Biochemistry, Biophysics, and Structural Biology Commons^™

Characterization Of Expression Of The Kcne Gene Family In Zebrafish, Danio Rerio, Lauren Vernlund

Honors Senior Capstones and Theses

The KCNE gene family codes for five transmembrane accessory proteins, "minK related peptides" or Mirps, involved in the modification of voltage-gated potassium (Kv) channels, K+ selective pores vital in the regulation of membrane potential and repolarization in all organisms. In mammals, all five KCNE gene members are conserved and active in the heart. In the zebrafish Danio rerio, there are no apparent orthologs for KCNE2 or KCNE5, yet they contain Kv channels with homologous structure, function, and Mirp regulatory behavior to other organisms. Sequence analysis of wildtype zebrafish KCNE1, 3 and 4, and rtPCR on RNA from zebrafish tissues …

Analysis Of The Mechanism By Which Ykl-40 Promotes Glioma Cell Migration, Bahiya Osrah

Theses and Dissertations

This thesis elucidates the crucial role of YKL-40 in enhancing glioma cell migration and invasion in vitro. Increased levels of YKL-40 are specifically associated with the increased invasive capacity of glioma multiforme (GBM) tumors and lower survival rate of GBM patients. In order to examine the effects of YKL-40 on the migration and invasion of GBM cells, we overexpressed YKL-40 in three different glioma cell lines. The overexpression of YKL-40 significantly enhanced glioma cells migration and invasion in vitro and also increased ERK phosphorylation, which is believed to enhance glioma cell survival, and invasiveness. Although receptors for YKL-40 are still …

Analysis Of Nfi-X3 And Stat3 Interaction And Its Functions, Etsegenet Tizazu

Theses and Dissertations

YKL-40 is a secreted protein that is highly up-regulated in malignant glioblastoma (GBM). Its expression is correlated with the invasive nature of GBMs and poor diagnosis of patients (Nigro et al., 2005). Previous research has shown that in astrocytes and GBM cells, YKL-40 expression is regulated by two transcription factors, NFI-X3 and STAT3, which form a complex with each other (Singh et al., 2011). Here, we show that the N-terminal domain of NFI-X3 is sufficient and required for its interaction with STAT3. We also show that the DNA-binding domain of NFI-X3 is required to induce YKL-40 expression. Thus, the interaction …

Hypervirulent Chlamydia Trachomatis Clinical Strain Is A Recombinant Between Lymphogranuloma Venereum (L(2)) And D Lineages, Naraporn Somboonna, Raymond Wan, David M. Ojcius, Matthew A. Pettengill, Sandeep J. Joseph, Alexander Chang, Ray Hsu, Timothy D. Read, Deborah Dean

All Dugoni School of Dentistry Faculty Articles

Chlamydia trachomatis is an obligate intracellular bacterium that causes a diversity of severe and debilitating diseases worldwide. Sporadic and ongoing outbreaks of lymphogranuloma venereum (LGV) strains among men who have sex with men (MSM) support the need for research on virulence factors associated with these organisms. Previous analyses have been limited to single genes or genomes of laboratory-adapted reference strain L₂/434 and outbreak strain L₂b/UCH-1/proctitis. We characterized an unusual LGV strain, termed L₂c, isolated from an MSM with severe hemorrhagic proctitis. L₂c developed nonfusing, grape-like inclusions and a cytotoxic phenotype in culture, …

Cerium Oxide Nanoparticles For The Detection Of Antimicrobial Resistance, Alexander J. Noll

HIM 1990-2015

The rise of antimicrobial resistance demands the development of more rapid screening methods for the detection of antimicrobial resistance in clinical samples to both give the patient the proper treatment and expedite the treatment of patients. Cerium oxide nanoparticles may serve a useful role in diagnostics due to their ability to exist in a mixed valence state and act as either oxidizing agents or reducing agents. Considering that cerium oxide nanoparticles have been shown to shift in absorbance upon oxidation, a useful method of antimicrobial resistance detection could be based on the oxidation of cerium oxide nanoparticles. Herein, an assay …

Role Of The Mar-Sox-Rob Regulon In Regulating Outer Membrane Porin Expression, Lon Chubiz, Christopher Rao

Biology Department Faculty Works

Multiple factors control the expression of the outer membrane porins OmpF and OmpC in Escherichia coli. In this work, we investigated the role of the mar-sox-rob regulon in regulating outer membrane porin expression in response to salicylate. We provide both genetic and physiological evidence that MarA and Rob can independently activate micF transcription in response to salicylate, leading to reduced OmpF expression. MarA was also found to repress OmpF expression through a MicF-independent pathway. In the case of OmpC, we found that its transcription was moderately increased in response to salicylate. However, this increase was independent of MarA and Rob. …

Identification Of Physiological Substrates Of Plasmodium Falciparum Pfpk5, A Cdk-Like Kinase, Catherine Sullenberger

