subject:( SUMO consensus sequence)

University of St. Andrews

1. Carr, Sharon. Adenovirus and its interaction with host cell proteins .

Degree: 2007, University of St. Andrews

► The E1B55k gene in adenovirus type 5 was studied by generating recombinant viruses in which the E1B55k gene was N-terminally tagged with either a cyan… (more)

Subjects/Keywords: Adenovirus; E1B55k; SUMO; Recombinant; Tandem affinity purification; TAP; CFP; Cyan fluorescent protein; Lysine to arginine mutation; SUMO consensus sequence

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APA (6^th Edition):

Carr, S. (2007). Adenovirus and its interaction with host cell proteins . (Thesis). University of St. Andrews. Retrieved from http://hdl.handle.net/10023/219

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):

Carr, Sharon. “Adenovirus and its interaction with host cell proteins .” 2007. Thesis, University of St. Andrews. Accessed January 18, 2021. http://hdl.handle.net/10023/219.

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

MLA Handbook (7^th Edition):

Carr, Sharon. “Adenovirus and its interaction with host cell proteins .” 2007. Web. 18 Jan 2021.

Vancouver:

Carr S. Adenovirus and its interaction with host cell proteins . [Internet] [Thesis]. University of St. Andrews; 2007. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/10023/219.

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

Council of Science Editors:

Carr S. Adenovirus and its interaction with host cell proteins . [Thesis]. University of St. Andrews; 2007. Available from: http://hdl.handle.net/10023/219

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

University of Adelaide

2. James, Sarah Ellen. Consensus sequence estimation methods for DNA sequence data sets.

Degree: 2017, University of Adelaide

URL: http://hdl.handle.net/2440/114060

► A combination of ancient and modern DNA sequences and geographical information is used in phylogenetics, to study the evolutionary relationships between individuals or species. A… (more)

Subjects/Keywords: consensus sequence estimation; DNA; ancient DNA

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APA (6^th Edition):

James, S. E. (2017). Consensus sequence estimation methods for DNA sequence data sets. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/114060

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):

James, Sarah Ellen. “Consensus sequence estimation methods for DNA sequence data sets.” 2017. Thesis, University of Adelaide. Accessed January 18, 2021. http://hdl.handle.net/2440/114060.

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

MLA Handbook (7^th Edition):

James, Sarah Ellen. “Consensus sequence estimation methods for DNA sequence data sets.” 2017. Web. 18 Jan 2021.

Vancouver:

James SE. Consensus sequence estimation methods for DNA sequence data sets. [Internet] [Thesis]. University of Adelaide; 2017. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/2440/114060.

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

Council of Science Editors:

James SE. Consensus sequence estimation methods for DNA sequence data sets. [Thesis]. University of Adelaide; 2017. Available from: http://hdl.handle.net/2440/114060

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

University of Sydney

3. Tanaka, Emi. Statistical Methods for Improving Motif Evaluation .

Degree: 2014, University of Sydney

URL: http://hdl.handle.net/2123/13922

► Gene regulation, especially cis-regulation of gene expression by the binding of transcription factors, is a critical component of cellular physiology. Transcription regulation is heavily influenced… (more)

▼ Gene regulation, especially cis-regulation of gene expression by the binding of transcription factors, is a critical component of cellular physiology. Transcription regulation is heavily influenced by the binding of transcription factors, and as such, it is of great interest to characterise these binding sites. The binding sites of a transcription factor are collectively referred to as a regulatory motif. Recent advancement in sequencing technology generated vast amounts of biological data. Thus computational tools are required to process and analyse this massive information. In particular, computational tools were developed to search for over-represented words among a set of co-regulated sequences. Such tools would be somewhat incomplete without a statistical analysis that allows researchers to discern between real biological significant sites and random artefacts. By analogy, it is difficult to imagine evaluating a BLAST result without its accompanying E-value. Of the many motif finders, MEME, with over 9000 unique users recorded in the first half of 2013, is one of the most popular motif finding tools available. Currently MEME evaluates its candidate motifs using an extension of BLAST's E-value to the motif finding context. Ng et al. (2006) previously showed the drawbacks of MEME's current significance evaluation scheme, however because MEME relies on the same E-value to internally rank competing candidate motifs, the alternative evaluation offered by Keich and Ng (2007) was not a practical substitute. Here we offer a two-tiered significance analysis that can replace the E-value in selecting the best candidate motif as well as in evaluating its overall statistical significance. We show that our new approach substantially improves MEME's motif finding performance and also provides the user with a reliable significance analysis. In addition, for large input sets our new approach is faster than the currently implemented E-value analysis. After applying a motif finder to a set of co-regulated DNA sequences, researchers often are interested to know whether the reported putative motif is similar to any known motif. While several tools have been designed for this task, Habib et al. (2008) pointed out that the scores that are commonly used for measuring similarity between motifs do not distinguish between a good alignment of two informative columns (say, all-A) and one of two uninformative columns. This observation explains why motif comparison tools such as Tomtom occasionally return an alignment of uninformative columns which is clearly spurious. To address this distinguishability problem Habib et al. (2008) suggested a new score, the BLiC. This score uses a Bayesian information criterion to penalise matches that are similar to the background distribution. We show that the BLiC score exhibits other, highly undesirable properties. Therefore as an alternative, we offer a general approach to adjust any motif similarity score so as to reduce the number of reported spurious alignments of uninformative columns. We…

Subjects/Keywords: motif finding; MEME; autonomously replicating sequence; ARS consensus sequence; motif significance analysis; motif comparison

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

APA (6^th Edition):

Tanaka, E. (2014). Statistical Methods for Improving Motif Evaluation . (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/13922

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):

Tanaka, Emi. “Statistical Methods for Improving Motif Evaluation .” 2014. Thesis, University of Sydney. Accessed January 18, 2021. http://hdl.handle.net/2123/13922.

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

MLA Handbook (7^th Edition):

Tanaka, Emi. “Statistical Methods for Improving Motif Evaluation .” 2014. Web. 18 Jan 2021.

Vancouver:

Tanaka E. Statistical Methods for Improving Motif Evaluation . [Internet] [Thesis]. University of Sydney; 2014. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/2123/13922.

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

Council of Science Editors:

Tanaka E. Statistical Methods for Improving Motif Evaluation . [Thesis]. University of Sydney; 2014. Available from: http://hdl.handle.net/2123/13922

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

University of Ottawa

4. Rossl, Anthony. A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast.

Degree: 2018, University of Ottawa

URL: http://hdl.handle.net/10393/38300

► Acetylation was previously thought to occur exclusively on histones, but recent high-throughput screens have identified thousands of non-histone substrates. Despite the identification of these sites,… (more)

Subjects/Keywords: Gcn5; Acetylation; Targeting; Consensus sequence; Ada3; SILAC; SAGA; Sirtuin

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APA (6^th Edition):

Rossl, A. (2018). A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/38300

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):

Rossl, Anthony. “A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. ” 2018. Thesis, University of Ottawa. Accessed January 18, 2021. http://hdl.handle.net/10393/38300.

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

MLA Handbook (7^th Edition):

Rossl, Anthony. “A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. ” 2018. Web. 18 Jan 2021.

Vancouver:

Rossl A. A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. [Internet] [Thesis]. University of Ottawa; 2018. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/10393/38300.

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

Council of Science Editors:

Rossl A. A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. [Thesis]. University of Ottawa; 2018. Available from: http://hdl.handle.net/10393/38300

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

University of Tasmania

5. Woodworth, AM. Gene regulation by RUNX1 in the absence of consensus sequences.

Degree: 2020, University of Tasmania

URL: Woodworth, AM ORCID: 0000-0002-3798-4627 <https://orcid.org/0000-0002-3798-4627> 2020 , 'Gene regulation by RUNX1 in the absence of consensus sequences', PhD thesis, University of Tasmania.

► Runt-related transcription factor 1 (RUNX1) is a transcription factor that has an important role in haematopoietic cell development and function and is frequently disrupted in… (more)

▼ Runt-related transcription factor 1 (RUNX1) is a transcription factor that has an important role in haematopoietic cell development and function and is frequently disrupted in leukaemia. RUNX1 is commonly described as a sequence-specific DNA binding factor which recognises the consensus sequence TG(T/C)GGT in the promoter and enhancer regions of its target genes to affect changes in gene expression. However, the advent of techniques to study DNA-protein interactions on a genome-wide scale has provided the opportunity to re-assess RUNX1 localisation and function, and this analysis suggests that the classical model of RUNX1 function is incomplete. By fully understanding the mechanisms by which RUNX1 maintains its target gene expression profiles under normal cellular conditions, insights into disrupted function can be gained and interventions can be developed. Analysis of publicly available RUNX1 ChIP-Seq data determined that the majority of RUNX1 binding in haematopoietic cells occurs outside of gene promoter regions, in intergenic or intronic regions. Furthermore, approximately one fifth of all RUNX1-DNA binding sites on a genome-wide scale were not associated with a canonical consensus sequence, and this was particularly prevalent in promoter regions, with almost half of RUNX1 binding in promoter regions occurring in the absence of consensus sequences. This suggests that recruitment of RUNX1 to gene targets occurs through multiple mechanisms and raises the possibility that it may function differently depending on its location and mode of recruitment. Similar results were obtained for localisation of the RUNX1 fusion protein RUNX1-ETO, the product of a common chromosomal translocation in leukaemia. This data set was used to investigate the different modes of binding and action of RUNX1 with the aim of establishing whether binding in the absence of consensus sequences constitutes a novel mechanism of RUNX1 binding and if genes regulated in this way respond differently to RUNX1 disruption. This study identified biological pathways enriched for genes with RUNX1 binding in their promoters, and in which only one type of binding (in the presence or absence of a consensus sequence) occurred. Clusters of functionally related RUNX1-bound genes were selected from two of these pathways; the RhoA and HMGB1 signalling pathways and used as models to investigate regulation by RUNX1. The RhoA signalling pathway genes, ARHGAP1, ARHGAP4 and ARHGAP12, all bound RUNX1 at their promoters, in association with a consensus sequence. However, while ARHGAP4 and ARHGAP12 responded to RUNX1 in reporter assays, ARHGAP1 did not, suggesting that a consensus sequence alone is not sufficient for a promoter to respond to RUNX1. In contrast, a group of histone acetyl transferase genes from the HMGB1 signalling pathway bound RUNX1 at their promoters in the absence of a consensus sequence. Both the KAT6B and KAT2B promoters were activated by RUNX1 in the absence of a consensus sequence, suggesting a mechanism whereby RUNX1 recruitment to DNA does not…

