+publisher:"Cornell University" +contributor:("Collins, Ruth N.")

Cornell University

1. Hah, Nasun. Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses.

Degree: PhD, Biochemistry, 2011, Cornell University

URL: http://hdl.handle.net/1813/33589

► Estrogens play crucial roles in regulating gene expression in physiological and disease states. Estrogens acts through estrogen receptors (ERs) and their binding sites in genomic… (more)

▼ Estrogens play crucial roles in regulating gene expression in physiological and disease states. Estrogens acts through estrogen receptors (ERs) and their binding sites in genomic DNA to modulate transcription by RNA polymerase II. Although recent gene-specific and genomic analyses have provided considerable information about of estrogen-dependent transcription, many aspects of the estrogen signaling network have not yet been elucidated. The goal of my studies was to uncover new information about the immediate and direct effects of estrogen signaling at the cell membrane, in the cytoplasm, and in the nucleus to elucidate the underlying regulatory networks. First, I investigated an ER transcriptional coregulators, SWI/SNF, an ATPdependent chromatin remodeling complex. I explored the molecular functions of the BAF57 and BAF180 subunits of SWI/SNF using a quantitative proteomic approach called SILAC (Stable Isotope Labeling by Amino Acids in Cell Culture). I found that depletion of BAF57 results in a significant depletion of BAF180 from the SWI/SNF complex without decreasing the total cellular BAF180 levels, resulting in an accumulation of cells in the G2/M phase. Knockdown of BAF57 also causes transcriptional misregulation of cell cycle-related genes involved in the late G2 checkpoint. Collectively, these studies have elucidated the role of BAF57 and BAF180 in the transcriptional control of cell proliferation. Second, I have used GRO-Seq (Global Nuclear Run-On and Massively Parallel Sequencing) to explore the immediate effects of estrogen signaling on the transcriptome of breast cancer cells. I found that estrogen directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. In addition to protein coding genes, estrogen regulates the distribution and activity of all three RNA polymerases, and virtually every class of non-coding RNA that has been described to date. I also identified a large number of previously undetected estrogen-regulated intergenic transcripts, many of which are found proximal to ER[alpha] binding sites. These results provide the most comprehensive measurement of the primary and immediate estrogen effects to date. I expect that genome-wide inferences based on the direct estrogen-regulated transcriptome in combination with estrogen-regulated signaling pathway will be useful for understanding estrogen biology. Advisors/Committee Members: Kraus, William Lee (chair), Collins, Ruth N. (committee member), Lis, John T (committee member).

Subjects/Keywords: estrogen; estrogen receptor; GRO-seq; swi/snf; baf57; baf180; silac; proteomic; enhancer; edc; estrogen signaling

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APA (6^th Edition):

Hah, N. (2011). Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33589

Chicago Manual of Style (16^th Edition):

Hah, Nasun. “Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses.” 2011. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/33589.

MLA Handbook (7^th Edition):

Hah, Nasun. “Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses.” 2011. Web. 22 Jan 2021.

Vancouver:

Hah N. Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/33589.

Council of Science Editors:

Hah N. Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/33589

Cornell University

2. Boroughs, Lindsey. Tissue Transglutaminase And Its Effects On Cell Migration And Survival.

Degree: PhD, Biochemistry, 2013, Cornell University

URL: http://hdl.handle.net/1813/34302

► Tissue transglutaminase (tTG) is a GTPase and acyl transferase which catalyzes the formation of covalent crosslinks between two protein substrates. tTG expression and activation are… (more)

▼ Tissue transglutaminase (tTG) is a GTPase and acyl transferase which catalyzes the formation of covalent crosslinks between two protein substrates. tTG expression and activation are frequently up-regulated in different types of human cancer, where it has been shown to be important for enhancing cell motility. Using HeLa cervical carcinoma cells as a model system, I show that a membrane-associated pool of tTG becomes activated and re-distributes to the leading edges of migrating cells upon EGF stimulation. Immunoprecipitations of tTG from the membrane fractions of EGF-treated HeLa cells led to the discovery that tTG binds the heat shock protein (Hsp)70 family of molecular chaperones. tTG and Hsp70 co-localize at leading edges, and this localization is dependent on the ATP hydrolytic activity of Hsp70, as inhibitors against this function prevent both tTG and Hsp70 from localizing to leading edges. More importantly, these inhibitors also block the EGF-dependent migration of HeLa cells and the constitutive migration of MDA-MB231 cells, suggesting that Hsp70 helps localize tTG to leading edges to facilitate its role in promoting cell migration. While tTG has been shown to influence a number of aspects of cancer progression, to what degree tTG works with oncogenic proteins to elicit these outcomes versus its intrinsic ability to impact malignant transformation is unknown. Thus, I have examined how ectopic expression of tTG in a normal (non-transformed) cellular context influences the behavior of these cells. Using NIH3T3 fibroblasts stably expressing the vector alone or a Myc-tagged form of wild-type tTG, I found that tTG strongly protected these cells from serum-starvation-induced apoptosis by activating the PI3-kinase/mTOR/p70 S6-kinase pathway. tTG binds c-Src and PI3kinase, and the formation of this complex is critical for the activation of the PI3-kinase signaling pathway. Activation of PI3-kinase signaling is essential for tTG's ability to promote cell survival, as inhibition of any component in this pathway, including Src, PI3-kinase, or mTOR, eliminates the protective effect afforded to the cells by tTG expression. Advisors/Committee Members: Cerione, Richard A (chair), Baird, Barbara Ann (committee member), Collins, Ruth N. (committee member).

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APA (6^th Edition):

Boroughs, L. (2013). Tissue Transglutaminase And Its Effects On Cell Migration And Survival. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/34302

Chicago Manual of Style (16^th Edition):

Boroughs, Lindsey. “Tissue Transglutaminase And Its Effects On Cell Migration And Survival.” 2013. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/34302.

MLA Handbook (7^th Edition):

Boroughs, Lindsey. “Tissue Transglutaminase And Its Effects On Cell Migration And Survival.” 2013. Web. 22 Jan 2021.

Vancouver:

Boroughs L. Tissue Transglutaminase And Its Effects On Cell Migration And Survival. [Internet] [Doctoral dissertation]. Cornell University; 2013. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/34302.

Council of Science Editors:

Boroughs L. Tissue Transglutaminase And Its Effects On Cell Migration And Survival. [Doctoral Dissertation]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/34302

Cornell University

3. Johnson, Jared. Reconstitution Of Rho Gtpase Interactions At The Membrane.

Degree: PhD, Molecular and Cell Biology, 2011, Cornell University

URL: http://hdl.handle.net/1813/30669

► In order for fibroblasts to migrate, budding yeast to polarize, and macrophages to undergo phagocytosis, each cell must coordinate a membrane-localized signal with a robust… (more)

