Biochemistry, Biophysics, and Structural Biology Commons^™

Identification And Characterization Of The Cis-Acting Elements Around The Murine Cd4 Cnhancer, Xin Dong

Loma Linda University Electronic Theses, Dissertations & Projects

The cluster determinant 4 (CD4) molecule is a transmembrane glycoprotein. CD4 is essential for normal T helper cell function and plays an important role in T cell development and activation. CD4 is encoded by a single gene located on chromosome 6 in the mouse and chromosome 12 in the human. Both human and murine CD4 genes are divided into ten exons spanning more than 25 kb and have a large non-coding region in the first and third intron. CD4 gene expression is controlled primarily at the transcriptional level during T cell development and activation.

An enhancer has been identified approximately …

The Peroxisome Proliferator-Activated Receptor Alpha (Ppar ) Regulates Bile Acid Biosynthesis., Mary Hunt, Yi-Zeng Yang, Gosta Eggertsen, Claes Carneheim, Mats Gafvels, Curt Einarsson, Stefan Alexson

Articles

Fibrates are a group of hypolipidemic agents which efficiently lower serum triglyceride levels by affecting the expression of many genes involved in lipid metabolism. These effects are exerted via the peroxisome proliferator-activated receptor alpha (PPARa). In addition, fibrates also lower serum cholesterol levels, suggesting a possible link between the PPARa and cholesterol metabolism. Bile acid formation represents an important pathway for elimination of cholesterol, and the sterol 12a-hydroxylase is a branch-point enzyme in the bile acid biosynthetic pathway, which determines the ratio of cholic acid to chenodeoxycholic acid. Treatment of mice for one week with the peroxisome proliferator WY-14,643 or …

Crystallization And Structure Determination Of The Catalytic Trimer Of Methanococcus Jannaschii Aspartate Transcarbamoylase, Jacqueline Vitali, Tatyana Vorobyova, Gordon Websterb, Evan R. Kantrowitza

Physics Faculty Publications

Aspartate transcarbamoylase (ATCase) catalyzes the first step in the pyrimidine biosynthetic pathway, the reaction between carbamoyl phosphate and L-aspartate to form N-carbamoyl-L-aspartate and phosphate. The structural analysis of the ATCase catalytic trimer from Methanococcus jannaschii, a unicellular thermophilic archaeabacterium, has been undertaken in order to gain insight into the structural features that are responsible for the thermostability of the enzyme. As a first step, the catalytic trimer was crystallized in space group R32, with unit-cell parameters a = b = 265.3, c = 195.5 Å and two trimers in the asymmetric unit. Its structure was determined using …

La Notion De Danger, Jean M. Kanellopoulos, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

Pendant de nombreuses années, les recherches en immunologie ont été centrées sur la réponse immunitaire adaptative, et la plupart des immunologistes considéraient que sa fonction principale était de faire la distinction entre soi et non soi. Plus récemment, plusieurs équipes ont proposé que la fonction principale du système immunitaire est en réalité d’éliminer les agents pathogènes. Or, c’est le système immunitaire inné, longtemps négligé, qui joue un rôle essentiel dans l’induction d’une réponse contre les microorganismes. Ce système réagit précocement aux infections, voire instantanément, puis il induit et oriente la réponse du système adaptatif. Plusieursthéories ont été élaborées pour expliquer …

Mechanistic Characterization Of The Mitochondrial Type I Dna Topoisomerase And A Study Of Genes Containing Type I Dna Topoisomerase-Related Domains, Jaydee Dones Cabral

Theses and Dissertations in Biomedical Sciences

The mitochondrial type I DNA topoisomerase (mt-topo I) serves an important function in the mitochondrion by relaxing mtDNA supercoils to allow for replication of the mitochondrial genome as well as for gene expression. The mt-topo I's role in essential processes, such as replication and transcription, makes it an ideal candidate as a target for antitumor or antifungal drugs. To gain further insight into mt-topo I mechanism, a cleavage assay and drug inhibition studies were performed. As well, a search for the mt-topo I gene or genes containing type I topoisomerase-related domains was conducted. To characterize the mt-topo I mechanism, the …

Investigations On The Use Of Ion Mobility Spectrometry For Clinical Chemistry Applications, Henri Parson Patten

Theses and Dissertations in Biomedical Sciences

The major objective of this research is to examine ion mobility spectrometry as a rapid screening tool for specific application to clinical chemistry research and laboratory use. Methodology was developed for target analytes representing several classes of physiologically active substances, including anesthetics, illicit drugs, and their metabolites. The IMS characteristics of animal tissues and other compounds such as amino acids and proteins were determined. Quality assurance and control procedures were developed for specific quality data objectives. Criteria were established relating to use of IMS for assessing the precision and accuracy of data, qualitative screening, and semi-quantitative analyses.

