Biochemistry, Biophysics, and Structural Biology Commons^™

Evolutionary Conservation And Times Of Action Of Heterochronic Genes, Maria Ivanova

Theses and Dissertations

The heterochronic pathway of C. elegans is the most well-characterized system to date for controlling the sequence and timing of developmental events. However, we still have critical unanswered questions to address. First, little is known about the evolution of the heterochronic pathway, and of developmental timing in general. To determine if the roles of major heterochronic genes are conserved, I made mutants in orthologs of these genes in C. briggsae, using CRISPR/Cas9. My studies revealed a significant drift in the roles of some of the genes, although all of them are still involved in the developmental timing regulation, and several …

Evaluating The Response Of Glycine Soja Accessions To Fungal Pathogen Macrophomina Phaseolina During Seedling Growth, Shirley Jacquet, Layla Rashad, Sonia Viera, Francisco Reta, Juan Reta

Biological Science Student Working Papers

Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. …

Langevin Dynamic Models For Smfret Dynamic Shift, David Frost, Keisha Cook Dr, Hugo Sanabria Dr

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Targeting Bet Proteins Downregulates Mir-33a To Promote Synergy With Pim Inhibitors In Cmml, Christopher T. Letson

USF Tampa Graduate Theses and Dissertations

Chronic Myelomonocytic Leukemia (CMML) is a rare myeloid malignancy with a dismal prognosis and no therapeutic options which are capable of altering the natural course of the disease. There remains a significant need for novel therapies that are able to meaningfully improve patient outcomes. In this study we explore the effectiveness of Bromodomain and Extra-Terminal domain protein inhibitor (BETi) combinations in CMML. Preclinical studies in myeloid neoplasms have demonstrated efficacy of BETi. However, BETi demonstrate poor single agent activity in clinical trials. Several studies suggest that combinations with other anti-cancer inhibitors may enhance the efficacy of BETi. To nominate BETi …

Association Of Elevated Serum Aldosterone Concentrations In Pregnancy With Hypertension, Robin C. Shoemaker, Marko Poglitsch, Dolph Lewis Davis Iii, Hong Huang, Aric Schadler, Neil Patel, Katherine Vignes, Aarthi Srinivasan, Cynthia Cockerham-Morris, John Anthony Bauer, John M. O’Brien

UK CARES Faculty Publications

Emerging evidence indicates a previously unrecognized, clinically relevant spectrum of abnormal aldosterone secretion associated with hypertension severity. It is not known whether excess aldosterone secretion contributes to hypertension during pregnancy. We quantified aldosterone concentrations and angiotensin peptides in serum (using liquid chromatography with tandem mass spectrometry) in a cohort of 128 pregnant women recruited from a high-risk obstetrics clinic and followed prospectively for the development of gestational hypertension, pre-eclampsia, superimposed pre-eclampsia, chronic hypertension, or remaining normotensive. The cohort was grouped by quartile of aldosterone concentration in serum measured in the first trimester, and blood pressure, angiotensin peptides, and hypertension outcomes …

Benchmark Dataset For Training Machine Learning Models To Predict The Pathway Involvement Of Metabolites, Erik D. Huckvale, Christian D. Powell, Huan Jin, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Metabolic pathways are a human-defined grouping of life sustaining biochemical reactions, metabolites being both the reactants and products of these reactions. But many public datasets include identified metabolites whose pathway involvement is unknown, hindering metabolic interpretation. To address these shortcomings, various machine learning models, including those trained on data from the Kyoto Encyclopedia of Genes and Genomes (KEGG), have been developed to predict the pathway involvement of metabolites based on their chemical descriptions; however, these prior models are based on old metabolite KEGG-based datasets, including one benchmark dataset that is invalid due to the presence of over 1500 duplicate entries. …

Evaluation Of Rotenone Mediated Α-Synuclein Spreading And Neurotoxicity In Intra-Striatal Injection Of Α-Synuclein Pff Model Of Parkinson’S Disease, Engila Khan

Theses

In the last 25 years, the prevalence of Parkinson’s Disease (PD) across the globe has doubled. Clinical manifestations of this progressive neurodegenerative disorder include motor symptoms such as tremors, bradykinesia, postural instability, etc., which occur due to selective loss of dopaminergic neurons in the Substantia nigra (SNC) in the brain. The histopathological feature of PD is the presence of intra-neuronal aggregates of proteins called Lewy bodies, a major constituent of which is α-synuclein (α-syn).

