Biochemistry Commons^™

Ion Transport Behaviors Upstream And Downstream From The Sampling Cone Of An Inductively Coupled Plasma Mass Spectrometer, Haibin Ma

Theses and Dissertations

Inductively coupled plasma - mass spectrometry (ICP-MS) is the technique of choice worldwide for trace elemental determinations because of its excellent ionization ability, low detection limits and fast analysis speeds. However, the ICP-MS still suffers from some disadvantages, such as spectral overlap and severe matrix effects. Matrix effects or interferences, partly arise from changes in the analyte transmission through the interfacial region between the ICP and mass spectrometer with changes in sample matrix. Better understanding of the transmission behaviors of analyte through the sampling and skimmer cones will provide the insights needed to alleviate matrix interferences and to improve the …

Relaxation Of Vibrationally Excited Trifluorobenzene And Tetrafluorobenzene By Collisions With Carbon Dioxide, Alan M. Johnson

Theses and Dissertations

An investigation into the relaxation of highly vibrationally excited trifluorobenzene and tetrafluorobenzene following collisions with carbon dioxide was performed using diode laser transient absorption spectroscopy. A 248 nm excimer laser prepared the vibrationally hot (E'~41,000 cm-1) fluorobenzene molecules. Large amounts of translational and rotational energy are transferred through collisions between the hot donor molecule and CO2. Rate constants and collisional probabilities were calculated by probing the high J states (J=58~80) of CO2 in the vibrational ground state, 0000, with measurements taken 1 µsec, ¼ the mean gas collision time, following each excimer laser pulse. The energy transfer probability distribution function, …

The Role Of Smpb In The Early Stages Of Trans-Translation, Deanna June Cazier

Theses and Dissertations

Ribosomes stall on defective messenger RNA transcripts in eubacteria. Without a mechanism to release stalled ribosomes, these cells would die. Transfer-messenger RNA (tmRNA) and small protein B (SmpB) reactivate stalled ribosomes in a process known as trans-translation. Together, tmRNA and SmpB mimic alanyl-tRNA, entering the A site of stalled ribosomes and accepting transfer of the stalled polypeptide. A portion of tmRNA is then positioned as a template for the ribosome to resume translating. The tmRNA open reading frame encodes a proteolysis tag to mark the aberrant polypeptide for degradation and a stop codon to release the ribosome. How are tmRNA …

Applications And Potentials For Biogenic Methane Recovery Operations In Nebraska Agriculture, Industry, And Economic Development, David Micheal Dingman

Department of Environmental Studies: Undergraduate Student Theses

ABSTRACT: This thesis report illustrates the applications and potentials of biogenic methane recovery in Nebraska’s agricultural and industrial sectors and as a means for increasing sustainable economic development in the state’s rural communities. As the nation moves toward a new green economy, biogenic methane recovery as a waste management strategy and renewable energy resource presents significant opportunities for Nebraska to be a national and world leader in agricultural and industrial innovation, advanced research and development of renewable energy technology, and generation of new product markets. Nebraska’s agricultural economy provides a distinct advantage to the state for supporting methane recovery operations …

Novel Cinchona Alkoloid Derived Ammonium Salts As Phase-Transfer Catalysts For The Asymmetric Synthesis Of Beta-Hydroxy Alpha-Amino Acids Via Aldol Reactions And Total Synthesis Of Celogentin C., Bing Ma

Theses and Dissertations

Project I. Cinchona alkaloid-derived quaternary ammonium salts have been successfully used as phase-transfer catalysts, particularly in asymmetric alkylations. Our group applied this type of catalyst in the synthesis of β-hydroxy α-amino acids via aldol reactions and discovered that the Park-Jew catalyst afforded good yields and good enantiomeric excess of the syn diasteromers, but negligible diastereoselectivity. This project was therefore focused on the synthesis of novel cinchonidine-derived catalysts with the Park-Jew catalyst as the lead structure. The C3 position of cinchonidine nucleus was modified to achieve dimers and catalysts possessing electron-deficient alkyne and alkene moieties. Synthesized catalysts were tested in the …