Subjects/Keywords: RUNXI; Gene Regulation; AKL; consensus sequence; ChIP-seq

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APA (6^th Edition):

Woodworth, A. (2020). Gene regulation by RUNX1 in the absence of consensus sequences. (Thesis). University of Tasmania. Retrieved from Woodworth, AM ORCID: 0000-0002-3798-4627 <https://orcid.org/0000-0002-3798-4627> 2020 , 'Gene regulation by RUNX1 in the absence of consensus sequences', PhD thesis, University of Tasmania.

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):

Woodworth, AM. “Gene regulation by RUNX1 in the absence of consensus sequences.” 2020. Thesis, University of Tasmania. Accessed January 18, 2021. Woodworth, AM ORCID: 0000-0002-3798-4627 <https://orcid.org/0000-0002-3798-4627> 2020 , 'Gene regulation by RUNX1 in the absence of consensus sequences', PhD thesis, University of Tasmania..

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

MLA Handbook (7^th Edition):

Woodworth, AM. “Gene regulation by RUNX1 in the absence of consensus sequences.” 2020. Web. 18 Jan 2021.

Vancouver:

Woodworth A. Gene regulation by RUNX1 in the absence of consensus sequences. [Internet] [Thesis]. University of Tasmania; 2020. [cited 2021 Jan 18]. Available from: Woodworth, AM ORCID: 0000-0002-3798-4627 <https://orcid.org/0000-0002-3798-4627> 2020 , 'Gene regulation by RUNX1 in the absence of consensus sequences', PhD thesis, University of Tasmania..

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

Council of Science Editors:

Woodworth A. Gene regulation by RUNX1 in the absence of consensus sequences. [Thesis]. University of Tasmania; 2020. Available from: Woodworth, AM ORCID: 0000-0002-3798-4627 <https://orcid.org/0000-0002-3798-4627> 2020 , 'Gene regulation by RUNX1 in the absence of consensus sequences', PhD thesis, University of Tasmania.

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

University of Georgia

6. Kolychev, Dmitri Sergeevich. Microsatellite detection and consensus sequence verification by virtual PCR and machine learning.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/21091

► Microsatellites, or simple sequence repeats, are genetic loci where several nucleotide bases are repeated in tandem. Since they can be easily found by Polymerase Chain… (more)

Subjects/Keywords: microsatellite detection; neural networks; polymerase chain reaction; consensus sequence verification

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

APA (6^th Edition):

Kolychev, D. S. (2014). Microsatellite detection and consensus sequence verification by virtual PCR and machine learning. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/21091

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):

Kolychev, Dmitri Sergeevich. “Microsatellite detection and consensus sequence verification by virtual PCR and machine learning.” 2014. Thesis, University of Georgia. Accessed January 18, 2021. http://hdl.handle.net/10724/21091.

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

MLA Handbook (7^th Edition):

Kolychev, Dmitri Sergeevich. “Microsatellite detection and consensus sequence verification by virtual PCR and machine learning.” 2014. Web. 18 Jan 2021.

Vancouver:

Kolychev DS. Microsatellite detection and consensus sequence verification by virtual PCR and machine learning. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/10724/21091.

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

Council of Science Editors:

Kolychev DS. Microsatellite detection and consensus sequence verification by virtual PCR and machine learning. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/21091

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

The Ohio State University

7. Mohan, Sidharth. Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability.

Degree: PhD, Biophysics, 2017, The Ohio State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1503054678218166

► Proteins represent the most diverse class of molecules that form the biochemical basis of life, and are products of the innumerable ways in which the… (more)

▼ Proteins represent the most diverse class of molecules that form the biochemical basis of life, and are products of the innumerable ways in which the 20 canonical amino acids link to each other. The specific sequences of amino acids are the sole determinants of the 3-dimensional properties and functions of proteins. While it is imperative that we develop a holistic model to comprehend and predict the effects of amino acids and changes in protein sequences, our current understanding tends to be context-sensitive and limited to only a few properties over which we have exerted very little control. The structural homology of proteins is an outcome of natural evolution and forms the basis for our classification of these molecules. Parsing these 'families' of proteins has yielded interesting knowledge that has enabled us to make ascribe due importance to specific positions and their amino acid identities in determining many biophysical characteristics, such as thermodynamic stability, solubility, catalysis, and binding. Of the many approaches that aim to supplement our knowledge of this sequence-structure-function relationship, we have used statistical methods that rely on protein multiple-sequence alignments to uncover the underlying evolutionary mechanisms of amino acid interactions in the 3-dimensional context of a model protein, Triosephosphate Isomerase (TIM). Positions that are relatively invariant across a family of homologous proteins are said to be conserved across a fold. On the other hand, positions that co-vary with each other are said to be correlated. In the extreme cases where one can ascribe a 'consensus' amino acid to a position in a protein family, one can interrogate the roles of such positions and amino acids. In some cases, such patterns are obvious, but in many situations, the subtle effects of poorly conserved and correlated positions are more challenging to demonstrate, obfuscating their biological importance. Two key TIM variants from the Magliery Lab have created a 'sandbox' where the outcomes from the statistical design are investigated in the context of protein stability and reported in this dissertation. One outcome of this investigation was an empirical approach to engineer protein stability in specific target proteins (including those outside the TIM-family) using the information-theory metrics of Relative Entropy and Mutual Information to determine mutational windows that draw on extant knowledge of the effects of consensus and correlations. We have employed rational and combinatorial approaches to explore the mutational and fitness landscape between the 2 TIM sequences 'cTIM' and 'ccTIM', and report findings that justify the idea that protein stability has complex and global sequence dependencies, displaying an emergent-property like behavior. The work presented here highlights the need for more nuanced methodologies to probe the roles of conserved and co-varying residues. Advisors/Committee Members: Magliery, Thomas (Advisor).

Subjects/Keywords: Biophysics; protein engineering, statistical sequence design, consensus, correlations, triosephosphate isomerase, stability

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

APA (6^th Edition):

Mohan, S. (2017). Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1503054678218166

Chicago Manual of Style (16^th Edition):

Mohan, Sidharth. “Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability.” 2017. Doctoral Dissertation, The Ohio State University. Accessed January 18, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1503054678218166.

MLA Handbook (7^th Edition):

Mohan, Sidharth. “Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability.” 2017. Web. 18 Jan 2021.

Vancouver:

Mohan S. Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability. [Internet] [Doctoral dissertation]. The Ohio State University; 2017. [cited 2021 Jan 18]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1503054678218166.

Council of Science Editors:

Mohan S. Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability. [Doctoral Dissertation]. The Ohio State University; 2017. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1503054678218166

8. Uzoma, Ijeoma K. GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION.

Degree: 2014, Johns Hopkins University

URL: http://jhir.library.jhu.edu/handle/1774.2/37923

► Over 100 kinases were recovered as SUMO substrates in our assays which points to a global phenomenon of kinase regulation by SUMO modification. The studies… (more)

Subjects/Keywords: Proteomics; SUMO

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APA (6^th Edition):

Uzoma, I. K. (2014). GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION. (Thesis). Johns Hopkins University. Retrieved from http://jhir.library.jhu.edu/handle/1774.2/37923

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):

Uzoma, Ijeoma K. “GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION.” 2014. Thesis, Johns Hopkins University. Accessed January 18, 2021. http://jhir.library.jhu.edu/handle/1774.2/37923.

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

MLA Handbook (7^th Edition):

Uzoma, Ijeoma K. “GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION.” 2014. Web. 18 Jan 2021.

Vancouver:

Uzoma IK. GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION. [Internet] [Thesis]. Johns Hopkins University; 2014. [cited 2021 Jan 18]. Available from: http://jhir.library.jhu.edu/handle/1774.2/37923.

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

Council of Science Editors:

Uzoma IK. GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION. [Thesis]. Johns Hopkins University; 2014. Available from: http://jhir.library.jhu.edu/handle/1774.2/37923

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

9. Malaby, Heidi L. H. Identification of Molecular Determinants that Shift Co- and Post-Translational N-Glycosylation Kinetics in Type I Transmembrane Peptides: A Dissertation.

