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You searched for +publisher:"Georgia Tech" +contributor:("Adegboyega Oyelere"). Showing records 1 – 3 of 3 total matches.

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1. Boz, Mustafa Burak. Modeling and simulations of single stranded rna viruses.

Degree: PhD, Chemistry and Biochemistry, 2012, Georgia Tech

The presented work is the application of recent methodologies on modeling and simulation of single stranded RNA viruses. We first present the methods of modeling RNA molecules using the coarse-grained modeling package, YUP. Coarse-grained models simplify complex structures such as viruses and let us study general behavior of the complex biological systems that otherwise cannot be studied with all-atom details. Second, we modeled the first all-atom T=3, icosahedral, single stranded RNA virus, Pariacoto virus (PaV). The x-ray structure of PaV shows only 35% of the total RNA genome and 88% of the capsid. We modeled both missing portions of RNA and protein. The final model of the PaV demonstrated that the positively charged protein N- terminus was located deep inside the RNA. We propose that the positively charged N- terminal tails make contact with the RNA genome and neutralize the negative charges in RNA and subsequently collapse the RNA/protein complex into an icosahedral virus. Third, we simulated T=1 empty capsids using a coarse-grained model of three capsid proteins as a wedge-shaped triangular capsid unit. We varied the edge angle and the potentials of the capsid units to perform empty capsid assembly simulations. The final model and the potential are further improved for the whole virus assembly simulations. Finally, we performed stability and assembly simulations of the whole virus using coarse-grained models. We tested various strengths of RNA-protein tail and capsid protein-capsid protein attractions in our stability simulations and narrowed our search for optimal potentials for assembly. The assembly simulations were carried out with two different protocols: co-transcriptional and post-transcriptional. The co-transcriptional assembly protocol mimics the assembly occurring during the replication of the new RNA. Proteins bind the partly transcribed RNA in this protocol. The post-transcriptional assembly protocol assumes that the RNA is completely transcribed in the absence of proteins. Proteins later bind to the fully transcribed RNA. We found that both protocols can assemble viruses, when the RNA structure is compact enough to yield a successful virus particle. The post-transcriptional protocol depends more on the compactness of the RNA structure compared to the co-transcriptional assembly protocol. Viruses can exploit both assembly protocols based on the location of RNA replication and the compactness of the final structure of the RNA. Advisors/Committee Members: Stephen C. Harvey (Committee Chair), Adegboyega Oyelere (Committee Member), Loren Williams (Committee Member), Rigoberto Hernandez (Committee Member), Roger Wartell (Committee Member).

Subjects/Keywords: Virus assembly; Coarse-grained models; RNA virus; RNA viruses; RNA; Nucleic acids

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APA (6th Edition):

Boz, M. B. (2012). Modeling and simulations of single stranded rna viruses. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/44815

Chicago Manual of Style (16th Edition):

Boz, Mustafa Burak. “Modeling and simulations of single stranded rna viruses.” 2012. Doctoral Dissertation, Georgia Tech. Accessed November 27, 2020. http://hdl.handle.net/1853/44815.

MLA Handbook (7th Edition):

Boz, Mustafa Burak. “Modeling and simulations of single stranded rna viruses.” 2012. Web. 27 Nov 2020.

Vancouver:

Boz MB. Modeling and simulations of single stranded rna viruses. [Internet] [Doctoral dissertation]. Georgia Tech; 2012. [cited 2020 Nov 27]. Available from: http://hdl.handle.net/1853/44815.

Council of Science Editors:

Boz MB. Modeling and simulations of single stranded rna viruses. [Doctoral Dissertation]. Georgia Tech; 2012. Available from: http://hdl.handle.net/1853/44815

2. Shaffer, Hally A. Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.

Degree: PhD, Chemistry and Biochemistry, 2011, Georgia Tech

Nuclear receptors are ligand-activated transcription factors that play significant roles in various biological processes within the body, such as cell development, hormone metabolism, reproduction, and cardiac function. As transcription factors, nuclear receptors are involved in many diseases, such as diabetes, cancer, and arthritis, resulting in approximately 10-15% of the pharmaceutical drugs presently on the market being targeted toward nuclear receptors. Structurally, nuclear receptors consist of a DNA-binding domain (DBD), responsible for binding specific sequences of DNA called response elements, fused to a ligand-binding domain (LBD) through a hinge region. The LBD binds a small molecule ligand. Upon ligand binding, the LBD changes to an active conformation leading to the recruitment of coactivator (CoAC) proteins and initiation of transcription. As a result of their involvement in disease, there is an emphasis on engineering nuclear receptors for applications in gene therapy, drug discovery and metabolic engineering. Advisors/Committee Members: Bahareh Azizi (Committee Chair), Donald Doyle (Committee Chair), Andreas Bommarius (Committee Co-Chair), Loren Williams (Committee Co-Chair), Adegboyega Oyelere (Committee Member), Nick Hud (Committee Member), Sheldon May (Committee Member).

