Biochemistry, Biophysics, and Structural Biology Commons^™

The Rna-Binding Site Of Bacteriophage Qβ Coat Protein, Francis Lim, Marc Spingola, David Peabody

Biology Department Faculty Works

The coat proteins of the RNA bacteriophages Qβ and MS2 are specific RNA binding proteins. Although they possess common tertiary structures, they bind different RNA stem loops and thus provide useful models of specific protein-RNA recognition. Although the RNA-binding site of MS2 coat protein has been extensively characterized previously, little is known about Qβ. Here we describe the isolation of mutants that define the RNA-binding site of Qβ coat protein, showing that, as with MS2, it resides on the surface of a large β-sheet. Mutations are also described that convert Qβ coat protein to the RNA binding specificity of MS2. …

Distribution Of R-Banded Chromosome Variants In A Bottlenose Dolphin (Tursiops Truncatus) Population, Kristine Anne Gunter

Dissertations and Theses

When combined with observational and behavioral data, chromosome variant analysis provides a means of assessing population structure in bottlenose dolphins, Tursiops truncatus. In this cytogenetic analysis of thirty-six bottlenose dolphins, a distribution of fluorescent R-band variants was catalogued and used as a way to characterize the genetic structure of a Tursiops population inhabiting the Matagorda Bay, Texas, area. Three different population genetic analytical techniques were evaluated for their usefulness in analyzing cytogenetic data. The chromosome variant data obtained from this study was then compared with cytogenetic data gathered from a resident dolphin population residing near Sarasota, Florida.

The purpose …

Mechanisms Of Cytokine-Mediated Localized Immunoprotection., Nora Sarvetnick

Journal Articles: Regenerative Medicine

No abstract provided.

Pancreatic Expression Of Interleukin-4 Abrogates Insulitis And Autoimmune Diabetes In Nonobese Diabetic (Nod) Mice., Regula Mueller, Troy Krahl, Nora Sarvetnick

Journal Articles: Regenerative Medicine

Diabetes in nonobese diabetic (NOD) mice is a T cell-dependent autoimmune disease. The destructive activities of autoreactive T cells have been shown to be tightly regulated by effector molecules. In particular, T helper (Th) 1 cytokines have been linked to diabetes pathogenesis, whereas Th2 cytokines and the cells that release them have been postulated to be protective from disease. To test this hypothesis, we generated transgenic NOD mice that express interleukin (IL) 4 in their pancreatic beta cells under the control of the human insulin promoter. We found that transgenic NOD-IL-4 mice, both females and males, were completely protected from …

Il-10 Is Necessary And Sufficient For Autoimmune Diabetes In Conjunction With Nod Mhc Homozygosity., Myung-Shik Lee, Regula Mueller, Linda S. Wicker, Laurence B. Peterson, Nora Sarvetnick

Journal Articles: Regenerative Medicine

Contrary to expectations based on in vitro experiments, we previously found that pancreatic IL-10 did not inhibit autoimmune diabetes but accelerated it in an MHC-dependent manner. Therefore, the ability of IL-10 to overcome the absence of all non-MHC diabetes susceptibility (Idd) alleles was studied in transgenic mice expressing pancreatic IL-10 backcrossed to B10.H2g7 congenic mice, which have no Idd alleles other than NOD MHC (H2g7). IL-10 transgenic backcross 1 (BC1) mice with H2g7/g7 haplotype developed clear-cut insulitis and diabetes, but neither transgenic mice with the H2g/b haplotype nor nontransgenic BC1 mice did so. Further implicating IL-10 in autoimmune diabetes, anti-IL-10 …

Anion Induced Blue To Purple Transition In Bacteriorhodopsin, Mrunalini Pattarkine, Anil K. Singh