Epidemiological studies to date have reported a connection between exposure to environmental neurotoxins such as Rotenone (a mitochondrial complex 1 inhibitor) and increased risk of PD …

Modulation Of Chronic Allergic Contact Dermatitis Through B Cells, Sara Saeed Alhmoudi

Theses

Allergic contact dermatitis (ACD) is a common inflammatory disease caused by contact with an allergen and is a T-cell-mediated type IV hypersensitivity reaction. Shortchain fatty acids (SCFAs) showed the ability to modulate immune cells in case of inflammation. Pentanoate is one of the abundant SCFA that showed therapeutic ability by inducing interleukin-10 (IL-10) secretion in lymphocytes. IL-10-producing regulatory B cells have been shown to decrease different inflammatory responses; however, the overall role of B cells in ACD is not well studied. This project aims to explore the role of B cells during chronic ACD and their modulation with the SCFA …

Anti Cancer Activity Of Rhus Coriaria (Sumac) Against 5-Fluorouracil-Resistant Colorectal Cancer Cells, Zohra Nausheen Nizami

Theses

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, both worldwide and in the UAE. 5-Fluorouracil (5-FU), a pyrimidine analogue, is a chemotherapeutic agent that is an integral component of chemotherapy regimens for CRC treatment. However, 5-FU resistance (intrinsic and/or acquired) inhibits their clinical efficacy. In recent years, there has been a growing popularity for plant-based cancer therapeutics, specifically using phytochemical compounds. Rhus coriaria (Sumac) is a Mediterranean plant whose fruits are used as a spice and medicinal herb. Extracts of Rhus coriaria fruits (RCE) have been reported to exhibit anti-cancer activity against breast cancer and CRC. In …

Canagliflozin Ameliorates Autistic-Like Features And Mitigates Brain Oxidative Stress Levels In Valproic Acid-Induced Autism In Rats, Mohammad Moutaz Nakhal

Theses

Autism spectrum disorder (ASD) is a neurodevelopmental disease with a substantially increasing incidence rate. It is mainly characterized by repetitive behavior, intellectual difficulties, social communication and interactions deficits. Many medications, dietary supplements, and behavioral treatments have been recommended for ASD management, however, there is no cure yet. Recent studies have examined the therapeutic potential of the sodium-glucose cotransporter 2 (SGLT2) inhibitors in neurodevelopmental diseases, based on their proved anti-inflammatory and antioxidant effects. The main objective of this study is to assess the ability of canagliflozin in improving the behavioural characteristics of autistic rats and investigate the efficacy of canagliflozin in …

Human Schwann Cells In Vitro I. Nerve Tissue Processing, Pre-Degeneration, Isolation, And Culturing Of Primary Cells, Gabriela I. Aparicio, Paula V. Monje

Markey Cancer Center Faculty Publications

This paper presents versatile protocols to prepare primary human Schwann cell (hSC) cultures from mature peripheral nervous system tissues, including fascicles from long spinal nerves, nerve roots, and ganglia. This protocol starts with a description of nerve tissue procurement, handling, and dissection to obtain tissue sections suitable for hSC isolation and culturing. A description follows on how to disintegrate the nerve tissue by delayed enzymatic dissociation, plate the initial cell suspensions on a two-dimensional substrate, and culture the primary hSCs. Each section contains detailed procedures, technical notes, and background information to aid investigators in understanding and managing all steps. Some …

Phosphorylation Of Ahr By Plk1 Promotes Metastasis Of Luad Via Dio2-Th Signaling, Chaohao Li, Derek B. Allison, Daheng He, Fengyi Mao, Xinyi Wang, Piotr G. Rychahou, Ibrahim A. Imam, Yifan Kong, Qiongsi Zhang, Yanquan Zhang, Jinghui Liu, Ruixin Wang, Xiongjian Rao, Sai Wu, B. Mark Evers, Qing Shao, Chi Wang, Zhiguo Li, Xiaoqi Liu