Louisiana: A Model For Advancing Regional E-Research Through Cyberinfrastructure, Daniel S. Katz, Gabrielle Allen, Ricardo Cortez, Carolina Cruz-Neira, Raju Gottumukkala, Zeno D. Greenwood, Les Guice, Shantenu Jha, Ramsesh Kolluru, Tevfik Kosar, Lonnie Leger, Honggao Liu, Charlie Mcmahon, Jarek Nabrzyski, Bety Rodriguez-Milla, Ed Seidel, Greg Speyrer, Michael Stubblefield, Brian Voss, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

Louisiana researchers and universities are leading a concentrated, collaborative effort to advance statewide e-Research through a new cyberinfrastructure: computing systems, data storage systems, advanced instruments and data repositories, visualization environments and people, all linked together by software programs and high-performance networks. This effort has led to a set of interlinked projects that have started making a significant difference in the state, and has created an environment that encourages increased collaboration, leading to new e-Research. This paper describes the overall effort, the new projects and environment and the results to date.

Mnte-2-Pyp And Radiation In A Prostate Cancer Model: Implications For Radiotherapy, Adeola Y. Makinde

Loma Linda University Electronic Theses, Dissertations & Projects

A major limitation of successful radiation therapy in cancer treatment is the increase in normal tissue damage as higher doses are used to achieve greater tumor destruction. Radiation dose optimization in cancer therapy requires achieving maximum tumor destruction with minimal damage to normal tissue Antioxidants have been shown to protect normal tissues against radiation damage, as radiation-induced tissue damage results predominantly from reactive oxygen species that directly damage cellular components. However, for effective use as normal tissue radioprotectants in radiotherapy, these antioxidants must not protect the tumors. Mn (III) tetrakis (N-ethylpyridinium-2-yl) porphyrin (MnTE-2-PyP) is a metalloporphyrin antioxidant that has been …

Genetic Analysis Of Ribosome Stalling And Rescue, Douglas Ray Tanner

Theses and Dissertations

In eubacteria, ribosome stalling on broken messenger RNA transcripts can lead to cell death. The trans-translation quality control mechanism rescues many of these stalled ribosomes. In this process, tmRNA enters stalled ribosomes by mimicking a transfer RNA, accepting the stalled nascent peptide. The ribosome then releases the broken mRNA and resumes translation on a coding region within tmRNA itself. Translation of tmRNA marks the nascent peptide for destruction by the addition of a short proteolysis tag and the ribosome is released at a stop codon within the tmRNA open reading frame. An intriguing aspect of trans-translation is that …

Synthesis And Evaluation Of Stimulatory Properties Of Glycolipids For Natural Killer T Cells, Xiangtian Long

Theses and Dissertations

Natural killer T cells (NKT cells) are a subset of T cells. They regulate a wide range of diseases including infection, tumor growth, and autoimmune diseases, through recognizing glycolipid antigens in the context of CD1d. An understanding of the scope of glycolipid antigens would facilitate use of this cell type in controlling immune responses. Till today, a lysosomal glycolipid, isoglobotrihexosylceramide (iGb3), is the only natural glycolipid that has been found to be recognized by both human and mouse NKT cells. To elucidate the molecular basis of this specific recognition, iGb3 variants were designed and prepared: i) replacement of the C26 …

Methyl Septanoside Hydrolysis As A Measure Of Carbohydrate Ring Flexibility: Substrate Synthesis And Kinetics Analysis, Shawn Michael Miller

Honors Scholar Theses

A number of seven-membered ring systems have been found to have promising enzyme inhibiting properties. The common explanation for their efficacy is the apparent improved flexibility that the ring-system has over smaller rings. In an attempt to probe the validity of this hypothesis, unnatural seven-membered ring carbohydrates have been generated and subjected to kinetics analysis using hydrolysis. In particular, methyl α- and β-D-glycero-D-guloseptanoside were subjected to acid-catalyzed hydrolysis and monitored via HNMR experiments. The rate constants of the reactions were determined and compared to the hydrolysis rate constants of comparable pyranose carbohydrates and found to be significantly faster, indicating an …

