Biochemistry, Biophysics, and Structural Biology Commons^™

An Analysis Of Mitochondrial Dna In Rett Syndrome And Other Neurodegenerative Disorders, Catherine Erickson Burgess

Theses and Dissertations in Biomedical Sciences

Mitochondrial dysfunction resulting from mutations on mitochondrial DNA (mtDNA) is being recognized in a growing spectrum of diseases. These diseases, resulting from single base mutations, large deletions, or insertions, have been largely neuromuscular in origin. However, as an understanding of the effects of mtDNA mutations progresses, attention is now focusing on neurodegenerative diseases. Rett Syndrome (RS), a progressive neurodegenerative disease with predominantly female cases, demonstrates morphologic mitochondrial changes, mitochondrial enzyme deficiencies and maternal inheritance (characteristic of mtDNA diseases). No investigation of mtDNA involvement has been previously conducted and, to date, no biological marker exists for this disorder.

Our preliminary studies …

Severe Bone Marrow Suppression In A Patient With Rheumatoid Arthritis On Methotrexate, M P. Iqbal, A A. Ali, A A. Alvi

Department of Biological & Biomedical Sciences

No abstract provided.

Tyrosyl Protein Phosphorylation In Human Bone Cells : Its Potential Role In Mediating Fluoride Induced Osteoblast Proliferation, Alan Blair Thomas

Loma Linda University Electronic Theses, Dissertations & Projects

This dissertation was designed to test the hypothesis that fluoride-stimulated osteoblast proliferation is mediated by specific inhibition of a phosphotyrosyl protein phosphatase, resulting in increased steady state levels of tyrosyl phosphorylation of key cellular proteins. Cellular levels of tyrosyl phosphorylation were determined by an immunoblot detection assay in which cellular proteins were separated by SDS-PAGE, transblotted to nitrocellulose membranes and the phosphotyrosyl proteins were identified by anti-phosphotyrosine monoclonal antibodies. The relative amount of tyrosyl phosphorylation was quantitated by laser densitometric analysis of the autoradiograms. This method showed that fluoride induced dose- and time-dependent changes in the level of tyrosyl phosphorylation …

A Characterization Of Extractable, Hydroxylated Fatty Acid Bearing Components In Legionella Pneumophila, Jonathan R. Lane

Electronic Theses and Dissertations

Extraction of the lipids of Legionella pneumophila yields phases unlike those produced from other Gram-negative bacteria. A viscous interface forms between the aqueous (wash) and organic phases. More than half of the hydroxylated fatty acids were found distributed between the aqueous phase and the interfacial material, fractions in which such constituents have not been reported in other Gram-negative species. It was further observed that after the material from the aqueous/interfacial phase was dissolved in methanol or chloroform/methanol (2:1 (V/V)), the addition of acetone would create a white, flocculent precipitate. Analyses showed that the supernatant contained fatty acids that were nonhydroxylated …

A Molecular Basis For Erythromycin Sensitivity And Resistance In Escherichia Coli, Harold S. Chittum

Electronic Theses and Dissertations

The effect of erythromycin on the 50S ribosomal subunit during cell growth has been extensively investigated. Sucrose density gradient analysis of ribosomes formed in the presence and absence of the drug revealed a 50S specific assembly defect is partially responsible for erythromycin's inhibitory effects on wild type cells. Examination of two erythromycin-resistant mutants of E. coli (N281 and N282) revealed that mutant N281 (L22 mutant) but not N282 (L4 mutant) was assembly defective in the presence of the drug, although only at much higher drug concentrations (300 ug/ml vs. 75 ug/ml for wild type cells). The altered genes from each …