It was found …

Increased Levels Of Multiple Forms Of Dihydrofolate Reductase In Peripheral Blood Leucocytes Of Cancer Patients Receiving Haematopoietic Colony-Stimulating Factors: Interim Analysis, M P. Iqbal, I A. Burney, F Sultana, N Mehboobali, T Siddiqui

Department of Biological & Biomedical Sciences

The precise mechanism whereby granulocytes proliferate when haematopoietic colony stimulating factors (CSFs) are used in neutropenic cancer patients is poorly understood. The purpose of this study was to investigate whether these cytokines bring about leucocyte proliferation by increasing the levels of multiple forms of dihydrofolate reductase (DHFR). Blood samples were collected from 36 cancer patients (25 males and 11 females) with chemotherapy-induced neutropenia. One sample of blood from each patient was obtained before therapy either with CSF, such as granulocyte colony stimulating factor (G-CSF) and granulocyte-macrophage colony stimulating factor (GM-CSF) or with placebo, and another one at the time of …

Identification And Characterization Of Control Elements Within The Murine Cd4 Gene, Zhong Deng

Loma Linda University Electronic Theses, Dissertations & Projects

The control of CD4 gene expression is essential for T lymphocyte development. Since the molecular mechanism for the control of CD4 gene expression during T cell development had not been elucidated, a study of the factors that control CD4 gene expression may lead to further. Toward these goals, we have made a series of recombinant DNA constructs to define the cis-acting transcriptional control elements in the murine CD4 locus that control CD4 gene expression during T cell development. In this study, we have identified multiple cis-acting control elements, which are critical for regulating the expression of the murine …

Telomerase Activity In Prostatic Fluid And Tissue As A Marker For Prostate Cancer, Zhilian Wang

Loma Linda University Electronic Theses, Dissertations & Projects

Telomerase is a ribonucleoprotein enzyme that is able to add telomeric repeats to the ends of eukaryotic DNA to stabilize chromosomes. Telomerase is active in germline cells, stem cells and tumor cells, but not in most human somatic cells. In this study we report the extended use of the Telomeric Repeat Amplification Protocol (TRAP) assay for the detection of telomerase activity in prostate needle biopsy specimens and freshly collected prostatic fluid. Clinical application of a newly developed PCR-ELISA telomerase assay method is also evaluated. Multiple sextant needle biopsy specimens from 56 subjects and prostatic secretion specimens from 72 subjects, with …

Electrically Mediated Plasmid Dna Delivery To Hepatocellular Carcinomas In Vivo, L. Heller, M. J. Jaroszeski, D. Coppola, C. Pottinger, R. Gilbert, Richard Heller

Bioelectrics Publications

Gene therapy by direct delivery of plasmid DNA has several advantages over viral gene transfer, but plasmid delivery is less efficient. In vivo electroporation has been used to enhance delivery of chemotherapeutic agents to tumors in both animal and human studies. Recently, this delivery technique has been extended to large molecules such as plasmid DNA. Here, the successful delivery of plasmids encoding reporter genes to rat hepatocellular carcinomas by in vivo electroporation is demonstrated.

Comparison Of The Mutant Frequency And Mutation Spectra Of Three Non-Genotoxic Carcinogens Oxazepam, Phenobarbital, And Wyeth 14,643 At The Λcii Locus In Big Blue Transgenic Mice, Vijaypreet K. Singh

Honors Capstones

No abstract provided.