Identifying Biomarkers For Resistance To Novel Cisplatin Analogues In Human Lung, Breast And Prostate Cancers, Becky Michelle Hess

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cisplatin is a common therapeutic agent used in cancer treatment. Unfortunately, resistance to cisplatin in addition to severe side effects limits its use in cancer treatment. Two novel cisplatin analogues, 4DB and 4TB were shown to have varying cytotoxicity in lung, breast and prostate cancer cells. The hypothesis for this study states that the differences in 4DB and 4TB cytotoxicity among different tissue types is due to the type and efficiency of DNA repair mechanisms involved in response to these drugs.

To test the hypothesis, proteins involved in the rate limiting step of nucleotide excision repair (NER) and mismatch repair …

A Comparative Study Of The Structural Features And Kinetic Properties Of The Mofe And Vfe Proteins From Azotobacter Vinelandii, Miguel Alejandro Pabon Sanclemente

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Biological nitrogen fixation is accomplished in the bacterium Azotobacter vinelandii by means of three metalloenzymes: The molybdenum, vanadium, and iron-only nitrogenase. The knowledge regarding biological nitrogen fixation has come from studies on the Mo-dependent reaction. However, the V- and Fe-only-dependent reduction of nitrogen remains largely unknown.

By using homology modeling techniques, the protein folds that contain the metal cluster active sites for the V- and Fe-only nitrogenases were constructed. The models uncovered similarities and differences existing among the nitrogenases regarding the identity of the amino acid residues lining pivotal structural features for the correct functioning of the proteins. These differences, …

Ionic Selectivity In L-Type Calcium Channels By Electrostatics And Hard-Core Repulsion, Dezso Boda, Douglas Henderson, Monika Valisko, Bob Eisenberg, Dirk Gillespie

Faculty Publications

A physical model of selective "ion binding" in the L-type calcium channel is constructed, and consequences of the model are compared with experimental data. This reduced model treats only ions and the carboxylate oxygens of the EEEE locus explicitly and restricts interactions to hard-core repulsion and ion–ion and ion–dielectric electrostatic forces. The structural atoms provide a flexible environment for passing cations, thus resulting in a self-organized induced-fit model of the selectivity filter. Experimental conditions involving binary mixtures of alkali and/or alkaline earth metal ions are computed using equilibrium Monte Carlo simulations in the grand canonical ensemble. The model pore rejects …

Synthesis Of 2,4,5-Triaminocyclohexane Carboxylic Acid As A Novel 2-Deoxystreptamine Mimetic, Sarah Elizabeth Roberts

Theses and Dissertations

RNAs have become increasingly recognized as possible drug targets due to their involvement in important biochemical functions, as well as their unique but well-defined structures. Recently published crystal structures depict the binding of a series of aminoglycosides- or more specifically- 2-deoxystretamine (2-DOS), the most preserved central scaffold of aminoglycosides, to a conserved 5'-GU-3'region on their target RNAs. A novel unnatural γ-amino acid, 1, has been synthesized using 2-deoxystreptamine as a template through structure-based rational design. The unnatural amino acid has been designed to replace a glycosidic linkage with an amide bond, which may limit the promiscuous binding characteristics of aminoglycosides …

Role Of Molecular Chaperones In G Protein B5-Regulator Of G Protein Signaling Dimer Assembly And G Protein By Dimer Specificity, Alyson Cerny Howlett

