Molecular Biology Commons^™

Structural And Biochemical Characterization Of Epigenetic And Fusion Tyrosine Kinase Cancer Targets For Drug Development, Melissa Bikowitz

USF Tampa Graduate Theses and Dissertations

Cancer is a significant global health burden, as ~40% of the human population is diagnosed with cancer over a lifetime, half of which succumb to the disease. To develop novel compounds as potential cancer therapeutics, an in-depth structural and biochemical understanding of proteins involved in oncogenesis is key. This dissertation centers around the comprehensive structural and biochemical characterization of two classes of proteins critical for cancer cell survival: bromodomain-containing proteins (BRDs) and fusion tyrosine kinases (FTKs).In 2010, small molecule inhibitors targeting bromodomains (epigenetic reader proteins) became heavily popularized due to the druggability and potent anticancer effects of BET inhibitors. …

The Childhood Acute Illness And Nutrition (Chain) Network Nested Case-Cohort Study Protocol: A Multi-Omics Approach To Understanding Mortality Among Children In Sub-Saharan Africa And South Asia, James M. Njunge, Kirkby Tickell, Abdoulaye Hama Diallo, Abu Sadat Mohammad Sayeem Bin Shahi, Md Amran Gazi, Ali Faisal Saleem, Zaubina Kazi, Syed Ali, Caroline Tigoi, Ezekiel Mupere

Department of Paediatrics and Child Health

Introduction: Many acutely ill children in low- and middle-income settings have a high risk of mortality both during and after hospitalisation despite guideline-based care. Understanding the biological mechanisms underpinning mortality may suggest optimal pathways to target for interventions to further reduce mortality. The Childhood Acute Illness and Nutrition (CHAIN) Network ( www.chainnnetwork.org) Nested Case-Cohort Study (CNCC) aims to investigate biological mechanisms leading to inpatient and post-discharge mortality through an integrated multi-omic approach.
Methods and analysis; The CNCC comprises a subset of participants from the CHAIN cohort (1278/3101 hospitalised participants, including 350 children who died and 658 survivors, and …

Occurrence Of Kanamycin-Resistant Bacteria Relative To Anthropogenic Pollution Along Richland Creek In Nashville, Tn​, Jolene Ho Mach, Annie Le, Brandon Torres Ramirez

Science University Research Symposium (SURS)

The overuse of antibiotics has caused an increase in antibiotic-resistant (AR) bacteria, which is a serious public health concern. Previous studies showed a significant correlation between anthropogenic pollution and AR bacteria. This project aims to identify AR bacteria in Richland Creek relative to local anthropogenic pollution. Water samples were collected at four locations along Richland Creek in Nashville, Tennessee. Bacteria resistant to the antibiotic kanamycin were isolated from the water samples, identified to genera using DNA barcoding, and compared among the sites. We expect to see a greater abundance and diversity of kanamycin-resistant bacteria closer to the end than near …

The Effect Of Licogliflozin (Sglt1/2 Inhibitor) On Diabetes And Cardiac Complications, Alanoud Gharib Alblooshi

Theses

Diabetes mellitus (DM) is a chronic endocrine disease affecting millions of people worldwide. In spite of the advances made in the management of DM, poor glycemic control and diabetes complications are still very common. There is a continuous search for new and more effective drugs to treat DM. One of the drugs currently in clinical trials for the treatment of DM is licogliflozin (LIK066), a dual SGLT1/2 inhibitor, which can be used to treat obesity and diabetes. LIK066 inhibits glucose reabsorption in the kidney and small intestine, thereby reducing hyperglycemia. This study aims to investigate the efficacy of licogliflozin on …

Distribution Of Erm Proteins In The Stomach Mucosa Of Normal And Diabetic Rats, Asmaa Salem Al Sereidi

