Biochemistry, Biophysics, and Structural Biology Commons^™

Adenovirus Entry From The Apical Surface Of Polarized Epithelia Is Facilitated By The Host Innate Immune Response, Poornima L.N. Kotha, Priyanka Sharma, Abimbola O. Kolawole, Ran Yan, Mahmoud Alghamri, Trisha L. Brockman, Julian Gomez-Cambronero, Julian Cambronero

Biological Sciences Faculty Publications

Prevention of viral-induced respiratory disease begins with an understanding of the factors that increase or decrease susceptibility to viral infection. The primary receptor for most adenoviruses is the coxsackievirus and adenovirus receptor (CAR), a cell-cell adhesion protein normally localized at the basolateral surface of polarized epithelia and involved in neutrophil transepithelial migration. Recently, an alternate isoform of CAR, CAREx8, has been identified at the apical surface of polarized airway epithelia and is implicated in viral infection from the apical surface. We hypothesized that the endogenous role of CAR^Ex8 may be to facilitate host innate immunity. We show that IL-8, …

The Fragile Fiber1 Kinesin Contributes To Cortical Microtubule-Mediated Trafficking Of Cell Wall Components, Chuanmei Zhu, Anindya Ganguly, Tobias I. Baskin, Daniel D. Mcclosky, Charles T. Anderson, Cliff Foster, Kristoffer A. Meunier, Ruth Okamoto, Howard Berg, Ram Dixit

Biology Faculty Research

The cell wall consists of cellulose microfibrils embedded within a matrix of hemicellulose and pectin. Cellulose microfibrils are synthesized at the plasma membrane, whereas matrix polysaccharides are synthesized in the Golgi apparatus and secreted. The trafficking of vesicles containing cell wall components is thought to depend on actin-myosin. Here, we implicate microtubules in this process through studies of the kinesin-4 family member, Fragile Fiber1 (FRA1). In an fra1-5 knockout mutant, the expansion rate of the inflorescence stem is halved compared with the wild type along with the thickness of both primary and secondary cell walls. Nevertheless, cell walls in fra1-5 …

Protein Sectors: Statistical Coupling Analysis Versus Conservation, Tiberiu Teşileanu, Lucy J. Colwell, Stanislas Leibler

Publications and Research

Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors”. The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be …

A Functional Chlorophyll Biosynthesis Pathway Identified In The Kleptoplastic Sea Slug, Elysia Chlorotica, Julie A. Schwartz

USF Tampa Graduate Theses and Dissertations

The sacoglossan sea slug, Elysia chlorotica, feeds upon and sequesters plastids from the heterokont alga, Vaucheria litorea, and maintains the metabolically active organelles for up to nine months under starvation conditions while utilizing the photosynthate to survive and reproduce. The photosynthetic pigment, chlorophyll a (Chla), is found in all oxygenic photosynthetic organisms and is responsible for capturing photons of light and converting them into chemical energy. Chlorophyll and its associated proteins involved in the light capturing process are subject to photo oxidative damage and must be continually replaced for ongoing photosynthesis to continue; however, genes encoding these proteins are present …

Functional Characterization Of The Plant 15-Cis-Zeta-Carotene Isomerase Z-Iso, Jesus Alonso Beltran Zambrano

Dissertations, Theses, and Capstone Projects

Vitamin A deficiency is a widespread health issue in the tropics. To solve this issue, efforts are underway to increase provitamin A carotenoids such as β-carotene in staple crops which can be achieved by breeding, metabolic engineering or a combination of both approaches. However, rational strategies to improve carotenoid content in crops require sufficient knowledge of pathway regulation. Therefore, to better understand how plants synthesize provitamin A and to guide metabolic engineering strategies in crops such as maize, the functional characterization of the new ζ-carotene isomerase (Z-ISO) is of significant importance.

Z-ISO was recently discovered in maize and Arabidopsis (Chen …

2015 Oklahoma Research Day Full Program, Northeastern State University

Oklahoma Research Day Abstracts

This document contains all abstracts from the 2015 Oklahoma Research Day held at Northeastern State University.

