Biochemistry, Biophysics, and Structural Biology Commons^™

College Of Natural Sciences Newsletter, July 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 7.

Page 1 Dean's Message
Page 2 Celebrating Three Years
Page 3 Summer School Travel
Page 4 Media Coverage of CNS
Page 5 Chemistry Teachers Visit
Page 5 Remembering Dr. Warren Hein
Page 6 Research Spotlights: Undergraduate Summer Experiences
Page 7 Open PRAIRIE Data; Grants Awarded in CNS

Host-Parasite Interactions Within Food Webs, Adam Zvanut Hasik

Graduate Theses and Dissertations

Parasitism is one of the most common life history strategies employed in nature, yet the effects of parasites are often thought to be minimal, and the vast majority of studies fail to consider parasites and their effects on host organisms. This is likely a problem, as the magnitude of parasite-mediated effects on their hosts can be quite large. Additionally, the effects of parasites are known to extend beyond the host to affect other species interactions. I used a series of approaches to gain a more integral understanding of host-parasite interactions by studying (1) the effects of parasites on biotic interactions …

Divergent Regulatory Roles Of Nurd Chromatin Remodeling Complex Subunits Gatad2 And Chd4 In Caenorhabditis Elegans, Nicole Lynn Golden

Theses and Dissertations

During stress, a protective cellular network known as the heat shock response (HSR) is induced to maintain protein-folding homeostasis, or proteostasis. While the HSR is essential for stress resistance, its misregulation is associated with neurodegenerative disease and cancer. Using the nematode model organism Caenorhabditis elegans, we have identified the chromatin remodeling complex NuRD (nucleosome remodeling and deacetylase) as a novel regulator of the HSR. Here, we begin with a brief introduction of the HSR and chromatin remodeling complexes in C. elegans, prior to presenting our findings in a series of two chapters. In chapter one, we outline a set of …

Distinct Spatiotemporal Regulation Of The Cytoprotective Heat Shock Response In Caenorhabditis Elegans, Rosemary Nadine Plagens

Theses and Dissertations

Every organism studied to-date utilizes the heat shock response (HSR) to maintain protein-folding homeostasis (proteostasis) during temperature or other protein-folding stress. The HSR has been well characterized using acute heat stress (HS) in single-celled models, but less is known about how distinct cell types and tissues respond to HS. Furthermore, how metazoans respond to prolonged HS at the molecular level remains relatively unexplored. The model organism C. elegans, with its genetic tractability and distinct tissues and behaviors, has been used extensively in the field to characterize the acute HSR, but with considerable variability across labs regarding HS temperature and duration. …

Characterization Of Iron-Sulfur Cluster Biogenesis In Methanogenic Archaea, Thomas Modlin Deere

Graduate Theses and Dissertations

Iron-sulfur (Fe-S) clusters are among the oldest cofactors on the planet, used by proteins in almost all forms of life on Earth to carry out processes ranging from energy transfer to DNA replication. Among the organisms believed to use these Fe-S proteins more extensively than almost any others are the methanogens, an ancient lineage of archaeal microbes that produce methane as a required product of their metabolism. Methane, the primary component of commercial natural gas, is both a potent greenhouse gas and an important fossil fuel. It can also be renewably produced as a biofuel. Biogenic methane is almost entirely …

The Characterization Of Angiopoietin-Like Protein 4 Overexpression In Triple Negative Breast Cancer, Jodi Simeon

Graduate Theses and Dissertations

Triple Negative Breast Cancer (TNBC) is highly invasive and metastatic with approximately 15% of patients developing liver metastases. The primary treatment of metastatic TNBC is chemotherapy, however, there is an increased chance of resistance to this therapeutic technique. If Breast Cancer Liver Metastasis (BCLM) is left untreated most patients survive only 4 to 8 months with a very rare 5-year survival. Therefore, it is imperative to analyze markers and molecular pathways that TNBC cells use to progress, invade, and metastasize to the liver. The aim of this study was to examine the overexpression of angiopoietin-like 4 (ANGPTL4) in TNBC cells …

Evaluating Bioenergetics And Mitochondrial Dynamics In Patient Fibroblasts With Pathogenic Mitochondrial Dna Mutations Causing Leigh Syndrome, Ajibola Bakare