Theses

Diabetes mellitus (DM), or simply diabetes, refers to a group of metabolic disorders that include a variety of diseases that disrupt our body's metabolism. The long-term uncontrolled disease can lead to stomach complications such as gastroparesis, as well as disruption in several proteins, such as ERM (Ezrin, radixin, moesin) proteins. ERM proteins are three proteins that are structurally and functionally related. ERM proteins have molecular masses of 82, 80, and 75 kDa, respectively. Ezrin is highly expressed in the stomach, especially in parietal cells that secrete gastric acid. ERM proteins function as scaffolding proteins in lipid rafts and granule trafficking …

Successful Use Of Continuous Erector Spinae Plane Blocks In A Patient With Variant Angina After Large Ventral Hernia Repair, Alexandra L Belfar, Yi Deng, Raymond C Yu, Annas Sabbagh

Faculty, Staff and Students Publications

Coronary artery spasm constitutes the primary underlying pathology of variant angina. Because provocation of coronary artery spasm may occur with both excess sympathetic and excess parasympathetic stimulation, patients with this disorder have extremely limited options for perioperative pain control. This is especially true for procedures involving extensive abdominal incision/manipulation. Whereas neuraxial analgesia might otherwise be appropriate in these cases, several studies have demonstrated that coronary artery spasm can occur as a result of epidural placement, and therefore, that this may not be an optimal choice for patients with variant angina. This report discusses the case of a patient with a …

To Be Or Not To Be: A Tale Of Staphylococcal Gpsb, Lauren R. Hammond

USF Tampa Graduate Theses and Dissertations

There are two big drivers motivating studies into bacterial cell division. The first is a desire to understand life around us. One of the defining characteristics of life is the ability for a cell to grow and divide, and without in-depth knowledge of this process, we cannot truly understand the complexities that allow for life on this planet. The second motivator is to identify new drug targets in the ongoing fight against antimicrobial resistance. Many infectious organisms have become resistant to commonly used antibiotics, and the bacterial cell division machinery is a largely untapped essential process with many potential therapeutic …

Lord Of The Z-Rings: Uncovering The Role Of Mraz And Ftsl In Bacillus Subtilis Cell Division, Maria Louise White

USF Tampa Graduate Theses and Dissertations

Cell division is a complex and highly orchestrated process that requires careful coordination. The process of cell division in prokaryotes primarily occurs via binary fission, where one mother cell becomes two genetically identically and equally sized daughter cells. In most bacteria a key protein, FtsZ, forms a FtsZ ring (Z-ring) to mark the division site and recruit proteins involved in cytokinesis. Whilst much has been learned about the contents and assembly of the divisome in model organisms such as Escherichia coli and Bacillus subtilis factors governing the regulation of divisome are much more poorly understood. …

Using The Embl-Ebi Clustal Omega Tool To Calculate Diversity Of Heavy Chain Phage-Display Libraries, Michael Bodri, Shane A. Webb

Georgia Journal of Science

Here we show that traditional Sanger sequencing combined with analysis tools available from the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), specifically EMBOSS Transeq and Clustal Omega, is extremely effective in the analysis of naïve phage display antibody libraries for the determination of library size and diversity. The free tools are easy to use and require little manipulation of reads by hand, allowing analysis to be performed on a standard personal computer. Utilization of this technique has applicability to researchers with limited access to deep sequencing. The primary drawback to this analysis methodology is that antibodies with particular molecular or …

Enhancing Production Of Functional Proteins In Plant Cell Culture Through Cellular Engineering And Rational Protein Design, Uddhab Karki

Student Theses and Dissertations

Plant cell culture is emerging as a promising alternative bioproduction platform for valuable proteins due to its low cost of production, safety (free from animal pathogen contamination) and ease of scale-up. However, there are common challenges for commercialization, including low protein yields, difficulty in cryopreservation, and non-human glycosylation, etc. This research project addresses the overarching research hypothesis that strategically modifying the plant cell genome using CRISPR/Cas9 technology and rationally designing protein molecules by fusing with a functional module enhance the production of protein in plant cell culture and improve protein function. There are two specific aims addressed in this project: …