Regulation Of Synaptogenesis By The Mirna Pathway And Fmr/P Bodies, Jacqueline Rochelle Furlong

Electronic Theses and Dissertations

Post-transcriptional regulation of mRNA is facilitated by different mechanisms, such as microRNA (miRNA) induced gene silencing or fragile X mental retardation protein (FMRP) mediated repression either independent of or acting through cytoplasmic RNA Processing bodies (P bodies). DPTP99A, Lar, and Wg have known functions during synaptogenesis and may be targets of miR-8. Here, we provide evidence that miR-8 regulates DPTP99A in vitro. Non-endogenous miR-8 expressed using an UAS driver regulates Lar. Endogenous miR-8 may regulate DPTP99A in vivo. Here we show that FMRP is capable of colocalizing with the P body components: DCP1, HPat, and Me31B, but not …

2015 Annual Report Department Of Biological Sciences, Ronald L. Frank, Chen Hou, Yue-Wern Huang, Adam R. Martin, Melanie R. Mormile, Dev Niyogi, Julie A. Semon, Katie S. Shannon, Matthew S. Thimgan, David J. Westenberg, Terry Wilson

Biological Sciences Faculty Research & Creative Works

No abstract provided.

A Protective Role Of Autophagy In A Drosophila Model Of Friedreich's Ataxia (Frda), Luan Wang

Wayne State University Dissertations

Friedreich’s ataxia (FRDA) is an inherited autosomal recessive neurodegenerative disease. It affects 1 in every 50,000 people in central Europe and North America. FRDA is caused by deficiency of Frataxin, an essential mitochondrial iron chaperone protein, and the associated oxidative stress damages. Autophagy, a housekeeping process responsible for the bulk degradation and turnover of long half-life proteins and organelles, is featured by the formation of double-membrane vacuoles and lysosomal degradation. Previous researches indicate that Danon’s disease, the inherited neural disorder disease that shares similar symptoms with FRDA, is due to the malfunction of autophagy. Based on this, we raise the …

Electroporation Of Mammalian Cells By Nanosecond Electric Field Oscillations And It's Inhibition By The Electric Field Reversal, Elena C. Gianulis, Jimo Lee, Chunqi Jiang, Shu Xiao, Bennet L. Ibey, Andrei G. Pakhomov

Bioelectrics Publications

The present study compared electroporation efficiency of bipolar and unipolar nanosecond electric field oscillations (NEFO). Bipolar NEFO was a damped sine wave with 140 ns first phase duration at 50% height; the peak amplitude of phases 2-4 decreased to 35%, 12%, and 7% of the first phase. This waveform was rectified to produce unipolar NEFO by cutting off phases 2 and 4. Membrane permeabilization was quantified in CHO and GH₃ cells by uptake of a membrane integrity marker dye YO-PRO-1 (YP) and by the membrane conductance increase measured by patch clamp. For treatments with 1-20 unipolar NEFO, at 9.6-24 …

Mysteries Of The Trypanosomatid Maxicircles: Characterization Of The Maxicircle Genomes And The Evolution Of Rna Editing In The Order Kinetoplastida, Preethi Ranganathan Iyengar

Theses and Dissertations

The trypanosomatid protists belonging to Order Kinetoplastida are some of the most successful parasites ever known to mankind. Their extreme physiological diversity and adaptability to different environmental conditions and host systems make them some of the most widespread parasites, causing deadly diseases in humans and other vertebrates.

This project focuses on their unique mitochondrion, called the kinetoplast, and more specifically involves the characterization of a part of their mitochondrial DNA (also called kinetoplast DNA or kDNA), the maxicircles, which are functional homologs of eukaryotic mitochondrial DNA in the kinetoplastid protists. We have sequenced and characterized the maxicircle genomes of 20 …

The Role Of Rnai In Downregulation Of Physcomitrella Patens Defense Genes And The Preliminary Steps Of Peg Mediated Transformation Of Mosses, Adam Beswick

Undergraduate Honors Thesis Collection

When attacked by a pathogen, the moss Physcomitrella patens will undergo both a hypersensitive response (HR) as well as a systematic acquired resistance (SAR) response. The SAR response turns on genes that ready the plant for future pathogen attacks. The hormone jasmonic acid (JA) is one of the products of SAR response in P. patens. In this study interference RNA (RNAi) was used to decrease gene expression of the allene oxide cyclase (ACe) gene, a key gene in the production pathway of JA. Using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), RNAi was found to significantly lower ACC gene levels …

Rna Aptamer Mediated Manipulation Of The 70 Kilodalton Heat Shock Protein Chaperone Machinery, Deepak Thirunavukarasu

Legacy Theses & Dissertations (2009 - 2024)