Effect Of Chlamydia Trachomatis Infection And Subsequent Tnfa Secretion On Apoptosis In The Murine Genital Tract, Jean-Luc Perfettini, Toni Darville, Gabriel Gachelin, Philippe Souque, Michel Huerre, Alice Dautry-Varsat, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

The pathology observed during Chlamydia infection is due initially to localized tissue damage caused by the infection itself, followed by deleterious host inflammatory responses that lead to permanent scarring. We have recently reported that the infection byChlamydia in vitro results in apoptosis of epithelial cells and macrophages and that infected monocytes secrete the proinflammatory cytokine interleukin-1β. At the same time, proinflammatory cytokines such as tumor necrosis factor alpha (TNF-α) can also trigger apoptosis of susceptible cells. To study the possible relationship between Chlamydia trachomatis infection and apoptosis in vivo, we used the terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling technique to …

Characterization Of Human T-Cell Leukemia Virus 1 Reverse Transcriptase, Pinky Gundayao Agbuya

Theses and Dissertations in Biomedical Sciences

Human T-cell leukemia virus 1 (HTLV-1) is a type C human retrovirus which has been the causative agent of Adult T-cell leukemia. Replication of the retrovirus; requires a reverse transcriptase which converts the retroviral RNA into DNA which is later incorporated into the host's genome. Very little is known about the reverse transcriptase of HTLV-1. Researchers have attempted to purify HTLV-1 RT by isolating the enzyme from human cell lines. Because large amounts of protein could not be produced by this isolation method, the reverse transcriptase cannot be fully characterized. In this research, a recombinant protein expressed in E. coli …

Crystal Structure Of Bis(7-Nitro-8-Quinolinolato)Copper(Ii), Cuc18h10o6n4 / M. Shoja, H. Gershon And D. D. Clarke Fordham University, Department Of Chemistry, Fordham Road, Bronx, Ny 10458, Usa, Massud Shoja, Herman Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

C1sHwCuN406, monoclinic, P121/cl (No. 14), a= 4.567(9) Å, b = 10.723(8) Å, c = 17.095(6) Å, ~ = 100.0(1)0 , v = 824.5 Å3 , Z = 2, Rgt(F) = 0.043, wRgt(F) = 0.067, T = 293 K

Synthesis Of 2-Acetamido-5,6-Dihalophenyl Acetates / Donald D. Clarke, Herman Gershon, And John J. Mcmahon Department Of Chemistry, Fordham University, Bronx, Ny 10458, Usa, Donald Dudley Clarke Phd, Herman Gershon, John J. Mcmahon

Chemistry Faculty Publications

2-Acetamido-5,6-dihalophenyl acetates were synthesized as intermediates for the preparation of 6, 7-dihalo-8-quinolinols via the Skraup procedure

The Influence Of Leptin On Metabolic Expenditure And Thermogenesis During Thyroid Hormone (T₃) Suppression In The Obese (Ob/Ob) Mouse, Brian Kimball Underhill

Theses Digitization Project

No abstract provided.

N-Methyl-D-Aspartate Receptor Subunit Nr2b Is Widely Expressed Throughout The Rat Diencephalon: An Immunohistochemical Study, Arshad Khan, B. Stanley, Lisa Bozzetti, Christina Chin, Cyndi Stivers, Margarita Curras-Collazo

Selected Works Temporary Series

No abstract provided.

N-Methyl-D-Aspartate Receptor Subunit Nr2b Is Widely Expressed Throughout The Rat Diencephalon: An Immunohistochemical Study, Khan, B. Stanley, Lisa Bozzetti, Christina Chin, Cyndi Stivers, Margarita Curras-Collazo

Departmental Papers (Biology)

No abstract provided.

The Holliday Junction In An Inverted Repeat Dna Sequence: Sequence Effects On The Structure Of Four-Way Junctions, Brandt F. Eichman, Jeff Vargason, Blaine H.M. Mooers, P. Shing Ho

Faculty Publications - Department of Biological & Molecular Science

Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair. We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2.1 Å. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson–Crick base pairs; it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination. The junction is in the stacked-X conformation, with two interconnected duplexes formed by coaxially stacked arms, and is crossed at an angle of 41.4° as a right-handed X. A sequence comparison with previous …

Cytotoxic T Cell Response To Influenza Vaccination In Older Adults, Caroline R. Letter

Chemistry & Biochemistry Theses & Dissertations

Influenza infections result in activation of cellular and humoral immune responses, leading to stimulation of cytotoxic T cells (CTL) and helper T cells with subsequent viral clearance.