Ngly1 Deficiency Affects Glycosaminoglycan Biosynthesis And Wnt Signaling Pathway In Mice, Amy Batten

PANDION: The Osprey Journal of Research and Ideas

Individuals affected by NGLY1 Deficiency cannot properly deglycosylate and recycle certain proteins. Even though less than 100 people worldwide have been diagnosed with this rare autosomal recessive condition, thousands are affected by similar glycosylation disorders. Common phenotypic manifestations of NGLY1 Deficiency include severe neural and intellectual delay, impaired muscle and liver function, and seizures that may become intractable. Very little is currently known about the various mechanisms through which NGLY1 deficiency affects the body and this has led to a lack of viable treatment options for those afflicted. This experiment uses a loss-of-function (LOF) mouse model of NGLY1 Deficiency homologous …

Polyamine Enzymes As Potential Targets For Cancer Therapeutics To Mitigate Diabetic Triple Negative Breast Cancer Advancement, Hadassha Tofilau

Biology Theses, Dissertations, and Student Creative Activity

Breast cancer (BC) is the second leading cause of death in women. Co-existence of diabetes and BC can be lethal, leading to higher mortality than BC alone. TNBC is highly refractive, heterogenous, and resistant to most chemotherapies. Polyamines play a role in cell growth and are elevated in cancer, though their role in diabetic TNBC has not been explored. We hypothesized that high glucose/diabetic conditions increase TNBC cell proliferation through modification of enzymes in the polyamine pathway and that miR-133a would decrease TNBC cell proliferation. For this study, MDA-MB-231 and MCF-10A cell lines were both treated with normal (5mM) and …

X-Linked Ubiquitin-Specific Peptidase 11 Increases Tauopathy Vulnerability In Women, Yan Yan

USF Tampa Graduate Theses and Dissertations

Women experience significantly higher tau burden and increased risk for Alzheimer’s disease (AD) than men, yet the underlying mechanism for this vulnerability has not been explained. Here, we demonstrate through in vitro and in vivo models, as well as human AD brain tissue, that X-linked ubiquitin specific peptidase 11 (USP11) augments pathological tau aggregation via tau deubiquitination initiated at lysine-281. Removal of ubiquitin provides access for enzymatic tau acetylation at lysines 281 and 274. USP11 escapes complete X-inactivation, and female mice and people both exhibit higher USP11 levels than males. Genetic elimination of usp11 in a tauopathy mouse model preferentially …

The Roles Of A Probiotic Exopolysaccharide In Breast Cancer, Mai Rachel Nguyen

Dissertations

breast cancer, exopolysaccharide, probiotic

Data Supporting A Saturation Mutagenesis Assay For Tat-Driven Transcription With The Gigaassay, Ronald Benjamin, Christopher J. Giacoletto, Zachary T. Fitzhugh, Danielle Eames, Lindsay Buczek, Xiaogang Wu, Jacklyn Newsome, Mira V. Han, Tony Pearson, Zhi Wei, Atoshi Banerjee, Lancer Brown, Liz J. Valente, Shirley Shen, Hong-Wen Deng, Martin R. Schiller

Life Sciences Faculty Research

The data in this article are associated with the research paper “GigaAssay – an adaptable high-throughput saturation mutagenesis assay". The raw data are sequence reads of HIV-1 Tat cDNA amplified from cellular genomic DNA in a new single-pot saturation mutagenesis assay designated the “GigaAssay”. A bioinformatic pipeline and parameters used to analyze the data. Raw, processed, analyzed, and filtered data are reported. The data is processed to calculate the Tat-driven transcription activity for cells with each possible single amino acid substitution in Tat. This data can be reused to interpret Tat intermolecular interactions and HIV latency. This is one of …

Seqcode: A Nomenclatural Code For Prokaryotes Described From Sequence Data, Brian P. Hedlund, Maria Chuvochina, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach, Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain C. Sutcliffe, Stephanus N. Venter, William B. Whitman

