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Biochemistry Commons™

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2007

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Articles 1 - 30 of 110

Full-Text Articles in Biochemistry

Preparation Of Divalent And Trivalent Antigens For Immunogical Studies On Degranulation Of Mast Cells And Preparation Of Ceragenins For Antiviral Studies Against Vaccinia Virus., Dianliang Geng Dec 2007

Preparation Of Divalent And Trivalent Antigens For Immunogical Studies On Degranulation Of Mast Cells And Preparation Of Ceragenins For Antiviral Studies Against Vaccinia Virus., Dianliang Geng

Theses and Dissertations

CHAPTER 1

Aggregation of receptors for IgE (Fc RI) causes mast cells and basophils to release preformed contents of granules, including histamine and a variety of enzymes. This process, called degranulation plays a central role in allergic reactions. Methods to study this process are to create multivalent ligands which can interact with the receptors and, in turn, lead to aggregation of the receptors. We prepared a series of fluorophore-labeled divalent and trivalent antigens to study the degranulation of mast cells. Trivalent antigens proved to be much better stimulators for degranulation of mast cells than divalent antigens. These results indicate that …

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Pyridinium Bisretinoids: Synthesis And Photoactivated Cytotoxicity, Junping Gao Dec 2007

Pyridinium Bisretinoids: Synthesis And Photoactivated Cytotoxicity, Junping Gao

Theses and Dissertations

This thesis discusses pyridinium bisretinoid compounds (PBRs), which were prepared for two purposes: 1) to use them as standards for detection of novel fluorophores in human RPE cells, which may be involved in age-related macular degeneration (AMD), and 2) to use them in the development of a targeted and triggered drug delivery system for cancer therapy. We prepared a selection of PBRs using a one-pot biomimetic method; synthesis, mechanisms for formation, and characterization of these compounds is described. We also explored the photoreactivity of three novel PBR compounds and found that these PBRs form oxidation products under blue-light irradiation. The …

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Study Of The Reproducibility Of Proteomics Methods And Variability Of Fruit Fly Proteomes., Thomas Franklin Culwell Dec 2007

Study Of The Reproducibility Of Proteomics Methods And Variability Of Fruit Fly Proteomes., Thomas Franklin Culwell

Theses and Dissertations

The reliability of biomarker discovery by means of proteomics has been called into question. It was speculated that "background noise" variation resulting from differences in preparation and handling of samples and proteome dynamics may mask subtle, yet important, differences due to the biological condition. Little is understood about complex proteomes and their variability. A critical aspect of proteomic biomarker research that is largely unexplored is the comparative reproducibility of certain methods such as two-dimensional gel electrophoresis and liquid chromatography/mass spectrometry. In particular, with liquid chromatography/mass spectrometry, it is not known whether variability in peptide quantitation is dependent on any of …

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Pyridinium Bis-Retinoids A2-Dopamine And A2-Cadaverine: Implications In Age-Related Macular Degeneration And Cancer, Mckenzie Ruth Pew Dec 2007

Pyridinium Bis-Retinoids A2-Dopamine And A2-Cadaverine: Implications In Age-Related Macular Degeneration And Cancer, Mckenzie Ruth Pew

Theses and Dissertations

Age-related macular degeneration (AMD) is the leading cause of blindness in the United States of America. The pyridinium bis-retinoid A2-ethanolamine (A2E) has been implicated to play a role in AMD. We have observed novel pyridinium bis-retinoids through melanolipofuscin and human RPE extractions that may also play a role in the pathology of AMD. We have begun the construction of an amino-retinoid library in order to identify these ocular compounds. The compounds from the amino-retinoid library are also used in a targeted and triggered drug delivery system for treating cancer. Folic acid is coupled with the amino-retinoids to specifically target cancer …

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Studies In The Biochemistry And Cell Biology Of Trypanosoma Brucei Hexokinases, Jeremy Chambers Dec 2007