Unusual Structure Of A Human Middle Repetitive Dna, Duminda D. Ratnasinghe

Electronic Theses and Dissertations

The L2Hs sequences are a polymorphic, interspersed, middle repetitive DNA family unique to human genomes. Genomic fingerprinting indicates that these DNAs vary from one individual to another and between tissues of the same individual. Sequence analysis reveals that they are AT-rich (76%) and contain many unusual sequence arrangements (palindromes, inverted and direct repeats). These sequence properties confer on the L2Hs elements the potential to fold into non-B-form structures, a characteristic of recombination hot spots. To test this hypothesis carbodiimide, osmium tetroxide and S$\sb1$ nuclease were used as single-strand specific probes to study a recombinant plasmid, pN6.4.39, containing a single L2Hs …

The 2′-Phosphate Of Nadp Is Critical For Optimum Productive Binding To 6-Phosphogluconate Dehydrogenase From Candida Utilis, Anthony J. Berdis, Paul F. Cook

Chemistry Faculty Publications

Initial velocity studies obtained with alternative dinucleotide substrates for the 6-phosphogluconate dehydrogenase reaction suggest that the 2′-phosphate is critical for the optimum productive binding of the dinucleotide substrate. Initial velocity patterns obtained by varying 6-phosphogluconate at different fixed levels of NAD are nearly parallel with apparent competitive substrate inhibition by 6-phosphogluconate at pH 7 and below but intersect to the left of the ordinate at pH 8 and above. Dead-end inhibition studies indicate that the mechanism is random at all pH values. Data are interpreted in terms of a random mechanism with marked antagonism in the binding of NAD and …

The Primary Structure Of A Fungal Chitin Deacetylase Reveals The Function For Two Bacterial Gene Products., Dimitris Kafetzopoulos, George Thireos, John N. Vournakis, Vassilis Bouriotis

Dartmouth Scholarship

Chitin deacetylase (EC 3.5.1.41) hydrolyzes the N-acetamido groups of N-acetyl-D-glucosamine residues in chitin. A cDNA to the Mucor rouxii mRNA encoding chitin deacetylase was isolated, characterized, and sequenced. Protein sequence comparisons revealed significant similarities of the fungal chitin deacetylase to rhizobial nodB proteins and to an uncharacterized protein encoded by a Bacillus stearothermophilus open reading frame. These data suggest the functional homology of these evolutionarily distant proteins. NodB is a chitooligosaccharide deacetylase essential for the biosynthesis of the bacterial nodulation signals, termed Nod factors. The observed similarity of chitin deacetylase to the B. stearothermophilus gene product suggests that this gene …

Sds Non-Acrylamide Polymeric Gel-Filled Capillary Electrophoresis For Molecular Size Separation Of Protein, Devon Andres

Honors Theses

Sodium dodecyl sulfide (SDS) non-acrylamide gel-filled capillary columns are a new technology being used for analysis and separation of biotechnology-derived proteins. This research was to compare this new technology to the current methods of SDS polyacrylamide gel electrophoresis (SDS-PAGE) and high-performance size-exclusion chromatography (HPSEC). The molecular mass of four different recombinant proteins were determined by two commercialized SDS non-acrylamide gel-filled capillary columns, SDS-PAGE, and HPSEC. The data obtained showed that the SDS non-acrylamide gel-filled capillary columns were compatible with the SDS-PAGE technique for molecular mass determination. HPSEC was shown to be unreliable for molecular weight determination. SDS non-acrylamide gel-filled capillary …

Aerotaxis In Bacillus Subtilis, Laurence Samuel Wong

Loma Linda University Electronic Theses, Dissertations & Projects

B. subtilis, like Escherichia coli and Salmonella typhimurium, responded to a step increase in oxygen concentration by swimming smoothly (~ 35 s duration) and to a decrease in oxygen by tumbling. In a spatial gradient of oxygen in liquid media, a band of cells congregated near the air interface. Aerotaxis required a functioning respiratory chain. Adaptation of B. subtilis, E. coli and S. typhimurium to media containing amino acids requires methylation of receptors/methyl-accepting chemotaxis proteins. Adaptation to oxygen and phosphotransferase sugar substrates in B. subtilis was dependent on methylation, unlike similar adaptation in E. coli and S. typhimurium. …

