acetyltransferase in Chromatin Organization and the Response to Beta-Amyloid. [Internet] [Thesis]. University of Western Ontario; 2016. [cited 2019 Oct 22]. Available from: https://ir.lib.uwo.ca/etd/4215.

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

Council of Science Editors:

Winick-Ng WR. A Non-Canonical Role for Choline Acetyltransferase in Chromatin Organization and the Response to Beta-Amyloid. [Thesis]. University of Western Ontario; 2016. Available from: https://ir.lib.uwo.ca/etd/4215

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

University of Western Ontario

25. Anguraj Vadivel, Arun Kumaran. GmMYB176 Interactome and Regulation of Isoflavonoid Biosynthesis in Soybean.

Degree: 2017, University of Western Ontario

URL: https://ir.lib.uwo.ca/etd/4639

► MYB transcription factors are one of the largest transcription factor families characterized in plants. They are classified into four types: R1 MYB, R2R3 MYB, R3… (more)

▼ MYB transcription factors are one of the largest transcription factor families characterized in plants. They are classified into four types: R1 MYB, R2R3 MYB, R3 MYB and R4 MYB. GmMYB176 is an R1MYB transcription factor that regulates Chalcone synthase (CHS8) gene expression and isoflavonoid biosynthesis in soybean. Silencing of GmMYB176 suppressed the expression of the GmCHS8 gene and reduced the accumulation of isoflavonoids in soybean hairy roots. However, overexpression of GmMYB176 does not alter either GmCHS8 gene expression or isoflavonoid levels suggesting that GmMYB176 alone is not sufficient for GmCHS8 gene regulation. I hypothesized that GmMYB176 acts cooperatively with another factor(s) for the regulation of GmCHS8 gene expression and it may also regulate other isoflavonoid biosynthetic genes in soybean. The objective of this research was to identify the GmMYB176 interactome for GmCHS8 gene regulation and elucidate the role of GmMYB176 in isoflavonoid biosynthesis in soybean. GmMYB176 interacting proteins were identified using two translational fusion baits (GmMYB176-YFP and YFP-GmMYB176) by co-immunoprecipitation, followed by liquid chromatography-tandem mass spectrometry. The interaction of selected candidates with GmMYB176 was validated in planta and their DNA binding activities determined. GmMYB176 may form a transcriptional complex with Gm04bZIP and/or Gm05bZIP for the regulation of GmCHS8 gene expression. RNA-seq and metabolomics analyses of soybean hairy roots in which GmMYB176 was either silenced or over-expressed revealed that GmMYB176 regulates multiple genes in the isoflavonoid biosynthesis pathway, affecting the production of metabolites in phenylpropanoid pathway such as phenylalanine, liquiritigenin, daidzin, genistin, glycitein, and glyceollin. The knowledge and information generated on the role of GmMYB176 in the regulation of isoflavonoid biosynthesis will allow genetic manipulation of isoflavonoid level in soybean and/or introduce isoflavonoid pathway in non-legumes.

Subjects/Keywords: Co-immunoprecipitation; MYB; isoflavonoid biosynthesis; transcriptional complex; gene regulation; soybean; Molecular Biology; Plant Biology

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

APA (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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Anguraj Vadivel AK. GmMYB176 Interactome and Regulation of Isoflavonoid Biosynthesis in Soybean. [Internet] [Thesis]. University of Western Ontario; 2017. [cited 2019 Oct 22]. 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 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).

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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

McMurray EN. Identification of Imprinting Regulators at the Meg3 Differentially Methylated Region. [Internet] [Thesis]. University of Illinois – Chicago; 2013. [cited 2019 Oct 22]. 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

27. 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 October 22, 2019. 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. 22 Oct 2019.

Vancouver:

Feijóo Buján A. Comprobación de una interacción física de HMGB1 con su diana . [Internet] [Masters thesis]. Universidad da Coruña; 2017. [cited 2019 Oct 22]. 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

University of the Western Cape

28. 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 October 22, 2019. 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. 22 Oct 2019.

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 2019 Oct 22]. 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

29. 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 October 22, 2019. 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. 22 Oct 2019.