Degree: Biochemistry and Molecular Pharmacology, Biochemistry and Molecular Pharmacology, 2014, U of Massachusetts : Med

URL: http://escholarship.umassmed.edu/gsbs_diss/702

► Asparagine (N)-linked glycosylation occurs on 90% of membrane and secretory proteins and drives folding and trafficking along the secretory pathway. The N-glycan can be… (more)

▼ Asparagine (N)-linked glycosylation occurs on 90% of membrane and secretory proteins and drives folding and trafficking along the secretory pathway. The N-glycan can be attached to an N-X-T/S-Y (X,Y ≠ P) consensus site by one of two oligosaccharyltransferase (OST) STT3 enzymatic isoforms either during protein translation (co-translational) or after protein translation has completed (post-translational). While co-translational N-glycosylation is both rapid and efficient, post-translational N-glycosylation occurs on a much slower time scale and, due to competition with protein degradation and forward trafficking, could be detrimental to the success of a peptide heavily reliant on post-translational N-glycosylation. In evidence, mutations in K⁺ channel subunits that shift N-glycosylation kinetics have been directly linked to cardiac arrhythmias. My thesis work focuses on identifying primary sequence factors that affect the rate of N-glycosylation. To identify the molecular determinants that dictate whether a consensus site acquires its initial N-glycan during or after protein synthesis, I used short (~ 100-170 aa) type I transmembrane peptides from the KCNE family (E1-E5) of K⁺ channel regulatory subunits. The lifetime of these small membrane proteins in the ER translocon is short, which places a significant time constraint on the co-translational N-glycosylation machinery and increases the resolution between co- and post-translational events. Using rapid metabolic pulse-chase experiments described in Chapter II, I identified several molecular determinants among native consensus sites in the KCNE family that favor co-translational N-glycosylation: threonine containing-consensus sites (NXT), multiple N-terminal consensus sites, and long C-termini. The kinetics could also be shifted towards post-translational N-glycosylation by converting to a serine containing-consensus site (NXS), reducing the number of consensus sites in the peptide, and shortening the C-termini. In Chapter III, I utilized an E2 scaffold peptide to examine the N-glycosylation kinetics of the middle X residue in an NXS consensus site. I found that large hydrophobic and negatively charged residues hinder co-translational N-glycosylation, while polar, small hydrophobic, and positively charged residues had the highest N-glycosylation efficiencies. Poorly N-glycosylated NXS consensus sites with large hydrophobic and negatively charged X residues had a significantly improved co-translational N-glycosylation efficiency upon conversion to NXT sites. Also in Chapter III, I adapted a siRNA knockdown strategy to definitively identify the OST STT3 isoforms that perform co- and post-translational N-glycosylation for type I transmembrane substrates. I found that the STT3A isoform predominantly performs co-translational N-glycosylation while the STT3B isoform predominantly performs post-translational N-glycosylation, in agreement with the roles of these enzymatic subunits on topologically different substrates. … Advisors/Committee Members: William R. Kobertz, PhD.

Subjects/Keywords: Asparagine; Consensus Sequence; Glycosylation; Kinetics; Membrane Proteins; Voltage-Gated Potassium Channels; RNA; Small Interfering; Biochemistry; Molecular Biology; Organic Chemistry

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

APA (6^th Edition):

Malaby, H. L. H. (2014). Identification of Molecular Determinants that Shift Co- and Post-Translational N-Glycosylation Kinetics in Type I Transmembrane Peptides: A Dissertation. (Doctoral Dissertation). U of Massachusetts : Med. Retrieved from http://escholarship.umassmed.edu/gsbs_diss/702

Chicago Manual of Style (16^th Edition):

Malaby, Heidi L H. “Identification of Molecular Determinants that Shift Co- and Post-Translational N-Glycosylation Kinetics in Type I Transmembrane Peptides: A Dissertation.” 2014. Doctoral Dissertation, U of Massachusetts : Med. Accessed January 18, 2021. http://escholarship.umassmed.edu/gsbs_diss/702.

MLA Handbook (7^th Edition):

Malaby, Heidi L H. “Identification of Molecular Determinants that Shift Co- and Post-Translational N-Glycosylation Kinetics in Type I Transmembrane Peptides: A Dissertation.” 2014. Web. 18 Jan 2021.

Vancouver:

Malaby HLH. Identification of Molecular Determinants that Shift Co- and Post-Translational N-Glycosylation Kinetics in Type I Transmembrane Peptides: A Dissertation. [Internet] [Doctoral dissertation]. U of Massachusetts : Med; 2014. [cited 2021 Jan 18]. Available from: http://escholarship.umassmed.edu/gsbs_diss/702.

Council of Science Editors:

Malaby HLH. Identification of Molecular Determinants that Shift Co- and Post-Translational N-Glycosylation Kinetics in Type I Transmembrane Peptides: A Dissertation. [Doctoral Dissertation]. U of Massachusetts : Med; 2014. Available from: http://escholarship.umassmed.edu/gsbs_diss/702

10. SUN WEI. A TABU SEARCH ALGORITHM FOR FINDING CONSENSUS SEQUENCES.

Degree: 2003, National University of Singapore

URL: https://scholarbank.nus.edu.sg/handle/10635/153888

Subjects/Keywords: Tabu Search; Consensus Sequence; Meta Heuristic; Multi Sequence Alignment; Object Oriented; C++

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APA (6^th Edition):

WEI, S. (2003). A TABU SEARCH ALGORITHM FOR FINDING CONSENSUS SEQUENCES. (Thesis). National University of Singapore. Retrieved from https://scholarbank.nus.edu.sg/handle/10635/153888

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):

WEI, SUN. “A TABU SEARCH ALGORITHM FOR FINDING CONSENSUS SEQUENCES.” 2003. Thesis, National University of Singapore. Accessed January 18, 2021. https://scholarbank.nus.edu.sg/handle/10635/153888.

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

MLA Handbook (7^th Edition):

WEI, SUN. “A TABU SEARCH ALGORITHM FOR FINDING CONSENSUS SEQUENCES.” 2003. Web. 18 Jan 2021.

Vancouver:

WEI S. A TABU SEARCH ALGORITHM FOR FINDING CONSENSUS SEQUENCES. [Internet] [Thesis]. National University of Singapore; 2003. [cited 2021 Jan 18]. Available from: https://scholarbank.nus.edu.sg/handle/10635/153888.

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

Council of Science Editors:

WEI S. A TABU SEARCH ALGORITHM FOR FINDING CONSENSUS SEQUENCES. [Thesis]. National University of Singapore; 2003. Available from: https://scholarbank.nus.edu.sg/handle/10635/153888

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

NSYSU

11. Lin, Tse-yu. Investigation of the SUMO-interacting motif of p38.

Degree: Master, Institute of Biomedical Sciences, 2015, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721115-145645

► SUMOylation is a posttranslational modification by the small ubiquitin-related modifier (SUMO), SUMOylation plays important roles in the regulation of diverse cellular processes. SUMO can interact… (more)

Subjects/Keywords: p38; SUMO-interacting motif; non-covalent interaction; SUMO-1; SUMO-2

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APA (6^th Edition):

Lin, T. (2015). Investigation of the SUMO-interacting motif of p38. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721115-145645

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):

Lin, Tse-yu. “Investigation of the SUMO-interacting motif of p38.” 2015. Thesis, NSYSU. Accessed January 18, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721115-145645.

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

MLA Handbook (7^th Edition):

Lin, Tse-yu. “Investigation of the SUMO-interacting motif of p38.” 2015. Web. 18 Jan 2021.

Vancouver:

Lin T. Investigation of the SUMO-interacting motif of p38. [Internet] [Thesis]. NSYSU; 2015. [cited 2021 Jan 18]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721115-145645.

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

Council of Science Editors:

Lin T. Investigation of the SUMO-interacting motif of p38. [Thesis]. NSYSU; 2015. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721115-145645

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

North-West University

12. Mlera, Luwanika. Preparatory investigations for developing a transcript-based rotavirus reverse genetics system / Luwanika Mlera .

Degree: 2012, North-West University

URL: http://hdl.handle.net/10394/9523

► Reverse genetics systems that are based on either viral transcripts or cDNA genome segments cloned in plasmids have recently been reported for some of the… (more)

▼ Reverse genetics systems that are based on either viral transcripts or cDNA genome segments cloned in plasmids have recently been reported for some of the dsRNA viruses of the Reoviridae family, namely African horsesickness virus, bluetongue virus and orthoreovirus. For rotaviruses, three reverse genetics systems which only allow the manipulation of a single genome segment have been described. These rotavirus single genome segment reverse genetics systems are not true stand-alone systems because they require a helper virus and a recombinant virus selection step. A true selection-free, plasmid- only or transcript-based reverse genetics system for rotaviruses is lacking. This study sought to identify and characterise the factors that need to be understood and overcome for the development of a rotavirus reverse genetics system using mRNA derived from the in vitro transcription of a consensus nucleotide sequence as well as from double-layered particles. The consensus whole genome sequence of the prototype rotavirus DS-1 and SA11 strains was determined using sequenceindependent whole genome amplification and 454® pyrosequencing. For the rotavirus DS-1 strain, a novel isoleucine in a minor population variant was found at position 397 in a hydrophobic region of VP4. NSP1 contained seven additional amino acids MKSLVEA at the N-terminal end due to an insertion in the consensus nucleotide sequence of genome segment 5. The first 34 nucleotides at the 5'- terminus and last 30 nucleotides at the 3'-terminal end of genome segment 10 (NSP4) of the DS-1 strain were determined in this study. The consensus genome segment 11 (NSP5/6) sequence was 821 bp in length, 148 bp longer than previously reported. The 454® pyrosequence data for a rotavirus SA11 sample with no known passage history revealed a mixed infection with two SA11 strains. One of the strains was a reassortant which contained genome segment 8 (NSP2) from the bovine rotavirus O agent. The other ten consensus genome segments of the two strains could not be differentiated. Novel minor population variants of genome segments 4 (VP4), 9 (VP7) and 10 (NSP4) were identified. Molecular clock phylogenetic analyses of the rotavirus SA11 genomes showed that the two SA11 strains were closely related to the original SA11-H96 strain isolated in 1958. Plasmids containing inserts of the consensus cDNA of the rotavirus DS-1 strain were purchased and used to generate exact capped transcripts by in vitro transcription with a T7 polymerase. Wild-type transcripts of rotavirus SA11 were obtained from in vitro transcription using purified rotavirus SA11 double-layered particles. The purified rotavirus DS-1 and SA11 transcripts were transfected into BSR, COS-7 and MA104 cells. Work on MA104 cells was discontinued due their very low transfection efficacy. In BSR and COS-7 cells, rotavirus DS-1 and SA11 transcripts induced cell death. However, no viable rotavirus was recovered following attempts to infect MA104 cells with the BSR and COS-7 transfected cell…