Theses and Dissertations

In order for G protein signaling to occur, the G protein heterotrimer must be assembled from its nascent polypeptides. The most difficult step in this process is the formation of the Gβγ dimer from the free subunits since both are unstable in the absence of the other. Recent studies have shown that phosducin-like protein (PhLP1) works as a co-chaperone with the cytosolic chaperonin complex (CCT) to fold Gβ and mediate its interaction with Gγ. However, these studies did not address questions concerning the scope of PhLP1 and CCT-mediated Gβγ assembly, which are important questions given that there are four Gβs …

Light-Regulated Sampling Of Protein Kinase Activity (Ii), Collaborative Project

Dyson College- Seidenberg School of CSIS : Collaborative Projects and Presentations

This entry adheres to the use of the quad chart template to provide a succinct description only of the current research project undertaken by the participants. It provides for the following information

1. Participants and Affiliations
2. Overall Project Goals
3. Illustrative picture
4. Specific research/artistic/pedagogic foci

Functionalization, Characterization, And Applications Of Diamond Particles, Modification Of Planar Silicon, And Chemoetrics Analysis Of Ms Data, Li Yang

Theses and Dissertations

In spite of the stablility (lack of reactivity) of diamond powder, I have developed a method for tethering alkyl chains and polymers to deuterium/hydrogen-terminated diamond. One method is through ether linkages via thermolysis of di-tert-amyl peroxide (DTAP). This reaction with DTAP has also been applied to grow polymers on the diamond surface. The other method is atom transfer radical polymerization (ATRP), which was applied to grow polystyrene at the surface of diamond. Both polystyrene-modified diamond and sulfonated polystyrene-modified diamond can be prepared by either method, and can be used for solid phase extraction. Diamond stationary phases are stable under basic …

The First Attachment And Post-Functionalization Of Polybutadiene And Thio-Click Functionalized Polybutadiene On H-Terminated Si(111), Todd Devere Wickard

Theses and Dissertations

I report the attachment of polymers with pendant vinyl groups to hydrogen-terminated silicon(111) (Si(111)-H) under mild conditions. 1,2-addition polybutadiene (Mw 3200-3500) was attached to Si(111)-H at room temperature with visible light. I also report the partial functionalization, in solution, of 1,2-addition polybutadiene with various thiols using thiol-click chemistry. These compounds bind to Si(111)-H via visible light activation. The partially functionalized polybutadienes allow further functionalization at the surface through unreacted carbon-carbon double bonds. Surfaces were characterized with contact angle goniometry, spectroscopic ellipsometry, X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), and atomic force microscopy (AFM).

Catena-Poly[[(Pyridine-Κn)Copper(Ii)]-Μ3-Pyridine-2,6-Dicarboxylato-Κ3o2:O2′,N,O6:O6′], Manoj Trivedi, Daya Pandey, Nigam Rath

Chemistry & Biochemistry Faculty Works

In the title compound, [Cu(C7H3NO4)(C5H5N)]n, the CuII atom is in a slightly distorted octa­hedral coordination environment. Each CuII atom is bound to two N atoms and one O atom of the pyridine­dicarboxyl­ate (PDA) ligand in a tridentate manner, one N atom of the pyridine mol­ecule and two bridging carboxyl­ate O atoms of adjacent PDA ligands, leading to a linear one-dimensional chain running along the c axis. These chains are further assembled via weak C-H...O and [pi]-[pi] inter­actions into a three-dimensional supra­molecular network structure. The centroid-centroid distance between the [pi]-[pi] inter­acting pyridine rings is 3.9104 (13) Å. The two N atoms …

From Gene Mutation To Protein Characterization, David A. Moffet

Chemistry and Biochemistry Faculty Works

A seven-week “gene to protein” laboratory sequence is described for an undergraduate biochemistry laboratory course. Student pairs were given the task of introducing a point mutation of their choosing into the well studied protein, enhanced green fluorescent protein (EGFP). After conducting literature searches, each student group chose the mutation they wanted to introduce into EGFP. Students designed their sequence-specific mutagenic primers and constructed their desired mutation. The resulting EGFP mutant proteins were expressed in E. coli, purified and characterized. This laboratory sequence connected the major concepts of molecular biology and biochemistry, while incorporating the thrill of novel discovery in …