▼ In order for fibroblasts to migrate, budding yeast to polarize, and macrophages to undergo phagocytosis, each cell must coordinate a membrane-localized signal with a robust morphological change. The Rho Family of GTPases play critically important roles in mediating these cellular processes. However, in order for the Rho GTPases to help regulate these processes in a tightly coordinated spatial and temporal manner, they need to be properly localized to specific membrane signaling sites. The mechanisms by which this precise localization is achieved are still not fully understood, but represent the subject of this thesis. The Rho GTPases are post-translationally modified at their C-terminus by the covalent attachment of a 20 carbon lipid tail, called a geranylgeranyl moiety, which allows them to associate with membranes. To facilitate their cytosolic localization, the Rho GTPases require the assistance of a ubiquitously-expressed regulatory protein, the Rho guanine nucleotide-dissociation inhibitor (RhoGDI). The mechanism by which the Rho GTPases move between distinct locations in the cell, and in particular, how they are able to cycle on and off between different membranes, has been a challenging question. I have set out to begin to define this mechanism by reconstituting in vitro the interactions between the geranylgeranylated Rho GTPase Cdc42, RhoGDI, and liposomes of well-defined lipid composition. In taking advantage of the sensitivity and real-time capabilities of these reconstituted systems, some unexpected findings emerged regarding how RhoGDI influences the membraneto-cytosol distribution of Rho GTPases like Cdc42. One such unexpected discovery involves my finding that RhoGDI can distinguish between the signaling-inactive (GDP-bound) and signaling active (GTPbound) forms of Cdc42 when they are associated with a lipid bilayer. In particular, despite having similar affinities for the GDP- and GTP-bound forms of Cdc42 in solution, I found that when RhoGDI interacts with Cdc42 along the membrane surface, it has a much higher affinity for GDP-bound Cdc42 compared to its GTPbound counterpart. Moreover, the membrane-release of Cdc42-RhoGDI complexes occurs at a similar rate as the release of Cdc42 alone, with the major effect of RhoGDI then being to significantly slow the re-association of Cdc42 with membranes. These findings lead us to propose a new model for how RhoGDI influences the ability of Cdc42 to move between membranes and the cytosol. I further demonstrated that the cycling of Rho GTPases like Cdc42 and Rac1 between the membrane and cytosol can be strongly influenced by RhoGEFs and RhoGAPs, as well as RhoGDI, such that the membrane association-dissociation cycle of the Rho GTPases is directly coupled to their GTP-binding/GTPase cycle. Most of the Rho family GTPases contain a cluster of positive-charged residues (i.e. a 'polybasic domain'), directly preceding their geranylgeranyl moiety. It has been suggested that this domain serves to fine-tune their localization among different cellular membranes. I have… Advisors/Committee Members: Cerione, Richard A (chair), Collins, Ruth N. (committee member), Baird, Barbara Ann (committee member).

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APA (6^th Edition):

Johnson, J. (2011). Reconstitution Of Rho Gtpase Interactions At The Membrane. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/30669

Chicago Manual of Style (16^th Edition):

Johnson, Jared. “Reconstitution Of Rho Gtpase Interactions At The Membrane.” 2011. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/30669.

MLA Handbook (7^th Edition):

Johnson, Jared. “Reconstitution Of Rho Gtpase Interactions At The Membrane.” 2011. Web. 22 Jan 2021.

Vancouver:

Johnson J. Reconstitution Of Rho Gtpase Interactions At The Membrane. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/30669.

Council of Science Editors:

Johnson J. Reconstitution Of Rho Gtpase Interactions At The Membrane. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/30669

Cornell University

4. Wu, Jun. L-Arginine And L-Phenylalanine Based Poly (Ester Amide)S, Their Synthesis, Characterization, Formulations And Applications As Gene Delivery Vectors And Tissue Engineering Scaffolds.

Degree: PhD, Biomedical Engineering, 2011, Cornell University

URL: http://hdl.handle.net/1813/33553

► A family of water soluble and positively charged L-arginine based poly (ester amide)s (Arg-PEAs) was synthesized by solution polycondensation. These biodegradable Arg-PEAs consist of 3… (more)

▼ A family of water soluble and positively charged L-arginine based poly (ester amide)s (Arg-PEAs) was synthesized by solution polycondensation. These biodegradable Arg-PEAs consist of 3 nontoxic building blocks: L-arginine, diols and dicarboxylic acids. The Arg-PEAs were prepared by the reaction of tetra-p- toluenesulfonic acids salts of bis-(L-arginine) [alpha], [omega]-alkylene diesters and di-pnitrophenyl esters of dicarboxylic acids. Optimal conditions of the monomers and polymers synthesis were investigated, and the monomers and Arg-PEAs were chemically characterized. Arg-PEAs were found to have good solubility in water and many other polar solvents. . Arg-PEAs were evaluated by many biological assays for the gene delivery applications. Structure-function relationship of the Arg-PEAs revealed that changing the number of methylene groups in the diol or/and diacid segment could finely tune the hydrophobic and cationic properties of the Arg-PEAs, and then affect the gene delivery efficiency. MTT assay showed that all the prepared Arg-PEAs and Arg-PEA/DNA complexes were non-toxic to the cell lines even at very large doses. Some of Arg-PEAs showed comparable or higher transfection efficiency than the commercial transfection agents, Superfect® and Lipofectamine2000®. Based on the above results, a new generation of Arg-PEAs, oligoethylene glycols and L-arginine based poly (ether ester amide)s (Arg-PEEAs) were developed. The new Arg-PEEAs had more flexible chain due to the introduction of oligoethylene glycols. Structure-function relationship of the Arg-PEEAs was intensively studied. MTT assay showed that all the and Arg-PEEA/DNA complexes were non-toxic to the cell lines, primary cells and stem cells even at very large doses. The Arg-PEEAs expanded the gene transfection from cell lines to primary cells/stem cells, and showed comparable or higher transfection efficiency than the commercial transfection agents, Superfect® and Lipofectamine2000®. Arg-PEAs with double bond functionality (Arg-UPEAs) could be photocrosslinked with Pluronic- diacrylate (Pluronic-DA) to form cationic hybrid hydrogels. The physicochemical and mechanical properties of the hybrid hydrogels were studied. The fibroblast and endothelial cells were cultured on the hybrid hydrogel surface and inside the hydrogel, respectively. The results indicated that the introduction of ArgUPEAs could significantly increase the cell attachment performance on hydrogel surface and viability inside the hydrogel. Some new L-phenylalanine based poly (ester amide)s (Phe-PEA) or derivatives were developed as the coating materials causing low inflammatory response. One example is the block copolymer of Phe-PEA and poly ([epsilon] -caprolactone) (PCL) [PEAb-PCL], another example is the L-Arginine and L-phenylalanine based hybrid poly (ester amide)s (Arg-Phe-PEAs). The new biomaterials were characterized and studied the cellular responses, such as cell attachment and macrophage inflammatory response. The results indicated that they could promote the cell attachment and cause… Advisors/Committee Members: Chu, Chih-Chang (chair), Collins, Ruth N. (committee member), Bonassar, Lawrence (committee member).

Subjects/Keywords: Arginine; Poly (ester amide); Gene delivery

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APA (6^th Edition):

Wu, J. (2011). L-Arginine And L-Phenylalanine Based Poly (Ester Amide)S, Their Synthesis, Characterization, Formulations And Applications As Gene Delivery Vectors And Tissue Engineering Scaffolds. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33553

Chicago Manual of Style (16^th Edition):

Wu, Jun. “L-Arginine And L-Phenylalanine Based Poly (Ester Amide)S, Their Synthesis, Characterization, Formulations And Applications As Gene Delivery Vectors And Tissue Engineering Scaffolds.” 2011. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/33553.

MLA Handbook (7^th Edition):

Wu, Jun. “L-Arginine And L-Phenylalanine Based Poly (Ester Amide)S, Their Synthesis, Characterization, Formulations And Applications As Gene Delivery Vectors And Tissue Engineering Scaffolds.” 2011. Web. 22 Jan 2021.

Vancouver:

Wu J. L-Arginine And L-Phenylalanine Based Poly (Ester Amide)S, Their Synthesis, Characterization, Formulations And Applications As Gene Delivery Vectors And Tissue Engineering Scaffolds. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/33553.