Subjects/Keywords: Rotavirus; Rotavirus DS-1 strain; Rotavirus SA11 strain; dsRNA; Sequenceindependent genome amplification; 454® pyrosequencing; Consensus genome sequence; In vitro transcription; Reverse genetics; Transfection; Innate immune response; Antiviral state

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APA (6^th Edition):

Mlera, L. (2012). Preparatory investigations for developing a transcript-based rotavirus reverse genetics system / Luwanika Mlera . (Thesis). North-West University. Retrieved from http://hdl.handle.net/10394/9523

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):

Mlera, Luwanika. “Preparatory investigations for developing a transcript-based rotavirus reverse genetics system / Luwanika Mlera .” 2012. Thesis, North-West University. Accessed January 18, 2021. http://hdl.handle.net/10394/9523.

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

MLA Handbook (7^th Edition):

Mlera, Luwanika. “Preparatory investigations for developing a transcript-based rotavirus reverse genetics system / Luwanika Mlera .” 2012. Web. 18 Jan 2021.

Vancouver:

Mlera L. Preparatory investigations for developing a transcript-based rotavirus reverse genetics system / Luwanika Mlera . [Internet] [Thesis]. North-West University; 2012. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/10394/9523.

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

Council of Science Editors:

Mlera L. Preparatory investigations for developing a transcript-based rotavirus reverse genetics system / Luwanika Mlera . [Thesis]. North-West University; 2012. Available from: http://hdl.handle.net/10394/9523

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

University of North Texas

13. Parvez, Imtiaz. Data Transmission in Quantized Consensus.

Degree: 2013, University of North Texas

URL: https://digital.library.unt.edu/ark:/67531/metadc271874/

► In the world of networked system, average consensus is an important dimension of co-ordinate control and cooperation. Since the communication medium is digital, real value… (more)

Subjects/Keywords: Data transmission; quantized consensus; consensus

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APA (6^th Edition):

Parvez, I. (2013). Data Transmission in Quantized Consensus. (Thesis). University of North Texas. Retrieved from https://digital.library.unt.edu/ark:/67531/metadc271874/

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):

Parvez, Imtiaz. “Data Transmission in Quantized Consensus.” 2013. Thesis, University of North Texas. Accessed January 18, 2021. https://digital.library.unt.edu/ark:/67531/metadc271874/.

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

MLA Handbook (7^th Edition):

Parvez, Imtiaz. “Data Transmission in Quantized Consensus.” 2013. Web. 18 Jan 2021.

Vancouver:

Parvez I. Data Transmission in Quantized Consensus. [Internet] [Thesis]. University of North Texas; 2013. [cited 2021 Jan 18]. Available from: https://digital.library.unt.edu/ark:/67531/metadc271874/.

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

Council of Science Editors:

Parvez I. Data Transmission in Quantized Consensus. [Thesis]. University of North Texas; 2013. Available from: https://digital.library.unt.edu/ark:/67531/metadc271874/

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

KTH

14. Ng, Harald. Distributed Consensus: Performance Comparison of Paxos and Raft.

Degree: Electrical Engineering and Computer Science (EECS), 2020, KTH

URL: http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-281973

►

With the growth of the internet, distributed systems have become increasingly important in order to provide more available and scalable applications. Con- sensus is… (more)

▼

With the growth of the internet, distributed systems have become increasingly important in order to provide more available and scalable applications. Con- sensus is a fundamental problem in distributed systems where multiple pro- cesses have to agree on the same proposed value in the presence of partial failures. Distributed consensus allows for building various applications such as lock services, configuration manager services or distributed databases.Two well-known consensus algorithms for building distributed logs are Multi-Paxos and Raft. Multi-Paxos was published almost three decades before Raft and gained a lot of popularity. However, critics of Multi-Paxos consider it difficult to understand. Raft was therefore published with the motivation of being an easily understood consensus algorithm. The Raft algorithm shares similar characteristics with a practical version of Multi-Paxos called Leader- based Sequence Paxos. However, the algorithms differ in important aspects such as leader election and reconfiguration.Existing work mainly compares Multi-Paxos and Raft in theory, but there is a lack of performance comparisons in practice. Hence, prototypes of Leader- based Sequence Paxos and Raft have been designed and implemented in this thesis. The prototypes were implemented using the Rust programming lan- guage and the message-passing framework Kompact and then benchmarked in real-world scenarios to compare the performance of Leader-based Sequence Paxos and Raft.The results show that Leader-based Sequence Paxos and Raft have simi- lar performance in geographically distributed deployments. However, the un- predictable leader election in Raft could greatly affect the performance if the elected leader is in an undesired location. In our experiments, the location of the Raft leader affected the average throughput by up to 35%. Furthermore, the results indicate that implementation details could have a significant impact on performance even in the parts where the algorithms are similar. By batch- ing messages more efficiently, Leader-based Sequence Paxos achieved up to 17% higher average throughput than Raft.

Med tillväxten av internet har distribuerade system blivit allt mer viktiga för att bygga mer tillgängliga och skalbara applikationer. Konsensus är ett funda- mentalt problem i distribuerade system där flera processer ska komma överens om samma föreslagna värde, samtidigt som partiella fel kan ske. Distribuerad konsensus kan appliceras till olika användningsomården som låstjänster, kon- figurationshanterare och distribuerade databaser.Två välkända konsensusalgoritmer för att bygga distribuerade loggar är Multi-Paxos och Raft. Multi-Paxos publicerades nästintill tre årtionden före Raft och blev populär. Men kritiker av Multi-Paxos anser att algoritmen är svår att förstå. Av denna anledning publicerades Raft med motivationen att vara en konsensusalgoritm som är enkel att förstå. Raft delar likheter med Leader- based Sequence Paxos, en praktisk version av Multi-Paxos. Dock skiljer sig algoritmerna i viktiga…

Subjects/Keywords: Paxos; Multi-Paxos; Leader-based Sequence Paxos; Raft; Distributed Systems; Consensus; Replicated State Machine; Paxos; Multi-Paxos; Leader-based Sequence Paxos; Raft; Distribuearade System; Konsensus; Replikerad Tillståndsmaskin; Computer and Information Sciences; Data- och informationsvetenskap

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APA (6^th Edition):

Ng, H. (2020). Distributed Consensus: Performance Comparison of Paxos and Raft. (Thesis). KTH. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-281973

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):

Ng, Harald. “Distributed Consensus: Performance Comparison of Paxos and Raft.” 2020. Thesis, KTH. Accessed January 18, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-281973.

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

MLA Handbook (7^th Edition):

Ng, Harald. “Distributed Consensus: Performance Comparison of Paxos and Raft.” 2020. Web. 18 Jan 2021.

Vancouver:

Ng H. Distributed Consensus: Performance Comparison of Paxos and Raft. [Internet] [Thesis]. KTH; 2020. [cited 2021 Jan 18]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-281973.

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

Council of Science Editors:

Ng H. Distributed Consensus: Performance Comparison of Paxos and Raft. [Thesis]. KTH; 2020. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-281973

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

University of Alberta

15. Beatty, Jessica. Examining the Potential Modification of the Protein Tyrosine Kinase Pyk2 by SUMO-1.

Degree: MS, Department of Medical Microbiology and Immunology, 2013, University of Alberta

URL: https://era.library.ualberta.ca/files/sf2685977

► Proline-rich tyrosine kinase 2 (Pyk2) is a non-receptor protein tyrosine kinase that is highly expressed in hematopoietic cells. Our lab generated two polyclonal antibodies to… (more)

Subjects/Keywords: Pyk2; SUMO-1; PIAS1

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APA (6^th Edition):

Beatty, J. (2013). Examining the Potential Modification of the Protein Tyrosine Kinase Pyk2 by SUMO-1. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/sf2685977

Chicago Manual of Style (16^th Edition):

Beatty, Jessica. “Examining the Potential Modification of the Protein Tyrosine Kinase Pyk2 by SUMO-1.” 2013. Masters Thesis, University of Alberta. Accessed January 18, 2021. https://era.library.ualberta.ca/files/sf2685977.

MLA Handbook (7^th Edition):

Beatty, Jessica. “Examining the Potential Modification of the Protein Tyrosine Kinase Pyk2 by SUMO-1.” 2013. Web. 18 Jan 2021.

