Molecular Biology Commons^™

Localization And Functional Analysis Of Raby Gtpase In Dictyostelium Discoideum, Lisa Rene' Williams

Theses and Dissertations

Localization and functional analysis of the small monomeric GTPase RabY in the unicellular amoeba Dictyostelium discoideum was investigated. I constructed 2 cell lines that overexpressed GFP tagged RabY (OE) and expressed a dominant negative form of GFP-RabY (T25N). Sequence analysis revealed homology to Rab1a genes in several organisms (ER/Golgi localized in humans). Therefore, I hypothesize the GFP tagged RabY protein is within the Golgi and/or Endoplasmic Reticulum. Analysis using immunofluorescence, quantitative and other techniques revealed GFP-RabY (OE) is localized at the Dictyostelium Golgi apparatus and within the endosomes. However, the GFP-RabY (T25N) protein was found to be dispersed intracellularly. Thus, …

Conserved Glycine Residues Control Transient Helicity And Disorder In The Cold Regulated Protein, Cor15a, Oluwakemi Sowemimo

USF Tampa Graduate Theses and Dissertations

COR15A is a cold regulated disordered protein from Arabidopsis thaliana that contributes to freezing tolerance in plants by protecting membranes. It belongs to the (LEA) Late Embryogenesis Abundant group of proteins that accumulate during the later stage of seed development and are expressed in various parts of the plant. During freezing-induced cellular dehydration, COR15A transitions from a disordered structure to a mostly α-helical structure that binds and stabilizes chloroplast membranes when cells dehydrate due to freezing. We hypothesize that increasing the transient α-helicity of COR15A under normal conditions will increase its ability to bind and protect chloroplast membranes when cells …

Biochemical And Proteomic Approaches To Determine The Impact Level Of Each Step Of The Supply Chain On Tomato Fruit Quality, Robert T. Madden

USF Tampa Graduate Theses and Dissertations

Fresh fruits and vegetables (FFVs) are the most frequently wasted foods because of their perishability and handling requirements. However, there is a lack of information on how much each step of the supply chain impacts FFVs quality, particularly on tomatoes, and what measures need to be taken for an immediate and effective impact on waste reduction. There is also no information on how the supply chain affects the proteome of the tomato and what proteins are differentially regulated by the most impactful steps of the supply chain. The objectives of the work presented on this thesis were to evaluate the …

Further Understanding Of Bacteriophages That Infect The Bacterial Family Enterobacteriaceae, Paul Flake

Undergraduate Honors Theses

Despite the eclectic nature of bacteriophage genomes, nucleotide comparison is an effective method for grouping phages into cluster and subcluster classifications. This process is facilitated by making preliminary cluster assignations based on the identity of the major capsid protein. As more phages continue to be sequenced and integrated into cluster/subcluster groupings, adjustments may need to be made to the genomic similarity percentages that have previously defined cluster/subcluster classifications. Implementing proteomic comparison in addition to nucleotide homology may provide added clarity to this process. Protein conservation and diversity among lytic phages that infect the bacterial family Enterobacteriaceae is discussed and the …

The Drosophila Neuroblasts: A Model System For Human Ribosomopathies, Sonu Shrestha Baral

LSU Doctoral Dissertations

This dissertation describes the use of Drosophila neuroblasts (NBs) to model human ribosomopathies; the overall goal is to understand why specific stem cell and progenitor cell populations are the primary targets in nucleolar stress as seen in the ribosomopathies. Chapter 1 provides an overview of relevant literature. Chapter 2 describes nucleolar stress in Drosophila neuroblasts as a model for human ribosomopathies. For this, we induce nucleolar stress by using the UAS-GAL4 system to express RNAi that depletes Nopp140 transcripts, and we also employ homozygous, CRISPR-Cas9-generated Nopp140 gene disruptions with a systemic null phenotype (Nopp140-/-). Embryonic lethality was observed …

Identification And Characterization Of Novel Transporters Involved In The Co2 Concentrating Mechanism Of Chlamydomonas Reinhardtii, Ananya Mukherjee