Studies In The Biochemistry And Cell Biology Of Trypanosoma Brucei Hexokinases, Jeremy Chambers

All Dissertations

Trypanosoma brucei expresses two hexokinases (TbHK1 and TbHK2) that are 98% identical at the amino acid level. We previously found that recombinant TbHK1 (rTbHK1) has hexokinase activity, while rTbHK2 did not, a finding attributed to differences in the C-termini of the proteins. We found that the C-terminal tails of TbHK contained a novel motif specific for eukaryotic hexokinases found within the final helix of an ATP-binding domain. By altering the residues in the C-terminal tail of TbHK1 to resemble the residues found in TbHK2, we found that D454, F462, M466, and N469 were essential to TbHK1 catalysis. Additionally, we found …

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Effects Of Water Vapor On The Kinetics Of The Methylperoxy Radical Self-Reaction And Reaction With Hydroperoxy, Alecia Mower Dec 2007

Effects Of Water Vapor On The Kinetics Of The Methylperoxy Radical Self-Reaction And Reaction With Hydroperoxy, Alecia Mower

Theses and Dissertations

The gas phase reactions of CH3O2 + CH3O2, HO2 + HO2, and CH3O2 + HO2 in the presence of water vapor have been studied at temperatures between 263 and 303 K using laser flash photolysis coupled with UV time-resolved absorption detection at 220 nm and 260 nm. Water vapor concentration was quantified using tunable diode laser spectroscopy operating in the mid-IR. The HO2 self-reaction rate constant is significantly enhanced by water vapor, consistent with what others have reported, whereas CH3O2 self-reaction and the cross-reaction (CH3O2 + HO2) rate constants are nearly unaffected. The enhancement in the HO2 self-reaction rate coefficient …

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The Tropical Forest And Fire Emissions Experiment: Method Evaluation Of Volatile Organic Compound Emissions Measured By Ptr-Ms, Ftir, And Gc From Tropical Biomass Burning, T. G. Karl, Ted J. Christian, Robert J. Yokelson, Paulo Artaxo, Wei Min Hao, Alex Guenther Nov 2007

The Tropical Forest And Fire Emissions Experiment: Method Evaluation Of Volatile Organic Compound Emissions Measured By Ptr-Ms, Ftir, And Gc From Tropical Biomass Burning, T. G. Karl, Ted J. Christian, Robert J. Yokelson, Paulo Artaxo, Wei Min Hao, Alex Guenther

Chemistry and Biochemistry Faculty Publications

Volatile Organic Compound (VOC) emissions from fires in tropical forest fuels were quantified using Proton-Transfer-Reaction Mass Spectrometry (PTRMS), Fourier Transform Infrared Spectroscopy (FTIR) and gas chromatography (GC) coupled to PTRMS (GC-PTR-MS). We investigated VOC emissions from 19 controlled laboratory fires at the USFS (United States Forest Service) Fire Sciences Laboratory and 16 fires during an intensive airborne field campaign during the peak of the burning season in Brazil in 2004. The VOC emissions were dominated by oxygenated VOCs (OVOC) (OVOC/NMHC similar to 4:1, NMHC: non-methane hydrocarbons) The specificity of the PTR-MS instrument, which measures the mass to charge ratio of …

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1,3,7,10,14,17,21,28,31,42,52,55-Dodeca­Kis(Trifluoro­Meth­Yl)- 1,3,7,10,14,17,21,28,31,42,52,55-Dodeca­Hydro­(C60-IH)[5,6]Fullerene, Natalia B. Shustova Prof. Dr., O.P. Anderson, O. V. Boltalina, S. H. Strauss, I. E. Kareev Nov 2007

1,3,7,10,14,17,21,28,31,42,52,55-Dodeca­Kis(Trifluoro­Meth­Yl)- 1,3,7,10,14,17,21,28,31,42,52,55-Dodeca­Hydro­(C60-IH)[5,6]Fullerene, Natalia B. Shustova Prof. Dr., O.P. Anderson, O. V. Boltalina, S. H. Strauss, I. E. Kareev