Inheritance Of Freezing Resistance In Tuber-Bearing Solanum Species: Evidence For Independent Genetic Control Of Nonacclimated Freezing Tolerance And Cold Acclimation Capacity, Julie M. Stone, Jiwan P. Palta, John B. Bamberg, Laurie S. Weiss, James F. Harbage

Department of Biochemistry: Faculty Publications

Frost or winter survival is regarded as a complex trait with polygenic inheritance. Two maijor components of this survival in crop plants are freezing tolerance in the nonacclimated state and cold acclimation capacity. To date researchers have not distinguished the two components as separate heritable traits. The mode of inheritance of these two traits was investigated in F1 and backcross populations of two wild diploid potato species (Solanum commersonii and Solanum cardiophyllum) exhibiting extremes of freezing tolerance and acclimation capacity. Precise assessment of these two traits allowed distinction of small but significant differences among genotypes. The two traits …

The Interplay Of Light And The Circadian Clock. Independent Dual Regulation Of Clock-Controlled Gene Ccg-2(Eas), Guiseppina Arpaia, Jennifer J. Loros, Jay C. Dunlap, Giorgio Morelli, Guiseppe Macino

Dartmouth Scholarship

Ambient light is the major agent mediating entrainment of circadian rhythms and is also a major factor influencing development and morphogenesis. We show that in Neurospora crassa the expression of clock-controlled gene 2 (ccg-2), a gene under the control of the circadian clock and allelic to the developmental gene easy wettable (eas), is regulated by light in wild-type strains. Light elicits a direct and important physiological effect on ccg-2(eas) expression as demonstrated using several mutant Neurospora strains. In white collar mutants (wc-1 and wc-2) that are “blind” to blue light, ccg-2(eas) mRNA shows no variation following illumination with saturating light. …

Leukocyte Extravasation Into The Pancreatic Tissue In Transgenic Mice Expressing Interleukin 10 In The Islets Of Langerhans., Lise Wogensen, Xiaojian Huang, Nora Sarvetnick

Journal Articles: Regenerative Medicine

Transgenic expression of interleukin 10 (IL-10) in the islets of Langerhans leads to a pronounced pancreatic inflammation, without inflammation of the islets of Langerhans and without diabetes. A scattered infiltration of macrophages (M pi) precedes localized accumulations of CD4+ and CD8+ T lymphocytes, B lymphocytes, and M pi. This recruitment of inflammatory cells to the pancreas is somewhat surprising, since the biological activities of IL-10 in vitro indicate that IL-10 is a powerful immunosuppressive cytokine. Since endothelial cells play a major role in leukocyte extravasation, we examined if vascular changes and extralymphoid induction of peripheral and mucosal type vascular addressins …

Studies On Type I And Type Ii Dna Topoisomerases From Mammalian Mitochondria, Jia-Hwei Lin

Theses and Dissertations in Biomedical Sciences

Mammalian mitochondria contain a unique DNA topoisomerase I with characteristics of both nuclear and bacterial type I DNA topoisomerases. This enzyme, purified from bovine liver, requires cations as cofactors and possesses optimal activity at pH 7.0, 37°C and either 150 mM K+ or Na+ ions. Similar to nuclear enzymes and different from the bacterial enzyme, divalent ions such as Ca²⁺ or Mg²⁺ will stimulate but are not essential for the enzymatic activity.

Like the nuclear DNA topoisomerase I, the mitochondrial enzyme is capable of relaxing both negatively and positively supercoiled DNA. The relaxation of negatively supercoiled DNA is …

Genetic Analyses Of Photopigment Biosynthesis In Eubacteria: A Guiding Light For Algea And Plants, David Bollivar

Scholarship

No abstract provided.