Faculty Works

Purple membrane (PM, λ" role="presentation">λmax" role="presentation">max 570 nm) of H. halobium on treatment with sulphuric acid changes its colour to blue (λ" role="presentation">λmax" role="presentation">max 608 nm). The purple chromophore can be regenerated from the blue chromophore by exogeneous addition of anions such as CI−" role="presentation">− and HPO42−" role="presentation">2−4. Chloride ion is found to be more effective than the dibasic phosphate ion in regenerating the purple chromophore. Nevertheless, one thing common to the anion regeneration is that both CI−" role="presentation">− and HPO42−" role="presentation">2−4 show marked pH effect. At pH 1.0 the efficiency of …

Characterization Of The Tdd-4 Transposable Element From Dictyostelium Discoideum, David J. Wells

Biology

Transposable elements are DNA segments that possess the capability to move to new chromosomal or extrachromosomal locations. Tdd-4 is a newly isolated transposable element from Dictyostelium discoideum that was captured while studying maintenance properties of Dictyostelium plasmids. Approximately 20 copies are present in the D. discoideum AX4 genome. Two classes of elements were identified, which include a 3.8 kilobase full-length version and a 3.4 kilobase deleted version. Restriction fragment length polymorphism analysis demonstrates that Tdd-4 utilizes a cut-and-paste mode of transposition. Sequence analysis reveals that the 145 base pair inverted terminal repeats contain the 5'-TG...CA-3' conserved terminal dinucleotides found in …

Phylogenetic Studies Of The United States Bluetongue Viruses And Characterization Of The Viral Vp4 Protein, I-Jen Huang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bluetongue virus (BTV) is transmitted by arthropod vectors and causes bluetongue disease with serious economic loss in many regions of the world. The replication mechanism of bluetongue virus is still not clear. To have a better understanding regarding the viral replication, the function of each individual protein has to be identified. This study used molecular biology techniques to investigate the function of the inner core protein VP4.

The M1 genes of United States bluetongue virus serotypes-2, -10, -11, -13, and -17 were cloned and sequenced. The length of each of the five M1 genes is 1981 nucleotides. The coding region …

Interactions Involving The Human Rna Polymerase Ii Transcription/Nucleotide Excision Repair Complex Tfiih, The Nucleotide Excision Repair Protein Xpg, And Cockayne Syndrome Group B (Csb) Protein, Narayan Iyer, Michael S. Reagan, Kou-Juey Wu, Bertram Canagarajah, Errol C. Friedberg

Biology Faculty Publications

The human basal transcription factor TFIIH plays a central role in two distinct processes. TFIIH is an obligatory component of the RNA polymerase II (RNAP II) transcription initiation complex. Additionally, it is believed to be the core structure around which some if not all the components of the nucleotide excision repair (NER) machinery assemble to constitute a nucleotide excision repairosome. At least two of the subunits of TFIIH (XPB and XPD proteins) are implicated in the disease xeroderma pigmentosum (XP). We have exploited the availability of the cloned XPB, XPD, p62, p44, and p34 genes (all …

Modulated Structures In Electrodeposited Superconducting Ba(1-X)K(X)Bio(3), Chad Bryant Huffman

Theses, Dissertations and Capstones

Compositionally modulated crystals of the superconductor Ba_1-x K_xBiO₃ have been grown electrochemically. Modulation was produced through control of the deposition potential.

Modulated crystals were imaged using optical microscopy, backscattered SEM, and STM. The expected linear relationship between the amount of time that current was applied and the modulation thickness was observed, and the growth rates were determined.

Multilayers were differentially etched using an EDTA solution. Etched and unetched samples were imaged using backscattered SEM.

The transition temperature of a modulated sample was determined by SQUID magnetometry to equal the bulk value.

Effect Of Retinoic Acid On The Expression And Function Of Ap-1 Transcription Factor In B16 Mouse Melanoma Cells: Role Of Protein Kinase, Sejal H. Desai

Theses, Dissertations and Capstones

Retinoic acid (RA) induces differentiation of B16 mouse melanoma cells. This differentiation is accompanied by an increase in protein kinase Ca (PKCα) protein level and selective enrichment in nuclear-associated PKCα. PKC is thought to regulate gene expression through the TPA response element (TRE). This element is specifically recognized by the AP-1 transcription factor composed of jun and fos family members. In this study, I have analyzed the effect of RA on the expression and function of AP-1 in B16 mouse melanoma cells. Transient transfection analysis of B16 cells using leuciferase reporter gene constructs with or without AP-1 elements indicated that …