Vancouver:

Beatty J. Examining the Potential Modification of the Protein Tyrosine Kinase Pyk2 by SUMO-1. [Internet] [Masters thesis]. University of Alberta; 2013. [cited 2021 Jan 18]. Available from: https://era.library.ualberta.ca/files/sf2685977.

Council of Science Editors:

Beatty J. Examining the Potential Modification of the Protein Tyrosine Kinase Pyk2 by SUMO-1. [Masters Thesis]. University of Alberta; 2013. Available from: https://era.library.ualberta.ca/files/sf2685977

University of Dundee

16. Hands, Katherine J. Defining the mechanism of arsenic-induced degradation of PML.

Degree: PhD, 2012, University of Dundee

URL: https://discovery.dundee.ac.uk/en/studentTheses/a5b14b03-25b0-457f-8dd9-9facf98b6415 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578872

► Arsenic trioxide is a clinically effective treatment for the disease acute promyelocytic leukaemia (APL) which is caused by the chromosomal translocation t(15;17) which fuses the… (more)

▼ Arsenic trioxide is a clinically effective treatment for the disease acute promyelocytic leukaemia (APL) which is caused by the chromosomal translocation t(15;17) which fuses the promyelocytic leukaemia (PML) protein to the retinoic receptor alpha (RARa). The PML-RARa oncoprotein disrupts normal retinoic acid signalling and the function of PML nuclear bodies (PML-NBs), subnuclear protein complexes with roles in control of apoptosis and cellular senescence. Treatment with arsenic induces rapid post translational modification of PML and with the small ubiquitin like modifier (SUMO). SUMO modification of PML recruits the SUMO targeted ubiquitin E3 ligase RNF4 via four SUMO interaction motifs within the N-terminal region of RNF4. PML is then ubiquitylated and targeted for proteasomal degradation. In APL, these events trigger degradation of PML-RARa, curing the disease. To further investigate the process of arsenic induced degradation of PML, a high content siRNA screen was designed to monitor the fate of a YFP linked version of PML after siRNA mediated knockdown of components of the ubiquitin system and arsenic treatment. RNF4 depletion prior to arsenic treatment prevented PML degradation and resulted in accumulation of PML in large, bright PML-NBs. This was used as a positive control. A library of siRNAs targeting 1067 gene products were screened to identify those which perturbed the process of arsenic mediated degradation of PML, and those which affected the stability of PML in untreated cells. A number of putative hits were identified. Depletion of the cullin RING ligase scaffold CUL3, and the NEDD8 E3 ligase DCUN1D1 resulted in striking accumulation of PML, suggesting PML may be a substrate of a CUL3 RING ligase complex. Further experiments using the inhibitor of neddylation, MLN4924 support this hypothesis. PML is expressed as a various isoforms which encode a unique C-terminal region, due to alternative splicing. The second part of this study investigated the role of this variable C-terminal region in the response of the six major PML isoforms to arsenic treatment. Using a system in which only a single eYFP-linked PML isoform is expressed, differences in the localisation of PML isoforms following arsenic treatment were identified, with PML I, II and VI found to accumulate in the cytoplasm following arsenic treatment, whereas PML III, IV and V did not. A high content imaging assay identified PML V as the isoform most readily degraded following arsenic treatment, and PML IV as relatively resistant to degradation. Using siRNA it was demonstrated that arsenic induced degradation of all PML isoforms is dependent on the ubiquitin E3 ligase RNF4. Intriguingly, depletion of RNF4 resulted in marked accumulation of PML V, suggesting this isoform is an optimal substrate for RNF4. Thus the variable C-terminal domain influences the rate and location of degradation of PML isoforms following arsenic treatment.

Subjects/Keywords: 616.1; PML; Arsenic; SUMO

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APA (6^th Edition):

Hands, K. J. (2012). Defining the mechanism of arsenic-induced degradation of PML. (Doctoral Dissertation). University of Dundee. Retrieved from https://discovery.dundee.ac.uk/en/studentTheses/a5b14b03-25b0-457f-8dd9-9facf98b6415 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578872

Chicago Manual of Style (16^th Edition):

Hands, Katherine J. “Defining the mechanism of arsenic-induced degradation of PML.” 2012. Doctoral Dissertation, University of Dundee. Accessed January 18, 2021. https://discovery.dundee.ac.uk/en/studentTheses/a5b14b03-25b0-457f-8dd9-9facf98b6415 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578872.

MLA Handbook (7^th Edition):

Hands, Katherine J. “Defining the mechanism of arsenic-induced degradation of PML.” 2012. Web. 18 Jan 2021.

Vancouver:

Hands KJ. Defining the mechanism of arsenic-induced degradation of PML. [Internet] [Doctoral dissertation]. University of Dundee; 2012. [cited 2021 Jan 18]. Available from: https://discovery.dundee.ac.uk/en/studentTheses/a5b14b03-25b0-457f-8dd9-9facf98b6415 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578872.

Council of Science Editors:

Hands KJ. Defining the mechanism of arsenic-induced degradation of PML. [Doctoral Dissertation]. University of Dundee; 2012. Available from: https://discovery.dundee.ac.uk/en/studentTheses/a5b14b03-25b0-457f-8dd9-9facf98b6415 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578872

NSYSU

17. Wang, Pin-Yao. SUMOs mediate the nuclear transfer of p38 and p-p38 during Helicobacter pylori infection.

Degree: PhD, Institute of Biomedical Sciences, 2016, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0801116-023742

► p38 mitogen-activated protein kinase (MAPK) is of the essence in the cellâs response to environmental stresses, cytokines and DNA damage. p38 is distributed both in… (more)

Subjects/Keywords: SUMO-1; SIM; Helicobacter pylori; p38; nuclear translocalization; SUMO-2

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APA (6^th Edition):

Wang, P. (2016). SUMOs mediate the nuclear transfer of p38 and p-p38 during Helicobacter pylori infection. (Doctoral Dissertation). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0801116-023742

Chicago Manual of Style (16^th Edition):

Wang, Pin-Yao. “SUMOs mediate the nuclear transfer of p38 and p-p38 during Helicobacter pylori infection.” 2016. Doctoral Dissertation, NSYSU. Accessed January 18, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0801116-023742.

MLA Handbook (7^th Edition):

Wang, Pin-Yao. “SUMOs mediate the nuclear transfer of p38 and p-p38 during Helicobacter pylori infection.” 2016. Web. 18 Jan 2021.

Vancouver:

Wang P. SUMOs mediate the nuclear transfer of p38 and p-p38 during Helicobacter pylori infection. [Internet] [Doctoral dissertation]. NSYSU; 2016. [cited 2021 Jan 18]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0801116-023742.

Council of Science Editors:

Wang P. SUMOs mediate the nuclear transfer of p38 and p-p38 during Helicobacter pylori infection. [Doctoral Dissertation]. NSYSU; 2016. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0801116-023742

18. Baik, Hayeon. Role of the SUMO pathway in Acute Myeloid Leukemias response to treatments : Rôle de la sumoylation dans la réponse aux traitements des leucémies aiguës myéloïdes.

Degree: Docteur es, Biologie Santé, 2017, Montpellier

URL: http://www.theses.fr/2017MONTT016

►

Les thérapies de différenciation sont une alternative prometteuse aux drogues génotoxiques utilisées en chimiothérapie pour le traitement de nombreux cancers. En particulier, l’acide tout-trans rétinoïque… (more)

▼

Les thérapies de différenciation sont une alternative prometteuse aux drogues génotoxiques utilisées en chimiothérapie pour le traitement de nombreux cancers. En particulier, l’acide tout-trans rétinoïque (ATRA) est utilisé avec succès pour traiter la leucémie aiguë promyélocytaire, un sous-type des leucémies aiguës myéloïdes (LAM). Malheureusement, son efficacité clinique est limitée dans les autres sous-types des LAM. Cela est en particulier du à une répression épigénétique des gènes de réponse à l’ATRA. Les SUMO constituent une famille de modificateurs post-traductionnels apparentés à l’ubiquitine dont la conjugaison sur de nombreuses protéines, appelée sumoylation, est impliquée dans la régulation de nombreux processus cellulaires, dont la transcription. Dans ce contexte, l’objective de ma thèse a été de comprendre le rôle de la sumoylation dans la réponse des LAM aux thérapies de différenciation. Nous avons pu montrer que la sumoylation réprime la différenciation induite par ATRA dans plusieurs lignées cellulaires, des cellules primaires de patients y compris celles résistantes à la chimiothérapie. L’inhibition de la sumoylation par les inhibiteurs pharmacologiques ou la surexpression des désumoylases augmente de façon remarquable la différenciation par ATRA et, à l’inverse l’augmentation de la sumoylation suite à une surexpression de SUMO ou son enzyme de conjugaison Ubc9 réduit fortement l’efficacité d’ATRA. L’ATRA synergise avec l’inhibition de la sumoylation pour limiter la prolifération des cellules de LAM in vitro et in vivo. D’un point de vue mécanistique, l’inhibition de la sumoylation favorise la différenciation des cellules de LAM en facilitant l’expression des gènes responsables de la différenciation myéloïde. Ainsi, cibler la sumoylation constitue une approche prometteuse pour sensibiliser la LAM aux thérapies de différenciation.

