Biochemistry, Biophysics, and Structural Biology Commons^™

A Seascape Genetics Approach To Studying Genetic Differentiation In The Bull Kelp Nereocystis Luetkeana, Lily G. Gierke

Theses and Dissertations

The brown alga Nereocystis luetkeana is a foundation species found from Alaska to California. In the Salish Sea, N. luetkeana is declining, but little is known about its population structure. We explored N. luetkeana 1) allelic dissimilarity and richness using seven microsatellite markers, and 2) tested models of gene flow in the Salish Sea using a hydrodynamic transport model. Our results suggest that the N. luetkeana distribution is comprised of four genetic co-ancestry groups that are geographically coherent, apart from the separation of the Strait of Georgia/Puget Sound by the Strait of Juan de Fuca. Our model supported that environmental …

Effects Of The Dihydrouracil Lesion On Dna Using 1h/31p 1d And 2d Solution Nmr, Benjamin M. Boyd

MSU Graduate Theses

The effects of the dihydrouracil lesion in DNA were studied using two dimensional NMR spectroscopy. The sequence used was based off of the Drew-Dickerson Dodecamer, with the cytosine in the three position replaced by a dihydrouracil. All of the nonexchangeable proton chemical shifts, with the exception of the H2, H5’, and H5’’, of the lesioned DNA were identified using NOESY spectra and then compared to the chemical shift values of the Drew Dickerson Dodecamer. The largest differences in chemical shifts were observed in the nucleotides neighboring the lesion, both within the strand and on the opposite strand. The imino exchangeable …

Rotational Tuning Of Transmembrane Helix Properties Based On The Precise Placements Of Aromatic And Charged Residues, Matthew J. Mckay

Graduate Theses and Dissertations

Designed model transmembrane peptides and oriented 2H and 15N solid-state nuclear magnetic resonance (NMR) spectroscopy were used to analyze how simple sequence modifications can influence peptide structure, behavior and dynamics as well as for determining the pKa of glutamic acid at the membrane interface. The GW5,19ALP23 (acetyl-GGALW(LA)6LWLAGA-amide) peptide framework adopts a well-defined tilted orientation in lipid bilayers (DLPC, DMPC and DOPC) and undergoes low amounts of dynamic motion. The sequence was initially modified by moving the Trp residues outwards to positions 4 and 20. This new sequence GW4,20ALP23 (acetyl-GGAW(AL)7AWAGA-amide) displays high amounts of signal averaging of NMR observables caused by …

The Role Of Membrane Domains In Protein And Lipid Sorting During Endocytic Traffic, Blanca B. Diaz-Rohrer

Dissertations & Theses (Open Access)

The lipid and protein composition of the plasma membrane (PM) must be tightly controlled to maintain cellular functionality, despite constant, rapid endocytosis. Because de novo synthesis of proteins and lipids is energetically costly, the cell depends on active recycling to return endocytosed membrane components back to the PM. For most proteins, the mechanisms and pathways of their PM retention remain unknown. The work presented here shows that association with ordered membrane microdomains is fully sufficient for PM recycling and that abrogation of raft partitioning leads to their degradation in lysosomes. These findings support a model wherein ordered membrane domains mediate …

Influence Of Single And Multiple Histidine Residues And Their Ionization Properties On Transmembrane Helix Dynamics, Orientations And Fraying, Fahmida Afrose

Graduate Theses and Dissertations

Since aromatic and charged residues are often present in various locations of transmembrane helices of integral membrane proteins, their impacts on the molecular properties of transmembrane proteins and their interactions with lipids are of particular interest in many studies. In this work, I used solid-state deuterium NMR spectroscopy in designed model peptide GWALP23 [GGALW(LA)6LWLAGA] with selective deuterium labels to addresses the pH dependence and influence of single and multiple “guest” histidine residues in the orientation and dynamic behaviors of transmembrane proteins. The mutations include Gly to His (G2/22 to H2/22), Trp to His (W5/19 to H5/19) and Leu to His …

