Biochemistry Commons^™

Immunoadjuvanticity Of Chlorophyll, Jocelyn Helen Parks Ramos

All-Inclusive List of Electronic Theses and Dissertations

Background: Vaccines are formulations containing antigenic determinants (from non-self organic matters) and immuno-enhancers called adjuvants. Together, they evoke protective immune responses in hosts. Adjuvants are substances that further vaccines' capability to induce a robust immune response. Common side effects with conventional adjuvants used in most vaccines are toxicity, inflammation and granulomas. In this study we investigated the pigment chlorophyll (Chl) for immunoadjuvanticity. The selection of chlorophyll is based on the fact that it is a component in foods such as spinach, and that it contains an isoprenoid structure that is a feature of many conventional adjuvants, Pristane and Squalene. Chl …

Characterizing Ntrc-Like Activators Affecting Myxococcus Xanthus Development, Jessica Eisenstatt

Renée Crown University Honors Thesis Projects - All

Myxococcus xanthus is a soil bacterium that is a member of a group of organisms known as the myxobacteria. M. xanthus cells live in biofilms and feed on other bacteria to obtain nutrients. During times of inadequate nourishment, M. xanthus cells aggregate, build fruiting bodies, and fruiting body cells differentiate into spores that are highly resistant. In order to form the fruiting bodies, M. xanthus cells must be able to move across solid surfaces. There are two motility systems, the adventurous system (A-motility) and the social system (S-motility), used by M. xanthus cells to navigate across surfaces. The adventurous system …

Compensation Mechanisms For Altered Membrane Sterol Compositions In The Yeast: Saccharomyces Cerevisiae, David M. Dewolfe

Renée Crown University Honors Thesis Projects - All

Cell Membranes are composed of several different lipid and sterol products. Among these are, chiefly, phospholipids, glycolipids, sphingolipids, various proteins and sterols. The sterol that is prevalent in fungi, including yeast, is ergosterol. It plays the same physiological role as cholesterol in mammalian cells. That is, mainly, to control membrane fluidity. Membranes in general are extremely important to the normal functioning of any cell and its sub-cellular compartments. The primary factor in the normal functioning of a membrane is the relative composition of the previously mentioned components. Even though there is a high amount of traffic between different membranes within …

Characterization Of Type Ii Secretion Mutants Of Pseudomonas Aeruginosa, Sijung Suh

Renée Crown University Honors Thesis Projects - All

Pseudomonas aeruginosa mutants PA0686, PA3102, PA3103, and PA5210 carry transposon insertions in uncharacterized genes in the PA01 background. The biofilms formed by these mutants show different phenotypes than PA01, their wild-type counterpart. BLAST searches and phylogenomic mapping tools indicate that protein products of the mutated genes are involved in P. aeruginosa type-II secretion, which is linked to twitching motility. In this study, 96-well microtitre plate biofilm assays, UV/visible spectrophotometer analysis, and motility assays were used to demonstrate a link between type-II secretion, twitching motility and biofilm formation. The results show that the PA5210 mutant forms a biofilm that is less …

Characterization Of Hypersensitive Response Related Genes Of Arabidopsis Thaliana, Keluo Yao

Renée Crown University Honors Thesis Projects - All

Like most complex living organisms, plants have many mechanisms to prevent disease by microbial pathogens. One of the most important and well developed defense systems that involve recognition, identification and systematic response is the hypersensitive response.