Differentiation therapies are a promising alternative to genotoxic-based chemotherapies in the treatment of many cancers. In particular, All-trans-retinoic acid (ATRA) is successfully used for Acute Promyelocytic Leukemias, a subtype of Acute Myeloid Leukemias. However, its clinical efficiency is very limited in the other AML subtypes, in particular because of epigenetic repression of ATRA-responsive genes. SUMOs are a family of post-translational modifiers related to ubiquitin and their conjugation, sumoylation, to their substrate proteins regulate many processes including gene transcription. The aim of my thesis was to understand the role of sumoylation in AML responses to treatments. I showed that sumoylation represses ATRA-induced differentiation in many AML cell lines and primary patient samples, including those resistant to chemotherapies. Inhibition of sumoylation with pharmacological inhibitors or overexpression of desumoylases markedly increased their differentiation by ATRA and increasing sumoylation by overexpression of SUMO or its conjugating enzyme Ubc9 strongly reduce ATRA efficiency. Inhibition of sumoylation synergize with ATRA to arrest AML cells…

Advisors/Committee Members: Piechaczyk, Marc (thesis director).

Subjects/Keywords: Sumo; Atra; Lam; Différenciation; Sumo; Atra; Aml; Differentiation

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

APA (6^th Edition):

Baik, H. (2017). Role of the SUMO pathway in Acute Myeloid Leukemias response to treatments : Rôle de la sumoylation dans la réponse aux traitements des leucémies aiguës myéloïdes. (Doctoral Dissertation). Montpellier. Retrieved from http://www.theses.fr/2017MONTT016

Chicago Manual of Style (16^th Edition):

Baik, Hayeon. “Role of the SUMO pathway in Acute Myeloid Leukemias response to treatments : Rôle de la sumoylation dans la réponse aux traitements des leucémies aiguës myéloïdes.” 2017. Doctoral Dissertation, Montpellier. Accessed January 18, 2021. http://www.theses.fr/2017MONTT016.

MLA Handbook (7^th Edition):

Baik, Hayeon. “Role of the SUMO pathway in Acute Myeloid Leukemias response to treatments : Rôle de la sumoylation dans la réponse aux traitements des leucémies aiguës myéloïdes.” 2017. Web. 18 Jan 2021.

Vancouver:

Baik H. Role of the SUMO pathway in Acute Myeloid Leukemias response to treatments : Rôle de la sumoylation dans la réponse aux traitements des leucémies aiguës myéloïdes. [Internet] [Doctoral dissertation]. Montpellier; 2017. [cited 2021 Jan 18]. Available from: http://www.theses.fr/2017MONTT016.

Council of Science Editors:

Baik H. Role of the SUMO pathway in Acute Myeloid Leukemias response to treatments : Rôle de la sumoylation dans la réponse aux traitements des leucémies aiguës myéloïdes. [Doctoral Dissertation]. Montpellier; 2017. Available from: http://www.theses.fr/2017MONTT016

University of Dundee

19. Tammsalu, Triin. Global identification of SUMO modification sites.

Degree: PhD, 2016, University of Dundee

URL: https://discovery.dundee.ac.uk/en/studentTheses/5f8905a2-c31c-45ec-8173-4c91cf797342 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805988

► Post-translational modification by Small Ubiquitin-like modifiers (SUMOs) affects the behaviour of proteins involved in diverse cellular processes and is indispensable for cell survival. Proteomic studies… (more)

Subjects/Keywords: SUMO; SUMO modification sites; Mass Spectrometry; Heat stress; Subcellular fractionation

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APA (6^th Edition):

Tammsalu, T. (2016). Global identification of SUMO modification sites. (Doctoral Dissertation). University of Dundee. Retrieved from https://discovery.dundee.ac.uk/en/studentTheses/5f8905a2-c31c-45ec-8173-4c91cf797342 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805988

Chicago Manual of Style (16^th Edition):

Tammsalu, Triin. “Global identification of SUMO modification sites.” 2016. Doctoral Dissertation, University of Dundee. Accessed January 18, 2021. https://discovery.dundee.ac.uk/en/studentTheses/5f8905a2-c31c-45ec-8173-4c91cf797342 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805988.

MLA Handbook (7^th Edition):

Tammsalu, Triin. “Global identification of SUMO modification sites.” 2016. Web. 18 Jan 2021.

Vancouver:

Tammsalu T. Global identification of SUMO modification sites. [Internet] [Doctoral dissertation]. University of Dundee; 2016. [cited 2021 Jan 18]. Available from: https://discovery.dundee.ac.uk/en/studentTheses/5f8905a2-c31c-45ec-8173-4c91cf797342 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805988.

Council of Science Editors:

Tammsalu T. Global identification of SUMO modification sites. [Doctoral Dissertation]. University of Dundee; 2016. Available from: https://discovery.dundee.ac.uk/en/studentTheses/5f8905a2-c31c-45ec-8173-4c91cf797342 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805988

University of Illinois – Urbana-Champaign

20. Naqvi, Syed Shalan. Exact Byzantine consensus under local-broadcast channels.

Degree: MS, Computer Science, 2018, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/101234

► We consider the problem of achieving exact consensus with Byzantine faults under a local-broadcast communication channel. We prove necessary and sufficient conditions on the underlying… (more)

Subjects/Keywords: Consensus; Distributed Algorithms

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APA (6^th Edition):

Naqvi, S. S. (2018). Exact Byzantine consensus under local-broadcast channels. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/101234

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):

Naqvi, Syed Shalan. “Exact Byzantine consensus under local-broadcast channels.” 2018. Thesis, University of Illinois – Urbana-Champaign. Accessed January 18, 2021. http://hdl.handle.net/2142/101234.

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

MLA Handbook (7^th Edition):

Naqvi, Syed Shalan. “Exact Byzantine consensus under local-broadcast channels.” 2018. Web. 18 Jan 2021.

Vancouver:

Naqvi SS. Exact Byzantine consensus under local-broadcast channels. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2018. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/2142/101234.

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

Council of Science Editors:

Naqvi SS. Exact Byzantine consensus under local-broadcast channels. [Thesis]. University of Illinois – Urbana-Champaign; 2018. Available from: http://hdl.handle.net/2142/101234

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

University of Waterloo

21. Kazhamiaka, Mikhail. Sift: Achieving Resource-Efficient Consensus with RDMA.

Degree: 2019, University of Waterloo

URL: http://hdl.handle.net/10012/14596

► Sift is a new consensus protocol for replicating state machines. It disaggregates CPU and memory consumption by creating a novel system architecture enabled by one-sided… (more)

Subjects/Keywords: consensus; fault tolerance

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APA (6^th Edition):

Kazhamiaka, M. (2019). Sift: Achieving Resource-Efficient Consensus with RDMA. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/14596

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):

Kazhamiaka, Mikhail. “Sift: Achieving Resource-Efficient Consensus with RDMA.” 2019. Thesis, University of Waterloo. Accessed January 18, 2021. http://hdl.handle.net/10012/14596.

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

MLA Handbook (7^th Edition):

Kazhamiaka, Mikhail. “Sift: Achieving Resource-Efficient Consensus with RDMA.” 2019. Web. 18 Jan 2021.

Vancouver:

Kazhamiaka M. Sift: Achieving Resource-Efficient Consensus with RDMA. [Internet] [Thesis]. University of Waterloo; 2019. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/10012/14596.

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

Council of Science Editors:

Kazhamiaka M. Sift: Achieving Resource-Efficient Consensus with RDMA. [Thesis]. University of Waterloo; 2019. Available from: http://hdl.handle.net/10012/14596

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

Queens University

22. Condello, Alexander. Stability of Agreement in State-dependent Interaction Environments .

Degree: Mathematics and Statistics, 2013, Queens University

URL: http://hdl.handle.net/1974/8096

► We study stochastic stability for a class of agreement dynamics and define two forms of agreement which we call stochastic agreement and stochastic absolute agreement.… (more)

Subjects/Keywords: Mathematics ; Consensus ; Agreement

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APA (6^th Edition):

Condello, A. (2013). Stability of Agreement in State-dependent Interaction Environments . (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/8096

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):

Condello, Alexander. “Stability of Agreement in State-dependent Interaction Environments .” 2013. Thesis, Queens University. Accessed January 18, 2021. http://hdl.handle.net/1974/8096.

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

MLA Handbook (7^th Edition):

Condello, Alexander. “Stability of Agreement in State-dependent Interaction Environments .” 2013. Web. 18 Jan 2021.

Vancouver:

Condello A. Stability of Agreement in State-dependent Interaction Environments . [Internet] [Thesis]. Queens University; 2013. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/1974/8096.

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

Council of Science Editors:

Condello A. Stability of Agreement in State-dependent Interaction Environments . [Thesis]. Queens University; 2013. Available from: http://hdl.handle.net/1974/8096

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

Georgia Tech

23. Vázquez-Figueroa, Eduardo. Development of a novel dehydrogenase and a stable cofactor regeneration system.

Degree: PhD, Chemical Engineering, 2008, Georgia Tech

URL: http://hdl.handle.net/1853/31685

► The first goal of this work focused on the development of an amine dehydrogenase (AmDH) from a leucine dehydrogenase using site-directed mutagenesis. We aimed at… (more)

▼ The first goal of this work focused on the development of an amine dehydrogenase (AmDH) from a leucine dehydrogenase using site-directed mutagenesis. We aimed at reductively aminating a prochiral ketone to a chiral amine by using leucine dehydrogenase (LeuDH) as a starting template. This initial work was divided into two stages. The first focused mutagenesis to a specific residue (K68) that we know is key to developing the target functionality. Subsequently, mutagenesis focused on residues known to be in close proximity to a key region of the substrate (M65 and K68). This approach allowed for reduced library size while at the same time increased chances of generating alternate substrate specificity. An NAD+-dependent high throughput assay was optimized and will be discussed. The best variants showed specific activity in mU/mg range towards deaminating the target substrate. The second goal of this work was the development of a thermostable glucose dehydrogenase (GDH) starting with the wild-type gene from Bacillus subtilis. GDH is able to carry out the regeneration of both NADH and NADPH cofactors using glucose as a substrate. We applied the structure-guided consensus method to identify 24 mutations that were introduced using overlap extension. 11 of the tested variants had increased thermal stability, and when combined a GDH variant with a half-life ~3.5 days at 65℃ was generated – a ~10⁶increase in stability when compared to the wild-type. The final goal of this work was the characterization of GDH in homogeneous organic-aqueous solvent systems and salt solutions. Engineered GDH variants showed increased stability in all salts and organic solvents tested. Thermal stability had a positive correlation with organic solvent and salt stability. This allowed the demonstration that consensus-based methods can be used towards engineering enzyme stability in uncommon media. This is of significant value since protein deactivation in salts and organic solvents is not well understood, making a priori design of protein stability in these environments difficult. Advisors/Committee Members: Bommarius, Andreas S. (Committee Chair), Doyle, Donald F. (Committee Member), Koros, William J. (Committee Member), Moore, Jeffre C. (Committee Member), Prausnitz, Mark R. (Committee Member).

