Biochemistry, Biophysics, and Structural Biology Commons^™

Variation On A Theme: The Structures And Biosynthesis Of Specialized Fatty Acid Natural Products In Plants, Samuel Scott, Edgar B. Cahoon, Lucas Busta

Department of Biochemistry: Faculty Publications

Plants are able to construct lineage-specific natural products from a wide array of their core metabolic pathways. Considerable progress has been made toward documenting and understanding, for example, phenylpropanoid natural products derived from phosphoenolpyruvate via the shikimate pathway, terpenoid compounds built using isopentyl pyrophosphate, and alkaloids generated by the extensive modification of amino acids. By comparison, natural products derived from fatty acids have received little attention, except for unusual fatty acids in seed oils and jasmonate-like oxylipins. However, scattered but numerous reports show that plants are able to generate many structurally diverse compounds from fatty acids, including some with highly …

Crispr/Cas13 Effectors Have Differing Extents Of Off-Target Effects That Limit Their Utility In Eukaryotic Cells, Yuxi Ai, Dongming Liang, Jeremy E Wilusz

Faculty, Staff and Students Publications

CRISPR/Cas13 effectors have garnered increasing attention as easily customizable tools for detecting and depleting RNAs of interest. Near perfect complementarity between a target RNA and the Cas13-associated guide RNA is required for activation of Cas13 ribonuclease activity. Nonetheless, the specificity of Cas13 effectors in eukaryotic cells has been debated as the Cas13 nuclease domains can be exposed on the enzyme surface, providing the potential for promiscuous cleavage of nearby RNAs (so-called collateral damage). Here, using co-transfection assays in Drosophila and human cells, we found that the off-target effects of RxCas13d, a commonly used Cas13 effector, can be as strong as …

Ceramide-1-Phosphate: A Novel Regulator Of Golgi Fragmentation, Golgi-Er Vesicle Trafficking, And Anaplasma Phagocytophilum Pathogenesis, Anika Nayar Ali

USF Tampa Graduate Theses and Dissertations

Anaplasma phagocytophilum, the etiologic agent of human granulocytic anaplasmosis (HGA), is a tick transmitted obligate intracellular bacterium that infects granulocytes, bone marrow progenitor cells and endothelial cells. HGA exhibits symptoms of febrile illness including fever, chills, headache, malaise, leukopenia and elevated liver enzymes which are treatable by antibiotics. However, elderly and immunocompromised patients are at a greater risk of developing fatal complications. Inside the host cell A.phagocytophilum resides in host cell derived vacuole called A.phagocytophilum occupied vacuole (ApV) where it undergoes its biphasic lifecycle. Being an intracellular pathogen, A.phagocytophilum relies heavily on nutrient acquisition from host cell and to obtain …

Exploring Melatonin As A Treatment For Oral Ulcers, William H. Sutherland

Undergraduate Honors Theses

The hormone melatonin is best known for its role in the sleep-wake cycle, but its anti-inflammatory and antioxidant effects have significant implications that have not been fully explored in oral health. Some studies use melatonin to treat gastrointestinal ulcers, including duodenal ulcers and oral mucositis, but we found no study reporting its effects on more common oral ulcers, like aphthous stomatitis. We hypothesize that the anti-inflammatory and antioxidant characteristics of melatonin could effectively prevent and heal oral ulcers. In this paper, we review the literature on melatonin to propose its use as a treatment for oral ulcers. We also include …

17Β-Estradiol Treatment Improves Acetylcholine-Induced Relaxation Of Mesenteric Arteries In Ovariectomized Uc Davis Type 2 Diabetes Mellitus Rats In Prediabetic State, Md Rahatullah Razan, Farjana Akther, Rifat Ara Islam, James L. Graham, Kimber L. Stanhope, Peter J. Havel, Roshanak Rahimian