Asymmetric Synthesis Of The C29-C34 Moiety Of Fragment A Of The Antascomicin B & Thermal Azole Based Claisen Rearrangements, Dharma Theja Nannapaneni

Graduate Theses and Dissertations

The dissertation describes asymmetric synthesis towards C29-C34 moiety of fragment A of the Antascomicin B and Thermal azole based Claisen rearrangements. In chapter 1, we describes asymmetric synthesis towards C29-C34 moiety of fragment A of the Antascomicin B. The non-immunosuppressant Rapamycin, Ascomycin, and Tacrolimus (FK506), strongly binds with FKBP12, the ligand FKBP12 complexes responsible for immunosuppressive activity. Antascomicin B structurally related to Rapamycin, Ascomycin, and Tacrolimus (FK506), binds strongly to FKBP12, yet does not shown immunosuppressive activity. The ligand FKBP12 binding complexes shown to have potent neuroprotective and neurogenerative properties in mouse models of Parkinson’s disease. The linear synthesis of …

Single Molecule Fluorescence Studies Of Protein Structure And Dynamics Underlying The Chloroplast Signal Recognition Particle Targeting Pathway, Dustin R. Baucom

Graduate Theses and Dissertations

The work presented in this dissertation explores the structural dynamics in the chloroplast signal recognition particle pathway. Findings include cpSRP shows scanning functionality similar to that in the cytosolic SRP with the ribosome. The intrinsically disordered C-terminal tail of the Albino3 protein has some transient secondary structure. Upon binding to cpSRP43 in solution, separate secondary structure formation was identified in the C-terminal tail of Albino3. Finally, to increase efficiency of analyzing fluorescence time traces for this work, a modular software was produced.

Xenobiotic Exposure Requires Mitochondrial Metabolism For Redox Homeostasis And Survival In Astrocytes, Jordan Rose

Department of Biochemistry: Dissertations, Theses, and Student Research

Astrocytes are integral components of glutamatergic neurotransmission, providing essential metabolic processes for neuronal homeostasis and acting as the first line of defense against xenobiotics crossing the blood brain barrier. Arsenic is a xenobiotic with widespread natural and industrial prevalence, and has been linked to impaired neurodevelopment and neuronal death. Given the integrated metabolic nature of astrocytes and neurons, we sought to explore how arsenic impacts astrocyte metabolism in order to better understand the mechanisms of xenobiotic toxicity in the mammalian brain.

We demonstrate that astrocyte viability depends upon de novoglutathione (GSH) synthesis during arsenic exposure, and sub-lethal arsenic exposure …

Characterization Of The Dimerization Domains On The Mannose-6-Phosphate/Insulin-Like Growth Factor Ii Receptor, Tyler Degener

Theses/Capstones/Creative Projects

The mannose-6-phosphate/insulin-like growth factor II (M6P/IGF2) receptor is a transmembrane protein known to sequester growth factors from the extracellular matrix. This behavior suggests a mechanism of tumor suppression. Structurally, the receptor’s extracellular region is segmented into 15 homologous repeats, which are divided further into 5 triplet domains, labelled 1-3, 4-6, 7-9, 10-12, and 13-15. What is notable about the triplets is their propensity to form dimers with triplets on a second M6P/IGF2 receptor. In fact, previous studies indicate that this protein functions optimally when dimerized. Thus, the purpose of this experiment is to characterize these domain interactions. Using a urea …

Electropermeabilization Does Not Correlate With Plasma Membrane Lipid Oxidation, Olga Michel, Andrei G. Pakhomov, Maura Casciola, Jolanta Saczko, Julita Kulbacka, Olga N. Pakhomova