Faculty Publications

The title compound, C72F36, is one of four isomers of C60(CF3)12 for which crystal structures have been obtained. The fullerene mol­ecule has an idealized Ih C60 core with the 12 CF3 groups arranged in an asymmetric fashion on two ribbons of edge-sharing C6(CF3)2 hexa­gons, a para–meta–para–para–para–meta–para ribbon and a para–meta–para ribbon, giving an overall pmp 3 mp,pmp structure. There are no cage Csp 3 …

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Microchip Liquid Chromatography And Capillary Electrophoresis Separations In Multilayer Microdevices, Hernan Vicente Fuentes Nov 2007

Microchip Liquid Chromatography And Capillary Electrophoresis Separations In Multilayer Microdevices, Hernan Vicente Fuentes

Theses and Dissertations

In this dissertation, several microfabricated devices are introduced to develop new applications in the area of chemical analysis. Electrochemical micropumps, chip-based liquid chromatography systems and multilayer capillary electrophoresis microdevices with crossover channels were fabricated using various substrates such as poly(dimethylsiloxane) (PDMS), glass, and poly(methyl methacrylate) (PMMA). I have demonstrated pressure-driven pumping of liquids in microfabricated channels using electrochemical actuation. PDMS-based micropumps were integrated easily with channel-containing PMMA substrates. Flow rates on the order of ~10 µL/min were achieved using low voltages (10 V). The potential of electrolysis-based pumping in microchannels was further evaluated for pressure driven microchip liquid chromatography (LC). …

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Microfluidic Electro-Osmotic Flow Pumps, John Mason Edwards Nov 2007

Microfluidic Electro-Osmotic Flow Pumps, John Mason Edwards

Theses and Dissertations

The need for miniaturized, portable devices to separate and detect unknown compounds has greatly multiplied, leading to an increased interest in microfluidics. Total integration of the detector and pump are necessary to decrease the overall size of the microfluidic device. Using previously developed thin film technologies, an electroosmotic flow (EOF) pump was incorporated in a microfluidic liquid chromatography device. An EOF pump was chosen because of its simple design and small size. EOF pumps fabricated on silicon and glass substrates were evaluated. The experimental flow rates were 0.19-2.30 microliters/minute for 40-400 V. The theoretical pump efficiency was calculated along with …

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Discovery Of Platelet-Type 12-Human Lipoxygenase Selective Inhibitors By High-Throughput Screening Of Structurally Diverse Libraries., Joshua D. Deschamps, Jeffrey T. Gautschi, Stephanie Whitman, Tyler A. Johnson, Nadine C. Gassner, Phillip Crews, Theodore R. Holman Nov 2007

Discovery Of Platelet-Type 12-Human Lipoxygenase Selective Inhibitors By High-Throughput Screening Of Structurally Diverse Libraries., Joshua D. Deschamps, Jeffrey T. Gautschi, Stephanie Whitman, Tyler A. Johnson, Nadine C. Gassner, Phillip Crews, Theodore R. Holman

Natural Sciences and Mathematics | Faculty Scholarship

Human lipoxygenases (hLO) have been implicated in a variety of diseases and cancers and each hLO isozyme appears to have distinct roles in cellular biology. This fact emphasizes the need for discovering selective hLO inhibitors for both understanding the role of specific lipoxygenases in the cell and developing pharmaceutical therapeutics. To this end, we have modified a known lipoxygenase assay for high-throughput (HTP) screening of both the National Cancer Institute (NCI) and the UC Santa Cruz marine extract library (UCSC-MEL) in search of platelet-type 12-hLO (12-hLO) selective inhibitors. The HTP screen led to the characterization of five novel 12-hLO inhibitors …

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Counter-Flow Ion Mobility Analysis: Design, Instrumentation, And Characterization, Nosa Agbonkonkon Nov 2007