School of Pharmacy Faculty Articles

We recently reported sex differences in mesenteric arterial function of the UC Davis type-2 diabetes mellitus (UCD-T2DM) rats as early as the prediabetic state. We reported that mesenteric arteries (MA) from prediabetic male rats exhibited a greater impairment compared to that in prediabetic females. However, when females became diabetic, they exhibited a greater vascular dysfunction than males. Thus, the aim of this study was to investigate whether the female sex hormone, estrogen preserves mesenteric arterial vasorelaxation in UCD-T2DM female rats at an early prediabetic state. Age-matched female Sprague Dawley and prediabetic (PD) UCD-T2DM rats were ovariectomized (OVX) and subcutaneously implanted …

Luminescence And Scintillation In The Niobium Doped Oxyfluoride Rb4Ge5O9F6:Nb, Darren Carone, Vladislav V. Klepov, Scott T. Misture, Joseph C. Schaeperkoetter, Luiz G. Jacobsohn, Mina Aziziha, Juliano Schorne-Pinto, Stuart A. J. Thomson, Adrian T. Hines, Theodore M. Besmann, Hans Conrad Zur Loye

Faculty Publications

A new niobium-doped inorganic scintillating oxyfluoride, Rb₄Ge₅O₉F₆:Nb, was synthesized in single crystal form by high-temperature flux growth. The host structure, Rb₄Ge₅O₉F₆, crystallizes in the orthorhombic space group Pbcn with lattice parameters a = 6.98430(10) Å, b = 11.7265(2) Å, and c = 19.2732(3) Å, consisting of germanium oxyfluoride layers made up of Ge₃O₉ units connected by GeO₃F₃ octahedra. In its pure form, Rb₄Ge₅O₉F₆ shows neither luminescence nor scintillation but when doped …

Glucose Homeostasis In Human Diabetic Adipocytes: Role Of Glp1 In Sortilin Alternative Splicing, Ashley Lui

USF Tampa Graduate Theses and Dissertations

Type 2 diabetes mellitus (T2DM) is a chronic and progressive metabolic disease defined by systemic insulin resistance. The inability of cells to respond to insulin and take up glucose results in elevated blood sugar that is detrimental to the overall health of patients. There is no cure for T2DM. Identification of new targets to alleviate hyperglycemia are crucial for treatment and prevention of metabolic diseases. Adipocytes play a central role in glycemic regulation by insulin stimulated glucose uptake, storage of excess nutrients, and secretion of adipokines. Major glucose transporter-4 (Glut4) is the main transporter responsible for postprandial clearance of glucose …

Hepcidin Antimicrobial Peptide (Hamp) Screening For P.Cys70arg Variant And Iron Overload In Β -Thalassemia Major Patients, Ambreen Kanwal, Malik Siddique Mahmood, Saba Irshad

Journal of Bioresource Management

Hereditary Hemochromatosis is a rare genetic iron overload disorder characterized by iron accumulation in vital body organs such as the lungs, liver, and pancreas. HAMP mutations are reported as one of the principal sources for the disturbance of iron homeostasis. This study was designed to screen the involvement of p.Cys70Arg HAMP variant in iron overload in the β-thalassemia patients. For the purpose, bioinformatics tools were used for the structural and functional manifestation of mutated protein which revealed 1.93 kcal/mol energy differences between the wild-type and mutated proteins, causing the stability decline. Following that, clinical data was collected for 106 β-thalassemia …

Expression And Purification Of E. Coli Yoaa, A Putative Helicase, Mark Gregory, Vincent Sutera Mr., Susan Lovett Dr.