By using an assay of granzyme B activity, the in vivo cellular-mediated immune response of old adults was found to be significantly decreased in comparison to young adults. The effect of aging on the CTL response was further investigated via enzyme-linked immunospot technique. A significant increase in number of virus-specific T cells occurred in older adults after vaccination, although the magnitude of the CTL response decreased in comparison to young adults. These data …

Biochemical Composition Of Particles And Dissolved Organic Matter Slong An Estuarine Gradient: Sources And Implications For Dom Reactivity, Antonio Mannino, H. Rodger Harvey

OES Faculty Publications

The chemical composition of high molecular weight dissolved organic matter (DOM) and particulate organic matter (POM) was examined along the salinity gradient of the Delaware Estuary. DOM was collected and fractionated by tangential-flow ultrafiltration into 1-30 kDa (HDOM; high molecular weight) and 30 kDa to 0.2 μm (VHDOM; very high molecular weight) and compared to particles collected in parallel. Polysaccharides comprised 12-43% of particulate organic carbon (POC), 30-56% of VHDOM carbon, and 7.5-19% of HDOM carbon. Hydrolyzable amino acids comprised 17-38% of POC, 5.4-12% of VHDOM carbon, and 1.5-4.2% of HDOM carbon. Only 7-43% of dissolved organic nitrogen in VHDOM …

Multiple Factors Independently Regulate Hila And Invasion Gene Expression In Salmonella Enterica Serovar Typhimurium, Robin L. Lucas, C. Phoebe Lostroh, Concetta C. Dirusso, Michael P. Spector, Barry L. Wanner, Catherine A. Lee

Department of Biochemistry: Faculty Publications

HilA activates the expression of Salmonella enterica serovar Typhimurium invasion genes. To learn more

about regulation of hilA, we isolated Tn5 mutants exhibiting reduced hilA and/or invasion gene expression. In

addition to expected mutations, we identified Tn5 insertions in pstS, fadD, flhD, flhC, and fliA. Analysis of the

pstS mutant indicates that hilA and invasion genes are repressed by the response regulator PhoB in the absence

of the Pst high-affinity inorganic phosphate uptake system. This system is required for negative control of the

PhoR-PhoB two-component regulatory system, suggesting that hilA expression may …

Multiple Factors Independently Regulate Hila And Invasion Gene Expression In Salmonella Enterica Serovar Typhimurium, Robin L. Lucas, C. Phoebe Lostroh, Concetta C. Dirusso, Michael P. Spector, Barry L. Wanner, Catherine A. Lee

Department of Biochemistry: Faculty Publications

HilA activates the expression of Salmonella enterica serovar Typhimurium invasion genes. To learn more

about regulation of hilA, we isolated Tn5 mutants exhibiting reduced hilA and/or invasion gene expression. In

addition to expected mutations, we identified Tn5 insertions in pstS, fadD, flhD, flhC, and fliA. Analysis of the

pstS mutant indicates that hilA and invasion genes are repressed by the response regulator PhoB in the absence

of the Pst high-affinity inorganic phosphate uptake system. This system is required for negative control of the

PhoR-PhoB two-component regulatory system, suggesting that hilA expression may …

Two-Step Processing Of Human Frataxin By Mitochondrial Processing Peptidase, Patrizia Cavadini, Jiri Adamec, Franco Taroni, Oleksandr Gakh, Grazia Isaya

Department of Biochemistry: Faculty Publications

We showed previously that maturation of the human

frataxin precursor (p-fxn) involves two cleavages by the

mitochondrial processing peptidase (MPP). This observation

was not confirmed by another group, however,

who reported only one cleavage. Here, we demonstrate

conclusively that MPP cleaves p-fxn in two sequential

steps, yielding a 18,826-Da intermediate (i-fxn) and a

17,255-Da mature (m-fxn) form, the latter corresponding

to endogenous frataxin in human tissues. The two cleavages

occur between residues 41–42 and 55–56, and both

match the MPP consensus sequence RX ↓ (X/S). Recombinant

rat and yeast MPP catalyze the pài step 4 and 40 …

Urea Hydrolysis Using Immobilized Urease, Anita Arullan

Student Works (2000-2009)

An inexpensive carrier matrix. vermiculite was used for immobilizing urease. A cost effective and simple method of coupling was developed using vermiculite. Immobilization of urease on Amberlite MB-land Nylon-6 tube were also studied. Activities of free and immobilized urease were studied and compared: Among all methods used for immobilization of urease. the method of coupling the enzyme to vermiculite gave the highest retained activity of 82% (Method I) and 89% (Method 2) at pH 6.0 and 5.5 respectively. Urease immobilized by Method I retained 69% and 30% of its original activity and Method 2 (using glutaraldehyde as coupling agent) retained …