Markey Cancer Center Faculty Publications

Metastasis of lung adenocarcinoma (LUAD) is a major cause of death in patients. Aryl hydrocarbon receptor (AHR), an important transcription factor, is involved in the initiation and progression of lung cancer. Polo-like kinase 1 (PLK1), a serine/threonine kinase, acts as an oncogene promoting the malignancy of multiple cancer types. However, the interaction between these two factors and their significance in lung cancer remain to be determined. In this study, we demonstrate that PLK1 phosphorylates AHR at S489 in LUAD, leading to epithelial-mesenchymal transition (EMT) and metastatic events. RNA-seq analyses reveal that type 2 deiodinase (DIO2) is responsible for EMT and …

Increasing Glutathione Levels By A Novel Posttranslational Mechanism Inhibits Neuronal Hyperexcitability, Ashwini Sri Hari, Rajeswari Banerji, Li-Ping Liang, Ruth E Fulton, Christopher Quoc Huynh, Timothy Fabisiak, Pallavi Bhuyan Mcelroy, James R Roede, Manisha Patel

Faculty, Staff and Students Publications

Glutathione (GSH) depletion, and impaired redox homeostasis have been observed in experimental animal models and patients with epilepsy. Pleiotropic strategies that elevate GSH levels via transcriptional regulation have been shown to significantly decrease oxidative stress and seizure frequency, increase seizure threshold, and rescue certain cognitive deficits. Whether elevation of GSH per se alters neuronal hyperexcitability remains unanswered. We previously showed that thiols such as dimercaprol (DMP) elevate GSH via post-translational activation of glutamate cysteine ligase (GCL), the rate limiting GSH biosynthetic enzyme. Here, we asked if elevation of cellular GSH by DMP altered neuronal hyperexcitability in-vitro and in-vivo. Treatment of …

Newer Insights Into Mmtv Replication: The Human Retroviral Proteins Hiv-1 Tat And Htlv-1 Tax Can Transactivate The Mmtv Novel 5’ Element, Thanumol Abdul Khader

Dissertations

The mouse mammary tumor virus (MMTV) is a prototypic betaretrovirus that causes breast cancer in mice. MMTV regulates its gene expression both at the transcriptional and post transcriptional levels. It has hormonally-regulated promoters controlled by negative regulatory factors in a tissue-specific manner. Recently, we identified a novel 24-nucleotide region at the 5' end of the MMTV genome crucial for MMTV gene expression. Its deletion resulted in disruption of MMTV transcript elongation and stability, leading to a complete loss of Gag gene expression. This conserved element is present within the bifurcated stem loop 4, responsible for gRNA dimerization and encapsidation, into …

Yeast Crf1p: An Activator In Need Is An Activator Indeed, Sanjay Kumar

LSU Doctoral Dissertations

Ribosome biogenesis is an energetically costly process, and tight regulation is required for stoichiometric balance between components. This requires coordination of RNA polymerases I, II, and III. Lack of nutrients or the presence of stress leads to downregulation of ribosome biogenesis, a process for which mechanistic target of rapamycin complex I (mTORC1) is key. mTORC1 activity is communicated by means of specific transcription factors, and in yeast, which is a primary model system in which transcriptional coordination has been delineated, transcription factors involved in regulation of ribosomal protein genes include Fhl1p and its cofactors, Ifh1p and Crf1p. Ifh1p is an …

Neuroendocrine Regulation Of Chemokine Receptor-Mediated Leukocyte Migration Via Heteromeric G Protein-Coupled Receptor Complexes, Garrett Enten

