Biochemistry, Biophysics, and Structural Biology Commons^™

Pump-Probe And Mix-And-Inject Experiments At X-Ray Free Electron Lasers, Suraj Pandey

Theses and Dissertations

Time resolved serial femtosecond crystallography (TR-SFX) utilizes X-ray crystallography to visualize the reaction of molecules in real time at the atomic level. Crystals of biological macromolecules are exposed to powerful X-ray pulses. The X-ray radiation emitted by the crystal is then measured by an X-ray sensitive area detector that produces an image called a diffraction pattern. These patterns are analyzed to determine a three-dimensional atomic structure of the biological macromolecule.The ultimate goal of TR-SFX is to make a “molecular movie” that shows the reaction dynamics of a biological process. For this, a reaction is started in a macromolecular crystal and …

Structural And Functional Characterization Of L-Enduracididine Biosynthetic Enzymes, Nemanja Vuksanovic

Theses and Dissertations

The mannopeptimycins produced by Streptomyces hygroscopicus are non-ribosomal peptide antibiotics with activity against a number of Gram-positive pathogens, including drug-resistant strains like methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Attempts to synthesize more potent mannopeptimycin analogues have so far not been successful. One reason this has proven difficult is that the mannopeptimycins contain the unusual non-proteinogenic amino acid L-enduracididine (L-End), or its hydroxylated derivative β-hydroxy enduracididine (βhEnd,). This amino acid is not commercially available and, while synthetic routes have been developed, they are multi-step processes starting from an advanced intermediate. Understanding enzymatic synthesis of L-End is an important goal, …

Analytic Solutions For Diffusion On Path Graphs And Its Application To The Modeling Of The Evolution Of Electrically Indiscernible Conformational States Of Lysenin, K. Summer Ware

Boise State University Theses and Dissertations

Memory is traditionally thought of as a biological function of the brain. In recent years, however, researchers have found that some stimuli-responsive molecules exhibit memory-like behavior manifested as history-dependent hysteresis in response to external excitations. One example is lysenin, a pore-forming toxin found naturally in the coelomic fluid of the common earthworm Eisenia fetida. When reconstituted into a bilayer lipid membrane, this unassuming toxin undergoes conformational changes in response to applied voltages. However, lysenin is able to "remember" past history by adjusting its conformational state based not only on the amplitude of the stimulus but also on its previous …

Design Of Hfgf1 Variant(S) With Increased Stability And Enhanced Bioactivity, Shilpi P. Agrawal

Graduate Theses and Dissertations

Fibroblast growth factors (FGFs) are involved in various cellular processes such as cell growth,proliferation, differentiation, migration, angiogenesis, wound healing and embryonic development. Human acidic fibroblast growth factor (hFGF1) binds non-selectively to all the four FGF-receptors and is therefore considered as a powerful mitogen with broadest specificity. However, pharmacological applications of hFGF1 are restricted due to the low thermal stability of the growth factor. hFGF1 has low thermodynamic stability under physiological temperatures which leads to impairment of cellular signaling process thereby preventing its potential mitogenic properties. hFGF1 has a heparin binding pocket at the C-terminus which comprises of positively charges residues. …

Calcium Dyshomeostasis In Neurodegeneration, Nicholas Emanuel Karagas

Dissertations & Theses (Open Access)

Neurodegenerative diseases, despite constituting a major and growing cause of mortality globally, have few effective treatments. In order to develop novel therapeutics to combat neurodegeneration, a better understanding of the molecular mechanisms underlying these diseases is needed. Neurons rely on Ca²⁺ to mediate many of their unique functions, and aberrant Ca²⁺ signaling has been broadly implicated in neurodegeneration. The goal of this dissertation is to delineate specific examples of Ca²⁺ dyshomeostasis that I have uncovered in Drosophila models of neurodegeneration.

I first define the role a neurodegeneration-associated mutation plays in perturbing presynaptic [Ca²⁺], which is …

The Role Of Liver Sinusoidal Endothelial Cells In Liver Malady Homeostasis, Fatima Cabral

Department of Biochemistry: Dissertations, Theses, and Student Research

Current literature described techniques for the purification of liver cell types through text alone. The techniques described for the isolation of liver sinusoidal endothelial cells as well as hepatocytes described here are modified from a published article in the Journal of Visualized experiments. The video protocol allows for the user to successfully isolate cells as the most difficult parts of the procedure are demonstrated visually. The detection of liver maladies such as the non-alcoholic fatty liver disease, the stage if this disease and differentiation between non-alcoholic and alcoholic fatty liver disease is demonstrated in the development of a unique panel …

The Role Of Rna Editing Within Calcium-Dependent Activator For Secretion 1 In Large Dense Core Vesicle Fusion, Kaylee M. Mathiason