Subjects/Keywords: Nuclear receptors; Chemical complementation; Negative chemical complementation; Yeast-two hybrid selection; Pregnane X receptor; Estrogen receptor; Pregnane; Protein engineering; Nuclear receptors (Biochemistry); Transcription factors; Yeast Genetics

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

APA (6th Edition):

Shaffer, H. A. (2011). Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/39620

Chicago Manual of Style (16th Edition):

Shaffer, Hally A. “Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.” 2011. Doctoral Dissertation, Georgia Tech. Accessed November 27, 2020. http://hdl.handle.net/1853/39620.

MLA Handbook (7th Edition):

Shaffer, Hally A. “Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.” 2011. Web. 27 Nov 2020.

Vancouver:

Shaffer HA. Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. [Internet] [Doctoral dissertation]. Georgia Tech; 2011. [cited 2020 Nov 27]. Available from: http://hdl.handle.net/1853/39620.

Council of Science Editors:

Shaffer HA. Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. [Doctoral Dissertation]. Georgia Tech; 2011. Available from: http://hdl.handle.net/1853/39620


Georgia Tech

3. Scarberry, Kenneth Edward. Biomedical applications of cobalt-spinel ferrite nanoparticles for cancer cell extraction and drug delivery.

Degree: PhD, Chemistry and Biochemistry, 2009, Georgia Tech

In this presentation it is demonstrated that the unique magnetic properties of superparamagnetic cobalt-spinel ferrite nanoparticles can be employed in several novel applications. A method to selectively capture and remove pathogens from infected organisms to improve longevity is presented. Evidence is provided to show that automated methods using modified forms of hemofiltration or peritoneal dialysis could be used to eliminate the particle/pathogen or particle/infected cell conjugates from the organism postoperatively. It is shown that disparately functionalized nanoparticles can be used in concert as drug carrier and release mechanisms. Lastly, we provide preliminary evidence to support the use of magnetic nanoparticles for controlling reaction kinetics. Advisors/Committee Members: Dr. John Zhang (Committee Chair), Dr. John McDonald (Committee Co-Chair), Dr. Adegboyega Oyelere (Committee Member), Dr. Dennis Doyle (Committee Member), Dr. Nael McCarty (Committee Member).

Subjects/Keywords: Nanotechnology; Chemiluminescence; Biochemistry; Peptide; Aptamer; HIV; Drug delivery; Cancer; Magnetic nanoparticles; Nanobiotechnology; Magnetic materials; Ferrites (Magnetic materials); Chemiluminescence Diagnostic use; Nanomedicine; Nanoparticles; Drug delivery systems; Cobalt; Spinel group

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

APA (6th Edition):

Scarberry, K. E. (2009). Biomedical applications of cobalt-spinel ferrite nanoparticles for cancer cell extraction and drug delivery. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/33951

Chicago Manual of Style (16th Edition):

Scarberry, Kenneth Edward. “Biomedical applications of cobalt-spinel ferrite nanoparticles for cancer cell extraction and drug delivery.” 2009. Doctoral Dissertation, Georgia Tech. Accessed November 27, 2020. http://hdl.handle.net/1853/33951.

MLA Handbook (7th Edition):

Scarberry, Kenneth Edward. “Biomedical applications of cobalt-spinel ferrite nanoparticles for cancer cell extraction and drug delivery.” 2009. Web. 27 Nov 2020.

Vancouver:

Scarberry KE. Biomedical applications of cobalt-spinel ferrite nanoparticles for cancer cell extraction and drug delivery. [Internet] [Doctoral dissertation]. Georgia Tech; 2009. [cited 2020 Nov 27]. Available from: http://hdl.handle.net/1853/33951.

Council of Science Editors:

Scarberry KE. Biomedical applications of cobalt-spinel ferrite nanoparticles for cancer cell extraction and drug delivery. [Doctoral Dissertation]. Georgia Tech; 2009. Available from: http://hdl.handle.net/1853/33951

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