Graduate Theses and Dissertations

Leigh syndrome (LS) is a rare fatal mitochondrial disorder of infants caused by pathogenic mutations in the nuclear (nDNA) or mitochondrial DNA (mtDNA) leading to mitochondrial dysfunction. The extent to which pathogenic mtDNA variants regulate disease severity in LS is not well understood. The heterogeneous nature of this disorder, based in part by complex mitochondrial genetics, and the nuclear and mitochondrial cross-talk has made it particularly challenging to investigate and develop therapies for treating LS . While the prognosis is poor, several studies are underway to understand the pathophysiology of LS. This dissertation provides a comprehensive structural and functional analysis …

A Time-Course Characterization Of Muscle Function And Mitochondrial Markers During Colorectal Cancer-Induced Cachexia In Tumor-Bearing Male Mice, Ana Cabrera Ayuso

Graduate Theses and Dissertations

Cachexia is a multisystemic and multifactorial syndrome prevalent in cancer patients. It is clinically defined by involuntary loss of >5% weight in a six-month window, despite nutritional interventions. A negative energy balance characterizes cancer cachexia (CC), it is associated with weakness and fatigue in skeletal muscle. Impaired muscle function is associated with lower quality of life in cancer patients. Defects in mitochondrial function are strongly associated with muscle wasting. This study explored muscular contractile function and mitochondrial quality control (MQC) markers in soleus, gastrocnemius, and tibialis anterior (TA) muscles of C26-induced male tumor-bearing mice during a 25-day time course. It …

Cytoplasmic Polyadenylation Element Binding Protein 2 Alternative Splicing Regulates Hif1Α During Chronic Hypoxia, Emily M. Mayo

USF Tampa Graduate Theses and Dissertations

Chronic pulmonary hypoxia commonly results in the sustained expression of HIF1 (hypoxia inducible factor 1), a heterodimeric transcription factor, that, if unrestrained, can result in dramatic vasculature remodeling, pulmonary arterial hypertension, and right-sided heart failure. Together, these pulmonary disorders cost approximately $100 billion annually to treat due to the limited therapeutic targets designed to inhibit HIF1 expression. In this study, we introduce a translational regulator of HIF1 expression, known as Cytosolic polyadenylation element binding proteins 2 (CPEB2). Our lab has previously demonstrated in cancer cells that alternatively spliced isoforms of CPEB2 regulate the translation of the HIF1 oxygen-dependent subunit, HIF1α, …

Attenuated Strain Of Cvb3 With A Mutation In The Car‑Interacting Region Protects Against Both Myocarditis And Pancreatitis, Ninaad Lasrado, Arunakumar Gangaplara, Chandirasegaran Massilamany, Rajkumar Arumugam, Allison Shelbourn, Mahima T. Rasquinha, Rakesh H. Basavalingappa, Gustavo Delhon, Shi-Hua Xiang, Asit K. Pattnaik, David Steffen, Jay Reddy

School of Veterinary and Biomedical Sciences: Faculty Publications

Coxsackievirus B3 (CVB3), is commonly implicated in myocarditis, which can lead to dilated cardiomyopathy, in addition to causing acute pancreatitis and meningitis. Yet, no vaccines are currently available to prevent this infection. Here, we describe the derivation of a live attenuated vaccine virus, termed mutant (Mt) 10, encoding a single amino acid substitution H790A within the viral protein 1, that prevents CVB3 infection in mice and protects from both myocarditis and pancreatitis in challenge studies. We noted that animals vaccinated with Mt 10 developed virus neutralizing antibodies, predominantly containing IgG2a and IgG2b, and to a lesser extent IgG3 and IgG1. …

Circrev1 Expression In Triple-Negative Breast Cancer, Meagan P. Horton

USF Tampa Graduate Theses and Dissertations

Triple-negative breast cancer (TNBC) comprises only 24% of breast cancer cases, yet is the second leading cause of cancer mortality in women due to its aggressive nature (1). This increase in mortality is due to the lack of receptors for three targetable growth factors (HER2, progesterone, and estrogen receptors). Our previous studies have indicated that these cancers are highly dysregulated in respect to alternative splicing. Hence, we undertook a study aimed at identifying circular RNAs (circRNAs) generated from back-splicing events which were dysregulated in TNBC. We have identified a novel circRNA transcript, circular REV1 (circREV1), which is upregulated in our …

Temperature Regulation Of Plant Hormone Signaling During Stress And Development, Christian Castroverde, Damaris Dina

Biology Faculty Publications

Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview …

College Of Natural Sciences Newsletter, June 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 6.