USF Tampa Graduate Theses and Dissertations

Neuroendocrine regulation of the innate immune system is a well-documentedphenomenon. The underlying mechanisms, however, are not well understood. Here we show that at least 20 members of the human chemokine receptor (CR) family heteromerize with one or more members of the α1-adrenergic receptor (AR) family and that all CRs, apart from CXCR1, heteromerize with arginine vasopressin receptor 1A (AVPR1A) in recombinant systems. These heteromeric complexes are detectable in human monocytes and the monocytic leukemia cell line THP-1. Though currently technical limitations prevent the direct visualization of endogenously expressed higher-order hetero-oligomeric receptor complexes, we provide evidence through functional analysis and proximity-based …

Thermodynamic Frustration Of Tad2 And Prr Contribute To Autoinhibition Of P53, Emily Gregory

USF Tampa Graduate Theses and Dissertations

The intrinsically disordered transcription factor and tumor suppressor p53 binds to promoter response element DNA upon cellular stress and activates genes associated with cell cycle arrest, senescence, and apoptosis. Disruption of sequence specific binding to target gene promoters is heavily implicated in human health, where a majority of cancers contain mutations localized to the DNA binding domain (DBD) of p53. p53 DNA binding is regulated by posttranslational modifications, associations with cellular factors, and by an autoinhibitory intramolecular interaction. The autoinhibitory intramolecular interaction occurs when the disordered N-terminal transactivation domain (TAD) interacts with the ordered DBD. Previous work in the Daughdrill …

Novel Treatments For Pxe: Targeting The Systemic And Local Drivers Of Ectopic Calcification, Ida Joely Jacobs, Qiaoli Li

Department of Biochemistry and Molecular Biology Faculty Papers

Pseudoxanthoma elasticum (PXE) is a heritable multisystem ectopic calcification disorder. The gene responsible for PXE, ABCC6, encodes ABCC6, a hepatic efflux transporter regulating extracellular inorganic pyrophosphate (PPi), a potent endogenous calcification inhibitor. Recent studies demonstrated that in addition to the deficiency of plasma PPi, the activated DDR/PARP signaling in calcified tissues provides an additional possible mechanism of ectopic calcification in PXE. This study examined the effects of etidronate (ETD), a stable PPi analog, and its combination with minocycline (Mino), a potent inhibitor of DDR/PARP, on ectopic calcification in an Abcc6-/- mouse model of PXE. Abcc6-/- mice, at 4 weeks of …

Molecular Event In Hrp Apoptosis, Laura Valdez

Research Colloquium

Background: Human retinal pericytes (HRP) are contractile cells providing support for endothelial cells of capillaries, essential in the regulation of retinal vasculature. Early stages of DR are characterized by the loss of HRP, leading to angiogenesis. Our preliminary studies identified monocyte-derived macrophages secrete TGF-β1, inducing the expression and secretion of a TGFβ1-Induced, pro-apoptotic BIGH3 protein leading to apoptosis of HRP. Based on a preliminary study in renal cells (unpublished data), CTP with an RGD domain is released from BIGH3 by proteolysis leading to renal cell apoptosis. In the present study, we employed Western Blots to determine if a similar molecular …

Irbp In Diabetic Retinopathy – Cell Culture & Ophthalmic Pathology Studies, Laura Valdez

Research Colloquium

Background: Interphotoreceptor-Retinoid-Binding-Protein (IRBP) is restricted to the subretinal space by the external limiting membrane and RPE zonulae occludens. Its expression is reduced in diabetic retinopathy (DR) and increased expression is protective. Hypoxia decreases viable conelike photoreceptors (661W) but increased VEGF, suggesting a role of photoreceptors in proliferative DR (PDR) (Rodriguez et al, Arch Clin Exp. Ophthal 3:23,2021). Here, we investigated the effects of high glucose and VEGF on IRBP expression by 661W and rod-like Y79 cells and distribution of IRBP and albumin in human globes with PDR and NPDR.

Methods:  661W and Y79 cells were cultured in DMEM or RPMI …

Sars-Cov-2: Tale Of A Microscopic Murderer, Josiah P. Garner

Quest

Independent Study

Research in progress for BIOL1406: Biology for Science Majors I

Faculty Mentor: Amina Tassa, Ph.D.