Council of Science Editors:

Wu J. L-Arginine And L-Phenylalanine Based Poly (Ester Amide)S, Their Synthesis, Characterization, Formulations And Applications As Gene Delivery Vectors And Tissue Engineering Scaffolds. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/33553

Cornell University

5. Wang, Mengqiao. A Histone Deacetylase Hos3 Establishes Crosslink Between The Morphogenesis And Spindle Positioning Checkpoints.

Degree: PhD, Molecular and Cell Biology, 2013, Cornell University

URL: http://hdl.handle.net/1813/33908

► An increasing number of cellular activities are under the regulation of lysine acetylation. This post-translational modification (PTM) is reversibly catalyzed by histone acetyltransferases (HATs) and… (more)

Subjects/Keywords: Histone deacetylase Hos3; Morphogenesis checkpoint; Spindle positioning checkpoint

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APA (6^th Edition):

Wang, M. (2013). A Histone Deacetylase Hos3 Establishes Crosslink Between The Morphogenesis And Spindle Positioning Checkpoints. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33908

Chicago Manual of Style (16^th Edition):

Wang, Mengqiao. “A Histone Deacetylase Hos3 Establishes Crosslink Between The Morphogenesis And Spindle Positioning Checkpoints.” 2013. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/33908.

MLA Handbook (7^th Edition):

Wang, Mengqiao. “A Histone Deacetylase Hos3 Establishes Crosslink Between The Morphogenesis And Spindle Positioning Checkpoints.” 2013. Web. 22 Jan 2021.

Vancouver:

Wang M. A Histone Deacetylase Hos3 Establishes Crosslink Between The Morphogenesis And Spindle Positioning Checkpoints. [Internet] [Doctoral dissertation]. Cornell University; 2013. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/33908.

Council of Science Editors:

Wang M. A Histone Deacetylase Hos3 Establishes Crosslink Between The Morphogenesis And Spindle Positioning Checkpoints. [Doctoral Dissertation]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/33908

Cornell University

6. Lin, Miao-chong. Novel Heregulin-Mediated Pathways To Mammalian Target Of Rapamycin Complex 1.

Degree: PhD, Molecular and Cell Biology, 2013, Cornell University

URL: http://hdl.handle.net/1813/34050

► Heregulin (HRG) is a growth factor that mediates the activation of ErbB2/ErbB3 receptors. Aberrant signaling of HRG and the ErbB receptors give rise to human… (more)

▼ Heregulin (HRG) is a growth factor that mediates the activation of ErbB2/ErbB3 receptors. Aberrant signaling of HRG and the ErbB receptors give rise to human cancer. Our laboratory has previously identified mammalian target of rapamycin (mTOR), an essential hub for growth factor and nutrient sensing, as an important intermediate in HRG-signaling. This thesis focuses on the pathways that lead to the activation of mTORC1 (mTOR complex 1) in response to HRG. First, I identified the importance of mTORC2 signaling to mTORC1 in ErbB2/HRGmediated cellular transformation in SKBR3 breast cancer cells. mTORC2 was initially identified to play a role in actin cytoskeletal remodeling, but with the discovery of novel mTORC2 targets, mTORC2 has been implicated in cellular functions such as cell proliferation, survival, and metabolism. By utilizing rapamycin and an ATP-competitive inhibitor of mTOR, INK128, I was able to differentiate between mTORC1 and mTORC2 activation by HRG. In HRG/ErbB2mediated signaling to AKT, mTORC2 is required for the phosphorylation on AKT (S473) and this precedes the activating PDK1 phosphorylation at AKT (T308). AKT phosphorylates TSC2, making TSC2 unable to function on Rheb. Rheb remains in its GTP-bound form and activates mTORC1. By performing a Rictor knock-down, which decreased mTORC2 availability in the cell, the HRG-mediated transforming capability of SKBR3 cells was reduced. Next, I took a mechanistic approach to identify how small GTPases, namely Rheb, Rac, and i Cdc42, are playing a role in HRG-mediated mTORC1 activation. Using a knock-down and rescue approach, I was able to delineate that Rac and Cdc42 are upstream of Rheb, and that they signal independently of one another to mTORC1 in this context. Additionally, I found that Dock7, a GEF for Rac and Cdc42, serves as a unique scaffold for the G-proteins and mTORC1. The most intriguing finding, however, is that Dock7 also possesses properties of a Rheb GEF. It has long been hypothesized that only a GAP is needed for the regulation of Rheb, so the identification of a putative Rheb GEF is of significant interest to the field. ii Advisors/Committee Members: Cerione, Richard A (chair), Collins, Ruth N. (committee member), Baird, Barbara Ann (committee member).

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APA (6^th Edition):

Lin, M. (2013). Novel Heregulin-Mediated Pathways To Mammalian Target Of Rapamycin Complex 1. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/34050

Chicago Manual of Style (16^th Edition):

Lin, Miao-chong. “Novel Heregulin-Mediated Pathways To Mammalian Target Of Rapamycin Complex 1.” 2013. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/34050.

MLA Handbook (7^th Edition):

Lin, Miao-chong. “Novel Heregulin-Mediated Pathways To Mammalian Target Of Rapamycin Complex 1.” 2013. Web. 22 Jan 2021.

Vancouver:

Lin M. Novel Heregulin-Mediated Pathways To Mammalian Target Of Rapamycin Complex 1. [Internet] [Doctoral dissertation]. Cornell University; 2013. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/34050.

Council of Science Editors:

Lin M. Novel Heregulin-Mediated Pathways To Mammalian Target Of Rapamycin Complex 1. [Doctoral Dissertation]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/34050

Cornell University

7. Allen, Krystal. The Gnrh Receptor-Associated Membrane Raft Proteome In Mouse Gonadotrope Cells.

Degree: PhD, Veterinary Medicine, 2012, Cornell University

URL: http://hdl.handle.net/1813/31077

► Gonadotropin releasing hormone (GnRH) is the central hormone of reproduction in vertebrates. This hormone is secreted from the hypothalamus in response to environmental, steroid hormone… (more)

Subjects/Keywords: Gonadotropin Releasing Hormone Receptor; Proteomic; Membrane Raft

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APA (6^th Edition):

Allen, K. (2012). The Gnrh Receptor-Associated Membrane Raft Proteome In Mouse Gonadotrope Cells. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/31077

Chicago Manual of Style (16^th Edition):

Allen, Krystal. “The Gnrh Receptor-Associated Membrane Raft Proteome In Mouse Gonadotrope Cells.” 2012. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/31077.

MLA Handbook (7^th Edition):

Allen, Krystal. “The Gnrh Receptor-Associated Membrane Raft Proteome In Mouse Gonadotrope Cells.” 2012. Web. 22 Jan 2021.

Vancouver:

Allen K. The Gnrh Receptor-Associated Membrane Raft Proteome In Mouse Gonadotrope Cells. [Internet] [Doctoral dissertation]. Cornell University; 2012. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/31077.

Council of Science Editors:

Allen K. The Gnrh Receptor-Associated Membrane Raft Proteome In Mouse Gonadotrope Cells. [Doctoral Dissertation]. Cornell University; 2012. Available from: http://hdl.handle.net/1813/31077

Cornell University

8. Weiskoff, Amanda. Analysis Of The Transport Of Saccharomyces Cerevisiae Chitin Synthase 3 By The Exomer Secretory Vesicle Cargo Adaptor.