Regulation Of Melanogenesis In B16 Mouse Melanoma Cells By Protein Kinase C (Pkc), Harish Mahalingam

Theses, Dissertations and Capstones

The pigment cell-specific expression of tyrosinase and TRP1 has been shown to be important for the production of melanin in pigmented cells. Using a pigmented cell line, B16 mouse melanoma, we obtained evidence that PKC plays a major role in regulating melanogenesis. Chronic treatment with phorbol dibutyrate (PDBu) leads to downregulation of PKC activity and protein levels. This is accompanied by a loss of pigmentation which is correlated with a 50% reduction and a complete loss of TRP1 and tyrosinase respectively. Similar results were obtained with Northern and Western blotting indicating that PKC may regulate the steady state levels of …

Role Of Immunodominant T Cell Responses To Minor Histocompatibility Antigens In A Mouse Model Of Graft-Versus-Host Disease, Marc Adam Berger, B.S. Thomas Jefferson University

Full-Text Theses & Dissertations

Graft-versus-host-disease (GVHD) is a major complication of major histocompatibility complex (MHC) matched bone marrow transplantation. GVHD is the result of an immune-mediated attack, by T lymphocytes derived from donor bone marrow, against recipient tissues expressing minor histocompatibility antigen (miHA) differences. There is a lack of knowledge concerning the nature of in vivo immune responses to miHA during GVHD. C57BL/6By (B6/By) and BALB.B mouse strains both express the H-2B MHC haplotype but differ at more than 40 miHA loci. Both the in vitro and in vivo T cell responses to miHA expressed by BALB.B and CXB recombinant inbred (RI) strains of …

Analysis Of The Mechanisms Controlling Phospholipid Biosynthetic Gene Expression In The Yeast Saccharomyces Cerevisiae, Brian Patrick Ashburner

Dissertations

No abstract provided.

The Chlorophyll Biosynthetic Enzyme Mg-Protoporphyrin Ix Monomethyl Ester (Oxidative) Cyclase, David Bollivar

Scholarship

No abstract provided.

Application Of A Modified Ziehl-Neelsen's Carbol-Fuchsin Stain For Observing Nuclei In Vegetative Hyphae Of The Puffball Species Lycoperdon Pyriforme, Martin J. Huss

Journal of the Arkansas Academy of Science

Nuclei of vegetative hyphae of the puffball species Lycoperdon pyriforme are small and difficult to stain. A simple mitotic staining technique utilizing a modified version of Ziehl-Neelsen's carbol-fuchsin stain, originally developed for examining bacteria and small chromosomes of plants, has proven useful for observing fungal nuclei in this gasteromycete species. Cells of vegetative hyphae were pre-treated for 2 hours with an aqueous solution saturated with naphthalene, fixed in a 3:1 mixture of 100% ethanol and glacial acetic acid, and hydrolyzed for 10 minutes in a 1:1 mixture of 100% ethanol and 12 M hydrochloric acid. Cells were rinsed with distilled …

Destabilizing Effect Of Proline Substitutions In Two Helical Regions Of T4 Lysozyme: Leucine 66 To Proline And Leucine 91 To Proline, Terry M. Gray, Eric Arnoys, Stephen Blankespoor, Tim Born

University Faculty Publications and Creative Works

A class of temperature-sensitive (ts) mutants of T4 lysozyme with reduced activity at 30 °C and no activity at 43 °C has been selected. These mutants, designated 'tight' ts mutants, differ from most other T4 lysozyme mutants that are active at 43 °C, but only manifest their ts lesion by a reduced halo size around phage plaques after exposure of the growth plates to chloroform vapors. For example, in the series of T4 lysozyme mutants at position 157, the original randomly selected mutant, T1571, is the least stable of the series, yet, apart from the halo assay and subsequent in …