The Isolation And Identification Of Polyphenolics From Grape Seeds And Their Activity Towards Specific Cell Lines, Joseph A. Reddy

Chemistry & Biochemistry Theses & Dissertations

Grape seed extract is being marketed in France for cardiovascular use and skin care. The active constituents of both these drugs are certain polyphenols called procyanidins. A similar seed extract has now been obtained from Virginia Chardonnay grape seeds. Ten of the major components in this extract have been isolated in their pure form by the semi-preparative HPLC separation on a YMC ODS-AQ (Octadecylsilane-AQ) column. The ODS-Aq column has been shown to have a better resolving capacity compared to the Spherisorb ODS (Octadecylsilane) column previously described in the literature. This has been attributed to the ODSAQ support which has both …

The Cytotoxic Effect Of Tropical Plants On Human And Rat Hepatoma Cells, Mark Tafazoli

Honors Capstone Projects and Theses

No abstract provided.

Gal4 Disrupts A Repressing Nucleosome During Activation Of Gal1 Transcription In Vivo, Jeffrey D. Axelrod, Michael S. Reagan, John Majors

Biology Faculty Publications

Photofootprinting in vivo of GALl reveals an activation- dependent pattern between the UASG and the TATA box, in a sequence not required for transcriptional activation by GAL4. The pattern results from a nucleosome whose position depends on sequences within the UASG. In the wild-type gene, activation by GAL4 and derivatives disrupts this nucleosome. This activity is independent of interactions with DNA-bound core transcription factors and is proportional to the strength of the activator. Presence of the nucleosome correlates with low basal transcription levels under various conditions, suggesting a role in limiting basal expression. We propose a role for the GAL4 …

Human Lung Mast Cell Tryptase Isozymes: Separation And Examination Of Structural And Functional Differences, Susan S. Little

Electronic Theses and Dissertations

Tryptases are trypsin-like enzymes found in mast cell granules. Although in vivo substrates have not been positively identified, tryptases cleave a limited number of potential physiological substrates in vitro, including high molecular weight kininogen (HMWK) and vasoactive intestinal peptide (VIP). Purified human lung mast cell tryptase (HLT) apparently exists as a tetramer with an M$\sb{\rm r}$ of 135-144 kDa by gel filtration, whereas SDS-PAGE yielded two bands of M$\sb{\rm r}$ 29 Kda and 33 Kda. Tryptases are resistant to inhibition by most natural trypsin inhibitors and display some affinity for heparin. The existence of tryptase isozymes has been implied from …

Probing Protein-Protein Interactions Among Proteins Of A Nonaggregated Fatty Acid Synthetase From Euglena Gracilis Variety Bacillaris, Sande G. Williams

Electronic Theses and Dissertations

Enoyl-acyl carrier protein (ACP) reductase from chloroplast nonaggregated fatty acid synthetase (FAS) of Euglena gracilis variety bacillaris was purified to a single band on a denaturing polyacrylamide gel. The enzyme was partially characterized with respect to substrate specificity, reduced nucleotide requirement, and the effect of ACP and Ca$\sp{++}$ on enzyme activity. Antibodies against the purified protein were raised in hens and isolated from eggs. ACP was purified from Euglena in yields of about 1mg/100g (wet weight) of cells. Antibodies were raised against the purified protein. ACP antibodies inhibited the Euglena chloroplast FAS using Euglena or E. coli ACP as a …

Longitudinal Study Of Plasma And Erythrocyte Selenium Levels In Type I Diabetic Children During Development And Treatment Of Ketoacidosis, Pi-Hsia Fan

Chemistry & Biochemistry Theses & Dissertations

Most studies on the biological activity of selenium have focused on its role at the active site in the ubiquitous enzyme, glutathione peroxidase (GSH-Px) which catalyzes the removal of hydrogen peroxide and organic hydroperoxides (1). A connection between selenium deficiency and a wide range of diseases in animals and humans has been reviewed (2). Development of various forms of human cancer (3), failure of the immune system (4), as well as some cardiovascular diseases (5) have been reported or suspected to correlate with selenium deficiency. However, the physiological function of selenium in these different diseases is not fully understood, and …