Medical Student Research Symposium

All cells must maintain their genomic integrity to survive, which they achieve through several repair mechanisms that necessitate unwinding the damaged DNA by helicases. In Escherichia coli (E. coli), YoaA has been genetically shown to be involved in DNA repair and shares conserved sequences with helicase DinG. The goal of our study was to purify YoaA for further biochemical characterization. For expression, YoaA was fused to a His tag and overexpressed in MG1655 E.coli under the lacZ or T7 promoters for 2 hours, 4 hours, or overnight at 24oC, 30oC or 37oC. For purification, crude lysate was applied to a …

Variants In Asph Cause Exertional Heat Illness And Are Associated With Malignant Hyperthermia Susceptibility, Yukari Endo, Linda Groom, Alper Celik, Natalia Kraeva, Chang Seok Lee, Sung Yun Jung, Lois Gardner, Marie-Anne Shaw, Susan L Hamilton, Philip M Hopkins, Robert T Dirksen, Sheila Riazi, James J Dowling

Faculty, Staff and Students Publications

Exertional heat illness (EHI) and malignant hyperthermia (MH) are life threatening conditions associated with muscle breakdown in the setting of triggering factors including volatile anesthetics, exercise, and high environmental temperature. To identify new genetic variants that predispose to EHI and/or MH, we performed genomic sequencing on a cohort with EHI/MH and/or abnormal caffeine-halothane contracture test. In five individuals, we identified rare, pathogenic heterozygous variants in ASPH, a gene encoding junctin, a regulator of excitation-contraction coupling. We validated the pathogenicity of these variants using orthogonal pre-clinical models, CRISPR-edited C2C12 myotubes and transgenic zebrafish. In total, we demonstrate that ASPH variants represent …

Autofluorescence Microscopy: Identifying Bacterial Signals On Rock Samples, Noel Case

University Honors Theses

One common method for identifying microbes present in fluid and non-fluid samples is fluorescent dye staining, in which samples are stained with a fluorophore - a molecule excited by an external light source that re-emits energy as higher-wavelength light. The excitation wavelength used greatly impacts the observability of microbes in the resulting fluorescence images, and deep ultraviolet excitation (200-280 nm) seems to provide the highest signal-to-noise ratio of any excitation range. By inoculating rock samples (gypsum and marble) with B. subtilis, staining with SYTO 9, Acridine Orange and FM 1-43 dyes, and imaging with deep UV (275 nm), near …

Dj-1 Is Not A Deglycase And Makes A Modest Contribution To Cellular Defense Against Methylglyoxal Damage In Neurons, Melissa Conti Mazza, Sarah C. Shuck, Jiusheng Lin, Michael Moxley, John Termini, Mark R. Cookson, Mark A. Wilson

Department of Biochemistry: Faculty Publications

Human DJ-1 is a cytoprotective protein whose absence causes Parkinson's disease and is also associated with other diseases. DJ-1 has an established role as a redox-regulated protein that defends against oxidative stress and mitochondrial dysfunction. Multiple studies have suggested that DJ-1 is also a protein/nucleic acid deglycase that plays a key role in the repair of glycation damage caused by methylglyoxal (MG), a reactive α-keto aldehyde formed by central metabolism. Contradictory reports suggest that DJ-1 is a glyoxalase but not a deglycase and does not play a major role in glycation defense. Resolving this issue is important for understanding how …

The Regulation Of Atg9a-Mediated Aggrephagy By An Ulk1-Independent Atg13-Atg101 Complex, Joshua Youngs

Undergraduate Honors Theses

Aggrephagy, a type of autophagy, is an essential cellular process by which protein aggregates are collected and broken down in the lysosome. Protein aggregates are implicated in several diseases including Alzheimer’s disease, diabetes, and cancer. Here, we investigate the ATG13-ATG101 protein complex, a sub-complex of the canonical ULK1 complex whose regulatory role in aggrephagy is not completely understood. We also develop a protein fragment complementation (PFC) assay using the biotin ligase TurboID to study the functions of the ATG13-ATG101 complex with increased specificity. We demonstrate that ATG13 is required for optimal degradation of p62-ubiquitin condensates. We also show that a …

Overexpression Of Foxf2 In Prostate Cancer Cells Causes An Increase In Cancer Cell Apoptosis And A Decrease In Proliferation, Vaughn Poon