Degree: PhD, Molecular and Cell Biology, 2014, Cornell University

URL: http://hdl.handle.net/1813/38752

► A major feature of a eukaryotic cell is its ability to compartmentalize its functions by sequestering components into distinct membrane-bound organelles. Since membrane-embedded proteins cannot… (more)

▼ A major feature of a eukaryotic cell is its ability to compartmentalize its functions by sequestering components into distinct membrane-bound organelles. Since membrane-embedded proteins cannot diffuse through the cell to travel between organelles, they must be sorted into transport vesicles, typically by coat complexes and their adaptors. The transmembrane protein Chitin Synthase 3 (Chs3) in Saccharomyces cerevisiae is an excellent model system to study some of these complex sorting and transport processes. Chs3 cycles between specific locations on the plasma membrane (PM) where it synthesizes chitin for the yeast cell wall, and retention in trans-Golgi network (TGN) compartments where it is inactive. Exomer, a novel protein complex found in fungi, acts as an adaptor complex for the transport of Chs3 and several other proteins from the TGN to the PM. The exomer complex is composed of the core subunit protein Chs5 and paralagous adaptor proteins known as ChAPs (Chs5-Arf1-binding Proteins), and is recruited to the membrane by the small GTPase Arf1. I have determined the minimal functional fragment of Chs5, which I have shown interacts with Arf1, likely contributing to exomer recruitment. The ChAPs are responsible for binding cargo, and Chs6 is required for transport of Chs3. Therefore, I examined Chs6 protein levels throughout the cell cycle and incorporation into complexes. When Chs6 levels were held constant by replacing its promoter with another, there was an effect on Chs3 transport only in one yeast background, indicating this regulation is only required under certain conditions. I also show that different segments of the Chs3 N-terminus mediate distinct trafficking steps. I present a crystal structure of residues 10-27 bound to the exomer complex, which are residues known to mediate retention and also seem to play a role in internalization. Residues 2852 are involved in transport to the plasma membrane and recycling out of the endosomes to prevent degradation. Together, these findings contribute to our understanding of how proteins are transported by exomer, and how cycling of a transmembrane protein can be regulated. Advisors/Committee Members: Fromme, Joseph Chris (chair), Emr, Scott David (committee member), Collins, Ruth N. (committee member).

Subjects/Keywords: Cell Biology; Membrane trafficking; Yeast

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APA (6^th Edition):

Weiskoff, A. (2014). Analysis Of The Transport Of Saccharomyces Cerevisiae Chitin Synthase 3 By The Exomer Secretory Vesicle Cargo Adaptor. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/38752

Chicago Manual of Style (16^th Edition):

Weiskoff, Amanda. “Analysis Of The Transport Of Saccharomyces Cerevisiae Chitin Synthase 3 By The Exomer Secretory Vesicle Cargo Adaptor.” 2014. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/38752.

MLA Handbook (7^th Edition):

Weiskoff, Amanda. “Analysis Of The Transport Of Saccharomyces Cerevisiae Chitin Synthase 3 By The Exomer Secretory Vesicle Cargo Adaptor.” 2014. Web. 22 Jan 2021.

Vancouver:

Weiskoff A. Analysis Of The Transport Of Saccharomyces Cerevisiae Chitin Synthase 3 By The Exomer Secretory Vesicle Cargo Adaptor. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/38752.

Council of Science Editors:

Weiskoff A. Analysis Of The Transport Of Saccharomyces Cerevisiae Chitin Synthase 3 By The Exomer Secretory Vesicle Cargo Adaptor. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/38752

Cornell University

9. Plys, Aaron. Analysis Of The Movement Of Saccharomyces Cerevisiae Mismatch Repair Proteins On Dna.

Degree: PhD, Biochemistry, 2011, Cornell University

URL: http://hdl.handle.net/1813/30604

► Replication errors that escape DNA polymerase proof-reading activity are efficientl y recognized and repaired by conserved DNA mismatch repair factors. The overall result is a… (more)

▼ Replication errors that escape DNA polymerase proof-reading activity are efficientl y recognized and repaired by conserved DNA mismatch repair factors. The overall result is a drastic reduction in deletion mutations. The mechanistic details of how mismatch repair proteins execute mismatch removal have not been elucidated. The aim of my thesis is to better understand how mismatch repair factors interact with DNA in order to identify mismatch sites. My work reveals that the mismatch repair complex, MLH1-PMS1, has unique DNA diffusion characteristics facilitated by structural features of the two subunits. Through bulk assays and total internal reflectance fluorescence microscopy (TIRFM), I found that MLH1PMS1 could independently bind DNA and rapidly diffuse using the thermal energy of the system. Furthermore, MLH1-PMS1 was shown to be the first passively diffusing protein that could bypass stationary nucleosomes. In contrast, the DNA diffusion activity of the mismatch recognition complex MSH2-MSH6 was blocked by nucleosomes. The timing and nature of mismatch repair is linked with replication and is thus proposed that the differences seen for the two complexes have important implications for repair in the context of the chromatin state directly at the replication fork. Each subunit of the MLH1-PMS1 complex is composed of two defined globular domains connected by an unstructured linker arm. The linker arms of the complex are proposed to facilitate topological DNA binding and diffusion along DNA in a hopping/stepping mechanism. I found that TEV protease cleavage within the linker arms of MLH1-PMS1 disrupted DNA binding and mismatch repair in vitro and in vivo. Using a genetic mismatch repair assay I found that shortening of the linker arms in MLH1 had a drastic effect on function whereas similar changes in PMS1 had little or no effect. Purified truncated complexes were able to interact with DNA and form ternary complexes with MSH2-MSH6 at a mismatch. Future studies should focus on the diffusion characteristic for these complexes. Together, my work has important implications for understanding how mismatch repair proteins can rapidly identify their targets in a chromatin landscape. Advisors/Committee Members: Alani, Eric E (chair), Collins, Ruth N. (coChair), Weiss, Robert S. (committee member).

Subjects/Keywords: DNA mismatch repair; Replication; Cancer

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APA (6^th Edition):

Plys, A. (2011). Analysis Of The Movement Of Saccharomyces Cerevisiae Mismatch Repair Proteins On Dna. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/30604

Chicago Manual of Style (16^th Edition):

Plys, Aaron. “Analysis Of The Movement Of Saccharomyces Cerevisiae Mismatch Repair Proteins On Dna.” 2011. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/30604.

MLA Handbook (7^th Edition):

Plys, Aaron. “Analysis Of The Movement Of Saccharomyces Cerevisiae Mismatch Repair Proteins On Dna.” 2011. Web. 22 Jan 2021.

Vancouver:

Plys A. Analysis Of The Movement Of Saccharomyces Cerevisiae Mismatch Repair Proteins On Dna. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/30604.