I am delighted to introduce Josiah Garner’s “SARS-CoV-2: Tale of a Microscopic Murderer.” This independent study assignment explores the impact of a novel, deadly, and worldwide virus. The assignment also examines the fast development of vaccines to control the spread and reduce the symptoms of the virus.

Josiah’s paper focuses on the early history of the emergence of COVID-19, the world response, and vaccine development. He demonstrates critical thinking skills and effectively utilizes various research methods to obtain and communicate his information. Josiah …

Characterizing The Utility Of A Near Infrared Click Beetle Luciferase For Bli Applications, Giovanni Duca

Master's Theses

Bioluminescent imaging systems (BLI) have become a valuable tool for doing real-time in vivo studies. BLI systems typically allow for the imaging of surface and subsurface level tissues but as depth increases, the resolution decreases while the signal to noise ratio increases. Deep tissue imaging is therefore a major limitation for BLI. To address this limitation there has been a consistent movement in luciferase research to create long wavelength emitting luciferases that still have a high photon emission rate. Longer wavelengths of light are able to penetrate deeper tissues due to having a lower amount of absorbance and scattering from …

Combination Therapy Of Triple-Negative Breast Cancer With Paclitaxel And Ambrisentan, A Selective Antagonist Of The Endothelin Type A Receptor, Inhibits Tumor Growth And Metastasis, Farah Nasser Almahrook

Theses

Cancer treatment is a big challenge especially when associated with metastasis. Moreover, the importance of using combination therapy is increasing, especially for highly invasive, drug-resistant cancers, such as triple-negative breast cancer (TNBC). Ambrisentan, a selective antagonist of the endothelin type A receptor (ETAR) was previously shown to reduce metastasis of TNBC in a preclinical tumor model when used prophylactically. In the current study, we investigated the therapeutic potential of Ambrisentan, given as monotherapy or in combination with Paclitaxel, on TNBC. The data show that oral dosing with Ambrisentan led to a significant retardation in tumor growth and metastasis. Moreover, combining …

Functional Characterization Of The Human And Murine Schlafen Family Group Iii, Carlos A. Valenzuela

Open Access Theses & Dissertations

The Schlafen (SLFN) family of proteins are known for being encoded by interferon stimulated genes. The family is divided into three groups (I, II, III), for which the largest in size belong to the subgroup III. In humans, group III has the most members (SLFN5, SLFN11, SLFN13 and SLFN14); there is no member of group I and only one member of group II (SLFN12). All human SLFNs belonging to group III have been reported to impair viral protein expression or infection across a variety of viruses. The antiviral function is mediated in SLFN11 and SLFN13 by their tRNase activity, and …

Copy Number Variation That Influences The Ionizing Radiation Sensitivity Of Oral Squamous Cell Carcinoma, Tadahide Izumi, Piotr G. Rychahou, Li Chen, Molly H. Smith, Joseph Valentino

Markey Cancer Center Faculty Publications

Genome instability in cancer cells causes not only point mutations but also structural variations of the genome, including copy number variations (CNVs). It has recently been proposed that CNVs arise in cancer to adapt to a given microenvironment to survive. However, how CNV influences cellular resistance against ionizing radiation remains unknown. PRMT5 (protein arginine methyltransferase 5) and APE1 (apurinic/apyrimidinic endonuclease 1), which enhance repair of DNA double-strand breaks and oxidative DNA damage, are closely localized in the chromosome 14 of the human genome. In this study, the genomics data for the PRMT5 and APE1 genes, including their expression, CNVs, and …

Distinct Camp Signaling Microdomains Differentially Regulate Melanosomal Ph And Pigmentation, Maftuna Yusupova, Dalee Zhou, Jaewon You, Jeydi Gonzalez-Guzman, Megha B. Ghanta, Hong Pu, Zalfa Abdel-Malek, Qiuying Chen, Steven S. Gross, John August D'Orazio, Shosuke Ito, Kazumasa Wakamatsu, Melissa L. Harris, Jonathan H. Zippin