Counter-Flow Ion Mobility Analysis: Design, Instrumentation, And Characterization, Nosa Agbonkonkon

Theses and Dissertations

The quest to achieve high resolution in ion mobility spectrometry (IMS) has continued to challenge scientist and engineers in the field of separation science. The low resolution presently attainable in IMS has continued to negatively impact its utility and acceptance. Until now, efforts to improve the resolution have mainly focused on better instrumentation and detection methods. However, since the resolution of IMS is diffusion limited, it makes sense to address this limitation in order to attain high resolution. This dissertation presents a new IMS technique, which utilizes a high electric field and opposing high gas flow velocity with the aim …

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A Conserved Cam- And Radial Spoke–Associated Complex Mediates Regulation Of Flagellar Dynein Activity, Erin E. Dymek, Elizabeth F. Smith Nov 2007

A Conserved Cam- And Radial Spoke–Associated Complex Mediates Regulation Of Flagellar Dynein Activity, Erin E. Dymek, Elizabeth F. Smith

Dartmouth Scholarship

For virtually all cilia and eukaryotic flagella, the second messengers calcium and cyclic adenosine monophosphate are implicated in modulating dynein- driven microtubule sliding to regulate beating. Calmodulin (CaM) localizes to the axoneme and is a key calcium sensor involved in regulating motility. Using immunoprecipitation and mass spectrometry, we identify members of a CaM-containing complex that are involved in regulating dynein activity. This complex includes flagellar-associated protein 91 (FAP91), which shares considerable sequence similarity to AAT-1, a protein originally identified in testis as an A-kinase anchor protein (AKAP)- binding protein. FAP91 directly interacts with radial spoke protein 3 (an AKAP), which …

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Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis Oct 2007

Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the π-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of …

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A Simple Array Platform For Microrna Analysis And Its Application In Mouse Tissues, Xiaoqing Tang, Jozsef Gal, Xun Zhuang, Wang-Xia Wang, Haining Zhu, Guiliang Tang Oct 2007

A Simple Array Platform For Microrna Analysis And Its Application In Mouse Tissues, Xiaoqing Tang, Jozsef Gal, Xun Zhuang, Wang-Xia Wang, Haining Zhu, Guiliang Tang

Plant and Soil Sciences Faculty Publications

MicroRNAs (miRNAs) are a novel class of small noncoding RNAs that regulate gene expression at the post-transcriptional level and play a critical role in many important biological processes. Most miRNAs are conserved between humans and mice, which makes it possible to analyze their expressions with a set of selected array probes. Here, we report a simple array platform that can detect 553 nonredundant miRNAs encompassing the entire set of miRNAs for humans and mice. The platform features carefully selected and designed probes with optimized hybridization parameters. Potential cross-reaction between mature miRNAs and their precursors was investigated. The array platform was …

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High-Throughput Screening For Fatty Acid Uptake Inhibitors In Humanized Yeast Identifies Atypical Antipsychotic Drugs That Cause Dyslipidemias, Hong Li, Paul N. Black, Aalap Chokshi, Angel Sandoval-Alvarez, Ravi Vatsyayan, Whitney Sealls, Concetta Dirusso Oct 2007

High-Throughput Screening For Fatty Acid Uptake Inhibitors In Humanized Yeast Identifies Atypical Antipsychotic Drugs That Cause Dyslipidemias, Hong Li, Paul N. Black, Aalap Chokshi, Angel Sandoval-Alvarez, Ravi Vatsyayan, Whitney Sealls, Concetta Dirusso

Department of Biochemistry: Faculty Publications

Fatty acids are implicated in the development of dyslipidemias, leading to type 2 diabetes and cardiovascular disease. We used a standardized small compound library to screen humanized yeast to identify compounds that inhibit fatty acid transport protein (FATP)-mediated fatty acid uptake into cells. This screening procedure used live yeast cells expressing human FATP2 to identify small compounds that reduced the import of a fluorescent fatty acid analog, 4,4-difluoro-5-methyl-4-bora-3a,4a-diaza-s-indacene-3-dodecanoic acid (C1-BODIPY-C12). The library used consisted of 2,080 compounds with known biological activities. Of these, ~1.8% reduced cell-associated C1-BODIPY-C12 fluorescence and were selected as potential inhibitors of human FATP2- mediated fatty acid …