Bioelectrics Publications

The permeabilized condition of the cell membrane after electroporation can last minutes but the underlying mechanisms remain elusive. Previous studies suggest that lipid peroxidation could be responsible for the lasting leaky state of the membrane. The present study aims to link oxidation within the plasma membrane of live cells to permeabilization by electric pulses. We have introduced a method for the detection of oxidation by ratiometric fluorescence measurements of BODIPY-C11 dye using total internal reflection fluorescence (TIRF) microscopy, limiting the signal to the cell membrane. CHO-K1 cells were cultured on glass coverslips coated with an electroconductive indium tin oxide (ITO) …

Cpsa Protein-Protein Interactions In Group B Streptococcus, Ben Tero

Honors College

Group B Streptococcal (GBS) infections pose a great threat to mortality in neonates. Neonates are often exposed to GBS both before, during, and after delivery, which can cause a range of health problems including meningitis, sepsis, or stillbirth. One of the major virulence factors that contributes to the infectivity of the pathogen is the bacterial capsule. The capsule is a polysaccharide matrix surrounding the cell which helps in the evasion of host defenses, and penetration into normally sterile sites like the bloodstream. The highly conserved GBS protein CpsA has been shown to regulate expression of the capsule. The objective of …

Targeting The Γ-Aminobutyric Acid A Receptor (Gabaar) To Alleviate Inflammation For Asthma And Neuropathic Pain, Amanda Nicole Nieman

Theses and Dissertations

The γ-Aminobutyric Acid A Receptor (GABAAR) is a ligand-gated, pentameric chloride channel composed of subunits that include α1-6, β1-3, γ1-3, δ, ε, π, θ, ρ1-3.1-2 The most common arrangement includes two α subunits, two β subunits, and a γ subunit.3 This receptor includes two binding sites for the endogenous ligand γ-aminobutyric acid (GABA) between the α and β subunits and a binding site between the α and γ subunit for benzodiazepines, a large family of positive allosteric modulators.4-5

Benzodiazepines are one of the most prescribed classes of pharmaceuticals to treat anxiety, insomnia, and epilepsy as well as for muscle relaxation.6-7 …

Investigation Of Phosphoserine Aminotransferase 1(Psat1) In Breast Cancer Progression., Stephanie Metcalf

Electronic Theses and Dissertations

This dissertation describes my research into the involvement of phosphoserine aminotransferase 1 (PSAT1) in breast cancer progression; specifically, in triple negative breast cancer (TNBC) metastasis and endocrine resistance in estrogen receptor positive breast cancer (ER+BC). Breast cancer is the most common tumor diagnosis among women. While the overall 5-year survival for breast cancer is reaching 90%, the 5-year survival for metastatic disease is only 22%. Metastasis and endocrine resistance combined can affect over 50% of patients. One of the proteins and pathways implicated in both metastasis and endocrine resistance in breast cancer is phosphoserine aminotransferase 1 (PSAT1) and the serine …

Investigating The Effects Of Excitotoxic Stimuli On The Suprachiasmatic Nucleus, Rachel A. Brandes

Chancellor’s Honors Program Projects

No abstract provided.

Cell Separation Delay And Membrane Trafficking Defects In Cdc42 Gap Mutants, Haylee Young

Chancellor’s Honors Program Projects

No abstract provided.

Isotopic Characterization Of Nitrogen Oxides (NoX), Nitrous Acid (Hono), And Nitrate (PNo3-) From Laboratory Biomass Burning During Firex, Jiajue Chai, David J. Miller, Eric Scheuer, Jack Dibb, Vanessa Selimovic, Robert Yokelson, Kyle K. Zarzana, Steven Brown, Abigail R. Koss, Carsten Warneke, Meredith Hastings