The hypersensitive response is a complex, early defense response against pathogens that causes necrosis and cell death at the site of infection to restrict the spread of pathogen. Hypersensitive response is a type of programmed cell death, and its activation usually happens when the plant recognizes a pathogen through an elicitor. This recognition triggers a series of signal transductions events which end in the …

Biochemical Characteristics Of Inconsistent Free T₄ Assays, Kristofer S. Fritz

Loma Linda University Electronic Theses, Dissertations & Projects

Serum levels of free thyroxine (T₄) are helpful in the clinical evaluation of patients who are suspected of having thyroid disease, since free T₄ (unbound) is known to closely relate to hyper, eu and hypothyroidism. There are documented inconsistencies among commercially available direct free thyroxine immunoassays. The biochemical basis for these inconsistencies is not understood and has not been characterized. Direct free T₄ measurements have been linked to both T₄-binding serum protein concentrations and protein-bound T₄ concentrations. A free T₄ reference method using direct equilibrium dialysis radioimmunoassay has been well characterized. New …

Radiation-Induced Increases In Pkc Modulate Integrin Expression And Contribute To Fibrotic Changes, Pinal Rushikesh Pandya

Loma Linda University Electronic Theses, Dissertations & Projects

The sequences of events in fibrosis are similar to those in wound healing; however, the normal termination and resolution stages do not take place. The initial cellular response following ionizing radiation involves accumulation of the ECM (extracellular matrix) including collagen, fibronectin and the interaction of many growth factors (cytokines) with their receptors. There are a number of unanswered questions regarding many aspects of radiation-induced fibrosis, including the initial triggers and physical changes that initiate the process. We have confirmed that elevated pKC and other cellular changes following radiation are similar to those found at sites of inflammation. This information leads …

Iron Dysregulation And Inflammation In Alzheimer’S Disease, Shino D. Magaki

Loma Linda University Electronic Theses, Dissertations & Projects

Alzheimer’s disease (AD) is the most common form of senile dementia in the US and worldwide but the causes of its pathogenesis are currently unknown. In this study, we examined two processes that have been implicated in the early stages of AD and other forms of neurodegeneration, iron dysregulation and inflammation, both of which can promote the increased production of amyloid precursor protein (APP). We have measured different pools of brain iron in transgenic iron regulatory protein 2 knockout (IRP2-/-) mice in the early stages of neurodegeneration and in affected brain regions from AD patients at different stages of the …

Stoichiometric Controls Of Mercury Dilution By Growth, Roxanne Karimi, Celia Y. Chen, Paul C. Pickhardt, Nicholas S. Fisher, Carol L. Folt

Dartmouth Scholarship

Rapid growth could significantly reduce methylmercury (MeHg) concentrations in aquatic organisms by causing a greater than proportional gain in biomass relative to MeHg (somatic growth dilution). We hypothesized that rapid growth from the consumption of high-quality algae, defined by algal nutrient stoichiometry, reduces MeHg concentrations in zooplankton, a major source of MeHg for lake fish. Using a MeHg radiotracer, we measured changes in MeHg concentrations, growth and ingestion rates in juvenile Daphnia pulex fed either high (C:P = 139) or low-quality (C:P = 1317) algae (Ankistrodesmus falcatus) for 5 d. We estimated Daphnia steady-state MeHg concentrations, using a …

Multiplex Snp Discrimination, Daniel J. Fish, M. Todd Horne, Robert P. Searles, Greg P. Brewood, Albert S. Benight

Chemistry Faculty Publications and Presentations

Multiplex hybridization reactions of perfectly matched duplexes and duplexes containing a single basepair mismatch (SNPs) were investigated on DNA microarrays. Effects of duplex length, G-C percentage, and relative position of the SNP on duplex hybridization and SNP resolution were determined. Our theoretical model of multiplex hybridization accurately predicts observed results and implicates target concentration as a critical variable in multiplex SNP detection.