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Gene Synthesis, Cloning, Expression, Purification And Biophysical Characterization Of The C2 Domain Of Human Tensin, Kiran Sukumar Gajula Oct 2007

Gene Synthesis, Cloning, Expression, Purification And Biophysical Characterization Of The C2 Domain Of Human Tensin, Kiran Sukumar Gajula

Doctoral Dissertations

Tensin is a large "docking" protein found in the adhesive junctions of animal cells and recruited early in the development of cell-substrate contacts. There it binds to the cytoplasmic domain of integrin β1 and caps the barbed ends of filamentous actin. This forms a rational basis for its implication in a direct role in the mechanics of membrane-cytoskeleton interactions. Tensin provides a physical link between the actin cytoskeleton, integrins, and other proteins at the cell-substrate contacts. Its overall biochemical properties are a function of its domain composition and architecture, i.e., the domains that are present and their relative positions in …

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The Functional Role Of Cysteine Residues For C-Abl Kinase Activity., Amanda Leonberg, Yuh-Cherng Chai Sep 2007

The Functional Role Of Cysteine Residues For C-Abl Kinase Activity., Amanda Leonberg, Yuh-Cherng Chai

Yuh-Cherng Chai

S-glutathionylation, the formation of mixed disulfides of glutathione with cysteine residues of proteins, is a broadly observed physiological modification that occurs in response to oxidative stress. Since cysteine residues are particularly susceptible to oxidative modification by reactive oxygen species, S-glutathionylation can protect proteins from irreversible oxidation. In this study, we show that the kinase activity of the non-receptor tyrosine kinase c-Abl is inhibited by in vitro thiol modification; specifically, the cysteine residues of c-Abl are modified by S-glutathionylation and by thiol alkylating agents such as 4-acetamido-4′-maleimidylstilbene-2,2′-disulfonic acid and N-ethylmaleimide. Modification of cysteine residues of c-Abl tyrosine kinase using glutathione disulfide …

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The Tropical Forest And Fire Emissions Experiment: Trace Gases Emitted By Smoldering Logs And Dung From Deforestation And Pasture Fires In Brazil, Ted J. Christian, Robert J. Yokelson, João A. Carvalho, David W.T. Griffith, Ernesto C. Alvarado, José Carlos Santos, Turibio Gomes Soares Neto, Carlos A.Gurgel Veras, Wei Min Hao Sep 2007

The Tropical Forest And Fire Emissions Experiment: Trace Gases Emitted By Smoldering Logs And Dung From Deforestation And Pasture Fires In Brazil, Ted J. Christian, Robert J. Yokelson, João A. Carvalho, David W.T. Griffith, Ernesto C. Alvarado, José Carlos Santos, Turibio Gomes Soares Neto, Carlos A.Gurgel Veras, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

Earlier work showed that Amazonian biomass burning produces both lofted and initially unlofted emissions in large amounts. A mobile, Fourier transform infrared spectrometer (FTIR) measured the unlofted emissions of 17 trace gases from residual smoldering combustion (RSC) of logs as part of the Tropical Forest and Fire Emissions Experiment (TROFFEE) during the 2004 Amazonian dry season. The RSC emissions were highly variable and the few earlier RSC measurements lay near the high end of combustion efficiency observed in this study. Fuel consumption by RSC was ∼5% of total for a planned deforestation fire. Much regional RSC probably occurs in the …

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The Tropical Forest And Fire Emissions Experiment: Emission, Chemistry, And Transport Of Biogenic Volatile Organic Compounds In The Lower Atmosphere Over Amazonia, Thomas Karl, Alex Guenther, Robert J. Yokelson, Jim Greenberg, Mark Potosnak, Donald R. Blake, Paulo Artaxo Sep 2007

