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Old Dominion University

2021

Articles 1 - 14 of 14

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Genetically Engineered Thermosynechococcus Elongatus Bp1: Assessment Of Potential Biorisks And Biofuel Production, Thu Ho Anh Nguyen-Jones Dec 2021

Genetically Engineered Thermosynechococcus Elongatus Bp1: Assessment Of Potential Biorisks And Biofuel Production, Thu Ho Anh Nguyen-Jones

Chemistry & Biochemistry Theses & Dissertations

According to the International Energy Outlook 2019, released by the U.S. Energy Information Administration, it is projected that the energy consumption will increase up to 50% between 2018 and 2050 worldwide. As fossil fuel being a finite source of energy with the risk of depletion, many countries are now facing an energy security crisis. Therefore, it is important to develop other renewable and sustainable energy sources that will allow countries to shift away from depending on fossil fuels. Among several types of renewable energy, biofuel production using genetically engineered cyanobacteria is capturing much interest due to its many advantages. Different …

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Improvement Of Biochar Through Ozonization And Biosafety Of Genetically Engineered Cyanobacteria, Oumar Sacko Jul 2021

Improvement Of Biochar Through Ozonization And Biosafety Of Genetically Engineered Cyanobacteria, Oumar Sacko

Chemistry & Biochemistry Theses & Dissertations

Through the innovative technique of biochar post-production surface oxygenation by ozonization, we were able to improve certain properties of biochar. In project one, the incubation of an insoluble phosphate rock material (hydroxyapatite) with the wet ozonized pine 400 biochar and its filtrate resulted in a solubilization of 80 times more phosphate from hydroxyapatite (569.0 mg/L ± 6.4) compared to the pure water-hydroxyapatite control (7.2 mg/L ± 0.3). The ozonized biochar may provide a new possible way to unlock the phosphorus from insoluble phosphate mineral phases. The cation exchange capacity (CEC) is a key property of biochar when used as a …

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Electrohydrodynamic Simulations Of Capsule Deformation Using A Dual Time-Stepping Lattice Boltzmann Scheme, Charles Leland Armstrong Jul 2021

Electrohydrodynamic Simulations Of Capsule Deformation Using A Dual Time-Stepping Lattice Boltzmann Scheme, Charles Leland Armstrong

Mathematics & Statistics Theses & Dissertations

Capsules are fluid-filled, elastic membranes that serve as a useful model for synthetic and biological membranes. One prominent application of capsules is their use in modeling the response of red blood cells to external forces. These models can be used to study the cell’s material properties and can also assist in the development of diagnostic equipment. In this work we develop a three dimensional model for numerical simulations of red blood cells under the combined influence of hydrodynamic and electrical forces. The red blood cell is modeled as a biconcave-shaped capsule suspended in an ambient fluid domain. Cell deformation occurs …

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Computational Analysis Of Type 3 Iodothyronine Deiodinase: Potential Inhibitors, Substrate Binding, And Dimer Structure, Eric Scott Marsan Jul 2021

Computational Analysis Of Type 3 Iodothyronine Deiodinase: Potential Inhibitors, Substrate Binding, And Dimer Structure, Eric Scott Marsan

Chemistry & Biochemistry Theses & Dissertations

Thyroid hormones (THs) in mammalian tissues are crucial for development and maintaining metabolic homeostasis. Iodothyronine deiodinases (Dios) remove iodines from THs by a selenocysteine (Sec) residue, which either activates or inactivates them. Halogen bonding (XB) has been proposed to describe the interaction between the Se and I atoms of the T4-Dio complex. Disruption of TH homeostasis by xenobiotics, such as polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) can cause deleterious effects on the endocrine system. Experimental studies have indicated that PBDEs and PCBs could disrupt TH homeostasis by inhibiting Dio through XB formation. However, no current quantitative study exists …

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Computational And Experimental Investigation Into The Determinants Of Protein Structure, Folding, And Stability In The Β-Grasp Superfamily, John T. Bedford Ii Apr 2021

Computational And Experimental Investigation Into The Determinants Of Protein Structure, Folding, And Stability In The Β-Grasp Superfamily, John T. Bedford Ii

Chemistry & Biochemistry Theses & Dissertations

Elucidating the mechanisms of protein folding and unfolding is one of the greatest scientific challenges in basic science. The overarching goal is to predict three-dimensional structures from their amino acid sequences. Understanding the determinants of protein folding and stability can be facilitated through the study of evolutionarily related but diverse proteins. Insights can also be gained through the study of proteins from extremophiles that may more closely resemble the primordial proteins. In this doctoral research, three aims were accomplished to characterize the structure, folding and unfolding behavior within the β-grasp superfamily. We propose that the determinants of structure, stability, and …