Protein quality control involves refolding of damaged proteins and facilitating degradation of irreparable proteins. Understanding the protein quality control mechanism is critical, since defects in it has been implicated in a number of age-related diseases like neurodegenerative diseases and also in cancer. A vast network of molecular chaperones and proteolytic systems collaborate to maintain protein quality control. The 70 kilodalton Heat shock protein (Hsp70) is a highly conserved and ubiquitous chaperone, which interacts with a variety of protein substrates including newly synthesized polypeptides, unfolded, partially misfolded and native proteins to maintain protein quality control. Hsp70 chaperone function is coupled to …

Rna Aptamers For Molecular Chaperones Hsp27 And Hsp90, Sathishkumar Kumar Munusamy

Legacy Theses & Dissertations (2009 - 2024)

Hsp90 and Hsp27 are members of the heat shock protein family of chaperones that perform multiple roles in cellular maintenance through protein folding and inhibition of apoptosis. They are abundantly expressed in cells and are over-expressed during conditions of stress. Hsp90 requires ATP for its chaperone function while Hsp27 self-associates into higher order oligomers enclosing its substrate. Their ability to interact with other proteins or with themselves lies at the heart of their mechanisms. The specific consequences of each of their interactions on global cellular health have not yet been fully discovered. The sheer diversity of proteins that interact with …

Genome-Scale Analyses Of Transcription And Transcriptional Regulation In Bacteria, Devon Marie Fitzgerald

Legacy Theses & Dissertations (2009 - 2024)

The textbook model of bacterial transcription regulation posits that promoters occur immediately upstream of genes and that transcription factors (TFs) modulate transcription through promoter-proximal binding. However, the recent application of unbiased genome-wide approaches, such as ChIP-seq and RNA-seq, has revealed a much more complex picture, including TF binding and transcription initiation occurring in unexpected locations. This dissertation describes the use of deep sequencing-based approaches to evaluate the genome-wide binding of transcription-related proteins and identify locations of transcription initiation. I have assessed the genome-wide binding of three Escherichia coli TFs and an alternative σ factor. Additionally, I have analyzed genome-wide patterns …

Expression And Functional Analysis Of Lipids And Glycolipids From The Mammal-Dwelling Stages Of Trypanosoma Cruzi, Felipe Gazos Lopes

Open Access Theses & Dissertations

Trypanosoma cruzi is the causative agent of the life-threatening Chagas disease, in which increased platelet aggregation related to myocarditis is observed. Platelet-activating factor (PAF) is a potent intercellular lipid mediator and second messenger that exerts its activity through a PAF-specific receptor (PAFR). Previous data from our group suggested that T. cruzi synthesizes a phospholipid with PAF-like activity. The structure of T. cruzi PAF-like molecule, however, remains elusive. Here, we have purified and structurally characterized the putative T. cruzi PAF-like molecule by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). Our ESI-MS/MS data demonstrated that the T. cruzi PAF-like molecule is actually a lysophosphatidylcholine …

Cross-Talk Between The Tumor Suppressors Par-4 And P53, Tripti Shrestha Bhattarai

Theses and Dissertations--Toxicology and Cancer Biology

This work describes the fascinating interplay between two tumor suppressors Prostate apoptosis response-4 (Par-4) and p53. The guardian of the genome, p53, is frequently mutated in human cancers, and may contribute to therapeutic resistance. However, p53 is intact and functional in normal tissues, and we observed that specific activation of p53 in normal fibroblasts could induce apoptosis selectively in p53-deficient cancer cells. This paracrine apoptotic effect was executed by Par-4 secreted in response to p53 activation. Accordingly, activation of p53 in wild-type mice, but not in p53^-/- or Par-4^-/- mice, caused systemic elevation of Par-4 that induced apoptosis …

Drosophila Cyclin J And The Somatic Pirna Pathway Cooperate To Regulate Germline Stem Cells, Paul Michael Albosta

Wayne State University Dissertations

Cyclin J (CycJ) is a highly conserved cyclin that is uniquely expressed specifically in ovaries in Drosophila. Deletion of the genomic region containing CycJ and adjacent genes resulted in a genetic interaction with neighboring piRNA pathway gene, armitage (armi). Here I assessed oogenesis in CycJ null in the presence or absence of mutations in armi or other piRNA pathway genes. Although CycJ null flies had decreased egg laying and hatching rates, ovaries appeared normal indicating that CycJ is dispensable for oogenesis under normal conditions. Further double mutant analysis of CycJ and neighbor armi, as well as two other piRNA pathway …

Analyzing The Interactions Of Kdm5/Lid And Sin3 In Drosophila Melanogaster, Ambikai Gajan