Honors Projects

FOXF2 is a transcription factor that plays a crucial role in organ development, and recent studies have shown that it suppresses tumor growth and progression in mouse prostate models by attenuating the cancer-associated fibroblasts (CAF) phenotype and transcriptionally downregulating Cxcl5. However, the effects of FOXF2 overexpression in prostate cancer cells have not been extensively studied. Here, we investigate the impact of FOXF2 overexpression in prostate cancer cells and demonstrate that it leads to a significant increase in cell apoptosis and a decrease in proliferation. These findings suggest that FOXF2 may have potential as an immunotherapy drug target for prostate …

Evolutionary Action Of Mutations Reveals Antimicrobial Resistance Genes In Escherichia Coli, David C Marciano, Chen Wang, Teng-Kuei Hsu, Thomas Bourquard, Benu Atri, Ralf B Nehring, Nicholas S Abel, Elizabeth A Bowling, Taylor J Chen, Pamela D Lurie, Panagiotis Katsonis, Susan M Rosenberg, Christophe Herman, Olivier Lichtarge

Faculty, Staff and Students Publications

Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage …

Decoding The Pitx2-Controlled Genetic Network In Atrial Fibrillation, Jeffrey D Steimle, Francisco J Grisanti Canozo, Minjun Park, Zachary A Kadow, Md Abul Hassan Samee, James F Martin

Faculty, Staff and Students Publications

Atrial fibrillation (AF), the most common sustained cardiac arrhythmia and a major risk factor for stroke, often arises through ectopic electrical impulses derived from the pulmonary veins (PVs). Sequence variants in enhancers controlling expression of the transcription factor PITX2, which is expressed in the cardiomyocytes (CMs) of the PV and left atrium (LA), have been implicated in AF predisposition. Single nuclei multiomic profiling of RNA and analysis of chromatin accessibility combined with spectral clustering uncovered distinct PV- and LA-enriched CM cell states. Pitx2-mutant PV and LA CMs exhibited gene expression changes consistent with cardiac dysfunction through cell type-distinct, PITX2-directed, cis-regulatory …

Analysis Of Soxs In S. Typhimurium By Transposon Mutagenesis, Joel Hanns, Brenda Pratte, Lon Chubiz Phd, Lauren Daugherty

Undergraduate Research Symposium

The mar-sox-rob regulon has been implicated in transcriptional regulation of several stress responses, such efflux of antibiotics, enzymes that break down reactive oxygen species, repression of biofilm formation, or repression of motility through downregulation of flagellar expression. This system is conserved among enteric bacteria and has been studied in species, such as E. coli and S. typhimurium. Some of these mechanisms can be costly and slow cell growth while increasing the probability of survival through tolerance of toxic environments. SoxS works in coordination with SoxR to respond to redox stress encountered by the cell. Interestingly, the overexpression of SoxS …

Collaborative Research: Surface-Specific Aerosol Chemistry: Direct Observations, Kinetics, And Environmental Impact, Yi Rao

Funded Research Records

No abstract provided.

College Of Natural Sciences Newsletter, May & June 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 4

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3-4 The path to a Doctorate Degree
Page 4 American Indian Student Center Native Graduate Honoring Ceremony
Page 5 Celebrating the lives of those who touched the College
Page 6 Media coverage of CNS
Page 7 Open PRAIRIE
Page 8-10 CNS Graduation Festivities
Page 11-14 Spring 2022 Dean's List
Page 16 Richard and Janice Vetter Endowed Professorship in Biotechnology.position

Early Advanced Therapy For Diabetic Foot Ulcers In High Amputation Risk Veterans: A Cohort Study, Margaret Doucette, Kattie M. Payne, Walter Lough, Alison Beck, Kristi Wayment, John Huffman, Laura Bond, Aurora Thomas-Vogel, Susan Langley

Biomedical Research Institute Publications and Presentations

Veterans with diabetic foot ulcers (DFUs) represent the highest percentage of lower extremity amputations (LEAs) within the Veterans Affairs (VA) population. Many veterans have additional risk factors for amputation. Few studies focus on advanced therapies for this population. This study explores the impact of early application of dehydrated human amniotic membrane allograft (DAMA) with comprehensive care on preventing amputation. This prospective, single-center cohort study (ClinicalTrials.gov Identifier NCT02632929) was conducted through Boise VA Medical Center. Patients with DFUs were objectively stratified for LEA risk. Those with moderate to high amputation risk could participate. Participants received comprehensive care and weekly application of …