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Influence Of Monovalent And Divalent Ions In The Conformational Change Of Caspase-Cleaved Par-4 (Cl-Par-4) Tumor Suppressor Protein, Krishna K. Raut, Komala Ponniah, Steven M. Pascal Apr 2021

Influence Of Monovalent And Divalent Ions In The Conformational Change Of Caspase-Cleaved Par-4 (Cl-Par-4) Tumor Suppressor Protein, Krishna K. Raut, Komala Ponniah, Steven M. Pascal

College of Sciences Posters

Prostate apoptosis response-4 (Par-4) is a pro-apoptotic tumor suppressor protein. We have shown that this 38 kDa full-length Par-4 (Fl-Par-4) protein is predominantly intrinsically disordered in vitro. In vivo, Par-4 is cleaved by caspase-3 at Asp-131 to generate a 24 kDa functionally active cleaved Par-4 (cl-Par-4) fragment. The cl-Par-4 protein inhibits the NF-κB-mediated cell survival pathway and causes selective apoptosis in various tumor cells. Our laboratory is interested in how the disorder-order balance within Fl-Par-4 and cl-Par-4 may be related to the balance between cell survival and cell death. Currently, we are using biophysical techniques such as circular …

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Evaluating The Role Of The Stringent Response Mechanism In Clostridioides Difficile Survival And Pathogenesis, Astha Pokhrel Apr 2021

Evaluating The Role Of The Stringent Response Mechanism In Clostridioides Difficile Survival And Pathogenesis, Astha Pokhrel

Chemistry & Biochemistry Theses & Dissertations

The human pathogen Clostridioides difficile is increasingly tolerant of multiple antibiotics and causes infections with a high rate of recurrence, creating an urgent need for new preventive and therapeutic strategies. The stringent response, a universal bacterial response to extracellular stresses, governs antibiotic survival and pathogenesis in diverse organisms but has not previously been characterized in C. difficile. This dissertation explores the ability of C. difficile to mount the stringent response. The bacteria encode a full-length, canonical bifunctional Rel/Spo Homolog or RSH enzyme. C. difficile RSH is incapable of utilizing GTP as a substrate but readily synthesizes putative 5’-pGpp-3’ alarmones. …

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Biophysical Characterization Of The Par-4 Tumor Suppressor: Evidence Of Structure Outside The Coiled Coil Domain And Interactions With Platinum Chemotherapeutics, Andrea Megan Clark Apr 2021

Biophysical Characterization Of The Par-4 Tumor Suppressor: Evidence Of Structure Outside The Coiled Coil Domain And Interactions With Platinum Chemotherapeutics, Andrea Megan Clark

Chemistry & Biochemistry Theses & Dissertations

Prostate apoptosis response-4 (Par-4) is an apoptosis-inducing tumor suppressor protein. Full-length Par-4 has previously been shown to be a predominantly intrinsically disordered protein (IDP) under neutral conditions, with significant regular secondary structure evident only within the C-terminal coiled coil domain. However, IDPs can gain ordered structure through the process of induced folding, which often occurs under non-neutral conditions. Previous work has shown that the Par-4 leucine zipper, which is a subset of the C-terminal coiled coil domain, is disordered under neutral conditions, but forms a dimeric coiled coil at acidic pH. Increase in ionic strength was also shown to increase …

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Methylation Of The D2 Dopamine Receptor Affects Binding With The Human Regulatory Proteins Par-4 And Calmodulin, Alexander Bowitch, Ansuman Sahoo, Andrea M. Clark, Christiana Ntangka, Krishna K. Raut, Paul Gollnick, Michael C. Yu, Steven M. Pascal, Sarah E. Walker, Denise M. Ferkey Feb 2021

Methylation Of The D2 Dopamine Receptor Affects Binding With The Human Regulatory Proteins Par-4 And Calmodulin, Alexander Bowitch, Ansuman Sahoo, Andrea M. Clark, Christiana Ntangka, Krishna K. Raut, Paul Gollnick, Michael C. Yu, Steven M. Pascal, Sarah E. Walker, Denise M. Ferkey

Chemistry & Biochemistry Faculty Publications

No abstract provided.

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Scaling The Effects Of Ocean Acidification On Coral Growth And Coral-Coral Competition On Coral Community Recovery, Nicolas R. Evensen, Yves-Marie Bozec, Peter J. Edmunds, Peter J. Mumby Jan 2021

Scaling The Effects Of Ocean Acidification On Coral Growth And Coral-Coral Competition On Coral Community Recovery, Nicolas R. Evensen, Yves-Marie Bozec, Peter J. Edmunds, Peter J. Mumby