Life Sciences Faculty Research

Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and …

Examination Of The Time Delayed Induction Between Prior Encapsulation Of Catalytic Enzymes In P22 Virus-Like Particles, Andrea Hernandez Irias

Chemistry Theses

Protein cages found in nature have the ability to protect and develop new nanomaterials in order to enhance catalytic reactions. This is due to the ability of these organelle structures to mimic protein-based organelles such as Virus-Like Particles (VLPs). VLPs have the ability to not only resemble virus protein structures but to encapsulate enzymes while retaining their activity. This research examines the in vitro encapsulation withing the bacteriophage P22 derived VLP, and show that some enzymes may require a delay in encapsulation to allowed proper folding

and maturation before they can be encapsulated inside P22 as fully active enzymes. Exploring …

Finding Biomarkers From Long-Non-Coding Rnas In Serum Of Patients With Non-Alcoholic Fatty Liver Disease, Nouran Yonis

Theses and Dissertations

Nonalcoholic fatty liver disease (NAFLD) is becoming a serious global public health problem as it is a highly prevalent condition, that begins as simple liver steatosis and develops into an inflammatory steatosis form known as non-alcoholic steatohepatitis (NASH). NAFLD has been linked with multiple comorbidities, which in certain cases predisposes to mortality secondary to extrahepatic neoplasms and coronary diseases. On the other hand, NASH leaves patients at risk of developing hepatocellular carcinoma (HCC). The incidence of NAFLD- based HCC is steadily increasing and is projected to surpass the incidence of HCC from viral origins. Long non-coding RNAs (lncRNAs) have been …

The Emerging Spectrum Of Cardiopulmonary Pathology Of The Coronavirus Disease 2019 (Covid-19): Report Of 3 Autopsies From Houston, Texas, And Review Of Autopsy Findings From Other United States Cities, Manish Bodas, Bharathiraja Subramaniyan, Harry Karmouty-Quintana, Peter F Vitiello, Matthew S Walters

Faculty, Staff and Student Publications

The mammalian respiratory system or lung is a tree-like branching structure, and the main site of gas exchange with the external environment. Structurally, the lung is broadly classified into the proximal (or conducting) airways and the distal alveolar region, where the gas exchange occurs. In parallel with the respiratory tree, the pulmonary vasculature starts with large pulmonary arteries that subdivide rapidly ending in capillaries adjacent to alveolar structures to enable gas exchange. The NOTCH signalling pathway plays an important role in lung development, differentiation and regeneration post-injury. Signalling via the NOTCH pathway is mediated through activation of four NOTCH receptors …

Isolation And Characterization Of Fluorescent Proteins And Small Molecules From Marine Vertebrates, Sara Rose Krivoshik

Dissertations, Theses, and Capstone Projects

Fluorescence is a phenomenon in which a wavelength of light excites a fluorophore and then emits light at a higher, longer wavelength. This occurs throughout the biological world, in both the terrestrial and marine realms. Encompassing a diverse set of mechanisms from small molecules to large protein complexes; fluorescence has been used as a biological tool with a wide range of applications to study molecular and cellular biology for decades. This dissertation looks to identify and characterize novel fluorescent proteins and small molecules to allow for more efficient translation in developing new biotechnologies. Using a combination of RNA-Seq, Mass-Spec, protein …

Determining The Roles Of The Oligomerization And C-Terminal Domains In Mutant P53 Gain-Of-Function Activities, George K. Annor

Dissertations, Theses, and Capstone Projects

The tumor suppressor p53 (TP53) gene is often mutated in cancer, with missense mutations found in the central DNA binding domain, and less often in the oligomerization domain (OD) and C-terminal domain (CTD). The OD and CTD have been found to be critical for the tumor suppressor functionality of wild-type p53 (wtp53). Specific missense mutations in the DNA binding domain have been found to confer new gain-of-function (GOF) activities. Mutations that destabilize tetramer formation, or deletion of key lysine residues within the CTD, downregulate the ability of wtp53 to transactivate (increase the rate of transcription of) its target …