Chemistry and Biochemistry Faculty Publications

New techniques have recently been developed and applied to capture reactive nitrogen species, including nitrogen oxides (NOx D NOCNO2), nitrous acid (HONO), nitric acid (HNO3), and particulate nitrate (pNO3 ), for accurate measurement of their isotopic composition. Here, we report – for the first time – the isotopic composition of HONO from biomass burning (BB) emissions collected during the Fire Influence on Regional to Global Environments Experiment (FIREX, later evolved into FIREX-AQ) at the Missoula Fire Science Laboratory in the fall of 2016. We used our newly developed annular denuder system (ADS), which was verified to completely capture HONO associated …

Exploring Secondary Structure In Bacteriophage Programmed Frameshift Elements, Samuel Okabayashi, Sean Mcclory

HON499 projects

Bacteriophages are viruses that infect bacteria and reproduce using host bacterial components. Part of the bacteriophage reproduction is assembly of the tail complex, which requires two assembly chaperone (TAC) proteins. In many phages the TAC’s are produced from a single gene through a non-canonical process called programmed translational frameshifting (PTF). The SEA-PHAGES program has produced hundreds of TAC genes that are accessible through phagesdb, a database of sequenced and annotated phage genomes. The sequences for the TAC gene were gathered from phagesdb and analyzed using ClustalOmega; a multiple sequence alignment (MSA) tool which revealed several positions where total conservation was …

Autophagy Protein Nrbf2 Has Reduced Expression In Alzheimer's Brains And Modulates Memory And Amyloid-Beta Homeostasis In Mice, Veronik Lachance, Qian Wang, Eric Sweet, Insup Choi, Cui-Zan Cai, Xu-Xu Zhuang, Jessica Li Jiang, Robert D. Blitzer, Ozlem Bozdagi-Gunal, Bin Zhang, Jia-Hong Lu, Zhenyu Yue

Biology Faculty Publications

Background Dysfunctional autophagy is implicated in Alzheimer's Disease (AD) pathogenesis. The alterations in the expression of many autophagy related genes (ATGs) have been reported in AD brains; however, the disparity of the changes confounds the role of autophagy in AD. Methods To further understand the autophagy alteration in AD brains, we analyzed transcriptomic (RNAseq) datasets of several brain regions (BA10, BA22, BA36 and BA44 in 223 patients compared to 59 healthy controls) and measured the expression of 130 ATGs. We used autophagy-deficient mouse models to assess the impact of the identified ATGs depletion on memory, autophagic activity and amyloid-beta (A …

High Concentrations Of Trimethylamines In Slime Glands Inhibit Skein Unraveling In Pacific Hagfish, Gaurav Jain, Marie Starksen, Kashika Singh, Christopher Hoang, Paul Yancey, Charlene Mccord, Douglas S. Fudge

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Hagfish defend themselves from fish predators by producing large volumes of gill-clogging slime when they are attacked. The slime consists of seawater and two major components that are ejected from the slime glands: mucus and threads. The threads are produced within specialized cells and packaged into intricately coiled bundles called skeins. Skeins are kept from unraveling via a protein adhesive that dissolves when the skeins are ejected from the slime glands. Previous work revealed that hagfish slime glands have high concentrations of methylamines including trimethylamine N-oxide (TMAO), trimethylglycine (betaine) and dimethylglycine (DMG); however, the function of these compounds in the …

Covalently Functionalized Sawdust For The Remediation Of Phosphate From Agricultural Wastewater, Daniel Meister, David Ure, Angela Awada, Jean-Claude Barrette, Joel Gagnon, Bluent Mutus, John F. Trant

Chemistry and Biochemistry Publications

Phosphate remediation from wastewater is rapidly becoming an ever more attractive process due to a combination of both the economic pressure of increasing phosphate scarcity and the environmental damage caused by untreated agricultural runoff. Ideally, remediated phosphate will be recoverable and would be able to be reused as fertilizer. Many different resins have been investigated, but due to the scale of the challenge, any feasible solution will involve the use of very inexpensive waste products as the solid support. Sawdust, functionalized with iron-binding ligands, is such a potential resin. Sawdust alone binds 0.3 g/kg of phosphate which is insufficient. Iron …