Typical Friedreich’S Ataxia Without Gaa Expansions And Gaa Epansions Wthout Typical Friedreich’S Ataxia, Dominick Mccabe, Fergus Ryan, D. Moore, Shirley Mcquaid, M. King, A. Kelly, K. Daly, David Barton, R. Murphy

Articles

We clinically assessed and performed polymerase chain reaction analysis for the GAA trinucleotide repeat expansion in 103 patients from 73 families in Ireland, with a prior clinical diagnosis of Friedreich’s ataxia (FA) or an unclassified progressive ataxic syndrome. The patients were classified as “typical” or “atypical” FA according to Harding’s mandatory clinical diagnostic criteria. All patients underwent blood glucose analysis, and electrocardiography and echocardiography was performed in 99 and 101 patients, respectively. Mutation screening for expanded CAG trinucleotide repeats, associated with spinocerebellar ataxia (SCA) 1, 2, 3 and 6 was performed in 86 patients overall, including all GAA negative patients. …

Applications Of The Atomic Force Microscope Within The Fields Of Haematology And Cytogenetics, Margaret O'Reilly-Crowley

Theses

Atomic force microscopy [AFM] has become a rapidly developing interdisciplinary field of research in recent years. The technique, including instrumentation and specimen preparation methods, is now more sophisticated and its application has increased dramatically. The key advantage of AFM is in providing three-dimensional images of samples imaged. Both size and shape of samples imaged can be obtained allowing their subsequent quantification. Red blood cells [RBCs] and chromosomes were imaged in this work. A brief overview of the current status of biomedical AFM, has been presented in the review.

Measurement of mean cell volume [MCV] of immobilised red blood cells with …

Emissions Of Formaldehyde, Acetic Acid, Methanol, And Other Trace Gases From Biomass Fires In North Carolina Measured By Airborne Fourier Transform Infrared Spectroscopy, Robert J. Yokelson, Jon G. Goode, Darold E. Ward, Ronald A. Susott, Ronald E. Babbitt, D. D. Wade, Issac T. Bertschi, David W. T. Griffith, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

Biomass burning is an important source of many trace gases in the global troposphere. We have constructed an airborne trace gas measurement system consisting of a Fourier transform infrared spectrometer (FTIR) coupled to a “flow-through” multipass cell (AFTIR) and installed it on a U.S. Department of Agriculture Forest Service King Air B-90. The first measurements with the new system were conducted in North Carolina during April 1997 on large, isolated biomass fire plumes. Simultaneous measurements included Global Positioning System (GPS); airborne sonde; particle light scattering, CO, and CO₂; and integrated filter and canister samples. AFTIR spectra acquired within …

Three-Dimensional Structure Of The Gly121tyr Dimeric Form Of Ornithine Decarboxylase From Lactobacillus 30a, Jacqueline Vitali, Donald Carroll, Rochika G. Chaudhrya, Marvin L. Hackert

Physics Faculty Publications

Ornithine decarboxylases catalyze the conversion of ornithine to putrescine at the beginning of the polyamine pathway. Ornithine decarboxylase (ODC) from Lactobacillus 30a is a 990612 Da dodecamer composed of six homodimers. A single point mutation (Gly121Tyr) was found to prevent association of dimers into dodecamers. The dimeric protein has been crystallized at pH 7.0 in the presence of guanosine triphosphate (GTP). Crystals belong to space group P3₂21, with unit-cell parameters a = 111.8, c = 135.9 Å and one monomer in the asymmetric unit. The structure was determined by molecular replacement and refined using simulated annealing to …

Structural Studies Of Recombinant Human Β-Casein Proteins, Yilin Hu

Loma Linda University Electronic Theses, Dissertations & Projects

β-Casein is the major component (~80%) of the human casein system. Interacting with calcium and phosphates through its phosphorylated N-terminus, β-casein participates in the formation of micelles which carry these otherwise insoluble nutrients indispensable for the growth and development of newborns. Human β-casein, or fragments thereof, are also found to have biological effects such as enhancement of calcium absorption. So far, knowledge of micelle formation is limited and structural studies of β-casein, especially its N-terminal portion will provide a better understanding of the structure-function relationship of milk micelles.

To elucidate the role that the N-terminus of the protein plays in …