HIM 1990-2015

Malaria is one of the most devastating infectious diseases causing 1-3 million fatalities a year. The majority of these cases occur amongst children in developing countries. Malarial strains in these areas are exhibiting increasing resistance to canonical treatments proving the importance of new drug targets for anti-malarials. Identification of new drug targets is dependent upon a better understanding of the molecular biology of the parasitic agent of malaria, Plasmodium. The regulation of Plasmodium's complex life cycle is still not well understood. Elucidation of signaling pathways involved in Plasmodium cell cycle regulation will provide insights into how the parasite thrives in …

An Assessment Of Stable Hydrogen-Isotope Analysis Methods To Assign Geographic Origin To Migratory Red-Tailed Hawks (Buteo Jamaicensis), Carla Marie Ahlschwede

Department of Environmental Studies: Undergraduate Student Theses

Stable-hydrogen isotopes are becoming an increasingly popular method of studying migratory birds, though sample preparation methods may affect results.  In this study I examined feathers from red-tailed hawks (Buteo jamaicensis) to determine the relationship between measure of δD due to inter-feather variation or drying methods, assessed the accuracy of results by using two birds of known-origin and estimated possible natal origins of migratory red-tailed hawks.  Two feathers per individual were taken from 81 wild hawks caught at Hitchcock Nature Center near Crescent IA and from 2 rescued red-tailed hawks, Raptor Recovery Nebraska near Eagle, NE. 119 of the …

Stealth Carbon Nanotubes: Strategies To Coat Carbon Nanotubes To Prevent Opsonization And Improve Biodistribution, Nalinikanth Kotagiri

Graduate Theses and Dissertations

Carbon nanotubes (CNT) have recently been in the limelight for its potential role in disease diagnostics and therapeutics. Even before these medical applications can be realized, there is a need to address issues like opsonization, phagocytosis by macrophages and sequestration to liver and spleen for eventual elimination from the body. We believe coating CNT with biocompatible and opsonin resistant moieties will not only help CNT in traversing the blood stream to reach the target organ, but also improve biodistribution tremendously. We set out to achieve this by firstly identifying a new compound, mAmp, which is a fluorescent derivative of the …

Investigation Of Charge Recombination In Escherichia Coli Photolyase And Vibrio Cholera Cryptochrome Dash, Agnieszka Zieba

Theses, Dissertations and Culminating Projects

Proton-coupled electron-transfer (PCET) is a mechanism of great importance in protein electron transfer and enzyme catalysis, and the involvement of aromatic amino acids in this process is of much interest. The DNA repair enzyme photolyase provides a natural system that allows for the study of PCET using a neutral radical tryptophan (Trp‘). In Escherichia coli photolyase, photoreduction of the flavin adenine dinucleotide (FAD) cofactor in its neutral radical semiquinone form (FADH') results in the formation of FADH and Trp . Charge recombination between these two intermediates requires O A/T # the uptake of a proton by ~ Trp . The …

The Role Of Albino3 And The Lipid Environment In Chloroplast Signal Recognition Particle Targeting, Nathan Lewis

Graduate Theses and Dissertations

Signal recognition particles (SRPs) in pro- and eukaryotes function in cotranslational targeting of nascent poplypeptides to an SRP receptor at the target membrane. A unique chloroplast SRP (cpSRP) functions post-translationally to direct light-harvesting chlorophyll-binding proteins (LHCPs) to the receptor cpFtsY at the thylakoid membrane for LHCP insertion in a process involving the integral membrane protein Albino3 (Alb3) and requiring GTP. Work here focuses on understanding cpSRP targeting events at the thylakoid membrane, specifically those involving Alb3 and the lipid environment.

We show an interaction between the novel cpSRP subunit cpSRP43 and the soluble, stromal-exposed C terminus of Albino3 (Alb3-Cterm). We …

Structural And Functional Characterization Of A Putative Citmhs Protein From Bacillus Anthracis, Qi Wen Li

Renée Crown University Honors Thesis Projects - All

The growing number of strains of antibiotic-resistant bacteria poses a new threat to human health. The development of innovative strategies to treat bacterial infections is essential. The recent discovery of a new class of membrane transporters, CitMHS, unique to bacteria, presents a potential new target for antibacterial therapeutics. CitMHS is a class of secondary metal citrate membrane transporters, with only five members characterized to date (2,3,5,6,7). No crystal structures have been reported. Detailed structural and functional studies of CitMHS are essential to the understanding of infection pathways and, consequently, the ability to block such pathways. Cit_Ba is a CitMHS …

Effects Of Ethanol On Social Behavior & Brain Structure, Lua Jafari

Renée Crown University Honors Thesis Projects - All

Autism spectrum disorders are a developmental disorder characterized by abnormal social behavior. Those with autism have problems with social interactions, repetitive behaviors, and both verbal and non-verbal communication. While the cause of autism is not yet know, studies have shown that there are both genetic and environmental factors linked with autism. The amygdala is considered to be part of the “social brain”, and atypical activation and morphology of the amygdala has been seen in those with autism.