Council of Science Editors:

Plys A. Analysis Of The Movement Of Saccharomyces Cerevisiae Mismatch Repair Proteins On Dna. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/30604

Cornell University

10. Frizzell, Kristine. Mechanisms Of Transcriptional Regulation By Proteins In The Nad+ Metabolic Pathway.

Degree: PhD, Biochemistry, 2011, Cornell University

URL: http://hdl.handle.net/1813/33561

► Poly(ADP-ribosyl)ation (PARylation) is an enzymatic reaction whereby ADPribose units from donor NAD+ molecules are covalently attached onto target proteins. The regulation of this reaction is… (more)

▼ Poly(ADP-ribosyl)ation (PARylation) is an enzymatic reaction whereby ADPribose units from donor NAD+ molecules are covalently attached onto target proteins. The regulation of this reaction is overseen by two nuclear enzymes, Poly(ADP-ribose) polymerase-1 (PARP-1) and poly(ADP-ribose) glycohydrolase (PARG), that modify target proteins in the nucleus by the addition and removal, respectively, of ADP-ribose polymers. While PARP-1 has generally been studied with respect to its role in DNA damage repair and cell death pathways, recent studies have revealed a role for PARP-1 in transcriptional regulation. The role of PARG in transcriptional regulation, however, is less characterized. In this study, I have investigated the coordinate patterns of gene regulation by PARP-1 and PARG in vivo using genomic and gene-specific analyses. Specifically, I show that PARP-1 and PARG coordinately regulate global patterns of gene expression by affecting genes in the same direction and with similar magnitudes. Further analysis revealed that PARP-1 and PARG localized to the promoters of both positively and negatively regulated target genes in parallel binding patterns. I also show that PARP-1 and PARG enzymatic activities are required for some, but not all, target genes. My results indicate that PARP-1 and PARG, two nuclear enzymes with opposing enzymatic activities, localize to target promoters and act in a similar, rather than antagonistic, manner to regulate gene expression. In a follow-up study, I have used a novel method known as Global Run-on Sequencing (GRO-seq) to define the role of PARP-1 on the estrogen-regulated transcriptome at the level of the nascent transcript, rather than steady-state mRNA levels. I have produced libraries from MCF-7 cells treated with vehicle or 17[beta]estradiol (E2) under three conditions: (i) a control knockdown; (ii) a control knockdown plus a PARP inhibitor, PJ34; and (iii) a PARP-1 knockdown. I have determined that the estrogen response is highly maintained under PARP-1 knockdown or inhibition. Accordingly, upon estrogen treatment, PARP-1 localization patterns are largely unaffected. However, deeper analyses reveal a small number of genes where PARP-1 knockdown or inhibition reduces the estrogen response at the transcription level (GRO-seq) and at the steady state mRNA level (RT-qPCR). The NAD+ metabolite generated from the PARP-1/PARG reaction, ADPribose (ADPR), is a small molecule ligand that is used by macro domain-containing proteins. The histone variant macroH2A1 is one such protein that has generally been studied with respect to its role in transcriptional repression on the inactive X chromosome. However, recent studies have begun to explore a role for macroH2A1 in autosomal gene regulation, as a transcriptional repressor and a transcriptional activator. Recent results from the Kraus lab have shown that the transcriptional coactivator Proline-, glutamic acid-, and leucine-rich protein 1 (PELP1) interacts with the macro domain of macroH2A1 in a ligand-independent manner and shows a similar… Advisors/Committee Members: Kraus, William Lee (chair), Collins, Ruth N. (committee member), Lis, John T (committee member).

Subjects/Keywords: parp-1; gene regulation; estrogen signaling

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

APA (6^th Edition):

Frizzell, K. (2011). Mechanisms Of Transcriptional Regulation By Proteins In The Nad+ Metabolic Pathway. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33561

Chicago Manual of Style (16^th Edition):

Frizzell, Kristine. “Mechanisms Of Transcriptional Regulation By Proteins In The Nad+ Metabolic Pathway.” 2011. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/33561.

MLA Handbook (7^th Edition):

Frizzell, Kristine. “Mechanisms Of Transcriptional Regulation By Proteins In The Nad+ Metabolic Pathway.” 2011. Web. 22 Jan 2021.

Vancouver:

Frizzell K. Mechanisms Of Transcriptional Regulation By Proteins In The Nad+ Metabolic Pathway. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/33561.

Council of Science Editors:

Frizzell K. Mechanisms Of Transcriptional Regulation By Proteins In The Nad+ Metabolic Pathway. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/33561

Cornell University

11. Donovan, Kirk. Coordinating The Transport Cycle Of The Myosin-V Motor Myo2 With Secretory Vesicle Delivery And Exocytosis.

Degree: PhD, Molecular and Cell Biology, 2014, Cornell University

URL: http://hdl.handle.net/1813/38860

► The polarization of proteins, lipids, and organelles within a eukaryotic cell allows for the spatial regulation of numerous biological processes. Saccharomyces cerevisiae displays exaggerated polarized… (more)

▼ The polarization of proteins, lipids, and organelles within a eukaryotic cell allows for the spatial regulation of numerous biological processes. Saccharomyces cerevisiae displays exaggerated polarized growth of its plasma membrane during budding through the directed transport of secretory vesicles. In addition, several organelles are actively transported into the growing bud. These processes are accomplished using formin-nucleated actin cables extending from the bud tip and neck and the myosin-V motor Myo2p. While many of the components linking Myo2p to its various cargoes are known, the dynamic behavior of the motor and how its dynamics is regulated at the molecular level remains unclear. Here I define the in vivo delivery cycle of a myosin-V in its essential function of secretory vesicle transport, and show how that transport is coordinated with other events in exocytosis. I determined that Myo2p is activated from an inactive state by binding to competent secretory vesicles. This inactive state is caused by an autoinhibitory interaction between the head and tail of the motor. Mutations that disrupt this interaction render the motor constitutively active and compromise cargo transport functions. About 10 motors associate with each secretory vesicle during rapid transport to sites of cell growth. Motor release is temporally regulated by vesicle-bound Rab-GTP hydrolysis and requires vesicle tethering via the exocyst complex, but does not require vesicle fusion with the plasma membrane. Additionally, I developed a vesicletracking assay to study single-vesicle fusion dynamics at the cortex. This aided in the creation of a timeline of events for exocytosis, allowing for the dynamics of single-vesicle populations of the Rab Sec4p, the exocyst complex, and Myo2p to be visualized. The components of this transport cycle are highly conserved in mammalian cells, so these results should be generally applicable to other myosin-V delivery cycles. Advisors/Committee Members: Bretscher, Anthony Paul (chair), Fromme, Joseph Chris (committee member), Collins, Ruth N. (committee member).

Subjects/Keywords: Myo2; exocytosis; myosin-V

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

APA (6^th Edition):

Donovan, K. (2014). Coordinating The Transport Cycle Of The Myosin-V Motor Myo2 With Secretory Vesicle Delivery And Exocytosis. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/38860

Chicago Manual of Style (16^th Edition):

Donovan, Kirk. “Coordinating The Transport Cycle Of The Myosin-V Motor Myo2 With Secretory Vesicle Delivery And Exocytosis.” 2014. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/38860.

MLA Handbook (7^th Edition):

Donovan, Kirk. “Coordinating The Transport Cycle Of The Myosin-V Motor Myo2 With Secretory Vesicle Delivery And Exocytosis.” 2014. Web. 22 Jan 2021.

Vancouver:

Donovan K. Coordinating The Transport Cycle Of The Myosin-V Motor Myo2 With Secretory Vesicle Delivery And Exocytosis. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/38860.

Council of Science Editors:

Donovan K. Coordinating The Transport Cycle Of The Myosin-V Motor Myo2 With Secretory Vesicle Delivery And Exocytosis. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/38860

Cornell University

12. Pareja, Kristeen Alcaide. A ROLE FOR THE N-TERMINAL DOMAIN IN MODULATING THE ACTIVITIES OF THE NUCLEOTIDE EXCHANGE FACTOR SIL1.