The Tropical Forest And Fire Emissions Experiment: Emission, Chemistry, And Transport Of Biogenic Volatile Organic Compounds In The Lower Atmosphere Over Amazonia, Thomas Karl, Alex Guenther, Robert J. Yokelson, Jim Greenberg, Mark Potosnak, Donald R. Blake, Paulo Artaxo

Chemistry and Biochemistry Faculty Publications

Airborne and ground-based mixing ratio and flux measurements using eddy covariance (EC) and for the first time the mixed layer gradient (MLG) and mixed layer variance (MLV) techniques are used to assess the impact of isoprene and monoterpene emissions on atmospheric chemistry in the Amazon basin. Average noon isoprene (7.8 +/- 2.3 mg/m(2)/h) and monoterpene fluxes (1.2 +/- 0.5 mg/m(2)/h)compared well between ground and airborne measurements and are higher than fluxes estimated in this region during other seasons. The biogenic emission model, Model of Emissions of Gases and Aerosols from Nature (MEGAN), estimates fluxes that are within the model and …

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Novel Perturbation Approach For The Structure Factor Of The Attractive Hard-Core Yukawa Fluid, Andrij Trokhymchuk, Roman Melnyk, Filip Moucka, Ivo Nezbeda Sep 2007

Novel Perturbation Approach For The Structure Factor Of The Attractive Hard-Core Yukawa Fluid, Andrij Trokhymchuk, Roman Melnyk, Filip Moucka, Ivo Nezbeda

Faculty Publications

A novel perturbation approach for the structure factor S(k) of the Lennard-Jones-type Yukawa fluid with z=1.8 is presented. An approach is based on a new reference system, that is, the short-range Yukawa model with z0 > z=1.8. By choosing for the reference system the value z0=6, it is shown that (i) the proposed approach for S(k) performs much better than the traditional hard-sphere reference perturbation method does; (ii) the use of an approximate mean spherical (MSA) description of the reference structure factor provides the results for S(k) that are more accurate as those obtained from the direct MSA computations; and (iii) …

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A Role For The Forebrain In Mediating Time-Of-Day Differences In Glucocorticoid Counterregulatory Responses To Hypoglycemia In Rats, Lori M. Gorton, Arshad M. Khan, Maryann Bohland, Graciela Sanchez-Watts, Casey M. Donovan, Alan G. Watts Sep 2007

A Role For The Forebrain In Mediating Time-Of-Day Differences In Glucocorticoid Counterregulatory Responses To Hypoglycemia In Rats, Lori M. Gorton, Arshad M. Khan, Maryann Bohland, Graciela Sanchez-Watts, Casey M. Donovan, Alan G. Watts

Arshad M. Khan, Ph.D.

No abstract provided.

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Phenylalanyl-Trna Synthetase Editing Defects Result In Efficient Mistranslation Of Phenylalanine Codons As Tyrosine, Jiqiang Ling, Srujana S. Yadavalli, Michael Ibba Sep 2007

Phenylalanyl-Trna Synthetase Editing Defects Result In Efficient Mistranslation Of Phenylalanine Codons As Tyrosine, Jiqiang Ling, Srujana S. Yadavalli, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Translational quality control is monitored at several steps, including substrate selection by aminoacyl-tRNA synthetases (aaRSs), and discrimination of aminoacyl-tRNAs by elongation factor Tu (EF-Tu) and the ribosome. Phenylalanyl-tRNA synthetase (PheRS) misactivates Tyr but is able to correct the mistake using a proofreading activity named editing. Previously we found that overproduction of editing-defective PheRS resulted in Tyr incorporation at Phe-encoded positions in vivo , although the misreading efficiency could not be estimated. This raised the question as to whether or not EF-Tu and the ribosome provide further proofreading mechanisms to prevent mistranslation of Phe codons by Tyr. Here we show that, …