LSU Doctoral Dissertations

The green alga Chlamydomonas reinhardtii possesses a CO₂ concentrating mechanism (CCM) which helps in successful acclimation to low CO₂ conditions. One of the main aspects of the CCM is bringing in inorganic carbon (Ci) into the cell as bicarbonate using Ci transporters. Current models of the CCM postulate that a series of ion transporters bring HCO₃^- from outside the cell to the thylakoid lumen where the carbonic anhydrase, CAH3, dehydrates accumulated HCO₃^- to CO₂, raising the CO₂ concentration for Rubisco. Previously, HCO₃^- transporters have been identified at both the …

Integrated Molecular Characterization Of Lung Adenocarcinoma With Implications For Immunotherapy, Nicholas T. Gimbrone

USF Tampa Graduate Theses and Dissertations

This dissertation covers a variety of the genetic and molecular abnormalities of lung adenocarcinoma with an emphasis on STK11 loss and its implications on immunotherapy response. Given that lung cancer is the leading cancer killer, novel therapies are in great demand. In particular, immunotherapy has shown some of the most promise in the last decade but remains limited due to nearly 80% of patients not significantly responding. This dissertation aims to molecularly characterize lung adenocarcinoma while attempting to explain the reason why patients with STK11 loss do not respond to immunotherapy.

In the first chapter we discuss the relationship between …

Mechanisms To Regulate Genes Encoding Clinically Relevant Multidrug Transporters At The Crossroads Of Antibiotic Resistance And Oxidative Stress Detection, Afsana Sabrin

LSU Doctoral Dissertations

Multiple Antibiotic Resistance Regulators (MarRs) are DNA binding proteins involved in bacterial survival and pathogenesis. My PhD dissertation focuses on a MarR homolog, OstR, which regulates genes encoding major multidrug transporters, a resistance-nodulation-division (RND) and an E. coli multidrug resistance B (EmrB) efflux pump homolog in Burkholderia thailandensis. The ostR gene is divergently oriented from genes encoding a hypothetical protein (Hyp) and an RND transporter and adjacent to a gene encoding an EmrB transporter. OstR binds to the promoters of each gene (K_d = 64.9 ± 8.0 nM, K_d = 126.1 ± 10.9 nM and K …

High Expression Of Osm And Il-6 Are Associated With Decreased Breast Cancer Survival: Synergistic Induction Of Il-6 Secretion By Osm And Il-1Β, Ken Tawara, Hannah Scott, Jacqueline Emathinger, Cody Wolf, Dollie Lajoie, Danielle Hedeen, Laura Bond, Cheryl Jorcyk

Biomedical Research Institute Publications and Presentations

Chronic inflammation has been recognized as a risk factor for the development and maintenance of malignant disease. Cytokines such as interleukin-6 (IL-6), oncostatin M (OSM), and interleukin-1 beta (IL-1β) promote the development of both acute and chronic inflammation while promoting in vitro metrics of breast cancer metastasis. However, anti-IL-6 and anti-IL-1β therapeutics have not yielded significant results against solid tumors in clinical trials. Here we show that these three cytokines are interrelated in expression. Using the Curtis TCGA™ dataset, we have determined that there is a correlation between expression levels of OSM, IL-6, and IL-1β and reduced breast cancer patient …

Living, Learning, And Leading At Linfield College, Kelsey Bruce

Student Engagement Posters

Kelsey Bruce discusses student engagement at Linfield College with regard to leadership through student/faculty collaborative research with Dr. Megan Bestwick, speech and debate, and the Linfield Residence Life team.