Markey Cancer Center Faculty Publications

cAMP signaling is a well-established regulator of melanin synthesis. Two distinct cAMP signaling pathways—the transmembrane adenylyl cyclase pathway, activated primarily by the MC1R, and the soluble adenylyl cyclase (sAC) pathway—affect melanin synthesis. The sAC pathway affects melanin synthesis by regulating melanosomal pH, and the MC1R pathway affects melanin synthesis by regulating gene expression and post-translational modifications. However, whether MC1R genotype affects melanosomal pH is poorly understood. We now report that loss of function MC1R does not affect melanosomal pH. Thus, sAC signaling appears to be the only cAMP signaling pathway that regulates melanosomal pH. We also addressed whether MC1R genotype …

Phosphatidic Acid Binding To Patched Contributes To The Inhibition Of Smoothened And Hedgehog Signaling In Drosophila Wing Development, Jie Zhang, Yajuan Liu, Chi Wang, Craig W. Vander Kooi, Jianhang Jia

Markey Cancer Center Faculty Publications

Hedgehog (Hh) signaling controls growth and patterning during embryonic development and homeostasis in adult tissues. Hh binding to the receptor Patched (Ptc) elicits intracellular signaling by relieving Ptc-mediated inhibition of the transmembrane protein Smoothened (Smo). We uncovered a role for the lipid phosphatidic acid (PA) in the regulation of the Hh pathway in Drosophila melanogaster. Deleting the Ptc C-terminal tail or mutating the predicted PA-binding sites within it prevented Ptc from inhibiting Smo in wing discs and in cultured cells. The C-terminal tail of Ptc directly interacted with PA in vitro, an association that was reduced by Hh, and increased …

Standardization Of A Technique For Obtaining Dna From Footprints, Gibrán Galindo-Martinez, Karla Villarreal-Sotelo, Cynthia Marisol Vargas-Orozco, Ernesto Leal-Sotelo, Ignacio Hernandez-Rodriguez, José Francisco Flores-Gómez, Esperanza Milagros Garcia-Oropesa

Research Symposium

Currently our country has high numbers of missing persons, Tamaulipas being one of the states with the highest rate of disappearances. The identification of people has become more important thanks to the development of molecular techniques. However, the limitations are very high, because it is necessary to compare the genetic pattern of the disappeared with the parents. Therefore, the objective of this research is to standardize a genomic DNA extraction technique from contact surfaces for its subsequent implementation in the identification of disappeared, allowing the comparison of the genetic pattern with the disappeared itself. For this, genomic DNA extraction was …

Natural Remedies To Combat Aberrant Hallmark Signatures Including Altered Glycosylation In Oral Carcinoma, Kruti A. Mehta, Jayendra B. Patel, Prabhudas S. Patel

Research Symposium

Background: Tobacco associated oral cancers remain a major concern in India with higher incidence and mortality making it an Indian-centric burning issue. To combat this dreadful disease, we investigated effects of certain natural compounds on the hallmark signatures including glycosylation transcripts levels in oral carcinoma.

Methods: The tongue carcinoma cells- SAS cells were treated with tobacco compounds, natural compounds and Cisplatin. RNA was isolated from the cells and converted to cDNA. RT-qPCR was performed to evaluate expression levels of various genes.

Results: The treatment of tobacco compounds resulted in similar pattern of altered makers (ST3GAL1, NEU3, FUT5, FUT6, MMP2, BCL2) …

Hpv Imprints In Western India: The Overlooked Criteria For Cancer Profiling, Ashi R. Thobias, Jayendra B. Patel, Prabhudas P. Patel

Research Symposium

Background: In India, HPV infection detection for cancer-typing has been largely evaded. Especially, data on prevalence of HPV types other than the highly prevalent HPV 16 and 18 are lacking, particularly from the western region. Thus, present study aimed to evaluate prevalence of HPV strains in three most prevailing cancers in India i.e. cervical, oral and oropharyngeal cancer.

Materials & methods: DNA was isolated from tissue samples of 400 cervical cancer cases, 127 oral cancer cases and 75 oropharyngeal cancer cases and endpoint PCR was performed using degenerative primers MY 09/11, GP 5+/6+ and CP I/II. TS-PCR was conducted to …