Modulation Of Queuine Uptake And Incorporation Into Trna By Protein Kinase C And Protein Phosphatase, Rana C. Morris, Bonnie J. Brooks, K. Lenore Hart, Mark S. Elliot

Chemistry & Biochemistry Faculty Publications

It has been suggested that the rate of queuine uptake into cultured human fibroblasts is controlled by phosphorylation levels within the cell. We show that the uptake of queuine is stimulated by activators of protein kinase C (PKC) and inhibitors of protein phosphatase; while inhibitors of PKC, and down-regulation of PKC by chronic exposure to phorbol esters inhibit the uptake of queuine into cultured human fibroblasts. Activators of cAMP- and cGMP-dependent kinases exert no effect on the uptake of queuine into fibroblast cell cultures. These studies suggest that PKC directly supports the activity of the queuine uptake mechanism, and that …

Rosalyn Sussman Yalow (1921-) Endocrinologist, Medical Physicist, Margaret Sylvia

Faculty Publications

A biography of Rosalyn Yalow, Nobel Prize winner in Physiology/Medicine for the development of radioimmunoassay of peptides hormones. She was the second woman to win a Nobel Prize in Medicine and first American woman to do so.

Developmental, Tissue, And Sub-Tissue Specific Expression Of The Mammalian Apurinic/Apyrimidinic Endonuclease, Teresa Mari Wilson

Dissertations

No abstract provided.

Regulation Of Phospholipid Biosynthesis In The Yeast Saccharomyces Cerevisiae By The Ume6 Gene, John Charles Jackson

Dissertations

No abstract provided.

Biochemical And Molecular Characterization Of The Prostate-Specific Membrane Antigen (Psma), John Karl Troyer

Theses and Dissertations in Biomedical Sciences

Prostate cancer is the most common malignancy and the second leading cause of cancer death in males in the United States. Additionally, the number of deaths attributed to prostate cancer is increasing at a rate of approximately 8% a year. Development of new diagnostic and therapy strategies are needed in order to improve the life expectancy of patients with this disease. One tool which may allow for improvements in prostate cancer diagnosis and therapy is the monoclonal antibody (MAb) 7E11-C5.3 which was first described in 1987. Since then, the antigen recognized by MAb 7E11-C5.3 has been named the prostate specific …

Anaerobic Protoporphyrin Biosynthesis Does Not Require Incorporation Of Methyl Groups From Methionine, David Bollivar

Scholarship

No abstract provided.

The Cytoplasmic Tail Domain Of The Vacuolar Protein Sorting Receptor Vps10p And A Subset Of Vps Gene Products Regulate Receptor Stability, Function, And Localization, Joan Lin-Cereghino, Eric G. Marcusson, Scott D. Emr

College of the Pacific Faculty Articles

VPS10 of Saccharomyces cerevisiae encodes a type I transmembrane receptor protein required for the sorting of the soluble vacuolar hydrolase carboxypeptidase Y (CPY). To characterize the essential structural features and intercompartmental transport itinerary of the CPY receptor, we have constructed mutant forms of Vps10p that alter the carboxyterminal cytoplasmic tail of the protein. In addition, we have analyzed the effect these mutations as well as mutations in several VPS genes have on the function, stability, and localization of Vps10p. Although wild-type Vps10p is very stable over a 3-h chase period, overproduction of Vps10p results in PEP4-dependent degradation of the receptor. …

Investigation Of The Substrate Recognition Characteristics And Kinetics Of Mammalian Mitochondrial Dna Topoisomerase I, Zeki Topcu

Theses and Dissertations in Biomedical Sciences

Topoisomerases are DNA-modifying enzymes found in prokaryotes, eukaryotes, viruses and organelles such as chloroplast and mitochondria. Information about these enzymes in eukaryotic systems is mostly limited to nuclear enzymes, although our laboratory has been characterizing the biochemical and biophysical properties of the mammalian mitochondrial topoisomerases. We have determined the polarity of the attachment of mitochondrial topoisomerase I to its substrate DNA. To study the substrate preference and kinetic parameters of mitochondrial topoisomerase I, selected regions of mammalian mitochondrial DNA (mtDNA) were inserted into pGEM plasmid vectors following a series of modification and optimization experiments of currently available methods for PCR-cloning. …

In Vitro Expression Of Human Zona Pellucida Protein 3, Chih-Wei Chen

Theses and Dissertations in Biomedical Sciences

Human zona pellucida protein 3 (hZP3) is the putative receptor on the zona pellucida of the mature oocyte that recognizes and binds sperm, and therefore plays a critical role in fertilization.