Polymer Microfluidic Devices For Bioanalysis, Xuefei Sun

Theses and Dissertations

Polymeric microchips have received increasing attention in chemical analysis because polymers have attractive properties, such as low cost, ease of fabrication, biocompatibility and high flexibility. However, commercial polymers usually exhibit analyte adsorption on their surfaces, which can interfere with microfluidic transport in, for example, chemical separations such as chromatography or electrophoresis. Usually, surface modification is required to eliminate this problem. To perform stable and durable surface modification, a new polymer, poly(methyl methacrylate-co-glycidyl methacrylate) (PGMAMMA) was prepared for microchip fabrication, which provides epoxy groups on the surface. Whole surface atom transfer radical polymerization (ATRP) and in-channel ATRP approaches were employed to …

Structure Of Human Dna Polymerase Κ Inserting Datp Opposite An 8-Oxog Dna Lesion, Rodrigo Vasquez-Del Carpio, Timothy D. Silverstein, Samer Lone, Michael K. Swan, Jayati R. Choudhury, Robert E. Johnson, Satya Prakash, Louise Prakash, Aneel K. Aggarwal

Chemical Sciences Faculty Publications

Background: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polκ) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polκ's preference for insertion of an A opposite 8-oxoG lesion, …

Liposomes Recruit Ipac To The Shigella Flexneri Type Iii Secretion Apparatus Needle As A Final Step In Secretion Induction, C. R. Epler, Nicholas E. Dickenson, A. J. Olive, W. L. Picking, W. D. Picking

Chemistry and Biochemistry Faculty Publications

Shigella flexneri contact with enterocytes induces a burst of protein secretion via its type III secretion apparatus (TTSA) as an initial step in cellular invasion. We have previously reported that IpaD is positioned at the TTSA needle tip (M. Espina et al., Infect. Immuno. 74:4391-4400, 2006). From this position, IpaD senses small molecules in the environment to control the presentation of IpaB to the needle tip. This step occurs without type III secretion induction or IpaC recruitment to the S. flexneri surface. IpaC is then transported to the S. flexneri surface when target cell lipids are added, and this event …

Loop Dynamics Of The Extracellular Domain Of Human Tissue Factor And Activation Of Factor Viia, Agnese S. Minazzo, Reuben C. Darlington, J. B. A. Ross

Chemistry and Biochemistry Faculty Publications

In the crystal structure of the complex between the soluble extracellular domain of tissue factor (sTF) and activesite- inhibited VIIa, residues 91 and 92 in the Pro⁷⁹-Pro⁹² loop of sTF interact with the catalytic domain of VIIa. It is not known, however, whether this loop has a role in allosteric activation of VIIa. Time-resolved fluorescence anisotropy measurements of probes covalently bound to sTF mutants E84C and T121C show that binding uninhibited Factor VIIa affects segmental motions in sTF. Glu⁸⁴ resides in the Pro⁷⁹-Pro⁹² loop, and Thr¹²¹ resides in the turn between the …

Emissions From Biomass Burning In The Yucatan, Robert J. Yokelson, J. D. Crounse, P. F. Decarlo, T. Karl, S. P. Urbanski, E. Atlas, T. Campos, Y. Shinozuka, V. Kasputin, A. D. Clarke, A. Weinheimer, D. J. Knapp, D. D. Montzka, J. Holloway, P. Weibring, F. Flocke, W. Zheng, D. Toohey, P. O. Wennberg, C. Wiedinmyer, L. Mauldin, A. Fried, D. Richter, J. Walega, J. L. Jimenez, K. Adachi, P. R. Buseck, S. R. Hall, R. Shetter