Page 1 Dean's Message
Page 2-6 Remembering the Life of Dr. Pengra and Celebrating His legacy for Entire Generations to Come.

Reconstituting The Cyanobacterial Circadian Clock In Vitro, Pyong Hwa Kim

Dissertations

Cyanobacteria are photosynthetic organisms that are known to be responsible for oxygenating Earth’s early atmosphere. Having evolved to ensure optimal survival in the periodic light/dark cycle on this planet, their genetic codes are packed with various tools, including a sophisticated biological timekeeping system. Among the cyanobacteria is Synechococcus elongatus PCC 7942, the simplest clock-harboring organism with a powerful genetic tool that enabled the identification of its intricate timekeeping mechanism. The three central oscillator proteins—KaiA, KaiB, and KaiC—drive the 24 h cyclic gene expression rhythm of cyanobacteria, and the "ticking" of the oscillator can be reconstituted inside a test tube just …

Component Causes Of Infectious Bovine Keratoconjunctivitis—Non-Moraxella Organisms In The Epidemiology Of Infectious Bovine Keratoconjunctivitis, John Dustin Loy, Kristin A. Clothier, Gabriele Maier

School of Veterinary and Biomedical Sciences: Faculty Publications

• Non-Moraxella organisms are associated with infectious bovine keratoconjunctivitis (IBK).

• Mycoplasma bovoculi can cause conjunctivitis and has a potential role in IBK pathogenesis.

• Other Non-Mycoplasma agents can cause disease that resembles IBK but is clinically different.

• Genomics and molecular technology are advancing research in this area.

• Classification and determination of pathogenesis potential of these organisms may be better understood through metagenomics and whole genome sequencing.

Analysis Of Symptom Expressions And Transmission Rates Caused By The Plant Pathogen Phytophthora Ramorum On Native Chaparral Plants From The Genus Arctostaphylos, Bharati Gaonker

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Phytophthora ramorum is the causal agent of Sudden Oak death (SOD), ramorum dieback and ramorum leaf blight which affect both forest environments and nurseries. This oomycete pathogen has had a huge economic impact on the nursery and lumber industry. Forests in California have experienced substantial mortality of oaks affecting the forest dynamics and diversity. Our research investigates four native species and two ornamental cultivars of plants, which belong to the genus Arctostaphylos (manzanita) and are considered to be new hosts for P. ramorum in the chaparral ecosystem of California. Symptom expression and transmission rates were analyzed on Arctostaphylos glauca, …

Creating A Protein Chimera To Study Regulation Of Muscle Diversity, Shannon Scarboro

Symposium of Student Scholars

Creating a protein chimera to study regulation of muscle diversity.

Body muscles are made of many individual super-cells, called muscle fibers, that have distinct properties and determine every individual’s strength and endurance. Initially all muscle fibers have identical characteristics, but become differentiated into specific types in adults. The mechanism of such transition is not well understood, despite its obvious importance for shaping human physicality.

Remarkable conservation of the muscle tissue enables us to use fruit flies to study the mechanisms of muscle fiber diversity. We hypothesized that the transcription factor Mef2 acts as a molecular switch that activates structural genes …

Identifying The Cell Composition And Clonal Diversity Of Supratentorial Ependymoma Using Single Cell Rna-Sequencing, James He

Honors Scholar Theses

Ependymoma is a primary solid tumor of the central nervous system. Supratentorial ependymoma (ST-EPN), a subtype of ependymomas, is driven by an oncogenic fusion between the ZFTA and RELA genes in 70% of cases. We introduced this fusion into neural progenitor cells of mice embryos via in utero electroporation of a non-viral binary piggyBac transposon system containing ZFTA-RELA. From preliminary data in the LoTurco lab, inducing the expression of ZFTA-RELA into different neural progenitor cells produces tumors of varying lethality and cellular composition. To define the cellular composition and subclonal diversity of ST-EPN tumors, we used single cell RNA-sequencing …

Search For Palladin, An Actin-Associated Protein, In Pig Retinal Pigmented Epithelium And Its Role In Epithelial-Mesenchymal Transition, Katrina Powell