The Development Of A Gc/Ms Protocol For The Analysis Of Polysaccharides In Echinacea Purpurea, Michaela Knapp

Undergraduate Theses and Capstone Projects

Echinacea purpurea is an herbal supplement used to reduce symptoms of common colds and flu-like illnesses. As of right now, it is not well understood what chemical components in the plant are immunologically active. The four main potentially immunologically active chemical components in E. purpurea are caffeic acid derivatives, alkamides, polyacetylenes, and polysaccharides. In this investigation, a protocol was developed in an attempt to identify polysaccharides present in Puritan’s Pride E. purpurea (aerial) “non-irradiated” herbal supplement First, an estimate of the crude total polysaccharide content in Puritan’s Pride and in a ChromaDex certified botanical standard (E. purpurea -powdered root) was …

Kinetic Studies Of 6-Halopurine Nucleoside In Snar Reactions; 6-(Azolyl, Alkylthio And Fluoro)-Purine Nucleosides As Substrates For Suzuki Reactions, Jiangqiong Liu

Theses and Dissertations

In chapter 1, we describe development of a mild and efficient method for SNAr iodination of 6-chloropurine 2'-deoxynucleosides and nucleosides. Our studies demonstrate that 6-iodopurine nucleosides are excellent substrates for certain transition metal-catalyzed cross-coupling reactions. In chapter 2, we describe synthesis of protected 6-fluoro, 6-chloro, 6-bromo and 6-sulfonylpurine nucleosides. Comparisons among 6-fluoro-, 6-chloro-, 6-bromo, 6-iodo and 6-sulfonylpurine nucleosides for SNAr reactions with various N, O and S nucleophiles were investigated. Our results demonstrate that the 6-fluoropurine nucleoside is the best substrate for SNAr reactions among the four 6-halopurine nucleosides with oxygen, sulfur and aliphatic amine nucleophiles, and also with an …

Dna-Templated Nanomaterials, Hector Alejandro Becerril-Garcia

Theses and Dissertations

Nanomaterials display interesting physical and chemical properties depending on their shape, size and composition. Self assembly is an intriguing route to producing nanomaterials with controllable compositions and morphologies. DNA has been used to guide the self assembly of materials, resulting in: (1) metal nanowires; (2) metal or semiconductor nanorods; (3) carbon nanotubes; and (4) semiconductor, metal or biological nanoparticles. My work expands the range of DNA templated nanomaterials and develops novel ways of using DNA to pattern nanostructures on surfaces. I have performed the first synthesis of silver nanorods on single stranded DNA, an attractive material for localizing DNA coupled …

Investigation Of Novel Microseparation Techniques, Yansheng Liu

Theses and Dissertations

Ultrahigh pressure liquid chromatography (UHPLC) makes it possible to use very small particles (< 2 µm) as packing materials to provide high column efficiencies. Results from a careful comparison of small porous and nonporous particles show that when the particle size is small enough (< 2 µm), both porous and nonporous particles give excellent performance, and the differences in column efficiencies between porous and nonporous particles become insignificant. Columns packed with bare diamond particles could separate small molecules, especially polar molecules, however, severe tailing occurred for less polar compounds. The polybutadiene coated diamond particles gave greater retention and better separation of small molecules compared to bare particles, although no improvement in column efficiency was observed. Changes in surface bonding of thermally hydrogenated diamond particles was achieved by chemical modification using various organic peroxides with or without reagents containing long carbon chain functional groups. It appears that the alkyl groups were attached onto the diamond surface with limited coverage. LC experiments did not demonstrate good separation; however, changes in LC behavior were observed. A repetitive solvent programming approach was successfully applied to the analysis of a continuous sample stream in microbore LC. Each analysis cycle consisted of three steps: pseudo-injection, elution and rinse. In the pseudo-injection step, elution with a non- or poor-eluting solvent produced a concentrated sample plug due to on-column focusing. Factors influencing peak symmetry, resolution and analysis cycle length were investigated. Quantitative analysis of a continuous sample stream is possible under certain operating conditions. Electric field gradient focusing (EFGF) devices with distributed resistor substrates could focus proteins in the separation channel, however, the focused bands were not stable, and the repeatability was poor due to the formation of bubbles and pH gradient in the separation channel. Both fiber-based and porous glass capillary-based planar EFGF devices with changing cross-sectional area (CCSA) channels were constructed and evaluated with the aid of a home-made scanning laser-induced fluorescence detection system. The fiber-based CCSA EFGF devices gave poorer performance compared with glass capillary based devices. Porous glass capillary-based EFGF devices could focus single proteins and separate mixtures of two to three proteins.