Degree: PhD, Pharmacology, 2018, Cornell University

URL: http://hdl.handle.net/1813/59801

► Excessive cellular reactive oxygen species (ROS), or oxidative stress, can lead to cell damage and is implicated in diseases such as cancer, aging and neurodegenerative… (more)

▼ Excessive cellular reactive oxygen species (ROS), or oxidative stress, can lead to cell damage and is implicated in diseases such as cancer, aging and neurodegenerative disorders. Yet, although these highly reactive molecules can be damaging, ROS can also elicit beneficial effects in cells as signaling molecules. In the endoplasmic reticulum (ER), where ROS are produced from protein folding, the Hsp70 BiP plays a role in cell protection during ER oxidative stress. BiP is a chaperone that binds and release substrates, and these activities are regulated by its ATPase cycle. We have previously discovered that yeast BiP’s conserved cysteine gets modified by the ROS peroxide during oxidative stress conditions. Our lab discovered that the protein Sil1 functions in cells as a reductant that can remove the modification on BiP’s cysteine. The reductant activity of Sil1 is mediated through two N-terminal cysteines. Sil1 has been well- characterized as BiP’s nucleotide exchange factor (NEF) that facilitates ADP release. Sil1 is active as a NEF even in the absence of its N-terminal region. A molecular picture as to how the N terminus, which contains the redox-active cysteines, influences interaction with BiP remains unclear. Our biochemical characterization of the full-length Sil1 has revealed that the N-terminal domain plays a role in modulating Sil1 activities. We uncovered that the presence of the N-terminal domain decreases Sil1 NEF activity and impacts the structural conformation adopted by full-length Sil1. We have mapped the region of the N terminus that accounts for the auto-inhibition of Sil1 NEF activity to a stretch of 36 amino acids of highly conserved sequence. Mutations in human SIL1 have been found in patients with Marinesco-Sjogren syndrome (MSS). One such mutation, R92W, is in the conserved N-terminal region. Through the characterization of the yeast version, Sil1-R84W, we have demonstrated that the mutation increases NEF activity, impacts reductant activity, and changes the apparent conformation of Sil1. Our overall findings suggest that the N-terminal domain’s conserved region is important in regulating Sil1 activities. We predict that this region may undergo post-translational modifications in cells to modulate NEF and reductant functions of Sil1 under specific physiological conditions. Advisors/Committee Members: Sevier, Carolyn S. (chair), Collins, Ruth N. (committee member), Brown, William J. (committee member), Qian, Shu-Bing (committee member).

Subjects/Keywords: Cellular biology; Pharmacology

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

APA (6^th Edition):

Pareja, K. A. (2018). A ROLE FOR THE N-TERMINAL DOMAIN IN MODULATING THE ACTIVITIES OF THE NUCLEOTIDE EXCHANGE FACTOR SIL1. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/59801

Chicago Manual of Style (16^th Edition):

Pareja, Kristeen Alcaide. “A ROLE FOR THE N-TERMINAL DOMAIN IN MODULATING THE ACTIVITIES OF THE NUCLEOTIDE EXCHANGE FACTOR SIL1.” 2018. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/59801.

MLA Handbook (7^th Edition):

Pareja, Kristeen Alcaide. “A ROLE FOR THE N-TERMINAL DOMAIN IN MODULATING THE ACTIVITIES OF THE NUCLEOTIDE EXCHANGE FACTOR SIL1.” 2018. Web. 22 Jan 2021.

Vancouver:

Pareja KA. A ROLE FOR THE N-TERMINAL DOMAIN IN MODULATING THE ACTIVITIES OF THE NUCLEOTIDE EXCHANGE FACTOR SIL1. [Internet] [Doctoral dissertation]. Cornell University; 2018. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/59801.

Council of Science Editors:

Pareja KA. A ROLE FOR THE N-TERMINAL DOMAIN IN MODULATING THE ACTIVITIES OF THE NUCLEOTIDE EXCHANGE FACTOR SIL1. [Doctoral Dissertation]. Cornell University; 2018. Available from: http://hdl.handle.net/1813/59801

Cornell University

13. Blackwood, Christopher. The Role Of Jagged1 In The Subventricular Zone During Late Embryonic Development.

Degree: PhD, Pharmacology, 2014, Cornell University

URL: http://hdl.handle.net/1813/36056

► Notch signaling plays an important role in regulating olfactory neurogenesis during development of the mammalian subventricular zone. During development, the Notch signaling pathway is critical… (more)

Subjects/Keywords: JAGGED1; NEUROGENESIS; embryonic subventricular zone

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

APA (6^th Edition):

Blackwood, C. (2014). The Role Of Jagged1 In The Subventricular Zone During Late Embryonic Development. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/36056

Chicago Manual of Style (16^th Edition):

Blackwood, Christopher. “The Role Of Jagged1 In The Subventricular Zone During Late Embryonic Development.” 2014. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/36056.

MLA Handbook (7^th Edition):

Blackwood, Christopher. “The Role Of Jagged1 In The Subventricular Zone During Late Embryonic Development.” 2014. Web. 22 Jan 2021.

Vancouver:

Blackwood C. The Role Of Jagged1 In The Subventricular Zone During Late Embryonic Development. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/36056.

Council of Science Editors:

Blackwood C. The Role Of Jagged1 In The Subventricular Zone During Late Embryonic Development. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/36056

Cornell University

14. Huang, Weishan. Function Of Il-2-Inducible T Cell Kinase (Itk) In Innate T Cells And Mast Cells.

Degree: PhD, Pharmacology, 2014, Cornell University

URL: http://hdl.handle.net/1813/36191

► IL-2-inducible T cell kinase (ITK) is expressed in T lymphocytes and mast cells (MC), and functions as a critical signaling mediator downstream of numerous cell… (more)

▼ IL-2-inducible T cell kinase (ITK) is expressed in T lymphocytes and mast cells (MC), and functions as a critical signaling mediator downstream of numerous cell surface receptors. ITK regulates both adaptive and innate immunity, via regulation of cell differentiation and activation. Lack of ITK results in spontaneous memory acquisition in [alpha][beta] T cells termed "innate memory phenotype (IMP) T cells". The development and function of IMP T cells, and the role of ITK in their development remains unknown. This dissertation describes an alternative bone marrow transplantation system, which generates murine models with predominant naïve or IMP T cells, allowing comparative investigation of the functions of these cells in vivo; and demonstrates that: 1) IMP T cell development requires hematopoietic expression of major histocompatibility complexes; 2) IMP CD8+ T cells are not the result of T cell homeostatic proliferation (HP), and they can rapidly and potently respond to primary antigenic stimulation; and 3) IMP CD4+ T cells can suppress autoimmune graft-versus-host disease. In addition, this dissertation also investigates the T cell-intrinsic role of ITK in the development of both IMP and HP CD8+ T cells: 1) ITK tunes IL-4/TcR signaling synergy to regulate IMP CD8+ T cell differentiation; and 2) ITK suppresses CD8+ T cell HP and anti-tumor immunity. Loss of ITK in mice also results in hyper-production of immunoglobulin E (IgE), through which MC regulate the development of allergy. Differential functions of ITK and the homologous Bruton's tyrosine kinase (BTK) in MC response to allergen/IgE-mediated stimulation have been illustrated. This dissertation further shows a redundant function for ITK/BTK in MC response to the bacterial endotoxin lipopolysaccharide (LPS), in that lack of ITK and BTK leads to hyper-production of MC-derived TNF-[alpha], which exacerbates LPS-induced septic hypothermia. This work provides insights into the function of ITK in innate T cells, and the value of targeting ITK to enhance antigen-specific primary response by IMP CD8+ T cells, regulatory function of IMP CD4+ T cells, and expansion of anti-tumor HP CD8+ T cells, for therapeutic purposes. However, the MC response to LPS also raises concern on the potential use of ITK/BTK cross-reactive kinase inhibitors. Advisors/Committee Members: August, Avery (chair), Collins, Ruth N. (committee member), Yen, Andrew (committee member), Leifer, Cynthia Anne (committee member), Linder, Maurine E. (committee member).