Undergraduate Theses

This study investigates the expression of Palladin, a phosphoprotein product of the PALLD gene, in the retinal pigmented epithelium (RPE). Palladin is an actin cross-linking protein and plays a role in cell adhesion and motility. Published reports have demonstrated that a down regulation of Palladin in colon cancer cells results in a reorganization of the actin cytoskeleton, causing the cells to lose their typical shape, become proliferative and migratory. This process is otherwise known as epithelial-mesenchymal transition (EMT). A similar EMT phenomenon is observed when the RPE is exposed to the vitreous humor in patients with proliferative vitreoretinopathy (PVR). In …

Role Of Endocytic Machinery Regulators In Egfr Traffic And Viral Entry, Insha Mushtaq

Theses & Dissertations

STUDY 1: Role of endocytic regulator EHD1 and its binding partner RUSC2 in EGFR traffic

Abstract

Epidermal growth factor receptor (EGFR) is a prototype receptor tyrosine kinase and an oncoprotein in many solid tumors. Cell surface display of EGFR is essential for cellular responses to its ligands. While post activation endocytic trafficking of EGFR has been well elucidated, little is known about mechanisms of basal/pre-activation surface display of EGFR. Here, we identify a novel role of the endocytic regulator EHD1 and a potential EHD1 partner, RUSC2, in cell surface display of EGFR. EHD1 and RUSC2 colocalize with EGFR in vesicular/tubular …

Identification Of The E3 Ligase That Directs The Degradation Of Proteins That Control Cell Fate Decisions In Yeast, Prasanna Tati, Stephen D Willis, Katrina F. Cooper

Rowan-Virtua Research Day

The ubiquitin–proteasome system (UPS) and autophagy pathways are distinct, highly conserved proteolytic systems that play important roles in maintaining cellular homeostasis in response to environmental cues [1]. The goal of this project is to identify the E3 ligase that mediates the degradation of cyclin C following nitrogen starvation in yeast using quantitative Western blot analysis of cyclin C-myc following nitrogen starvation in mutants of known Ubc4/5 interacting E3 ligases. No potential E3 ligases were identified as stable after 4 hours of nitrogen starvation, suggesting redundancy in function.

Mitochondrial Distribution Of Glycine Receptors In Motor Neuron Cell Lines, Katsiaryna Milashevich

Student Theses and Dissertations

Although non-essential, glycine plays an important role in major metabolic reactions and is most known for its anti-inflammatory effects. An accumulation of contemporary research has shown that glycine is able to stabilize membrane potential using glycine receptors at the cellular level and to protect mitochondrial function directly, whether it is from inflammation, heavy metal poisoning, or ischemia-induced neuroinflammation. In this research, the existence of a hypothetical mitochondrial glycine receptor is examined. Immunofluorescence imaging was used to examine the presence of the glycine receptor subunits alpha 1 and alpha 2 in both non- differentiated and differentiated neuroblastoma cell lines. The preliminary …

Cyclin C Determines Cell Fate In Response To Oxidative Stress And Proteasome Inhibition, David C. Stieg

Graduate School of Biomedical Sciences Theses and Dissertations

In response to various sources of cellular stress, the coordination of intracellular events is necessary to elicit the appropriate molecular response. In particular, the reprogramming of gene expression by stress-specific transcription factors drives the activation of signaling pathways, triggering either cell survival or regulated cell death pathways. The Cdk8 kinase module (CKM) is a highly conserved transcriptional regulatory complex with a role in this decision. The CKM is composed of Cdk8, its activating partner cyclin C, and two scaffold proteins, Med12 and Med13. The CKM is a detachable subunit of the Mediator complex, which interacts with RNA polymerase II to …

The Role Of Med31 And Med12 In Directing Adipogenesis Of Human Adult-Derived Mesenchymal Stem Cells, Joseph Straub

Doctoral Dissertations

Selective gene expression is crucial in maintaining the self-renewing and multipotent properties of stem cells. Mediator is a large, evolutionarily conserved, multisubunit protein complex that modulates gene expression by relaying signals from cell type-specific transcription factors to RNA polymerase II. In humans, this complex consists of 30 subunits arranged in four modules: head, middle, tail, and kinase. In our introduction, we show the state of the field of Mediator study with a focus on the critical kinase module. In the following chapters, we used siRNA knockdowns to investigate the roles of the highly-conserved core subunit MED31 and the kinase module …

Component Causes Of Infectious Bovine Keratoconjunctivitis - The Role Of Moraxella Species In The Epidemiology Of Infectious Bovine Keratoconjunctivitis, John Dustin Loy, Matthew Hille, Gabriele Maier, Michael L. Clawson

School of Veterinary and Biomedical Sciences: Faculty Publications

Moraxella bovis can cause infectious bovine keratoconjunctivitis (IBK).