Constituent Partitioning Consensus Docking Models And Application In Drug Discovery, Rainer Metcalf

USF Tampa Graduate Theses and Dissertations

This work expounds on some of the current computational tools and programs available and the best practices associated with their use. A high-level introduction, intended for both novices and the semi-experienced, focusing on the more common programs used in scientific literature is the scope of this topic. Both classical and quantum techniques are described. Classical methodologies include Molecular Dynamics, Monte Carlo, energy minimization methods, molecular docking, low-mode, and homology modeling. Quantum chemistry techniques are also discussed encompassing Hartree-Fock, Post-Hartree-Fock theories, and Density Functional Theory along with associated basis sets.

Along with established methodologies, novel theoretical methods are introduced for furthering …

Stability Of Petal Color Polymorphism: The Significance Of Anthocyanin Accumulation In Photosynthetic Tissues, José Carlos Del Valle, Cristina Alcalde-Eon, Mª Teresa Escribano-Bailón, Mª Luisa Buide, Justen B. Whittall, Eduardo Narbona

Biology

Background: Anthocyanins are the primary source of colour in flowers and also accumulate in vegetative tissues, where they have multiple protective roles traditionally attributed to early compounds of the metabolic pathway (flavonols, flavones, etc.). Petal-specific loss of anthocyanins in petals allows plants to escape from the negative pleiotropic effects of flavonoid and anthocyanins loss in vegetative organs, where they perform a plethora of essential functions. Herein, we investigate the degree of pleiotropy at the biochemical scale in a pink-white flower colour polymorphism in the shore campion, Silene littorea. We report the frequencies of pink and white individuals across 21 populations …

The Role Of Atypical Protein Kinase C In Colorectal Cancer Cells Carcinogenesis, S M Anisul Islam

USF Tampa Graduate Theses and Dissertations

Colorectal cancer (CRC) is the third most common malignancy and the fourth most common cause of cancer-related death worldwide. CRC is a life-threatening disease due to therapy-resistant cancerous cells. The exact mechanisms of cell growth, survival, metastasis and inter & intracellular signaling pathways involved in CRC are still a significant challenge. Moreover, the treatment of metastatic CRC considered palliative for many years aimed for an improved life, with little hope of a cure, highlighting the need for developing novel targeted therapy for CRC. Hence, investigating new molecular mechanism(s) that lead to colorectal carcinogenesis may give insight into the therapeutic target. …

Amyloid Protein Aggregation And Associated Toxicity, Chamani A. Niyangoda

USF Tampa Graduate Theses and Dissertations

Amyloidosis is a group of diseases in which amyloid fibrils accumulate and deposit into plaques and intracellular inclusions which lead to disruption of the tissue architecture and function. Most of the amyloid diseases are incurable due to a lack of understanding of the amyloid formation, as well as associated toxicity. My research work is focused on three different aspects of amyloid aggregation.

The aim of the first project is to investigate the potential use of deep-blue autofluorescence (dbAF) as an intrinsic optical probe to study amyloid self-assembly. This novel fluorescence signal is excited at the long wavelength edge of the …

Hexavalent Chromium-Induced Cytotoxicity And Mutagenicity: A Study Of Protection By Ascorbic Acid And Epigallocatechin Gallate, Timothy P. Mayotte

ELAIA

Hexavalent chromium, or Cr(VI), is a potent oxidizer and known carcinogen that is found at varying levels in the water sources of more than 200 million Americans. However, the exact mechanism of carcinogenicity remains unknown, and though the government currently regulates total chromium levels they have yet to determine a permissible exposure limit for Cr(VI). Moreover, there is currently no preventative treatment for Cr(VI). Because of Cr(VI)’s strong oxidative power, we hypothesized that it causes DNA mutation and cell death via oxidation and that antioxidants could prevent this from occurring. To test this, we first assessed the viability of human …