MSU Graduate Theses

Calcium-dependent activator protein for secretion 1 (CAPS1) is involved in synaptic vesicle and large dense core vesicle fusion by bridging vesicles and the plasma membrane prior to vesicle fusion and cargo release. CAPS1 is subject to a post-transcriptional modification called RNA editing. RNA editing recodes a single amino acid in the region of the protein that interacts with the vesicle. This recoding event within CAPS1 has cellular consequences in neurons where edited CAPS1 overexpression increases basal secretion from neural synaptic vesicles. Our goal was to investigate how RNA editing within CAPS1 affects large dense core vesicle secretion in an insulinoma …

Investigating The Disorder And Compaction Of Designed Minielastin Using Nuclear Magnetic Resonance., Ma Faye Charmagne Aquino Carvajal

Electronic Theses and Dissertations

Minielastins are elastin-based proteins with alternating hydrophobic and cross-link modules similar to tropoelastin. Tropoelastin is the ~70 kDa soluble monomeric precursor of elastin. The extracellular matrix protein, elastin provides elasticity to tissues and organs such as lungs, arteries and ligaments. The elastic properties of natural elastin are believed to be entropic in origin. In vivo, the elastin matrix is approximately 50% water by weight. Without water, elastin is brittle and hard. Minielastins, like tropoelastin, undergo a liquid-liquid phase transition upon an increase in temperature. Factors such as hydrophobicity, chain length and concentration affect the coacervation temperature, T_c. The …

Determining A Method For Expressing And Purifying Cytochrome P450 4v2: A Protein Involved In Bietti's Crystalline Dystrophy, Cody Lane Turner

MSU Graduate Theses

Within the Cytochrome P450 class of enzymes, there are a group known as the “orphan” cytochromes. The “orphan” classification comes from the poorly understood in vivo functionality and substrate specificity. Cytochrome P450 4V2 (CYP4V2) is one of these “orphans” and belongs to the CYP4 family. The CYP4 family is known for the omega oxidation of endogenous fatty acids. This family is most commonly found on chromosome 1 (CYP4ABXZ). CYP4V2 is unique in that its location is bound to chromosome 4 as discovered by Jiao in 2004. Mutations within the CYP4V2 gene have been associated with the …

Predictors Of Student Success In An Upper Division Agriculture Chemistry Class, Maddison V. May

MSU Graduate Theses

To attempt to find what made students successful within a higher division class at Missouri State University’s (MSU) Darr College of Agriculture, de-identified academic records of 172 students enrolled in AGR 300 - Food and Agriculture Chemistry were studied over four semesters. Deidentified data were collected and compared to final letter grade received at the end of the class using correlation coefficients, analysis of variance, and stepwise regression. Analysis of variance was used to evaluate the influence of semester on letter grade. Correlation coefficients were used to determine and evaluate relationships between the variables and final grade. Stepwise regression was …

A Context-Forward In Vivo Functional Genomics Platform For Target Discovery And Establishing Vulnerability Context In Pancreatic Cancer, Johnathon Rose, Johnathon Lynn Rose

Dissertations & Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a very poor patient prognosis (5-year survival of ≤ 7%). While transcriptional profiling has aided in the classification of this disease into at least two broader subtypes, this alone has so far been insufficient to inform on more nuanced patterns of oncogenic dependency. We hypothesized that a more comprehensive and granular characterization of PDAC disease diversity is required to establish relevant context for targeted therapy. To this end, we sought to establish an integrated platform to: i) more comprehensively characterize differential oncogenic signaling across our tumor models, and ii) establish …

Ionic Mechanism Of Lysosomal Function And Cell Metabolism, Jian Xiong

Dissertations & Theses (Open Access)

Two Pore Channels (TPCs) are endolysosomal ion channels that are permeable to sodium and calcium. Defects in TPCs have been implicated to impair vesicle trafficking, autophagy and cell metabolism control; however, the detailed mechanism remains largely unknown. In this study, I show that TPCs are critical for appropriate cargo delivery to the lysosomes and deletion of either TPC1 or TPC2 leads to delayed clearance of autophagosomes, resulting in enlarged lysosomes and accumulated contents inside the lysosomes. Cells with both TPC deleted also exhibit 50% reduction in lysosomal amino acids under normal culture conditions, leading to reduced homeostatic mTORC1 activation.