Subjects/Keywords: IL-2-inducible T cell kinase (ITK); Innate T cells; Mast cells

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APA (6^th Edition):

Huang, W. (2014). Function Of Il-2-Inducible T Cell Kinase (Itk) In Innate T Cells And Mast Cells. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/36191

Chicago Manual of Style (16^th Edition):

Huang, Weishan. “Function Of Il-2-Inducible T Cell Kinase (Itk) In Innate T Cells And Mast Cells.” 2014. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/36191.

MLA Handbook (7^th Edition):

Huang, Weishan. “Function Of Il-2-Inducible T Cell Kinase (Itk) In Innate T Cells And Mast Cells.” 2014. Web. 22 Jan 2021.

Vancouver:

Huang W. Function Of Il-2-Inducible T Cell Kinase (Itk) In Innate T Cells And Mast Cells. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/36191.

Council of Science Editors:

Huang W. Function Of Il-2-Inducible T Cell Kinase (Itk) In Innate T Cells And Mast Cells. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/36191

Cornell University

15. Zhao, Yingying. A Ubiquitin-Dependent Surveillance System Mediates Plasma Membrane Protein Quality Control In Yeast.

Degree: PhD, Physiology, 2013, Cornell University

URL: http://hdl.handle.net/1813/33968

► A UBIQUITIN-DEPENDENT SURVEILLANCE SYSTEM MEDIATES PLASMA MEMBRANE PROTEIN QUALITY CONTROL IN YEAST Yingying Zhao, Ph. D. Cornell University 2013 A key function of the ubiquitin-proteasome system is targeting of misfolded proteins for degradation. In the cytosol, specialized E3 ligases target soluble misfolded proteins for ubiquitination and subsequent proteasomal degradation. However, the case is more complicated for integral membrane proteins. Following co- translational insertion in the ER membrane, proteins that fail to fold properly in the ER are subject to ER-assisted degradation (ERAD), which involves retrotranslocation of proteins back into the cytosol followed by ubiquitin- dependent proteasomal degradation. Properly folded PM proteins, such as signaling receptors, ion channels, and nutrient transporters, exit the ER and traffic through the Golgi to the cell surface where they mediate their specific functions. Maintenance of proper PM proteostasis, particularly with respect to ion channels and nutrient transporters, is crucial to prevent loss of PM integrity and dissipation of essential ion and chemical gradients. As such, when PM resident proteins become damaged or misfolded, they must be recognized, removed by endocytosis and delivered to the lysosome for degradation. Thus, cells maintain a "cradle to grave" quality monitoring system for integral membrane proteins, yet the mechanisms of iii quality surveillance, particularly at the PM, remain poorly understood. … (more)

▼ A UBIQUITIN-DEPENDENT SURVEILLANCE SYSTEM MEDIATES PLASMA MEMBRANE PROTEIN QUALITY CONTROL IN YEAST Yingying Zhao, Ph. D. Cornell University 2013 A key function of the ubiquitin-proteasome system is targeting of misfolded proteins for degradation. In the cytosol, specialized E3 ligases target soluble misfolded proteins for ubiquitination and subsequent proteasomal degradation. However, the case is more complicated for integral membrane proteins. Following co- translational insertion in the ER membrane, proteins that fail to fold properly in the ER are subject to ER-assisted degradation (ERAD), which involves retrotranslocation of proteins back into the cytosol followed by ubiquitin- dependent proteasomal degradation. Properly folded PM proteins, such as signaling receptors, ion channels, and nutrient transporters, exit the ER and traffic through the Golgi to the cell surface where they mediate their specific functions. Maintenance of proper PM proteostasis, particularly with respect to ion channels and nutrient transporters, is crucial to prevent loss of PM integrity and dissipation of essential ion and chemical gradients. As such, when PM resident proteins become damaged or misfolded, they must be recognized, removed by endocytosis and delivered to the lysosome for degradation. Thus, cells maintain a "cradle to grave" quality monitoring system for integral membrane proteins, yet the mechanisms of iii quality surveillance, particularly at the PM, remain poorly understood. Here we present evidence that the E3 ubiquitin ligase Rsp5, the yeast homolog of Nedd4, is part of a critical protein quality surveillance mechanism at the PM. We show that proteotoxic stress triggers global activation of Rsp5-dependent ubiquitination, endocytosis, and vacuolar trafficking of PM proteins. Mutants defective for this protective response exhibit toxic accumulation of integral membrane proteins at the cell surface and suffer catastrophic loss of PM integrity during misfolding stress, phenotypes that can be suppressed by the presence of chemical chaperones. We present the identification of specific Rsp5 adaptors which target the ubiquitination of misfolded PM proteins during proteotoxic stress. Genetic interaction analysis reveals that this PM quality surveillance mechanism exhibits striking synthetic defects with components of both ERAD and the unfolded protein response, indicating that different quality control pathways cooperate to protect cells during misfolding stress. We propose that this ubiquitin-mediated PM quality surveillance pathway, together with other quality control pathways like ERAD, protects cells from proteotoxic stress by limiting the toxic accumulation of misfolded integral membrane proteins at the PM. iv Advisors/Committee Members: Roberson, Mark Stephen (chair), Emr, Scott David (coChair), Collins, Ruth N. (committee member), Qian, Shu-Bing (committee member).

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

APA (6^th Edition):

Zhao, Y. (2013). A Ubiquitin-Dependent Surveillance System Mediates Plasma Membrane Protein Quality Control In Yeast. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33968

Chicago Manual of Style (16^th Edition):

Zhao, Yingying. “A Ubiquitin-Dependent Surveillance System Mediates Plasma Membrane Protein Quality Control In Yeast.” 2013. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/33968.

MLA Handbook (7^th Edition):

Zhao, Yingying. “A Ubiquitin-Dependent Surveillance System Mediates Plasma Membrane Protein Quality Control In Yeast.” 2013. Web. 22 Jan 2021.

Vancouver:

Zhao Y. A Ubiquitin-Dependent Surveillance System Mediates Plasma Membrane Protein Quality Control In Yeast. [Internet] [Doctoral dissertation]. Cornell University; 2013. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/33968.

Council of Science Editors:

Zhao Y. A Ubiquitin-Dependent Surveillance System Mediates Plasma Membrane Protein Quality Control In Yeast. [Doctoral Dissertation]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/33968

Cornell University

16. Cragun, David. Investigation Of The Molecular Role(S) Of Yop1 And Rtn1 Shaping The Peripheral Er.

Degree: PhD, Molecular and Cell Biology, 2011, Cornell University

URL: http://hdl.handle.net/1813/33508

► A defining feature of eukaryotic life is the presence of membrane-bound organelles. While the energetically most stable shape for a membrane is likely a sphere,… (more)

Subjects/Keywords: membrane; curvature; yop1

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APA (6^th Edition):

Cragun, D. (2011). Investigation Of The Molecular Role(S) Of Yop1 And Rtn1 Shaping The Peripheral Er. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33508

Chicago Manual of Style (16^th Edition):

Cragun, David. “Investigation Of The Molecular Role(S) Of Yop1 And Rtn1 Shaping The Peripheral Er.” 2011. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/33508.

MLA Handbook (7^th Edition):

Cragun, David. “Investigation Of The Molecular Role(S) Of Yop1 And Rtn1 Shaping The Peripheral Er.” 2011. Web. 22 Jan 2021.

Vancouver:

Cragun D. Investigation Of The Molecular Role(S) Of Yop1 And Rtn1 Shaping The Peripheral Er. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/33508.