Subjects/Keywords: Consensus sequence; Glucose dehydrogenase; Cofactor regeneration; Protein engineering; Salt and solvent stability; Biocatalysis; Enzymes; Mutagenesis; Enzymes Synthesis; Organic solvents

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

APA (6^th Edition):

Vázquez-Figueroa, E. (2008). Development of a novel dehydrogenase and a stable cofactor regeneration system. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/31685

Chicago Manual of Style (16^th Edition):

Vázquez-Figueroa, Eduardo. “Development of a novel dehydrogenase and a stable cofactor regeneration system.” 2008. Doctoral Dissertation, Georgia Tech. Accessed January 18, 2021. http://hdl.handle.net/1853/31685.

MLA Handbook (7^th Edition):

Vázquez-Figueroa, Eduardo. “Development of a novel dehydrogenase and a stable cofactor regeneration system.” 2008. Web. 18 Jan 2021.

Vancouver:

Vázquez-Figueroa E. Development of a novel dehydrogenase and a stable cofactor regeneration system. [Internet] [Doctoral dissertation]. Georgia Tech; 2008. [cited 2021 Jan 18]. Available from: http://hdl.handle.net/1853/31685.

Council of Science Editors:

Vázquez-Figueroa E. Development of a novel dehydrogenase and a stable cofactor regeneration system. [Doctoral Dissertation]. Georgia Tech; 2008. Available from: http://hdl.handle.net/1853/31685

NSYSU

24. Lee, Bi-yao. Investigations of The Effects of Glucocorticoid Receptor SNPs and SUMO-2 Autoantibody in Patients with Systemic Lupus Erythematosus.

Degree: Master, Institute of Biomedical Sciences, 2008, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0730108-135015

► For more than fifty years glucocorticoids (GCs) has been used to treat a wide range of inflammatory diseases, such as allergies, asthma, rheumatoid arthritis, and… (more)

Subjects/Keywords: polymorphism; SUMO-2; glucocorticoid receptor; SLE

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

APA (6^th Edition):

Lee, B. (2008). Investigations of The Effects of Glucocorticoid Receptor SNPs and SUMO-2 Autoantibody in Patients with Systemic Lupus Erythematosus. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0730108-135015

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):

Lee, Bi-yao. “Investigations of The Effects of Glucocorticoid Receptor SNPs and SUMO-2 Autoantibody in Patients with Systemic Lupus Erythematosus.” 2008. Thesis, NSYSU. Accessed January 18, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0730108-135015.

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

MLA Handbook (7^th Edition):

Lee, Bi-yao. “Investigations of The Effects of Glucocorticoid Receptor SNPs and SUMO-2 Autoantibody in Patients with Systemic Lupus Erythematosus.” 2008. Web. 18 Jan 2021.

Vancouver:

Lee B. Investigations of The Effects of Glucocorticoid Receptor SNPs and SUMO-2 Autoantibody in Patients with Systemic Lupus Erythematosus. [Internet] [Thesis]. NSYSU; 2008. [cited 2021 Jan 18]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0730108-135015.

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

Council of Science Editors:

Lee B. Investigations of The Effects of Glucocorticoid Receptor SNPs and SUMO-2 Autoantibody in Patients with Systemic Lupus Erythematosus. [Thesis]. NSYSU; 2008. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0730108-135015

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

NSYSU

25. Hsu, Chih-wei. Investigation of the SUMOylation sites of Gfi1.

Degree: Master, Institute of Biomedical Sciences, 2015, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0421115-100738

► The transcriptional repressor Growth Factor Independence 1 (Gfi1) regulates many biological functions, such as development of granulocytes, T-cell differentiation, macrophage-dependent cytokine production and the development… (more)

Subjects/Keywords: SIM; Colocalization; In vitro SUMOylation; SUMO; Gfi1

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APA (6^th Edition):

Hsu, C. (2015). Investigation of the SUMOylation sites of Gfi1. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0421115-100738

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):

Hsu, Chih-wei. “Investigation of the SUMOylation sites of Gfi1.” 2015. Thesis, NSYSU. Accessed January 18, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0421115-100738.

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

MLA Handbook (7^th Edition):

Hsu, Chih-wei. “Investigation of the SUMOylation sites of Gfi1.” 2015. Web. 18 Jan 2021.

Vancouver:

Hsu C. Investigation of the SUMOylation sites of Gfi1. [Internet] [Thesis]. NSYSU; 2015. [cited 2021 Jan 18]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0421115-100738.

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

Council of Science Editors:

Hsu C. Investigation of the SUMOylation sites of Gfi1. [Thesis]. NSYSU; 2015. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0421115-100738

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

NSYSU

26. Wu, Chun-Yi. Interaction between KLIP1 and SUMO-1.

Degree: Master, Biological Sciences, 2011, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905111-105014

► Nuclear protein KLIP1 cooperates with myeloid leukemia factor 1 (MLF1) to inhibit the programmed cell death resulting in tumor formation. It also inhibits the activity… (more)

▼ Nuclear protein KLIP1 cooperates with myeloid leukemia factor 1 (MLF1) to inhibit the programmed cell death resulting in tumor formation. It also inhibits the activity of thymidine kinase promoter of Kaposiâs sarcoma-associated Herpes Virus. KLIP1 functions as a centromere protein, hence acquires its name as CENP-U or CENP-50, to regulate the separation of sister-chromatids during mitosis. These results indicate that KLIP1 plays important roles in regulation of transcription and cell cycle. In this study, six potential SUMO modification sites, K33, K63, K126, K127, K185 and K210, were identified bioinformatically using SUMOplot. Many reports address that SUMO modification alters the transcriptional activity, protein-protein interaction, the subcellular localization and stability of its target protein. Recent data suggest that SUMO is required for centromere binding protein to mediate proper mitotic spindle attachment to the kinetochore, and previous research suggest that there has a SUMO-interaction motif (SIM) in KLIP1 protein sequence. To reveal the interaction between KLIP1 and SUMO-1, and study its effects on KLIP1 function, we co-express GFP-KLIP1 and His-tagged SUMO-1 in HEK 293 cells. After affinity purification of SUMOylated proteins from transfected cells using nickel conjugated beads and subsequent western blotted with anti-GFP. The results indicated the interaction between KLIP1 and SUMO-1 in co-transfected cells. Our confocal microscopy imaging also found colocalization of GFP-KLIP1 with RFP-SUMO-1 nuclear foci. In addition, we failed to detect the interaction between SUMO-1 and mutant KLIP1-M6 ,whose six potential SUMO modified lysine residues were mutated to arginine. Furthermore, we found a distinct nuclear localization of GFP-KLIP1-M6 as compared to the image of wildtype GFP-KLIP1, which show a significant higher frequency of colocalization with RFP-SUMO-1 foci. Taken together, our data suggest the interaction between KLIP1 and SUMO-1 may be related to these six potential lysine residues, which upon mutation blocks its colocalization with SUMO-1 in nuclear foci. The biological significance of their interaction are awaits for further investigation. Advisors/Committee Members: YI-REN HONG (chair), Jiin-Tsuey Cheng (committee member), Angela Chen (chair).

Subjects/Keywords: KLIP1; SUMO-1; site-directed mutagenesis

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

APA (6^th Edition):

Wu, C. (2011). Interaction between KLIP1 and SUMO-1. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905111-105014

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):

Wu, Chun-Yi. “Interaction between KLIP1 and SUMO-1.” 2011. Thesis, NSYSU. Accessed January 18, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905111-105014.

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

MLA Handbook (7^th Edition):

Wu, Chun-Yi. “Interaction between KLIP1 and SUMO-1.” 2011. Web. 18 Jan 2021.

Vancouver:

Wu C. Interaction between KLIP1 and SUMO-1. [Internet] [Thesis]. NSYSU; 2011. [cited 2021 Jan 18]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905111-105014.

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

Council of Science Editors:

Wu C. Interaction between KLIP1 and SUMO-1. [Thesis]. NSYSU; 2011. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905111-105014

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

Rochester Institute of Technology

27. Prokop, Matthew. Routing protocol evaluation and development of a fully functional simulation environment for vehicular ad hoc networks.