The Purification Of Helicobacter Pylori Urease Β Subunit Protein And Dna For Vaccine Production, Alyson Moll

Honors Capstones

No abstract provided.

The Role Of Phosducin-Like Protein As A Co-Chaperone With The Cytosolic Chaperonin Complex In Assembly Of The G Protein Βγ Subunit Dimer, Paul Jayson Ludtke

Theses and Dissertations

Phosducin-like protein (PhLP) has been shown to interact with the cytosolic chaperonin containing TCP-1 (CCT), and the βγ subunit dimer of heterotrimeric G proteins (Gβγ). Here we provide details obtained from cryo-electron microscopic and biochemical studies on the structure of the complex between the cytosolic chaperonin CCT and PhLP. Binding of PhLP to CCT occurs through only one of the two chaperonin rings, making multiple contacts with CCT through both its N- and C-terminal domains. In addition, we show that PhLP acts as a co-chaperonin along with CCT in mediating the assembly of the G protein βγ subunit and that …

Size Dependence Of Static And Dynamic Magnetic Properties In Nanoscale Square Permalloy Antidot Arrays, Minghui Yu, Leszek M. Malkinski, Leonard Spinu, Weilie Zhou, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

Permalloy antidot arrays with different square hole sizes ( , , and ) have been fabricated by means of electron-beam lithography and lift-off techniques. The smaller square hole size results in enhanced remanence and reduced coercivity in the antidot array. Multiple resonance modes were clearly observed for the magnetic field applied normal to the array plane, and double uniform resonance modes occurred when the field deviated more than 30° from the normal to the plane. Two distinct dipolar field patterns with different orientations and magnitudes split the uniform resonance into double resonance modes. The double resonance modes show uniaxial in-plane …

The Niemann-Pick Type C2 Protein Loads Isoglobotrihexosylceramide Onto Cd1d Molecules And Contributes To The Thymic Selection Of Nkt Cells, Paul B. Savage, Nicolas Schrantz, Yuval Sagiv, Yang Liu, Albert Bendelac, Luc Teyton

Faculty Publications

The Niemann-Pick type C2 (NPC2) protein is a small, soluble, lysosomal protein important for cholesterol and sphingolipid transport in the lysosome. The immunological phenotype of NPC2-deficient mice was limited to an impaired thymic selection of Valpha 14 natural killer T cells (NKT cells) and a subsequent reduction of NKT cells in the periphery. The remaining NKT cells failed to produce measurable quantities of interferon-gamma in vivo and in vitro after activation with alpha-galactosylceramide. In addition, thymocytes and splenocytes from NPC2-deficient mice were poor presenters of endogenous and exogenous lipids to CD1d-restricted Valpha 14 hybridoma cells. Importantly, we determined that similar …

Hiv/Aids In Pakistan: The Battle Begins, Mohammad A. Rai, Haider J. Warraich, Syed H. Ali, Vivek R. Nerurkar

Department of Biological & Biomedical Sciences

Pakistan, the second most populous Muslim nation in the world, has started to finally experience and confront the HIV/AIDS epidemic. The country had been relatively safe from any indigenous HIV cases for around two decades, with most of the infections being attributable to deported HIV positive migrants from the Gulf States. However, the virus finally seems to have found a home-base, as evidenced by the recent HIV outbreaks among the injection drug user community. Extremely high-risk behavior has also been documented among Hijras (sex workers) and long-distance truck drivers. The weak government response coupled with the extremely distressing social demographics …

Pressure Dissociation Of Integration Host Factor-Dna Complexes Reveals Flexibility-Dependent Structural Variation At The Protein-Dna Interface, Donald F. Senear, Vira Tretyachenko-Ladokhina, Michael L. Opel, Kimberly A. Aeling, G. Wesley Hatfield, Laurie M. Franklin, Reuben C. Darlington, J. B. A. Ross