Council of Science Editors:

Cragun D. Investigation Of The Molecular Role(S) Of Yop1 And Rtn1 Shaping The Peripheral Er. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/33508

Cornell University

17. Wang, Qi. Molecular Basis Of Bar Domain Super-Family Proteins And Genetically Encoded Calcium Indicators.

Degree: PhD, Biophysics, 2011, Cornell University

URL: http://hdl.handle.net/1813/33600

► Protein domains are the basic functional modules that maintain cell functions at a molecule level. Previous studies have mainly focused on the functions of isolated… (more)

▼ Protein domains are the basic functional modules that maintain cell functions at a molecule level. Previous studies have mainly focused on the functions of isolated protein domains. The general objective of this thesis is to understand functions and regulations of multi-domain containing proteins. The study is based on two protein classes: naturally occurred BAR domain-containing proteins and artificially engineered calcium indicators. BAR domain super-family proteins BAR (Bin/Amphiphysin/Rvs) domain super-family proteins are peripheral membrane proteins that regulate membrane curvatures during the membrane remodeling events such as endocytosis, vesicular trafficking and cell growth. Via multiple biophysical approaches, I systematically studied BAR domain functions in Sorting Nexin 9, Endophilin and Pacsins at the presence of other protein domains. Two major findings are presented in this thesis. First I show that the diverse membrane sculpture activity of BAR domains is encoded in their unique molecular structures, and is influenced by membrane properties. Second, I show that this function diversity is highly regulated by other protein domains. Some protein domains have synergetic effects and play important roles in regulating cellular membrane remodeling. This work is significant in that it provides the molecular basis for the functional diversity of BAR domains and established the regulatory mechanism of BAR domain mediated-membrane deformation process. Genetically Encoded Calcium Indicators Genetically encoded calcium indicator GCAMP is an artificially designed multi-domain containing protein that can be endogenously expressed in cells to monitor calcium signals. The molecular mechanisms of its signal response and fast kinetics are poorly understood. Using fluorescent spectrometry and site-directed mutagenesis, I show that the calcium-dependent brightness of GCAMP is due to the different protonation states of the chromophore. Structural characterization of GCAMP reveals that the calmodulin domain regulates chromophore protonation states via a sophisticated water-mediated hydrogen bond network. This finding provided a general scheme for designing GCAMP-like sensors. Furthermore, I show that distinct electron properties of the protonated and deprotonated chromophore can be applied to design color switchable fluorescent proteins. This finding provides a novel approach to design the ratio metric pH sensors with an improved sensitivity. Advisors/Committee Members: Sondermann, Holger (chair), Sethna, James Patarasp (committee member), Feigenson, Gerald W (committee member), Collins, Ruth N. (committee member).

Subjects/Keywords: bar; f-bar; calcium indicators; GECIs; pacsin; sorting nexin; gcamp; mkate; crystal structure; em

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APA (6^th Edition):

Wang, Q. (2011). Molecular Basis Of Bar Domain Super-Family Proteins And Genetically Encoded Calcium Indicators. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33600

Chicago Manual of Style (16^th Edition):

Wang, Qi. “Molecular Basis Of Bar Domain Super-Family Proteins And Genetically Encoded Calcium Indicators.” 2011. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/33600.

MLA Handbook (7^th Edition):

Wang, Qi. “Molecular Basis Of Bar Domain Super-Family Proteins And Genetically Encoded Calcium Indicators.” 2011. Web. 22 Jan 2021.

Vancouver:

Wang Q. Molecular Basis Of Bar Domain Super-Family Proteins And Genetically Encoded Calcium Indicators. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/33600.

Council of Science Editors:

Wang Q. Molecular Basis Of Bar Domain Super-Family Proteins And Genetically Encoded Calcium Indicators. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/33600

Cornell University

18. Li, Donghao. Investigating Kinesin-Like Protein Smy1P’S Function In Polarized Secretion.

Degree: M.S., Genetics, Genetics, 2013, Cornell University

URL: http://hdl.handle.net/1813/33843

► The budding yeast Saccharomyces cerevisiae shows substantial polarity during its growth. Membranes and proteins are constantly transported to the growth sites, almost exclusively mediated by… (more)

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APA (6^th Edition):

Li, D. (2013). Investigating Kinesin-Like Protein Smy1P’S Function In Polarized Secretion. (Masters Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/33843

Chicago Manual of Style (16^th Edition):

Li, Donghao. “Investigating Kinesin-Like Protein Smy1P’S Function In Polarized Secretion.” 2013. Masters Thesis, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/33843.

MLA Handbook (7^th Edition):

Li, Donghao. “Investigating Kinesin-Like Protein Smy1P’S Function In Polarized Secretion.” 2013. Web. 22 Jan 2021.

Vancouver:

Li D. Investigating Kinesin-Like Protein Smy1P’S Function In Polarized Secretion. [Internet] [Masters thesis]. Cornell University; 2013. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/33843.

Council of Science Editors:

Li D. Investigating Kinesin-Like Protein Smy1P’S Function In Polarized Secretion. [Masters Thesis]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/33843

Cornell University

19. Han, Seunghye. The Role Of Elongator Complex In The Regulation Of Neuronal Exocytosis.

Degree: M.S., Molecular and Cell Biology, Molecular and Cell Biology, 2014, Cornell University

URL: http://hdl.handle.net/1813/45351

Subjects/Keywords: Elongator Complex; Neuronal Exocytosis

Record Details Similar Records Cite « Share

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

APA (6^th Edition):

Han, S. (2014). The Role Of Elongator Complex In The Regulation Of Neuronal Exocytosis. (Masters Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/45351

Chicago Manual of Style (16^th Edition):

Han, Seunghye. “The Role Of Elongator Complex In The Regulation Of Neuronal Exocytosis.” 2014. Masters Thesis, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/45351.

MLA Handbook (7^th Edition):

Han, Seunghye. “The Role Of Elongator Complex In The Regulation Of Neuronal Exocytosis.” 2014. Web. 22 Jan 2021.

Vancouver:

Han S. The Role Of Elongator Complex In The Regulation Of Neuronal Exocytosis. [Internet] [Masters thesis]. Cornell University; 2014. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/45351.

Council of Science Editors:

Han S. The Role Of Elongator Complex In The Regulation Of Neuronal Exocytosis. [Masters Thesis]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/45351

Cornell University

20. Hsu, Pichiang. Regulation Of Ubiquitin-Mediated Endocytosis In Saccharomyces Cerevisiae.

Degree: PhD, Biochemistry, 2012, Cornell University

URL: http://hdl.handle.net/1813/31122

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Hsu, P. (2012). Regulation Of Ubiquitin-Mediated Endocytosis In Saccharomyces Cerevisiae. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/31122

Chicago Manual of Style (16^th Edition):

Hsu, Pichiang. “Regulation Of Ubiquitin-Mediated Endocytosis In Saccharomyces Cerevisiae.” 2012. Doctoral Dissertation, Cornell University. Accessed January 22, 2021. http://hdl.handle.net/1813/31122.

MLA Handbook (7^th Edition):

Hsu, Pichiang. “Regulation Of Ubiquitin-Mediated Endocytosis In Saccharomyces Cerevisiae.” 2012. Web. 22 Jan 2021.

Vancouver:

Hsu P. Regulation Of Ubiquitin-Mediated Endocytosis In Saccharomyces Cerevisiae. [Internet] [Doctoral dissertation]. Cornell University; 2012. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1813/31122.

Council of Science Editors:

Hsu P. Regulation Of Ubiquitin-Mediated Endocytosis In Saccharomyces Cerevisiae. [Doctoral Dissertation]. Cornell University; 2012. Available from: http://hdl.handle.net/1813/31122

Open Access Theses and Dissertations