Biochemistry, Biophysics, and Structural Biology Commons^™

A Bioinformatic And Biochemical Analysis Of Cruciviruses, George William Kasun

Dissertations and Theses

Cruciviruses are novel ssDNA viruses discovered through metagenomics and direct environmental DNA amplification and cloning. The genomes of cruciviruses suggest that gene transfer between RNA and DNA viruses occurred due to the presence of putative protein-encoding genes that are homologous to both ssRNA and ssDNA viruses. In order to gain a better understanding of this group of viruses both bioinformatic analyses and in vitro biochemical experiments were employed. The results of the bioinformatic analyses show that cruciviruses are a highly diverse group of ssDNA viruses. Their placement within established ssDNA phylogenies is difficult due to heterogeneity in their putative replication-associated …

Mechanisms Of Substrate Recognition By The Cul3-Based E3 Ligase, Katia Graziella De Oliveira Rebola

Dissertations and Theses

Cul3-based E3 ligase is responsible for regulating a variety of cellular pathways, many of which are known to have profound effects on the proper function of multicellular organisms. Although progress over the past years has been truly impressive, our understanding of the mechanisms of E2 recruitment and selection by the BCR complex and all the roles that Cul3 plays on kidneys remains in its infancy. To explore these aspects, this dissertation aims to analyze the Cul3 complex using two different approaches: (1) We used the powerful tool of chimeric analysis to map the essential domain binding characteristics of Cul3 taking …

Complete Mitochondrial Genome Sequence Of The Gulf Coast Tick (Amblyomma Maculatum), Amanda E. Brenner, Rahul Raghavan

Biology Faculty Publications and Presentations

The complete circularized mitochondrial genome sequence of Amblyomma maculatum is 14,803 bp long. It encodes 13 protein coding genes, 2 rRNA genes, 22 tRNA genes, 2 tick box motifs, and 2 control regions. The gene arrangement and content are consistent with those of previously reported Metastriata tick mitochondrial genomes.

Niche Partitioning And Utilization Of Different Nitrogen Sources By Marine Cyanobacteria Synechococcus, Angel Bui, Anne W. Thompson

McNair Symposium

The Cyanobacterium Synechococcus plays a major role in the ocean’s biochemical processes and is responsible for a significant amount of primary production, especially around coastal areas. Synechococcus has a wide geographical distribution that includes both polar and high-nutrient waters. Within the genus, there are defined subpopulations that are ecologically distinct that allow them to niche partition the dynamic oceans. To further explore niche partitioning of Synechococcus, this project combines a bioinformatic and culture-based approach. I examined data along the North Pacific Subtropical Front (NSPF) to analyze the community structure. This analysis demonstrated that a particular ecotype identified as clade II …

Cd40l And Tnf-Alpha Levels After Traumatic Injury, Queen Revollido, Martin Schreiber

McNair Symposium

The biomarkers CD40 ligand and TNF-alpha are proteins that exhibit proinflammatory and prothrombotic effects. A small clinical study has shown that soluble CD40 ligand may have a role in early coagulopathy and inflammatory complications in severely injured patients. It is known that a CD40 ligand increases the production of cytokines such as TNF-alpha, thus, the current study aims to investigate the kinetics of these biomarkers and the extent of upregulation after traumatic injury. Frozen samples collected from baseline, 8, 24, and 48 hours after admission will be used. CD40 ligand and TNF-alpha levels will be quantified using Luminex that will …

Mechanisms Of Connexin-46 And -50 Intercellular Channel Function And Stability By Molecular Dynamics Simulations, Bassam George Haddad

Dissertations and Theses

Gap junctions make up a class of intercellular channels that characteristically connect the cytoplasm of directly apposed cells through large assemblies, or plaques, constituted by a multitude of intercellular channels. Gap junction mediated intercellular communication is critical for a variety of physiological functions, from coordinating electrical impulses in the heart and brain to maintaining homeostasis in most tissues. There are 21 isoforms of connexins, the constituent subunit of the gap junction, expressed in a tissue dependent manner. Gap junctions formed from different isoforms exhibit distinct biophysical properties, such as gating kinetics and sensitivity, as well as unique permeability and selectivity …

Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan

University Honors Theses

Connexins form intercellular channels known as gap junctions that facilitate diverse physiological roles, from long-range electrical and chemical coupling to nutrient exchange. Recent structural studies on Cx46 and Cx50 have defined a novel and stable open state and implicated the amino-terminal (NT) domain as a major contributor to functional differences between connexin isoforms. This thesis presents two studies which use molecular dynamics simulations with these new structures to provide mechanistic insight into the function and behavior of the NTH in Cx46 and Cx50. In the first, residues in the NTH that differ between Cx46 and Cx50 are swapped between the …

The Role Of Native Lens Α-Crystallin In Amyloid Suppression Using Β-Amyloid As A Model Amyloid Client, Leilani Lopes

University Honors Theses

Cataracts are a result of age-related protein aggregate formation in the eye lens, and the leading cause of blindness worldwide. α-crystallin, a small heat shock protein, acts a molecular chaperone that serves as the primary defense mechanism against protein aggregate formation in the lens. Recent evidence suggest amyloid formation in the lens may contribute to cataract formation, and that β-amyloid is present in lens epithelia of age-related cataracts. Previous studies have shown that αB-crystallin in other parts of the body, such as the brain, is protective against neurodegenerative diseases such as Alzheimer’s disease that are associated with plaque deposits containing …

Steady-State Transmembrane Water Exchange In Proliferating Cultures Of Saccharomyces Cerevisiae, Joseph O'Malley Armstrong

Dissertations and Theses

Cellular water exchange is often considered in terms of a change in volume, where a net flux of water moves across the cell membrane due to a change in osmotic pressure. Osmotic pressure can cause a cell to shrink or swell, however, rapid water exchange persists across the membrane even when the volume of the cell is constant. Steady-state transmembrane water exchange describes the exchange of water across the cell membranes which results in no net change in cell volume. This exchange is astonishingly rapid; the entire pool of intracellular water of a Saccharomyces cerevisiae cell may exchange 2-5 times …

Thermodynamics Of Ligand Binding And Global Structural Stability Of Human Serum Albumin, Matthew Walter Eskew

Dissertations and Theses

Protein structure is integral to its function. For the past 70 years differential scanning calorimetry has been used to measure protein structural stability. More recently it has been used to study macromolecular interactions. Interactions between proteins and ligands can manifest on differential scanning calorimetry melting curves or thermograms. Utilizing differential scanning calorimetry thermograms to detect or diagnose diseases has been a major goal in disease diagnostics. However, correlating specific ligand-protein interactions, as manifested in a thermogram, with a disease-specific plasma thermogram, has proven elusive.

Modified human serum albumin was utilized to develop a process to capture and retrieve ligands from …