Large Scale Dynamical Model Of Macrophage/Hiv Interactions, Matthew M. Froid

UNO Student Research and Creative Activity Fair

Properties emerge from the dynamics of large-scale molecular networks that are not discernible at the individual gene or protein level. Mathematical models - such as probabilistic Boolean networks - of molecular systems offer a deeper insight into how these emergent properties arise. Here, we introduce a non-linear, deterministic Boolean model of protein, gene, and chemical interactions in human macrophage cells during HIV infection. Our model is composed of 713 nodes with 1583 interactions between nodes and is responsive to 38 different inputs including signaling molecules, bacteria, viruses, and HIV viral particles. Additionally, the model accurately simulates the dynamics of over …

Pas Kinase And Tor, Controllers Of Cell Growth And Proliferation, Brooke Jasmyn Cozzens

Theses and Dissertations

Nutrient sensing kinases lie at the heart of cellular health and homeostasis, allowing cells to quickly adapt to changing environments. Target of Rapamycin (TOR) and PAS kinase (PASK, or PASKIN) are two such nutrient kinases, conserved from yeast to man. In yeast, these kinases each have paralogs. The two TOR paralogs in yeast mimic the mammalian TORC1 and TORC2 complexes, except both Tor1 and Tor2 may contribute to TORC1 or TORC2 function. The two PAS kinase paralogs are paired with the TOR paralogs, meaning that both Psk1 and Psk2 regulate TORC1, while Psk2 suppresses a temperature-sensitive allele of Tor2. Herein …

Ribosomally Synthesized And Post-Translationally Modified Peptides As Potential Scaffolds For Peptide Engineering, Devan Bursey

Theses and Dissertations

Peptides are small proteins that are crucial in many biological pathways such as antimicrobial defense, hormone signaling, and virulence. They often exhibit tight specificity for their targets and therefore have great therapeutic potential. Many peptide-based therapeutics are currently available, and the demand for this type of drug is expected to continue to increase. In order to satisfy the growing demand for peptide-based therapeutics, new engineering approaches to generate novel peptides should be developed. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of peptides that have the potential to be effective scaffolds for in vivo peptide engineering projects. These …

Interactions Between The Organellar Pol1a, Pol1b, And Twinkle Dna Replication Proteins And Their Role In Plant Organelle Dna Replication, Stewart Anthony Morley

Theses and Dissertations

Plants maintain organelle genomes that are descended from ancient microbes. Ages ago, these ancient microbes were engulfed by larger cells, beginning a process of co-evolution we now call the endo-symbiotic theory. Over time, DNA from the engulfed microbe was transferred to the genome of the larger engulfing cell, eventually losing the ability to be free-living, and establishing a permanent residency in the larger cell. Similarly, the larger cell came to rely so much on the microbe it had engulfed, that it too lost its ability to survive without it. Thus, mitochondria and plastids were born. Nearly all multicellular eukaryotes possess …

Arabinose Substitution Effect On Xylan Rigidity And Self-Aggregation, Utsab Shrestha, Sydney Smith, Sai Venkatesh Pingali, Hui Yang, Mai Zahran, Llyod Breunig, Liza Wilson, Daniel Cosgrove, Hugh O'Neill, Loukas Petridis

Publications and Research

Substituted xylans play an important role in the structure and mechanics of the primary cell wall of plants. Arabinoxylans (AX) consist of a xylose backbone substituted with arabinose, while glucuronoarabinoxylans (GAX) also contain glucuronic acid substitutions and ferulic acid esters on some of the arabinoses. We provide a molecular-level description on the dependence of xylan conformational, selfaggregation properties and binding to cellulose on the degree of arabinose substitution. Molecular dynamics simulations reveal fully solubilized xylans with a low degree of arabinose substitution (lsAX) to be stiffer than their highly substituted (hsAX) counterparts. Small-angle neutron scattering experiments indicate that both wild-type …

Rna Sequencing, Selection Of Reference Genes And Demonstration Of Feeding Rnai In Thrips Tabaci (Lind.) (Thysanoptera: Thripidae), Satnam Singh, Mridula Gupta, Suneet Pandher, Gurmeet Kaur, Neha Goel, Pankaj Rathore, Subba Reddy Palli

Entomology Faculty Publications

Background: Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this insect, RNA was sequenced; de novo transcriptome assembly and analysis were performed. The RNAseq data was used to identify reference and RNAi pathway genes in this insect. Additionally, feeding RNAi was demonstrated in T. tabaci for the first time.