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A Rhizosphere Fungus Enhances Arabidopsis Thermotolerance Through Production Of An Hsp90 Inhibitor, Catherine A. Mclellan, Thomas J. Turbyville, E. M. Kithsiri Wijeratne, Arthur Kerschen, Elizabeth Vierling, Christine Queitsch, Luke Whitesell, A. A. Leslie Gunatilaka Sep 2007

A Rhizosphere Fungus Enhances Arabidopsis Thermotolerance Through Production Of An Hsp90 Inhibitor, Catherine A. Mclellan, Thomas J. Turbyville, E. M. Kithsiri Wijeratne, Arthur Kerschen, Elizabeth Vierling, Christine Queitsch, Luke Whitesell, A. A. Leslie Gunatilaka

Elizabeth Vierling

The molecular chaperone HEAT SHOCK PROTEIN90 (HSP90) is essential for the maturation of key regulatory proteins in eukaryotes and for the response to temperature stress. Earlier, we have reported that fungi living in association with plants of the Sonoran desert produce small molecule inhibitors of mammalian HSP90. Here, we address whether elaboration of the HSP90 inhibitor monocillin I (MON) by the rhizosphere fungus Paraphaeosphaeria quadriseptata affects plant HSP90 and plant environmental responsiveness. We demonstrate that MON binds Arabidopsis (Arabidopsis thaliana) HSP90 and can inhibit the function of HSP90 in lysates of wheat (Triticum aestivum) germ. MON treatment of Arabidopsis seedlings …

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Elongation Factor G Stabilizes The Hybrid-State Conformation Of The 70s Ribosome, P. Clint Spiegel, Dmitri N. Ermolenko, Harry F. Noller Sep 2007

Elongation Factor G Stabilizes The Hybrid-State Conformation Of The 70s Ribosome, P. Clint Spiegel, Dmitri N. Ermolenko, Harry F. Noller

Chemistry Faculty and Staff Publications

Following peptide bond formation, transfer RNAs (tRNAs) and messenger RNA (mRNA) are translocated through the ribosome, a process catalyzed by elongation factor EF-G. Here, we have used a combination of chemical footprinting, peptidyl transferase activity assays, and mRNA toeprinting to monitor the effects of EF-G on the positions of tRNA and mRNA relative to the A, P, and E sites of the ribosome in the presence of GTP, GDP, GDPNP, and fusidic acid. Chemical footprinting experiments show that binding of EF-G in the presence of the non-hydrolyzable GTP analog GDPNP or GDP·fusidic acid induces movement of a deacylated tRNA from …

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The Effect Of Residue C:N Ratio On The Turnover Of N And C In Various Soil Organic Matter Fractions, Ana B. Wingeyer Sep 2007

The Effect Of Residue C:N Ratio On The Turnover Of N And C In Various Soil Organic Matter Fractions, Ana B. Wingeyer

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Identifying soil organic matter (SOM) fractions that contribute to soil indigenous nitrogen (N) supply and understanding their turnover under different management constitute necessary tools toward an efficient N use. The objectives of this study were: i) trace the endpoint of carbon (C) flux from residue inputs into SOM; and ii) asses the role of the light fraction (LF), mobile humic acid (MHA) fraction and calcium humate (CaHA) fraction as N sources for heterotrophic decomposition of fresh plant residues with contrasting C:N ratio. A long-term aerobic soil incubation was carried out on 15N-labeled soil samples from Lincoln and Mead, NE. …

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An Aminoacyl-Trna Synthetase: Elongation Factor Complex For Substrate Channeling In Archaeal Translation, Corinne D. Hausmann, Mette Praetorius-Ibba, Michael Ibba Sep 2007