Wayne State University Dissertations

SIN3, the scaffold protein of a histone modifying complex is conserved from yeast to mammals. Drosophila SIN3 associates with both a histone deactylase RPD3 and a histone demethylase dKDM5/LID. Immunopurification of dKDM5/LID verifies a previously observed interaction with SIN3 and RPD3. Furthermore, deficiency of dKDM5/LID phenocopies deficiency of SIN3 in many cellular and developmental processes. Knockdown of both Sin3A and lid hinder cell proliferation in Drosophila cultured cells and developing flies. Knockdown of these genes also results in a curved wing phenotype implicating a role in wing development. Analysis of underlying gene expression changes upon decreased expression of SIN3, dKDM5/LID …

Human Anatomy And Physiology Preparatory Course (1st Edition), Carlos Liachovitzky

Open Educational Resources

The overall purpose of this preparatory course textbook is to help students familiarize with some terms and some basic concepts they will find later in the Human Anatomy and Physiology I course.

The organization and functioning of the human organism generally is discussed in terms of different levels of increasing complexity, from the smallest building blocks to the entire body. This Anatomy and Physiology preparatory course covers the foundations on the chemical level, and a basic introduction to cellular level, organ level, and organ system levels. There is also an introduction to homeostasis at the beginning.

Genetically Based Low Oxygen Affinities Of Felid Hemoglobins: Lack Of Biochemical Adaptation To High-Altitude Hypoxia In The Snow Leopard, Jan E. Janecka, Simone S. E. Nielsen, Sidsel D. Andersen, Federico G. Hoffmann, Roy E. Weber, Trevor Anderson, Jay F. Storz, Angela Fago

School of Biological Sciences: Faculty Publications

Genetically based modifications of hemoglobin (Hb) function that increase blood–O₂ affinity are hallmarks of hypoxia adaptation in vertebrates. Among mammals, felid Hbs are unusual in that they have low intrinsic O₂ affinities and reduced sensitivities to the allosteric cofactor 2,3-diphosphoglycerate (DPG). This combination of features compromises the acclimatization capacity of blood–O2 affinity and has led to the hypothesis that felids have a restricted physiological niche breadth relative to other mammals. In seeming defiance of this conjecture, the snow leopard (Panthera uncia) has an extraordinarily broad elevational distribution and occurs at elevations above 6000 m in the Himalayas. Here, …

Modeling Atp-Binding Cassette G2 (Abcg2) Substrate Specificity, Raghav D. Acharya, Aurijit Sarkar, Glen E. Kellogg

Undergraduate Research Posters

How well can we predict efflux by ATP-binding cassette G2?

It is estimated that there will be about 1.6 million new cases of cancer and half a million cancer deaths in the US during 2015.ATP-binding cassette (ABC) efflux transporters such as ABCG2 are overexpressed in chemotherapy-resistant cancer cells. Anticancer drugs are prone to efflux by these transporters. Being able to identify drugs that are effluxed is of great interest in drug discovery.The current arsenal of methods used to detect efflux are not easily adaptable to high throughput formats and are limited in scope, making experimental analysis an expensive prospect. Hence, …

The Effects Of Hibernation On The Hemostatic Properties Of The American Bullfrog, Rana Catesbeiana, Kiana Cullinan

Honors Program Theses

It is known that hibernating animals display a drastic reduction in metabolic rate, accompanied by reduced heart rate and rate of blood flow through vessels. Sluggish blood flow increases the risk for developing clots, yet it has been observed that hibernators conclusively display elongated clotting times. This observed impairment may be caused by the decrease in body temperature, due to a negative impact on the functioning of the enzymes involved in coagulation. Some hibernating endotherms, or “warm-blooded” animals, employ biological mechanisms as preventative means to prevent clotting during hibernation, such as the down-regulation of certain clotting factors or the production …

Non-Destructive Dna Extraction Methods That Yield Dna Barcodes In Spiders, Reva Ann Bork

Honors Program Theses

DNA barcodes are short sequences of nucleotides that differ from species to species (Hebert et al., 2003; Hebert & Gregory, 2005). DNA barcoding is very important in helping to reconstruct phylogenetic trees and to confirm the identity of threatened or endangered species in the wild. Additionally, it has become increasingly popular in the food industry to test the accuracy of the food being sold in fast food chains (Wong and Hanner, 2008). For scientific purposes, nondestructive DNA extraction techniques need to be explored because they allow for preservation of the voucher specimen, which is particularly important for rare or extinct …

Editors' Note, Laura B. Regassa, Delena Gatch

Biology: Faculty Publications

Dear colleagues,

The International Journal for the Scholarship of Teaching & Learning is undergoing some major changes.