Biochemical And Biophysical Characterization Of Replicative Helicase Loading By Vibrio Cholerae Dcia, Crystal Structure Of A Monoclonal Antibody Bound To A C-Terminal Fragment Of Ebna-1 From Epstein Barr Virus, Nicholas Gao

Dissertations, Theses, and Capstone Projects

DNA replication initiation is mediated by the binding of an initiator protein to genomic origins of replication to begin the process of loading replicative helicases onto the genome. The loading of the helicase requires the action of an accessory protein, named a “loader”. Studies on well-characterized loaders have outlined how the bacterial DnaB replicative helicase is loaded via mechanisms of “Ring-Breaking” by E. coli DnaC (EcDnaC)/protein P from bacteriophage lambda (LP) and “Ring-Making” by B. subtilis DnaI. Mounting evidence points to a recently discovered candidate loader, named DciA, that shows a more widespread distribution throughout bacteria than DnaC and DnaI …

Generation Of Mycobacterium Smegmatis Model Systems For Testing Inhibitors Of The Mycobactin Siderophore Of Mycobacterium Tuberculosis, Gabrielle A. Germain

Dissertations, Theses, and Capstone Projects

Mycobacterium tuberculosis (Mtb) is the pathogenic bacterium causative of tuberculosis. According to the 2021 World Health Organization (WHO) Global Tuberculosis (TB) Report, there were approximately 5.8 million TB cases in 2020, and 1.3 million TB deaths among HIV negative people in that year. The rise of multi-drug resistant Mtb strains has increased the need for more potent microbials against this pathogen. Biosynthesis of iron scavenging molecules, known as siderophores (e.g., mycobactin and carboxymycobactin), has been identified as a potential drug target candidate since iron acquisition has been directly linked to the survival and virulence of Mtb. Salicyl-AMS (Sal-AMS) is …

Transcriptional Mechanisms Of Neuroprotection In Excitotoxicity Driven Neurodegeneration In C. Elegans, Zelda Z. Mendelowitz

Dissertations, Theses, and Capstone Projects

Excitotoxicity is notorious for triggering neuronal cell death in both developmental and adult-onset neurodegenerative diseases. In excitotoxicity, excessive concentrations of Glutamate in the synapse overstimulate Glutamate Receptors (GluRs) on postsynaptic neurons. While GluR mediated degenerative mechanisms remain obscure, GluR activation was surprisingly found to also have a neuroprotective effect through activation of specific transcriptional programs. To identify evolutionarily conserved transcriptional programs in neuroprotection we use a C. elegans model of excitotoxic necrosis (glt-3;nuIs5). We have identified that non-canonical activation of the transcription factor CRH-1/CREB mediates neuroprotection in our excitotoxicity model. We found the Histone Acetyl Transferase, MYS-1/KAT6, and the neuronal …

Cell-Intrinsic Melanin Fails To Protect Melanocytes From Ultraviolet-Mutagenesis In The Absence Of Epidermal Melanin, Tirzah J. Weiss, Emma R. Crawford, Valentina Posada, Hafeez Rahman, Tong Liu, Brandon M. Murphy, Tiffany E. Arnold, Shannon Gray, Zhexuan Hu, Rebecca C. Hennessey, Lianbo Yu, John August D'Orazio, Craig J. Burd, Jonathan H. Zippin, Douglas Grossman, Christin E. Burd

Markey Cancer Center Faculty Publications

Melanin is a free-radical scavenger, antioxidant, and broadband absorber of ultraviolet (UV) radiation which protects the skin from environmental carcinogenesis. However, melanin synthesis and UV-induced reactive melanin species are also implicated in melanocyte genotoxicity. Here, we attempted to reconcile these disparate functions of melanin using a UVB- sensitive, NRAS-mutant mouse model, TpN. We crossed TpN mice heterozygous for an inactivating mutation in Tyrosinase to produce albino and black littermates on a C57BL/6J background. These animals were then exposed to a single UVB dose on postnatal day three when keratinocytes in the skin have yet to be melanized. Approximately one-third (35%) …