Altered Collective Mitochondrial Dynamics In The Arabidopsis Msh1 Mutant Compromising Organelle Dna Maintenance, Joanna M. Chustecki, Ross D. Etherington, Daniel J. Gibbs, Iain G. Johnston

Department of Biochemistry: Faculty Publications

Mitochondria form highly dynamic populations in the cells of plants (and almost all eukaryotes). The characteristics and benefits of this collective behaviour, and how it is influenced by nuclear features, remain to be fully elucidated. Here, we use a recently developed quantitative approach to reveal and analyse the physical and collective ‘social’ dynamics of mitochondria in an Arabidopsis msh1 mutant where the organelle DNA maintenance machinery is compromised. We use a newly created line combining the msh1 mutant with mitochondrially targeted green fluorescent protein (GFP), and characterize mitochondrial dynamics with a combination of single-cell time-lapse microscopy, computational tracking, and network …

Highly Swellable Hydrogels Prepared From Extensively Oxidized Lignin, Jihyeon Hwang, Daniella V. Martinez, Estevan J. Martinez, Gift Metavarayuth, Dustin Goodlett, Qi Wang, Mitra Ganewatta, Michael S. Kent, Chuanbing Tang

Faculty Publications

Biopolymers such as lignin are gaining renewed appeal due to the need for sustainable materials. Herein, we used chelator-mediated Fenton (CMF) chemistry to oxidize Kraft lignin to develop sustainable super absorbent materials. The CMF chemistry adds oxygen, opens aromatic rings and increases COOH content, producing hydrophilic lignin without depolymerization. UV absorption, molecular weight, elemental analysis, and titration were used to study the chemical compositions of CMF-processed lignin. Then the chemically modified hydrophilic lignin was used to produce lignin-based hydrogels utilizing an aqueous polymerization and cross-linking reaction that enabled tunable properties. The resulting lignin hydrogels absorbed water up to 96% and …

Utilizing Computational Methods To Study The Biomolecules, Wenhan Guo

Open Access Theses & Dissertations

COVID-19 is increasingly affecting human health and global economy. Understanding the fundamental mechanisms of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is highly demanded to develop treatments for COVID-19. SARS-CoV and SARS-CoV-2 share 92.06% identity in their N protein RBDs' sequences, which results in very similar structures. However, the SARS-CoV-2 is more easily to spread. Utilizing multi-scale computational approaches, this work studied the fundamental mechanisms of the nucleocapsid (N) proteins of SARS-CoV and SARS-CoV-2, including their stabilities and binding strengths with RNAs at different pH values. Electrostatic potential on the surfaces of N proteins show that both the N proteins …

Understanding Rapid Intercalation Materials One Parameter At A Time, Wessel Van Den Bergh, Morgan Stefik

Faculty Publications

Demand for fast, energy-dense storage drives the research into nanoscale intercalation materials. Nanomaterials accelerate kinetics and can modify reaction path thermodynamics, intercalant solubility, and reversibility. The discovery of intercalation pseudocapacitance has opened questions about their fundamental operating principles. For example, are their capacitor-like current responses caused by storing energy in special near-surface regions or rather is this response due to normal intercalation limited by a slower faradaic surface-reaction? This review highlights emerging methods combining tailored nanomaterials with the process of elimination to disambiguate cause-and-effect at the nanoscale. This method is applied to multiple intercalation pseudocapacitive materials showing that the timescales …

Expression And Purification Of The Bacterial Protein Curli Csga And Its Cross-Interactions With Amyloid-B, Leah Grace Cantrell