For this research project, I utilized rats subjected to acute ethanol exposure during gestation and examined exposure effects on the anatomy and biochemistry …

Germline Cyst Formation And Development In Zebrafish, Tess Cherlin

Renée Crown University Honors Thesis Projects - All

In developing pre-natal mice, germline cysts are clusters or packages of cells consisting of individual oocytes. They are formed after the primordial germ cells move to the ovary during embryogenesis. The primordial germ cells divide, but do not completely separate. The cells within the cysts are linked by intercellular bridges, which end up breaking down leading to the formation of primordial follicles. The primordial follicles are oocytes surrounded by somatic cells called granulosa cells. Only one third of the original oocytes survive cyst breakdown and become the eggs that will be used by the mouse for her reproduction. This developmental …

Determination Of The Amino Acids Involved In The Interactions Between Dpy-30 And Ash2l, Key Components Of The Mll1 Core Complex, Carey Stuart

Renée Crown University Honors Thesis Projects - All

The human version of the DPY-30 protein is homologous to the DPY-30 protein in Caenorhabditis elegans (nematode), along with other DPY-30 homologous proteins in other organisms. This protein is involved in dosage compensation of X-linked genes, balancing the levels of expression of these genes between the sexes. The mechanism by which the balancing is carried out varies from organism to organism. For example, in C. elegans hermaphrodites (XX), transcript levels of the X-linked genes are cut in half. In Drosophila, the genes on the male’s (XY) X chromosome are transcribed at twice the rate of the female’s (XX) genes. …

Protein-Lipid Interactions: Influence Of Anchoring Groups And Buried Arginine On The Properties Of Membrane-Spanning Peptides, Vitaly V. Vostrikov

Graduate Theses and Dissertations

Designed transmembrane peptides were employed for investigations of protein-lipid interactions by means of oriented solid-state deuterium NMR spectroscopy using isotope-enriched alanine residues. Using the model GWALP23 sequence (GGALW(LA)6LWLAGA) as a host peptide having single interfacial tryptophan anchor residues, the effects of different guest mutations were explored. Replacements of glycine residues 2 and 22 to positively charged lysine or arginine on both termini had little influence on the peptide average orientation. Conversely, glycine to tryptophan substitutions had profound effects, manifested in the increased dynamics and altered tilt direction of the peptide. While the charged residues at the peptide termini did not …

Microrna Regulation Of Prostate Cancer Desensitization To Androgen Receptor Antagonist Drugs During Androgen Deprivation Therapy, Robert A. Lorch

HIM 1990-2015

The current standard treatment of prostate cancer by androgen deprivation therapy involves using drugs such as bicalutamide (Casodex) to antagonistically block androgen receptors that are normally present within prostate cells. Usually, the therapy is successful in the short run at limiting the growth of prostate cancer. However, in virtually all cases tumors begin to grow aggressively again after several months of treatment and new therapies must be started. The mechanism by which these prostate cells transform from androgen sensitive to androgen independent and anti-androgen resistant is unclear. In this study, we investigated the role of microRNAs, small 15 to 18 …

Cross-Talk Of Retinoic Acid And Adrenergic Hormone Signaling May Influence Development Of Cardiac Conduction And Rhythmicity In Utero, Sabikha Alam

HIM 1990-2015

Stress hormones, adrenaline and noradrenaline, have been shown to be critical for heart development. Mice lacking dopamine greek lower case letter beta]-hydroxylase (Dbh), an enzyme responsible for synthesis of these adrenergic hormones, die during mid-gestation due to cardiac failure. Prior research showed that adrenergic cells are found within the electrical conduction system of the heart, and adrenergic deficiency leads to slowed cardiac conduction during embryogenesis. Microarray analysis of wild-type (Dbh+/+) and knockout (Dbh-/-) mouse hearts revealed significant differences in expression of retinoic acid (RA) signaling genes. RA signaling has also been shown to be critical for heart development. These data …

Analysis Of The Repair Of Topoisomerase Ii Dna Damage, Eric D. Goldstein

HIM 1990-2015

A large number of anti-cancer chemotherapeutics target DNA topoisomerases. Etoposide is a specific topoisomerase II poison which causes reversible double strand DNA breaks. The focus of this project is to analyze the repair of DNA damage induced by etoposide.. Double strand DNA break repair is mediated by through either non-homologous end joining (NHEJ) or homologous recombination. NHEJ repairs through direct ligation of a double stranded break while homologous recombination utilizes a homologous template to recover the wild type sequence. A reporter cassette, RYDR-GFP, has been stably integrated into HeLa cells. This reporter contains an ultra-high affinity topoisomerase II cleavage site …

A Tripartile Biosensor For Real-Time Snss Detection In Dna Hairpin Motif, Camha Nguyen

HIM 1990-2015

The hybridization between two complementary strands of nucleic acid is the basis for a number of applications in DNA and RNA analysis, including in vivo RNA monitoring, microarrays, SNPs detection, and so on. The short oligonucleotide probes form Watson/Crick base pairs (A-T and G-C) with the analyzed nucleic acid. Molecular beacon (MB) probe is one of the most advantageous tools for nucleic acid analysis in real-time. A traditional MB probe consists of a DNA strand folded in hairpin motif with a fluorophore attached to the 5'end and a quencher attached to the 3' end. The loop segment is complementary to …