Comparison Of Montage With Conventional Stereoscopic Seven‑Field Photographs For Assessment Of Etdrs Diabetic Retinopathy Severity, Nam V. Nguyen, Erin M. Vigil, Muhammad Hassan, Muhammad S. Halim, Sean C. Baluyot, Hugo A. Guzman, Rubbia Afridi, Diana V. Do, Yasir J. Sepah

Department of Biochemistry: Faculty Publications

Background: The ETDRS stereoscopic seven-field (7F) has been a standard imaging and grading protocol for assessment of diabetic retinopathy (DR) severity score in many clinical trials. To the best of our knowledge, the comparison between montage and stereoscopic 7F has not been reported in the literature. Therefore, the main purpose of this study is to compare agreement between montage and stereoscopic seven-field (7F) photographs in the assessment of DR severity.

Methods: Stereoscopic 7F photographs were captured from subjects with DR. Montages of monoscopic 7F images were created using Adobe Photoshop CS6 Extended©. The best quality image of each stereo pair …

The Role Of Secreted Proteases In Regulating Disease Progression In Staphylococcus Aureus, Brittney D. Gimza

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus is a highly successful pathogen capable of producing a wealth of virulence factors in the human host. Of note, ten extracellular proteases are produced alongside these virulence factors and play a multifaceted role during infection. They not only cleave host proteins to promote bacterial invasion, immune evasion and survival, but also control disease progression by modulating the stability of self-derived pathogenic determinants. The importance of the secreted proteases modulating virulence factor stability is evidenced by our groups previous finding that a protease-null strain has a substantially increased infectious capacity in a murine model of sepsis; resulting from the …

A Novel Cytokine Response Modulatory Function Of Mek Inhibitors Mediates Therapeutic Efficacy, Mengyu Xie

USF Tampa Graduate Theses and Dissertations

Despite the recent success of immune-checkpoint blockade therapy for late-stage non-small cell lung cancer (NSCLC), lung cancer is still the leading cause of cancer deaths worldwide. One of the most important characteristics of lung cancer in therapeutic decision-making are the targetable molecules, including EGFR, ALK, BRAF, and MEK. The excitement of immune-checkpoint blockade therapy has triggered concerted efforts that focus on exploring combinations of immune checkpoint therapy with other approved therapeutic regimens aiming at further augmenting positive outcomes and survival. However, the lack of understanding of underlying mechanisms and evidence-based clinical testing has hindered the progress to a cure. Hence, …

Aerial And Ground-Based Optical Gas Imaging Survey Of Uinta Basin Oil And Gas Wells, Seth N. Lyman, Trang Tran, Marc L. Mansfield, Arvind P. Ravikumar

Bingham Research Center

We deployed a helicopter with an infrared optical gas imaging camera to detect hydrocarbon emissions from 3,428 oil and gas facilities (including 3,225 producing oil and gas well pads) in Utah’s Uinta Basin during winter and spring 2018. We also surveyed 419 of the same well pads from the ground. Winter conditions led to poor contrast between emission plumes and the ground, leading to a detection limit for the aerial survey that was between two and six times worse than a previous summertime survey. Because the ground survey was able to use the camera’s high-sensitivity mode, the rate of detected …

Targeting Bacterial Resistance And Cancer Metastasis: A Structure Based Approach, Kyle Galen Kroeck

USF Tampa Graduate Theses and Dissertations

Current research in pharmaceutical development commonly utilizes a profusion of methods in molecular modeling in order to probe intricate biological problems. Many original and promising compounds have been identified and developed by integrating experimental and computational methods. Structural biology utilizes many different research techniques including x-ray crystallography, NMR, and electron microscopy in order to develop molecular models of macromolecules that are of biological interest. Such techniques can be used in conjunction with molecular docking, which utilizes those molecular models in order to target macromolecules of therapeutic interest by computationally analyzing the conformations adopted by ligands upon interaction with a desired …