Redundancy And Developmental Coordination In Myxococcus Xanthus: Insights From The Phenome, Jessica A. Comstock

Dissertations - ALL

Genotype-to-phenotype mapping can typically involve disrupting the function of a gene and observing the impact of mutation on phenotype. While this can be a powerful tool for uncovering gene function, complicating factors such as influences between genes and the environment, epistatic interactions with other genes, and genetic redundancy could all potentially mask the phenotype of a mutation such that functional inferences cannot be made. On the level of the single gene, this may not be particularly informative, but it is possible that studying phenotype in this way at a genome scale might allow for the observation of patterns between genes …

Mechanisms And Roles Of Dynamic Actin Assembly Around Dysfunctional Mitochondria, Tak Shun Fung

Dartmouth College Ph.D Dissertations

Possessing the ability to efficiently generate ATP required to sustain cellular functions, mitochondria are often considered the ‘powerhouses of the cell’. However, our understanding of mitochondria in cell biology was further expanded when we recognized that communication between this unique organelle and the rest of the cell regulates cellular bioenergetics, metabolism and signaling processes such as mitophagy and apoptosis. Here, I investigate signaling between mitochondria and the actin cytoskeleton, and how this signaling regulates mitochondrial dynamics and cellular function. Specifically, I find that, upon mitochondrial dysfunction, actin polymerizes rapidly around the dysfunctional organelle, which we term ‘acute damage-induced actin’ (ADA). …

Identification Of Secondary Structural Elements Contained Within The Intrinsically Disordered N-Terminal Tail Of The Bloom’S Syndrome Helicase., Vivek Somasundaram

USF Tampa Graduate Theses and Dissertations

The Bloom’s Syndrome Helicase (BLM) is one of five human RecQ helicases and is necessary for maintenance of genome stability. Whilst a crystal structure exists for the C-terminal domain of BLM, very limited structural knowledge is known about the intrinsically disordered N-terminal tail. This lack of insight exists, despite the fact that the N-terminus of BLM is essential for the overall biological activity of BLM. Here we provide an Nuclear Magnetic Resonance spectroscopy based approach that we used to identify two distinct ⍺-helices contained within the first 100 residues of BLM. In addition, we propose a mutagenesis-based approach involving rationally …

From The Headlines: A Textual Analysis Of Social Polarization And Discord In Times Of Pandemic Across A Century In The United States, Alexa Demarco

Undergraduate Honors Theses

Within the past century, three major pandemics have affected the United States – the Spanish Flu, AIDS, and COVID-19. Each of these pandemics has tested the capabilities of the public health sector and the social resilience of the population. Scientists have studied the viruses and implemented public health measures to limit viral transmission, but the social responses to these preventative measures proved to be difficult to predict and control. The dissonance and polarization between the public health initiatives and the response of the general public in the most recent pandemic was apparent. Was this a pattern in other pandemics? Was …

Ligand- And Strain-Specific Control Of Microbial Communities, Austin Grant Rottinghaus

McKelvey School of Engineering Graduate Student Theses & Dissertations

Microbes naturally coexist in complex, multi-strain communities that are valuable assets for their host. Commensal and probiotic microbes prevent pathogen colonization, reduce the frequency and severity of various ailments, provide essential nutrients, and offer various additional benefits. Understanding the dynamics of and tailoring microbial communities to provide additional beneficial functions is a primary focus of researchers in medicine and agriculture. To date, consortia have primarily been manipulated by supplementing the communities with microbes that were engineered in vitro or by introducing stimuli that alter the metabolism or composition of the community. This method has proven successful, with numerous microbes engineered …