Chemistry and Biochemistry Faculty Publications

In March 2006 two instrumented aircraft made the first detailed field measurements of biomass burning (BB) emissions in the Northern Hemisphere tropics as part of the MILAGRO project. The aircraft were the National Center for Atmospheric Research C-130 and a University of Montana/US Forest Service Twin Otter. The initial emissions of up to 49 trace gas or particle species were measured from 20 deforestation and crop residue fires on the Yucatan peninsula. This included two trace gases useful as indicators of BB (HCN and acetonitrile) and several rarely, or never before, measured species: OH, peroxyacetic acid, propanoic acid, hydrogen peroxide, …

Biomass Burning And Urban Air Pollution Over The Central Mexican Plateau, J. D. Crounse, P. F. Decarlo, Donald R. Blake, L. K. Emmons, T. L. Campos, E. C. Apel, A. D. Clarke, A. J. Weinheimer, D. C. Mccabe, Robert J. Yokelson, J. L. Jimenez, P. O. Wennberg

Chemistry and Biochemistry Faculty Publications

Observations during the 2006 dry season of highly elevated concentrations of cyanides in the atmosphere above Mexico City (MC) and the surrounding plains demonstrate that biomass burning (BB) significantly impacted air quality in the region. We find that during the period of our measurements, fires contribute more than half of the organic aerosol mass and submicron aerosol scattering, and one third of the enhancement in benzene, reactive nitrogen, and carbon monoxide in the outflow from the plateau. The combination of biomass burning and anthropogenic emissions will affect ozone chemistry in the MC outflow.

Influence Of Irradiance And Iron On The Growth Of Colonial Phaeocystic Antarctica: Implications For Seasonal Bloom Dynamics In The Ross Sea, Antarctica, Nathan S. Garcia, Peter N. Sedwick, Giacomo R. Ditullio

OES Faculty Publications

Laboratory culture experiments were used to investigate the growth rate of colonial Phaeocystis anarctica as a function of irradiance and dissolved iron concentration. The experiments were conducted with a P. antarctica strain isolated from the southern Ross Sea, Antarctica, and made use of natural, low-iron (P. antarctica attained an average maximum cell-specific growth rate of 0.37 d^-1at an irradiance of 68 μE m^-2s^-1, above which growth rates decreased to 0.27 d^-1 at an irradiance of 314 μE m^-2s^-1. The dependence of growth rate on ambient dissolved iron concentration was …

Genetically Engineered Repetitive Polypeptides : Design, Synthesis, Characterization, And Applications, Natalya I. Topilina

Legacy Theses & Dissertations (2009 - 2024)

This work is dedicated to the investigation of protein folding with the emphasis on the aggregation and amyloid fibrils formation. The focus of the research is to elucidate the relationship between polypeptide chain sequence and folding/aggregation properties. For this purpose, i) libraries of the de novo macromolecular repetitive β-sheet forming polypeptides were designed, and ii) the strategy for their rapid creation was developed. The strategy enables retention of a basic polypeptide core, yet allowing variations in the repetitive sequence, degree of polymerization and distribution of specific amino acids. The polypeptides were expressed in E. coli, purified, and characterized by various …

Asymmetric Transfer Hydrogenation Of Allylic Alcohols With Homogeneous Chiral Ruthenium Catalysts: A Proposed Mechanism, Marie G. Beauchamps

Seton Hall University Dissertations and Theses (ETDs)

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Pressure-Driven Transport Of Particles Through A Converging-Diverging Microchannel, Ye Ai, Sang W. Joo, Xiangchun Xuan, Shizhi Qian

Mechanical & Aerospace Engineering Faculty Publications

Pressure-driven transport of particles through a symmetric converging-diverging microchannel is studied by solving a coupled nonlinear system, which is composed of the Navier-Stokes and continuity equations using the arbitrary Lagrangian-Eulerian finite-element technique. The predicted particle translation is in good agreement with existing experimental observations. The effects of pressure gradient, particle size, channel geometry, and a particle's initial location on the particle transport are investigated. The pressure gradient has no effect on the ratio of the translational velocity of particles through a converging-diverging channel to that in the upstream straight channel. Particles are generally accelerated in the converging region and then …