Analysis Of The Proteoglycan Content In Fresh And Cryopreserved Porcine Cardiovascular Tissues, Yun Hee Shon

Theses and Dissertations in Biomedical Sciences

The purpose of this research was to study the effects of cryopreservation on the proteoglycan (PG) and mineral content of aorta conduit tissue. Proteoglycans from fresh and cryopreserved porcine aorta conduit tissues were isolated by extraction with 4 M guanidine (Gdn) - hydrochloride (HCl) for 48 hours. Quantitative analysis of extracted proteoglycans revealed that the content of proteoglycan material from cryopreserved tissue, measured as uronate and protein per unit weight of wet tissue, was similar to that from fresh tissue. Gel permeation column chromatography studies suggested that proteoglycans present in three CsCl fractions from cryopreserved tissues had molecular weights similar …

Separation And Quantification Of Queuine-Modified And Unmodified Transfer Rna Isoacceptors, Jorge Miguel Pereira De Oliveira Da Silva Santos

Chemistry & Biochemistry Theses & Dissertations

The discovery of a base-exchange modification in the first position of the anticodon of four transfer RNA (tRNA) isoacceptor families has been shown to be correlated with a decrease in the rate of cell division in several tumorigenic tissues. This fact led to the hypothesis that wobbling in the anticodon might be a control point wich mediates the rate of translation. A suitable method for separation of different tRNA isoacceptor families had to be created in order to generate a means for quantitatively measuring degrees of this base modification in tRNA. Radio labelled amino acids were used to charge tRNA …

Thrombin-Binding Dna Aptamer Forms A Unimolecular Quadruplex Structure In Solution, James A. Roe, Roman F. Macaya, Peter Schultze, Flint W. Smith, Juli Feigon

Chemistry and Biochemistry Faculty Works

We have used two-dimensional 1H NMR spectroscopy to study the conformation of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG) in solution. This is one of a series of thrombin-binding DNA aptamers with a consensus 15-base sequence that was recently isolated and shown to inhibit thrombin-catalyzed fibrin clot formation in vitro [Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H. & Toole, J. J. (1992) Nature (London) 355, 564-566]. The oligonucleotide forms a unimolecular DNA quadruplex consisting of two G-quartets connected by two TT loops and one TGT loop. A potential T.T bp is formed between the two TT loops across …

Cloning A Putative Dna-Binding Protein Controlling The 5'Ltr Of The Copia Element In Drosophila, Horng-Yuan Kan

Theses and Dissertations in Biomedical Sciences

Copia, a Drosophila retrotransposon, is constitutively expressed in all developmental stages, except the embryo in Drosophila melanogaster. The effect of random integration of the copia element results in phenotypic change in Drosophila. The regulatory sequences, controlling copia expression, are located within the 5'LTR. The DNA sequence in the 5'LTR and in the location between downstream of entire the 5' LTR and the initial translation site have been identified by mobilityshift binding assays and DNase I footprinting assays. The data reveals three protected regions: a TATA-binding site, the AT-1, and AT-2 binding sites. The TATA-binding site and AT-1 site are …

Hepatic Lipase Treatment Of Chylomicron Remnants Increases Exposure Of Apolipoprotein E, Dawn L. Brasaemle, Kathleen Cornely-Moss, André Bensadoun

Chemistry & Biochemistry Faculty Publications

The consequences of hepatic lipase treatment of chylomicron remnants were studied. Rats were fed corn oil to induce production and secretion of chylomicrons and were then injected with polyclonal antiserum raised against hepatic lipase to specifically and quantitatively inhibit hepatic lipase activity in vivo. A fraction enriched in chylomicron remnants was isolated from rat plasma by a brief centrifugation step that preferentially isolates triglyceride-rich apolipoprotein (apo) B-48-containing lipoproteins. The chylomicron remnants were then treated with hepatic lipase in vitro, or incubated under identical conditions in the absence of enzyme (control incubations). Hepatic lipase-treated and control chylomicron remnants were isolated by …