A full length cDNA of hZP3 (1278 bp) was amplified from the human ovary mRNA by reverse transcription-polymerase chain reaction (RT-PCR). The hZP3 cDNA was subcloned into PSK and pREP4 expression vectors. The cDNA of hZP3 was further characterized by restriction mapping, PCR, auto-sequencing and Southern blot analysis by using an internal oligonucleotide probe, and found to be identical to the one reported by J. Dean. Using autosequencing, 289 …

Identification And Characterization Of Mitochondrial Dna Variants In Alzheimer's Disease, Natasha Singh Hamblet

Theses and Dissertations in Biomedical Sciences

Alzheimer's Disease (AD) is a complex neurodegenerative disorder that affects a significant portion of the human population regardless of ethnicity or gender. A mitochondrial hypothesis of AD has been proposed based on a number of studies which establish altered oxidative phosphorylation (OXPHOS) and ATP synthesis in AD tissue. ATP demand is most prevalent in the brain; damage to OXPHOS could severely impair brain metabolism, thereby leading to a decline in cognitive function. Four out of five complexes in the OXPHOS pathway are partly encoded by mitochondrial DNA (mtDNA); thus, this may be a crucial site of lesions that alter brain …

Moraxella (Branhamella) Catarrhalis: A Molecular Epidemiology Study, Lyndell R. Gill

Electronic Theses and Dissertations

Moraxella (Branhamella) catarrhalis is the third-most-frequently isolated microorganism associated with acute exacerbations of chronic bronchitis in patients during their stay at the Mountain Home VA Medical Center (MHVAMC). In order to develop a practical, epidemiologically-meaningful typing method for M. (B.) catarrhalis, we tested two methods based on analysis of chromosomal DNA for typeability, reproducibility, and ability to differentiate between unrelated strains (discriminatory power, D). M. (B.) catarrhalis isolants from MHVAMC from 7/1/87-6/30/88 were grown overnight in broth and embedded in agarose. DNA was isolated by standard methods. The DNA was subjected to: (1) restriction endonuclease digestion (with either Bgl II …

Identification And Characterization Of Genes Associated With V-Jun Induced Cell Transformation, Martin Toralballa Hadman

Biological Sciences Theses & Dissertations

The v-jun oncogene was initially identified as the causative agent for fibrosarcomas in chickens. Studies show that overexpression of v-Jun proteins transforms chicken embryo fibroblasts (CEF) in vitro, and forms tumors in chickens in vivo. The mechanisms for this are not clearly defined. Conceivably, overexpression of an unregulated transcription factor would cause cell transfonnation by illicit regulation of its target genes. In support of this, we show that in vivo v-Jun complexes exhibit differential binding to in vitro generated AP-1 and 'AP-1 like' target sequences, suggesting that the pattern of target gene expression is altered during cell transformation. …

The Kinetic Characterization Of Mutant L289p Of Recombinant Hiv-1 Reverse Transcriptase, Tryn Thomas Stimart

Chemistry & Biochemistry Theses & Dissertations

The Human Immunodeficiency Virus, type 1 (HIV-1) is the causative agent of the Acquired immunodeficiency Syndrome (AIDS). Currently, AIDS is the leading cause of death amongst young people in the United States. The large increase of HIV-1 infections over the past decade has spawned considerable research in fighting the spread of this disease. One area of intense HIV-1 research has focused on the enzyme Reverse Transcriptase (RT) which is an essential enzyme involved in the replication and life cycle of HIV-1. HIV-1 RT is composed of p66 and p51 subunits and is only active as a heterodimer in vivo. …