An Aminoacyl-Trna Synthetase: Elongation Factor Complex For Substrate Channeling In Archaeal Translation, Corinne D. Hausmann, Mette Praetorius-Ibba, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Translation requires the specific attachment of amino acids to tRNAs by aminoacyl-tRNA synthetases (aaRSs) and the subsequent delivery of aminoacyl-tRNAs to the ribosome by elongation factor 1 alpha (EF-1α). Interactions between EF-1α and various aaRSs have been described in eukaryotes, but the role of these complexes remains unclear. To investigate possible interactions between EF-1α and other cellular components, a yeast two-hybrid screen was performed for the archaeon Methanothermobacter thermautotrophicus. EF-1α was found to form a stable complex with leucyl-tRNA synthetase (LeuRS; KD = 0.7 μ M). Complex formation had little effect on EF-1α activity, but increased the kcat …

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The Yeast Integral Membrane Protein Apq12 Potentially Links Membrane Dynamics To Assembly Of Nuclear Pore Complexes, John J. Scarcelli, Christin A. Hodge, Charles N. Cole Aug 2007

The Yeast Integral Membrane Protein Apq12 Potentially Links Membrane Dynamics To Assembly Of Nuclear Pore Complexes, John J. Scarcelli, Christin A. Hodge, Charles N. Cole

Dartmouth Scholarship

Although the structure and function of components of the nuclear pore complex (NPC) have been the focus of many studies, relatively little is known about NPC biogenesis. In this study, we report that Apq12 is required for efficient NPC biogenesis in Saccharomyces cerevisiae. Apq12 is an integral membrane protein of the nuclear envelope (NE) and endoplasmic reticulum. Cells lacking Apq12 are cold sensitive for growth, and a subset of their nucleoporins (Nups), those that are primarily components of the cytoplasmic fibrils of the NPC, mislocalize to the cytoplasm. APQ12 deletion also causes defects in NE morphology. In the absence of …

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Surface Modification Of Cetyltrimethylammonium Bromide-Capped Gold Nanorods To Make Molecular Probes, Chenxu Yu, Leo Varghese, Joseph Irudayaraj Aug 2007

Surface Modification Of Cetyltrimethylammonium Bromide-Capped Gold Nanorods To Make Molecular Probes, Chenxu Yu, Leo Varghese, Joseph Irudayaraj

Chenxu Yu

A chemical procedure to replace the cetyltrimethylammonium bromide (CTAB) cap on gold nanorods (GNRs) fabricated through seed-mediated growth with organothiol compounds [3-animo-5-mercapto-1,2,4-triazole (AMTAZ) and 11-mercaptoundecaonic acid (MUDA)] was developed to reduce the cytotoxity of GNRs and facilitate further biofunctionalization. Compared to phosphatidylcholine (PC) modification, our procedure yields stable GNRs that are biocompatible and suitable for whole-cell studies. The PC-, AMTAZ-, and MUDA-activated GNRs all showed low cytotoxicity. By choosing different organothiols, net positive or negative charges could be created on the nanorod surface, for different applications. Gold nanorod molecular probes (GNrMPs) were fabricated by subsequent attachment of antibodies to the …

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The Use Of Non-Natural Nucleotides To Probe Template-Independent Dna Synthesis, Anthony J. Berdis, David Mccutcheon Aug 2007

The Use Of Non-Natural Nucleotides To Probe Template-Independent Dna Synthesis, Anthony J. Berdis, David Mccutcheon

Chemistry Faculty Publications

The vast majority of DNA polymerases use the complementary templating strand of DNA to guide each nucleotide incorporation. There are instances, however, in which polymerases can efficiently incorporate nucleotides in the absence of templating information. This process, known as translesion DNA synthesis, can alter the proper genetic code of an organism. To further elucidate the mechanism of template-independent DNA synthesis, we monitored the incorporation of various nucleotides at the “blunt-end” of duplex DNA by the high-fidelity bacteriophage T4 DNA polymerase. Although natural nucleotides are not incorporated at the blunt-end, a limited subset of non-natural indolyl analogues containing extensive π-electron surface …

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