The role of M bovoculi in IBK is not fully understood.

M bovis and M bovoculi appear to undergo genetic recombination with each other or other members of the Moraxellaceae.

Recombination complicates their classification and potential role(s) in IBK pathogenesis.

MALDI-TOF MS is used to identify M bovis, 2 major strains or genotypes of M bovoculi, M ovis, and other members of the Moraxellaceae.

Classification and determination of pathogenesis potential within Moraxella species may be better understood through whole genome sequencing.

College Of Natural Sciences Newsletter, May 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 5.

Page 1 Dean's Message
Page 2 - 3 Awards & Recognition
Page 4 Research Spotlight: Dr. Xiaoyang Zhang
Page 5 Upcoming Retirements
Page 6 - 7 Geography Alumni Social, Recent Media Coverage
Page 8 Open PRAIRIE Data
Page 9 - 11 Spring 2021 Dean's List and Academic Recognitions

Molecular Characterization Of Galectin From Amblyomma Americanum In Context Of Α-Gal Syndrome, Sumar Beauti

Honors Theses

The lone star tick Amblyomma americanum is a vector of various disease-causing pathogens and tick-borne alpha-gal syndrome (AGS) with rapidly expanding populations in the south- and northeast regions of the United States. This study aimed to molecularly characterize galectin and determine its involvement in galactose-α-1,3-galactose (α-gal) synthesis, transport, reproductive fitness, and microbial homeostasis in this tick. The lone star tick galectin possesses two conserved carbohydrate recognition domains and shares homology with other Ixodid tick galectins. Time and tissue-dependent expression data shows that galectin is constantly expressed in salivary glands, midgut, and ovary tissues. An RNA interference approach was used to …

Investigating A Novel Function For Phosphoserine Aminotransferase 1 (Psat1) In Epidermal Growth Factor Receptor (Egfr)-Mediated Lung Tumorigenesis., Rumeysa Biyik-Sit

Electronic Theses and Dissertations

Phosphoserine aminotransferase 1 (PSAT1) catalyzes the second enzymatic step within the serine synthetic pathway (SSP) and its expression is elevated in numerous human cancers, including non-small cell lung cancer (NSCLC). Epidermal growth factor receptor (EGFR) mutant NSCLC is characterized by activating mutations within its tyrosine kinase domain and accounts for 17% of lung adenocarcinomas. Although elevated SSP activity has been observed in EGFR-mutant lung cancer cells, the involvement of PSAT1 in EGFR-mediated oncogenesis is still unclear. Here, we explore a putative non-canonical function for PSAT1 using biochemical approaches to elucidate unknown interacting proteins and genomic RNA-seq profiling to identify cellular …

The Biochemical Characterization Of Aza197 And A Ras Related Protein Cdc42, Alix Montoya-Beltran

Graduate Theses and Dissertations

Eukaryotic cells contain an extensive amount of GTP/GDP binding proteins. Proteins known as Ras GTPase primary function as a binary switch, where they cycle from an on and off state when GTP or GDP are bound, respectively. They are known to play a critical role in many cellular functions where a dysregulation could potentially lead to oncogenic behavior or other malignancies. In our laboratory, our focus is the study of a Ras related protein Cell division control 42 homolog (Cdc42) which belongs to the Rho subfamily. Cdc42 plays a critical role in many biological signaling processes; therefore, its uncontrol gene …

Investigations Into The Cellular Target Of 4-Trifluoromethoxy Chalcone Via Darts Method, Jordan Stacy

Undergraduate Theses

Cellular drug target discovery is an important step in any drugs journey from bench to bedside. This is true for our lab's molecule of interest, the Chalcone. The Chalcone molecule and its derivatives have been identified as small, plant-derived secondary metabolites that, when interacting with human cancer cell lines, trigger apoptotic pathways leading to varying levels of cell death. One derivative, 4-Trifluoromethoxy Chalcone (4TFM), was identified through screenings as inducing the highest death rate in A549 cancer cells, in conjunction with having the lowest IC50, making it a good candidate to use in searching for the currently unknown cellular target …