Chemistry and Biochemistry Faculty Publications

E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236-39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. In contrast, if all elements are present, net binding energy is unaffected by deformation energy. We tested two hypotheses for this observation: in complexes containing all elements, (1) stiff DNA sequences are less bent upon binding IHF than flexible ones; or (2) DNA sequences …

Dynamic Polarizabilities Of Rare-Earth-Metal Atoms And Dispersion Coefficients For Their Interaction With Helium Atoms, Xi Chu, Alexander Dalgarno, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

The dynamic scalar and tensor polarizabilities of the rare-earth-metal atoms are calculated with time-dependent density functional theory. The frequency-dependent polarizabilities at imaginary frequencies are used to determine the isotropic and orientation-dependent van der Waals coefficients for the interactions of the rare-earth-metal atoms with helium atoms. The static polarizabilities are compared with other theoretical values and with experimental results. The agreement is satisfactory in most cases but there are some exceptions where the discrepancy between theory and experiment is significant. The derived isotropic van der Waals coefficients range between 37 and 50 E(H)a(0)(6) and the orientation-dependent coefficients between 2 and -1 …

Atp Activates A Reactive Oxygen Species-Dependent Oxidative Stress Response And Secretion Of Pro-Inflammatory Cytokines In Macrophages, Christiane M. Cruz, Alessandra Rinna, Henry Jay Forman, Ana L. M. Ventura, Pedro M. Persechini, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

Secretion of the proinflammatory cytokines, interleukin (IL)-1β and IL-18, usually requires two signals. The first, due to microbial products such as lipopolysaccharide, initiates transcription of the cytokine genes and accumulation of the precursor proteins. Cleavage and secretion of the cytokines is mediated by caspase-1, in association with an inflammasome containing Nalp3, which can be activated by binding of extracellular ATP to purinergic receptors. We show that treatment of macrophages with ATP results in production of reactive oxygen species (ROS), which stimulate the phosphatidylinositol 3-kinase (PI3K) pathway and subsequent Akt and ERK1/2 activation. ROS exerts its effect through glutathionylation of PTEN …

Cost-Effective Engineering Of A Small-Scale Bioreactor, John Tansey, Sadie R. Bartholomew

Chemistry Faculty Scholarship

Several methods exist for increasing the scale of cell culture in the laboratory. While these methods provide significant increases in biomass, they are often prohibitively expensive for many laboratories. We have engineered a small-scale bioreactor with a novel means of introducing oxygen through the catalytic breakdown of hydrogen peroxide using a manganese oxide catalyst. We have also adapted and modified an existing assay for dissolved oxygen to be compatible with culture conditions. In this system we have been able to culture CHO cells at densities of up to 10⁷ cells/mL without the use of automated feedback systems.

Total Parotidectomy Under Local Anesthesia: A Novel Technique, Kamran Shahid, Bilal Karim Siddiqui, Muhammad Hammad Tahir, Salman Bin Ayub, Ghulam Murtaza Memon, Adnan Yousuf, Arif Hussain, Osmani, Abdul Karim Siddiqui

Department of Biological & Biomedical Sciences

Parotidectomy is a common procedure usually done for a parotid mass necessitating a histological diagnosis. Operation is normally performed under General anesthesia with a nerve stimulator to facilitate facial nerve stimulation. We describe a new technique with reports of three cases, making total parotidectomy under local anesthesia possible. The ascending cervical branch of cervical plexus and the auriculotemporal nerve were anesthetized by bupivacaine 0.25% (2mg/kg) and lignocaine with adrenaline 7 mg/kg. Effective onset of anesthesia was within 15-25 minutes and the operations lasted between 2-3 hours without any complications. This offers advantage in high-risk patients where general anesthesia is contraindicated. …

Optimization Of Cutaneous Electrically Mediated Plasmid Dna Delivery Using Novel Electrode, L. C. Heller, M. J. Jaroszeski, D. Coppola, A. N. Mccray, J. Hickey, R. Heller