Glutamine …

Stem Cell Technology For Age Related Macular Degeneration Intervention, Laura Valdez

Theses and Dissertations

The main focus of this thesis is to study RPE cell derived from IMR90 induced pluripotent stem cells in various physiological conditions mimicking RPE transplantation rejection. Retinal pigmented epithelium (RPE) cells are located between the choroid and photoreceptors in the eye and they are essential to provide nutrients from blood to rods and cones, as well retinoids of the visual cycle. Vision loss and various ocular diseases are attributable to the degeneration or dysfunction of the RPE cells, leading to blindness. One of the major ocular problem from RPE dysfunction is macular degeneration. Age-related macular degeneration (AMD) can be frequently …

Not Too Hot, Not Too Cold, But Moderately Variable: The Influence Of Environmental Variability On Coral Thermal Tolerance, Courtney Nicole Klepac

Biological Sciences Theses & Dissertations

Anthropogenic climate change is causing an increase in the frequency and severity of marine heat waves, resulting in declining health of coral reef ecosystems worldwide. Coral bleaching events – the breakdown in symbiosis between the coral host and their intracellular photosynthetic algae – are increasingly common in recent years and contribute to widespread losses in coral cover. However, bleaching and heat stress responses vary across spatial scales both within and among coral species. Coral populations native to highly variable environments can have greater bleaching resistance than corals from more stable habitats and corals transplanted into these variable reef sites can …

Drivers Of Rickettsial Pathogen Transmission And Spillover In Local Tick Populations In Southeastern Virginia, Alexandra Cumbie

Biomedical Sciences Theses & Dissertations

Cases of spotted fever group rickettsiosis are becoming more prevalent in the United States. In Virginia, there are three human-biting ticks which are largely responsible for the spread of rickettsial pathogens and the increase in disease cases. These species include Dermacentor variabilis, Amblyomma americanum, and Amblyomma maculatum; all of which are vectors of rickettsial agents to vertebrate hosts. These species are sympatric as adults and have the potential to share large and small mammal hosts. Their interactions on and off host and their associated rickettsiae were the focus of this dissertation work. Amblyomma americanum is the vector …

Editorial: Structure And Function Of Chloroplasts - Volume Ii, Yan Lu, Lu Ning Liu, Rebecca L. Roston, Jurgen Soll, Hongbo Gao

Department of Biochemistry: Faculty Publications

No abstract provided.

Interactions Of The Nlrp3 Inflammasome Complex, Nyasha Makoni

Dissertations

The innate immune system is the first line of defense in response to invasion by pathogens. One of the major pathways in the innate immune system involves a three-protein complex known as the NLRP3 inflammasome. This complex comprises of NLRP3, ASC, and procaspase-1. In response to stimuli, the inflammasome assembles to activate caspase-1 which subsequently facilitates production of interleukin-1β (IL-1β), an inflammatory cytokine. The NLRP3 inflammasome has been implicated in a variety of inflammatory disorders including Alzheimer’s disease (AD). Amyloid beta (Aβ) is the protein that causes AD and Aβ deposits in the brain activate microglia resulting in chronic inflammation. …

Dna Aptamer-Drug Targeting Chemotherapy: Investigation Of Cell Cycle Inhibition Via S15 Aptamer – Norcantharidin Complex, Shannon Fehr

Senior Honors Theses

Lung Cancer is the leading cause of cancer related death in both men and women in the United States (Bray et al., 2018). Cancer treatments are often non-specific and kill many dividing cells within a patient causing unwanted side effects. Norcantharidin (NCTD) is a synthetic FDA approved treatment for cancers including non-small cell lung cancers (NSCLC). NCTD suppresses cell proliferation by inhibiting cells from exiting the G2 phase of the cell cycle. Aptamers are short single-stranded DNA or RNA molecules with ligand directed self-annealing capabilities allowing selective binding to specific targets. This paper will discuss the hypothesized effects of using …

An Investigation Into The Adverse Effects Of Oxidative Stress From Exposure To Bisphenol A And Its Analogues, Rachel Nas

Senior Honors Theses

Oxidative stress is a physiological event caused by an overaccumulation of reactive oxygen species (ROS) within the body. While ROS are a natural by-product of oxygen metabolism, too many can lead to cell and tissue damage and contribute to many etiologies. Bisphenol A (BPA), a component of many plastic products, has been shown to induce oxidative stress. While the industrial usage of BPA usage has lessened, the safety of its replacements is unknown. This paper will primarily discuss ROS and mechanisms of oxidative stress, the usage of BPA and its analogues, etiologies associated with oxidative stress resulting from exposure to …

Biophysical Analysis Of Pseudomonas-Phage Pap3 Small Terminase Suggests A Mechanism For Sequence-Specific Dna-Binding By Lateral Interdigitation., Marzia Niazi, Tyler J. Florio, Ruoyu Yang, Ravi K. Lokareddy, Nicholas A. Swanson, Richard E. Gillilan, Gino Cingolani

Department of Biochemistry and Molecular Biology Faculty Papers

The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but …