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 2019 Oct 22]. 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

Virginia Tech

30. Cao, Zhenning. Microfluidic Engineering for Ultrasensitive Molecular Analysis of cells.

Degree: PhD, Biomedical Engineering, 2015, Virginia Tech

URL: http://hdl.handle.net/10919/76721

► The main focus of this research was the development of microfluidic technology for ultrasensitive and fast molecular analysis of cells. Chromatin immunoprecipitation (ChIP) assay followed… (more)

▼ The main focus of this research was the development of microfluidic technology for ultrasensitive and fast molecular analysis of cells. Chromatin immunoprecipitation (ChIP) assay followed by next generation sequencing serves as the primary technique to characterize the genomic locations associated with histone modifications. However, conventional ChIP-seq assay requires large numbers of cells. We demonstrate a novel microfluidics-based ChIP-seq assay which dramatically reduced the required cell number. Coupled with next generation sequencing, the assay permitted the analysis of histone modifications at the whole genome from as few as ~100 cells. Using the same device, we demonstrated that MeDIP-seq with tiny amount of DNA (<5ng) generated high quality genome-wide profiles of DNA methylation. Off-chip sonication often leads to sample loss due to multiple tube transferring. In addition, conventional sonicators are not able to manipulate samples with small volume. We developed a novel microfluidic sonicator, which is able to achieve on-chip DNA/chromatin shearing into ideal fragment size (100~600bp) for both chromatin immunoprecipitation (ChIP) and methylated DNA immunoprecipitation (MeDIP). The integrated on-chip sonication followed by immunoprecipitation (IP) reaction can significantly reduce sample loss and contamination. Simple and accessible detection methods that can rapidly screen a large cell population with single cell resolution have been seriously lacking. We demonstrate a simple protocol for detecting translocation of native proteins using a common flow cytometer which detects fluorescence intensity without imaging. Using our approach, we successfully detected the translocation of native NF-kappa B (an important transcription factor) at its native expression level and examine the temporal dynamics in the process. Droplets with encapsulated beads and cells have been increasingly used for studying molecular and cellular biology. However, a mixed population of droplets with an uneven number or type of encapsulated particles is resulted and used for screening. We developed a fluorescence-activated microfluidic droplet sorter that integrated a simple deflection mechanism. By passing droplets through a narrow interrogation channel, the encapsulated particles were detected individually. The microcontroller conducted the computation to determine the number and type of encapsulated particles in each droplet and made the sorting decision. Our results showed high efficiency and accuracy for sorting and enrichment. Advisors/Committee Members: Lu, Chang-Tien (committeechair), Agah, Masoud (committee member), Li, Liwu (committee member), Davalos, Rafael V. (committee member), Jung, Sunghwan (committee member).

Subjects/Keywords: chromatin immunoprecipitation(ChIP); next generation sequencing; microfluidics; droplet sorting; protein translocation; sonication

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

APA (6^th Edition):

Cao, Z. (2015). Microfluidic Engineering for Ultrasensitive Molecular Analysis of cells. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/76721

Chicago Manual of Style (16^th Edition):

Cao, Zhenning. “Microfluidic Engineering for Ultrasensitive Molecular Analysis of cells.” 2015. Doctoral Dissertation, Virginia Tech. Accessed October 22, 2019. http://hdl.handle.net/10919/76721.

MLA Handbook (7^th Edition):

Cao, Zhenning. “Microfluidic Engineering for Ultrasensitive Molecular Analysis of cells.” 2015. Web. 22 Oct 2019.

Vancouver:

Cao Z. Microfluidic Engineering for Ultrasensitive Molecular Analysis of cells. [Internet] [Doctoral dissertation]. Virginia Tech; 2015. [cited 2019 Oct 22]. Available from: http://hdl.handle.net/10919/76721.

Council of Science Editors:

Cao Z. Microfluidic Engineering for Ultrasensitive Molecular Analysis of cells. [Doctoral Dissertation]. Virginia Tech; 2015. Available from: http://hdl.handle.net/10919/76721

Open Access Theses and Dissertations