• The layout of the journal has been overhauled, giving it a look that better aligns with the quality of the content. As we continue to struggle with SoTL “counting” as scholarship at some institutions, it is important to package our work in a way that reinforces its value. We hope you enjoy the new look!

• Articles are being assigned DOI (digital object identifier) numbers. All articles, past and present, will be tagged and linked to metadata as indexing is completed over the next …

Constitutive Activity In Orphan G Protein Coupled Receptors, Adam Lee Martin

Doctoral Dissertations

"The goal of this research was to use a distal signaling pathway analysis to evaluate the extent of agonist independent constitutive signaling among orphan class-A G protein coupled receptors (GPCRs). These receptors translate extracellular signals via conformational change into intracellular activation of different G proteins and subsequent second messenger synthesis. These small molecules regulate cellular biochemistry, eventually leading to nuclear signaling that results in changes in gene expression. Some GPCRs are capable of signaling in the absence of an activating ligand, a phenomenon called constitutive activity that is inhibited via an "inverse-agonist". The use of cAMP dependent Luciferase expression is …

Functional Analysis Of The Ovarian Cancer Susceptibility Locus At 9p22.2 Reveals A Transcription Regulatory Network Mediated By Bnc2 In Ovarian Cells, Melissa Buckley

USF Tampa Graduate Theses and Dissertations

GWAS have identified several chromosomal loci associated with ovarian cancer risk. However, the mechanism underlying these associations remains elusive. We identify candidate functional Single Nucleotide Polymorphisms (SNPs) at the 9p22.2 ovarian cancer susceptibility locus, several of which map to transcriptional regulatory elements active in ovarian cells identified by FAIRE-seq (Formaldehyde assisted isolation of regulatory elements followed by sequencing) and ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) in relevant cell types. Reporter and electrophoretic mobility shift assays (EMSA) determined the extent to which candidate SNPs had allele specific effects. Chromosome conformation capture (3C) reveals a physical association between Basonuclin 2 (BNC2) and …

High-Throughput Screening Of Age-Related Changes In Caenorhabditis Elegans, Neil Copes

USF Tampa Graduate Theses and Dissertations

This project was developed to identify novel methods for high-throughput culturing and screening of C. elegans to investigate age-related metabolic changes and to survey the proteomic and metabolomic factors associated with age-related changes. To accomplish these goals we developed a novel way to grow C. elegans in liquid culture in 96-well microplates for several weeks without suffering significant fluid loss due to evaporation and without needing to shake or unseal the plates for aeration. We also developed methods for assaying the total volume of live C. elegans in microplate cultures using a fluorescence microplate reader and for performing RNAi experiments …

The Effects Of Supplemented Metabolites On Lifespan And Stress Response Pathways In Caenorhabditis Elegans, Clare B. Edwards

USF Tampa Graduate Theses and Dissertations

Understanding how metabolites contribute to anaplerosis, antioxidant effects, and hormetic pathways during aging is fundamental to creating supplements and dietary habits that may decrease age-associated disease and decline, thus improving the quality of life in old age. In order to uncover metabolic pathways that delay aging, the effects of large sets of metabolites associated with mitochondrial function on lifespan were investigated.

Malate, the tricarboxylic acid (TCA) cycle metabolite, increased lifespan and thermotolerance in C. elegans. Addition of fumarate and succinate also extended lifespan and all three metabolites activated nuclear translocation of the cytoprotective DAF-16/FOXO transcription factor and protected from paraquat-induced …

Purification And Characterization Of Bcsc; An Integral Component Of Bacterial Cellulose Export, Emily D. Wilson Ms

Theses and Dissertations (Comprehensive)

Biofilms are a growing concern in the medical field due to their increased resistance to antibiotics. When found in a biofilm, bacteria can have antibiotic resistance 10-1000 times that of their planktonic counterparts. Therefore, it is important to study the formation of biofilms. Cellulose biofilms are formed by Enterobacteriaceae, such as many Escherichia coli and Salmonella spp. strains. Biofilms provide these species with benefits including antimicrobial protection, development of bacterial communities, promotion of DNA exchange, uptake of nutrients, and, in the case of cellulose biofilms, immune system evasion. Cellulose biofilms are controlled by the Bacterial cellulose synthesis (Bcs) complex located …