Mouse Heparin Binding Protein-44 (Hbp-44) Associates With Brushin, A High-Molecular-Weight Glycoprotein Antigen Common To The Kidney And Teratocarcinomas, Masaru Nakamoto, Masayuki Ozawa, Sonia Jacinto, Tatsuhiko Furukawa, Yasuhiro Natori, Hiroshi Shirahama, Suguru Yonezawa, Tatsuo Nakayama, Takashi Muramatsu

Biology Faculty Publications

Heparin binding protein-44 (HBP-44) is a heparin binding protein of 44 kDa, found by cDNA cloning using antibodies against teratocarcinoma glycoproteins [Furukawa, T. et al. (1990) J. Biochem. 108, 297-302]. The N-terminal sequence analysis reported in this publication establishes the structure of its mature form. Immunohistochemical staining revealed that HBP-44 was located in the tubular brush border of the kidney. HBP-44 formed a complex with brushin, a high molecular weight (460 kDa) glycoprotein antigen common to the kidney and teratocarcinoma, but not with OR8 antigen, another antigen (350 kDa) of the same category. Brushin was shown to be the mouse …

Investigation Of The Structural Heterogeneity Of Lipooligosaccharides From Pathogenic Haemophilus And Neisseria Species And Of R-Type Lipopolysaccharides From Salmonella Typhimurium By Electrospray Mass Spectrometry, B W. Gibson, William Melaugh, Nancy J. Phillips, M A. Apicella, A A. Campagnari, J M. Griffiss

Chemistry Faculty Publications

Heterogeneity in the lipooligosaccharides (LOS) of pathogenic Haemophilus and Neisseria species is evident from the multiplicity of components observed with electrophoretic analyses. Knowledge of the precise structures that make up these diverse LOS molecules is clearly the key to reaching an understanding of pathogenic processes such as phase variation and molecular mimicry. Except for a few cases, little is known about the specific structural features of LOS that underlie phase variation and molecular mimicry, partly because of the inherent difficulties in the structural elucidation of these complex glycolipids. In the lipopolysaccharides (LPS) from Salmonella typhimurium and Escherichia coli, rough, or …

Site-Directed Mutagenesis By Double Polymerase Chain Reaction: Megaprimer Method, Sailen Barik

Biological, Geological, and Environmental Faculty Publications

The "megaprimer" method (1) based on polymerase chain reaction (PCR) is one of the simplest and most versatile procedures of site-specific in vitro mutagenesis available to date. The method utilizes three oligonucleotide primers and two rounds of PCR performed on a DNA template containing the cloned gene that is to be mutated. The rationale of the method is shown schematically in Fig. 1 where A and B represent the "flanking" primers that can map either within the cloned gene or outside the gene (i.e., within the vector sequence) and M represents the internal "mutant" primer containing the desired base change. …

Reexamination Of The Thermolytic Rearrangement Of 4-Halophenyl Azides To 2-Aminophenols And Other Products / H. Gershon, D. D. Clarke, And M. Gershon, Department Of Chemistry, Fordham University, Bronx, Ny 10458, Usa, New York Botanical Garden, Bronx, Ny 10458, Usa, Herman Gershon, Donald Dudley Clarke Phd, Muriel Gershon

Chemistry Faculty Publications

The halogenation of derivatives of 2-aminophenol with N-chloro- and N-bromosuccinimides at ambient temperatures in acetic acid was studied. With the necessary compounds available, a reexamination of the thermolytic rearrangement of 2-halophenyl azides to 2-aminophenols and other products was undertaken. It is certain that the rearrangement of 4-halophenyl azides to 2-aminophenols occurs but the products identified in this study differ significantly from those reported previously by Suschitzky et al. (1963, 1966)