Degree: Computer Engineering, 2011, Rochester Institute of Technology

URL: https://scholarworks.rit.edu/theses/3182

► A Vehicular Ad-hoc Networks (VANET) is an area of wireless technologies that are attracting a great deal of interest. There are still several areas of… (more)

Subjects/Keywords: AODV; DSR; DYMO; Omnet++; SUMO; VANET

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

APA (6^th Edition):

Prokop, M. (2011). Routing protocol evaluation and development of a fully functional simulation environment for vehicular ad hoc networks. (Thesis). Rochester Institute of Technology. Retrieved from https://scholarworks.rit.edu/theses/3182

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):

Prokop, Matthew. “Routing protocol evaluation and development of a fully functional simulation environment for vehicular ad hoc networks.” 2011. Thesis, Rochester Institute of Technology. Accessed January 18, 2021. https://scholarworks.rit.edu/theses/3182.

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

MLA Handbook (7^th Edition):

Prokop, Matthew. “Routing protocol evaluation and development of a fully functional simulation environment for vehicular ad hoc networks.” 2011. Web. 18 Jan 2021.

Vancouver:

Prokop M. Routing protocol evaluation and development of a fully functional simulation environment for vehicular ad hoc networks. [Internet] [Thesis]. Rochester Institute of Technology; 2011. [cited 2021 Jan 18]. Available from: https://scholarworks.rit.edu/theses/3182.

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

Council of Science Editors:

Prokop M. Routing protocol evaluation and development of a fully functional simulation environment for vehicular ad hoc networks. [Thesis]. Rochester Institute of Technology; 2011. Available from: https://scholarworks.rit.edu/theses/3182

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

Universiteit Utrecht

28. Poot, B.W.A. Norm-based distributed controllers in a Multi-Agent System.

Degree: 2015, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/320413

► Autonomous vehicles will most likely participate in traﬃc in the near future. These autonomous vehicles have private goals they want to achieve, which might conﬂict… (more)

Subjects/Keywords: Multi-Agent Systems; Norms; Traffic; SUMO

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APA (6^th Edition):

Poot, B. W. A. (2015). Norm-based distributed controllers in a Multi-Agent System. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/320413

Chicago Manual of Style (16^th Edition):

Poot, B W A. “Norm-based distributed controllers in a Multi-Agent System.” 2015. Masters Thesis, Universiteit Utrecht. Accessed January 18, 2021. http://dspace.library.uu.nl:8080/handle/1874/320413.

MLA Handbook (7^th Edition):

Poot, B W A. “Norm-based distributed controllers in a Multi-Agent System.” 2015. Web. 18 Jan 2021.

Vancouver:

Poot BWA. Norm-based distributed controllers in a Multi-Agent System. [Internet] [Masters thesis]. Universiteit Utrecht; 2015. [cited 2021 Jan 18]. Available from: http://dspace.library.uu.nl:8080/handle/1874/320413.

Council of Science Editors:

Poot BWA. Norm-based distributed controllers in a Multi-Agent System. [Masters Thesis]. Universiteit Utrecht; 2015. Available from: http://dspace.library.uu.nl:8080/handle/1874/320413

Universidade Nova

29. Bértolo, Diana Fernandes Quitério. Aplicação de quitosano na redução do escurecimento enzimático em sumo de maçã não pasteurizado (estabilizado por hiperpressão).

Degree: 2011, Universidade Nova

URL: http://www.rcaap.pt/detail.jsp?id=oai:run.unl.pt:10362/6718

►

Dissertação para obtenção do Grau de Mestre em Tecnologia e Segurança Alimentar

A maçã, sendo um dos frutos com maior produção em Portugal, detentor de… (more)

Subjects/Keywords: Conservação; Escurecimento enzimático; Maçã; Sumo; Quitosano

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APA (6^th Edition):

Bértolo, D. F. Q. (2011). Aplicação de quitosano na redução do escurecimento enzimático em sumo de maçã não pasteurizado (estabilizado por hiperpressão). (Thesis). Universidade Nova. Retrieved from http://www.rcaap.pt/detail.jsp?id=oai:run.unl.pt:10362/6718

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):

Bértolo, Diana Fernandes Quitério. “Aplicação de quitosano na redução do escurecimento enzimático em sumo de maçã não pasteurizado (estabilizado por hiperpressão).” 2011. Thesis, Universidade Nova. Accessed January 18, 2021. http://www.rcaap.pt/detail.jsp?id=oai:run.unl.pt:10362/6718.

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

MLA Handbook (7^th Edition):

Bértolo, Diana Fernandes Quitério. “Aplicação de quitosano na redução do escurecimento enzimático em sumo de maçã não pasteurizado (estabilizado por hiperpressão).” 2011. Web. 18 Jan 2021.

Vancouver:

Bértolo DFQ. Aplicação de quitosano na redução do escurecimento enzimático em sumo de maçã não pasteurizado (estabilizado por hiperpressão). [Internet] [Thesis]. Universidade Nova; 2011. [cited 2021 Jan 18]. Available from: http://www.rcaap.pt/detail.jsp?id=oai:run.unl.pt:10362/6718.

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

Council of Science Editors:

Bértolo DFQ. Aplicação de quitosano na redução do escurecimento enzimático em sumo de maçã não pasteurizado (estabilizado por hiperpressão). [Thesis]. Universidade Nova; 2011. Available from: http://www.rcaap.pt/detail.jsp?id=oai:run.unl.pt:10362/6718

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

University of Dundee

30. Chua, Shijia Joy. Establishing the role of RNF4 in the vertebrate DNA damage response.

Degree: PhD, 2012, University of Dundee

URL: https://discovery.dundee.ac.uk/en/studentTheses/20679582-0300-40ac-8d30-e733210c76b4 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578870

► RNF4 belongs to the family of SUMO-targeted ubiquitin E3 ligases (STUbLs). The role of STUbLs in maintaining genomic stability was first discovered in yeast. Theyeast… (more)

▼ RNF4 belongs to the family of SUMO-targeted ubiquitin E3 ligases (STUbLs). The role of STUbLs in maintaining genomic stability was first discovered in yeast. Theyeast STUbL mutants displayed genomic instability, elevated mutation rates, sensitivity to DNA damaging agents and also demonstrated synthetic lethality with other DNA repair genes. Although the role of vertebrate RNF4 in the DNA damage response was not yet established, it could rescue the Schizosaccaromyces pombe STUbL mutant phenotypes, showing that RNF4 is a functional homologue of the yeast STUbL proteins,and that it might be implicated in the vertebrate DNA damage response.A homozygous knockout of RNF4 in the DT40 chicken lymphocyte cell line was generated to investigate the involvement of vertebrate RNF4 in protecting cells against DNA damage. Although the complete loss of RNF4 did not affect cell proliferation or cell cycle distribution, the RNF4 -/- cells exhibited a selective hypersensitivity to some S-phase specific DNA damaging agents. This hypersensitivity could be rescued by introducing an ortholog of RNF4 from another vertebrate species, and this was dependent on a functional ubiquitin E3 ligase activity of RNF4.To explore the physiological function of RNF4 in the context of a wholeorganism, Danio rerio was chosen as an in vivo model. Danio rerio RNF4 sharedsimilar in vitro biochemical characteristics as RNF4 from other vertebrates – it was able to autoubiquitylate itself and also ubiquitylate SUMO2 chains. In Danio rerio, RNF4 is a maternally provided gene and is highly expressed in the adult gonads. In the ovaries, RNF4 expression was restricted to the early stage oocytes, suggesting a possible role in oocyte development. Loss-of-function studies in Danio rerio were performed using morpholino knockdown and zinc-finger knockout technologies, and the depletion of RNF4 in zebrafish did not affect early embryonic development or viability of the animal.The results presented in this thesis suggests that while vertebrate RNF4 is notlikely to be an essential gene in some vertebrates, it plays a role in the DNA damage response and might be implicated in gonad development in Danio rerio. The zinc-finger knockout model has just been established and a more in-depth analysis is necessary to shed more light on the in vivo functions of RNF4.

Subjects/Keywords: 572.8; DNA damage; Ubiquitin; SUMO; Zebrafish; DT40

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APA (6^th Edition):

Chua, S. J. (2012). Establishing the role of RNF4 in the vertebrate DNA damage response. (Doctoral Dissertation). University of Dundee. Retrieved from https://discovery.dundee.ac.uk/en/studentTheses/20679582-0300-40ac-8d30-e733210c76b4 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578870

Chicago Manual of Style (16^th Edition):

Chua, Shijia Joy. “Establishing the role of RNF4 in the vertebrate DNA damage response.” 2012. Doctoral Dissertation, University of Dundee. Accessed January 18, 2021. https://discovery.dundee.ac.uk/en/studentTheses/20679582-0300-40ac-8d30-e733210c76b4 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578870.

MLA Handbook (7^th Edition):

Chua, Shijia Joy. “Establishing the role of RNF4 in the vertebrate DNA damage response.” 2012. Web. 18 Jan 2021.

Vancouver:

Chua SJ. Establishing the role of RNF4 in the vertebrate DNA damage response. [Internet] [Doctoral dissertation]. University of Dundee; 2012. [cited 2021 Jan 18]. Available from: https://discovery.dundee.ac.uk/en/studentTheses/20679582-0300-40ac-8d30-e733210c76b4 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578870.

Council of Science Editors:

Chua SJ. Establishing the role of RNF4 in the vertebrate DNA damage response. [Doctoral Dissertation]. University of Dundee; 2012. Available from: https://discovery.dundee.ac.uk/en/studentTheses/20679582-0300-40ac-8d30-e733210c76b4 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.578870

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