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is an established technique for enhancing plasmid delivery to many tissues in vivo. A critical component of this technique is the electrode configuration. Electroporation parameters were optimized for transgene expression with minimal tissue damage with a novel electrode. The highest transgene expression and efficiency of individual cell transformation with minimal damage was produced with eight 150 ms pulses at field strength of …

The Yeast Orthologue Of Grasp65 Forms A Complex With A Coiled-Coil Protein That Contributes To Er To Golgi Traffic, Rudy Behnia, Francis A. Barr, John J. Flanagan, Charles Barlowe, Sean Munro

Dartmouth Scholarship

The mammalian Golgi protein GRASP65 is required in assays that reconstitute cisternal stacking and vesicle tethering. Attached to membranes by an N-terminal myristoyl group, it recruits the coiled-coil protein GM130. The relevance of this system to budding yeasts has been unclear, as they lack an obvious orthologue of GM130, and their only GRASP65 relative (Grh1) lacks a myristoylation site and has even been suggested to act in a mitotic checkpoint. In this study, we show that Grh1 has an N-terminal amphipathic helix that is N-terminally acetylated and mediates association with the cis-Golgi. We find that Grh1 forms a complex with …

A Watershed Analysis Of Long Pond South: Implications For Water Quality And Land-Use Management [Presentation], Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: Long Pond, South (2007, 1995)

No abstract provided.

A Watershed Analysis Of Long Pond South: Implications For Water Quality And Land Use Management, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: Long Pond, South (2007, 1995)

The water quality of the South Basin of Long Pond, located in the Belgrade Lakes region of Maine, was investigated by the Colby Environmental Assessment Team (CEAT) from May to September of 2007. The physical, chemical, and biological characteristics of water quality were analyzed to evaluate the current health of the lake. The Long Pond South watershed was examined to investigate the effect of land-use patterns, including residential and commercial development, on the lake water quality. Data were also collected from road and shoreline surveys to produce maps highlighting areas that could potentially contribute to the degradation of water quality. …

Selective Cholesterol Dynamics Between Lipoproteins And Caveolae/Lipid Rafts, Stephen M. Storey, Adalberto M. Gallegos, Barbara P. Atshaves, Avery L. Mcintosh, Gregory G. Martin, Rebecca D. Parr, Kerstin K. Landrock, Ann B. Kier, Judith M. Ball, Friedhelm Schroeder

Faculty Publications

Although low-density lipoprotein (LDL) receptor-mediated cholesterol uptake through clathrin-coated pits is now well understood, the molecular details and organizing principles for selective cholesterol uptake/efflux (reverse cholesterol transport, RCT) from peripheral cells remain to be resolved. It is not yet completely clear whether RCT between serum lipoproteins and the plasma membrane occurs primarily through lipid rafts/caveolae or from non-raft domains. To begin to address these issues, lipid raft/caveolae-, caveolae-, and non-raft-enriched fractions were resolved from purified plasma membranes isolated from L-cell fibroblasts and MDCK cells by detergent-free affinity chromatography and compared with detergent-resistant membranes isolated from the same cells. Fluorescent sterol …

Effect Of N-Halosucinimides On 5-, 7- And 5,7-8-Quinolinol Sulfonic Acids / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

8-Quinolinol 5-, 7- and 5,7-sulfonic acids were treated with N-halosuccinimides (NXS) where the halogen atom was chlorine, bromine or iodine under different conditions of solvent, temperature and time. Under neutral or basic conditions the sulfonic acid group was retained while in dilute acid the S03H group was largely displaced by halogen. Excess NXS caused additional electrophilic substitution. Mild hydrolysis of 5-iodo-8-quinolinol- 7-sulfonic acid and 7-iodo-8-quinolinol-5-sulfonic acid with 15% sulfuric acid in acetic acid formed the 5- and 7-iodo-8-quinolinol respectively in high yield