Biological Sciences Faculty Publications

Ocean acidification (OA) is negatively affecting calcification in a wide variety of marine organisms. These effects are acute for many tropical scleractinian corals under short-term experimental conditions, but it is unclear how these effects interact with ecological processes, such as competition for space, to impact coral communities over multiple years. This study sought to test the use of individual-based models (IBMs) as a tool to scale up the effects of OA recorded in short-term studies to community-scale impacts, combining data from field surveys and mesocosm experiments to parameterize an IBM of coral community recovery on the fore reef of Moorea, …

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Detrital Neodymium And (Radio)Carbon As Complementary Sedimentary Bedfellows? The Western Arctic Ocean As A Testbed, Melissa S. Schwab, Jörg D. Rickli, Robie W. Macdonald, H. Rodger Harvey, Negar Haghipour, Timothy I. Eglinton Jan 2021

Detrital Neodymium And (Radio)Carbon As Complementary Sedimentary Bedfellows? The Western Arctic Ocean As A Testbed, Melissa S. Schwab, Jörg D. Rickli, Robie W. Macdonald, H. Rodger Harvey, Negar Haghipour, Timothy I. Eglinton

OES Faculty Publications

Interactions between organic and detrital mineral phases strongly influence both the dispersal and accumulation of terrestrial organic carbon (OC) in continental margin sediments. Yet the complex interplay among biological, chemical, and physical processes limits our understanding of how organo-mineral interactions evolve during sediment transfer and burial. In particular, diverse OC sources and complex hydrodynamic processes hinder the assessment of how the partnership of organic matter and its mineral host evolves during supply and dispersal over continental margins. In this study, we integrate new and compiled sedimentological (grain size, surface area), organic (%OC, OC-δ13C, OC-F14C), and inorganic …

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Adenosine Triphosphate (Atp) As A Metric Of Microbial Biomass In Aquatic Systems: New Simplified Protocols, Laboratory Validation, And A Reflection On Data From The Literature, Alexander B. Bochdansky, Alison N. Stouffer, Nyjaee N. Washington Jan 2021

Adenosine Triphosphate (Atp) As A Metric Of Microbial Biomass In Aquatic Systems: New Simplified Protocols, Laboratory Validation, And A Reflection On Data From The Literature, Alexander B. Bochdansky, Alison N. Stouffer, Nyjaee N. Washington

OES Faculty Publications

The use of adenosine triphosphate (ATP) as a universal biomass indicator is built on the premise that ATP concentration tracks biomass rather than the physiological condition of cells. However, reportedly high variability in ATP in response to environmental conditions is the main reason the method has not found widespread application. To test possible sources of this variability, we used the diatom Thalassiosira weissflogii as a model and manipulated its growth rate through nutrient limitation and through exposure to three different temperatures (15°C, 20°C, and 25°C). We simplified the ATP protocol with hot‐water or chemical extraction methods, modified a commercially available …

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Marine Phytoplankton Functional Types Exhibit Diverse Responses To Thermal Change, S. I. Anderson, A. D. Barton, Sophie Clayton, S. Dutkiewicz, T. A. Rynearson Jan 2021

Marine Phytoplankton Functional Types Exhibit Diverse Responses To Thermal Change, S. I. Anderson, A. D. Barton, Sophie Clayton, S. Dutkiewicz, T. A. Rynearson

OES Faculty Publications

Marine phytoplankton generate half of global primary production, making them essential to ecosystem functioning and biogeochemical cycling. Though phytoplankton are phylogenetically diverse, studies rarely designate unique thermal traits to different taxa, resulting in coarse representations of phytoplankton thermal responses. Here we assessed phytoplankton functional responses to temperature using empirically derived thermal growth rates from four principal contributors to marine productivity: diatoms, dinoflagellates, cyanobacteria, and coccolithophores. Using modeled sea surface temperatures for 1950-1970 and 2080-2100, we explored potential alterations to each group's growth rates and geographical distribution under a future climate change scenario. Contrary to the commonly applied Eppley formulation, our …

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Structual Analysis Of The Cl-Par-4 Tumor Suppressor As A Function Of Ionic Environment, Krishna K. Raut, Komala Ponniah, Steven M. Pascal Jan 2021

Structual Analysis Of The Cl-Par-4 Tumor Suppressor As A Function Of Ionic Environment, Krishna K. Raut, Komala Ponniah, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Prostate apoptosis response-4 (Par-4) is a proapoptotic tumor suppressor protein that has been linked to a large number of cancers. This 38 kilodalton (kDa) protein has been shown to be predominantly intrinsically disordered in vitro. In vivo, Par-4 is cleaved by caspase-3 at Asp-131 to generate the 25 kDa functionally active cleaved Par-4 protein (cl-Par-4) that inhibits NF-κB-mediated cell survival pathways and causes selective apoptosis in tumor cells. Here, we have employed circular dichroism (CD) spectroscopy and dynamic light scattering (DLS) to assess the effects of various monovalent and divalent salts upon the conformation of cl-Par-4 in vitro. We have …

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