Honors Theses

One of the main causes of neurodegenerative diseases is aggregation of amyloid proteins that are toxic to the neurons. Proteins like amyloid-β (Aβ) and α-syneuclein (α-syn) form hallmark aggregate lesions that contribute to pathological processes in the brain in Alzheimer and Parkinson’s patients, respectively. Recent ground-breaking studies have suggested a link between the microbiota of the gut and neurodegenerative diseases, called the “gut-brain axis.” It has been long known that the protein, CsgA found in many enteric bacteria, forms amyloid fibers of its own called Curli. Curli fibrils are a structural component of bacterial colonies and maintain the integrity of …

Oligomerization Of Amyloid-Β Peptide In The Presence Of Gangliosides–Implications For Alzheimer Disease, Sydney Boyd

Honors Theses

Alzheimer disease (AD) is a neurodegenerative disorder that leads to memory impairment and cognitive dysfunction in elderly populations worldwide. A key characteristic of AD is the formation of neuritic plaques composed of extracellularly deposited aggregates of amyloid-β (Aβ), an intrinsically disordered protein. Although Aβ fibrils were once thought to be the prime initiators of the disease, research has since been shifted to consider soluble, low molecular weight Aβ oligomers as the driving force behind AD toxicity. Due to its origin as a cleavage product of amyloid precursor protein (APP), an integral membrane protein, Aβ is known to perpetually interact with …

Editorial: Engineering Nucleic Acids-Based Functional Nanomaterials, Nanodrugs, And Biosensors, Jabrane Jouha, Fengli Li, Wen-Ta Su, Chenguang Fan, Dayong Yang, Hai Xiong

Chemistry & Biochemistry Faculty Publications and Presentations

Editorial on the Research Topic: Engineering Nucleic Acids-Based Functional Nanomaterials, Nanodrugs, and Biosensors

Signature Peptide Identification For Body Fluids In Sexual Assault Cases By Liquid Chromatography Tandem Mass Spectrometry (Lc-Ms/Ms), Kelci Somers

Student Theses

Body fluids contain proteins that perform functions specific to different types of body fluids. Therefore, the detection of signature peptides for these proteins can potentially identify a body fluid in a forensic investigation. This project aimed to validate a method to detect signature peptides in body fluids commonly found in sexual assault cases by LC-MS/MS. Signature peptides for semen and saliva fluids were combined with two signature peptides for vaginal fluids. Samples created using two donors each for saliva, semen, and vaginal fluids were extracted using a trypsin digest, with separation of the protein and DNA fractions. The LC-MS/MS was …

Elucidating Mechanisms Of Biofluorescence And Bioluminescence In Marine Organisms, Andrew M. Guarnaccia

Dissertations, Theses, and Capstone Projects

Biofluorescence and bioluminescence are two methods of light emission that entail separate mechanisms of action but end at the same process: a colorful display that have tremendous ecological and behavioral benefits, whether it be used to communicate with conspecifics, camouflage into a multicolored background, attract unsuspecting prey, or alert others to a predator. In biofluorescence, higher-energy, shorter wavelength light is absorbed then re-emitted as lower-energy, longer-wavelength light. Bioluminescence on the other hand entails a chemical reaction in which a small molecule is oxidized by an enzyme, creating a high-energy intermediate that sheds the excess energy in the form of visible …

Molecular Mechanism Of Rapamycin Resistance In Cancer Cells, Sohag Chakraborty

Dissertations, Theses, and Capstone Projects

The mammalian target of rapamycin (mTOR) acts as the central regulator of multiple cellular processes including cell growth, proliferation, and survival by integrating signals via nutrients, growth factors, hormones, and energy sensing. In cancer cells, the mTOR pathway is highly dysregulated providing survival signals to the cells for their uncontrolled growth. Hence, mTOR has evolved to be a potential therapeutic target for cancer treatment for the past two decades. Application of micro-molar doses of Rapamycin in vitro has been found to successfully inhibit mTOR complex 1 (mTORC1) by blocking the phosphorylation of its downstream substrates- a) ribosomal protein p70 S6 …