Results: From the assembled transcriptome, 27,836 coding sequence (CDS) with an average size of 1236 bp per CDS were identified. About 85.4% of …

Evaluation Of Volatile Metabolites Emitted In-Vivo From Cold-Hardy Grapes During Ripening Using Spme And Gc-Ms: A Proof-Of-Concept, Somchai Rice, Devin L. Maurer, Anne Fennell, Murlidhar Dharmadhikari, Jacek A. Koziel

Agronomy, Horticulture and Plant Science Faculty Publications

In this research, we propose a novel concept for a non-destructive evaluation of volatiles emitted from ripening grapes using solid-phase microextraction (SPME). This concept is novel to both the traditional vinifera grapes and the cold-hardy cultivars. Our sample models are cold-hardy varieties in the upper Midwest for which many of the basic multiyear grape flavor and wine style data is needed. Non-destructive sampling included a use of polyvinyl fluoride (PVF) chambers temporarily enclosing and concentrating volatiles emitted by a whole cluster of grapes on a vine and a modified 2 mL glass vial for a vacuum-assisted sampling of volatiles from …

Lncegfl7os Regulates Human Angiogenesis By Interacting With Max At The Egfl7/Mir-126 Locus, Quinbo Zhou, Chastain Anderson, Zhan-Peng Huang, Jakub Hanus, Wensheng Zhang, Yu Han

Faculty and Staff Publications

In an effort to identify human endothelial cell (EC)-enriched lncRNAs,~500 lncRNAswere shown to be highly restricted in primary human ECs. Among them,lncEGFL7OS, located inthe opposite strand of theEGFL7/miR-126gene, is regulated by ETS factors through abidirectional promoter in ECs. It is enriched in highly vascularized human tissues, and upregulatedin the hearts of dilated cardiomyopathy patients. LncEGFL7OS silencing impairs angiogenesis asshown by EC/fibroblast co-culture, in vitro/in vivo and ex vivo human choroid sproutingangiogenesis assays, while lncEGFL7OS overexpression has the opposite function. Mechanistically,lncEGFL7OS is required for MAPK and AKT pathway activation by regulating EGFL7/miR-126expression. MAX protein was identified as a lncEGFL7OS-interacting protein that …

Ck2 Negatively Regulates 5-Ht4 Receptor Signaling In The Prefrontal Cortex And Mediates Depression-Like Behaviors, Julia Castello Saval

Dissertations, Theses, and Capstone Projects

The serotonergic system has been the major candidate in the pathophysiology of mood related disorders such as anxiety and major depressive disorder (MDD). Unfortunately, current antidepressant drugs are ineffective in 50% of the population and require chronic administration for a period of 3-6 weeks before the onset of therapeutic response. 5-HT4 receptor (5-HT₄R) agonists have emerged as potential candidates for fast antidepressant action, since an antidepressant response can be achieved after 3 days of pharmacological administration in rodents.

This dissertation aims to investigate the role of casein kinase 2 (CK2) as a regulator of 5-HT₄R expression …

Itch Nuclear Translocation And H1.2 Polyubiquitination Negatively Regulate The Dna Damage Response, Lufen Chang, Lei Shen, Hu Zhou, Jing Gao, Hangyi Pan, Li Zheng, Brian Armstrong, Yang Peng, Guang Peng, Binhua P. Zhou, Steven T. Rosen, Binghui Shen

Molecular and Cellular Biochemistry Faculty Publications

The downregulation of the DNA damage response (DDR) enables aggressive tumors to achieve uncontrolled proliferation against replication stress, but the mechanisms underlying this process in tumors are relatively complex. Here, we demonstrate a mechanism through which a distinct E3 ubiquitin ligase, ITCH, modulates DDR machinery in triple-negative breast cancer (TNBC). We found that expression of a nuclear form of ITCH was significantly increased in human TNBC cell lines and tumor specimens. Phosphorylation of ITCH at Ser257 by AKT led to the nuclear localization of ITCH and ubiquitination of H1.2. The ITCH-mediated polyubiquitination of H1.2 suppressed RNF8/RNF168-dependent formation of 53BP1 foci, …