Biochemistry, Biophysics, and Structural Biology Commons^™

Enhancing Fertiliser Use Efficiency For Transplanted Vegetables, Dennis Phillips, Aileen Reid, Gavin D'Adhemar

Horticulture research reports

Horticulture Australia (HAL) Project No. VG04018.

Project VG 04018 ‘Enhancing fertiliser use efficiency for transplanted vegetables’ showed that spraying highly concentrated solutions containing nitrogen over newly transplanted vegetable seedlings for between 14 and 21 days after planting can increase marketable yields by as much as 300% compared to other methods of fertiliser application. Crops that this method has been successfully tested on in this study by the W.A. Department of Agriculture and Food include iceberg and Cos lettuce, broccoli, cauliflower, Chinese cabbage (wombok), celery and cabbage.

The research was conducted on virgin sandy soils of the Swan Coastal Plain near …

Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha

Faculty Publications, Chemistry

Insertion of hydrophobic groups in a silica matrix, by addition of propyl- or trifluoropropyltrimethoxysilane, leads to a surprising increase in the helical content of apomyoglobin following encapsulation by the sol–gel technique

Characterization Of Power Induced Heating And Damage In Fiber Optic Probes For Near-Field Scanning Optical Microscopy, Nicholas E. Dickenson, E. S. Erickson, O. L. Mooren, R. C. Dunn

Chemistry and Biochemistry Faculty Publications

Tip-induced sample heating in near-field scanning optical microscopy (NSOM) is studied for fiber optic probes fabricated using the chemical etching technique. To characterize sample heating from etched NSOM probes, the spectra of a thermochromic polymer sample are measured as a function of probe output power, as was previously reported for pulled NSOM probes. The results reveal that sample heating increases rapidly to ~55–60°C as output powers reach ~50 nW. At higher output powers, the sample heating remains approximately constant up to the maximum power studied of ~450 nW. The sample heating profiles measured for etched NSOM probes are consistent with …

A New N-Terminal Recognition Domain In Caveolin-1 Interacts With Sterol Carrier Protein-2 (Scp-2), Rebecca D. Parr, Gregory G. Martin, Heather A. Hostetler, Megan E. Schroeder, Kiran D. Mir, Ann B. Kier, Judith M. Ball, Friedhelm Schroeder

Faculty Publications

Although plasma membrane domains, such as caveolae, provide an organizing principle for signaling pathways and cholesterol homeostasis in the cell, relatively little is known regarding specific mechanisms, whereby intracellular lipid-binding proteins are targeted to caveolae. Therefore, the interaction between caveolin-1 and sterol carrier protein-2 (SCP-2), a protein that binds and transfers both cholesterol and signaling lipids (e.g., phosphatidylinositides and sphingolipids), was examined by yeast two-hybrid, in vitro binding and fluorescence resonance energy transfer (FRET) analyses. Results of the in vivo and in vitro assays identified for the first time the N-terminal amino acids (aa) 1−32 amphipathic α helix of SCP-2 …

Emissions From Forest Fires Near Mexico City, Robert J. Yokelson, S. P. Urbanski, E. L. Atlas, D. W. Toohey, E. C. Alvarado, J. D. Crounse, P. O. Wennberg, M. E. Fisher, C. E. Wold, T. L. Campos, K. Adachi, P. R. Buseck, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

The emissions of NOx (defined as NO (nitric oxide) + NO2 (nitrogen dioxide)) and hydrogen cyanide (HCN), per unit amount of fuel burned, from fires in the pine forests that dominate the mountains surrounding Mexico City (MC) are about 2 times higher than normally observed for forest burning. The ammonia (NH3) emissions are about average for forest burning. The upper limit for the mass ratio of NOx to volatile organic compounds (VOC) for these MC-area mountain fires was similar to 0.38, which is similar to the NOx/VOC ratio in the MC urban area emissions inventory of 0.34, but much larger …

The Tropical Forest And Fire Emissions Experiment: Overview And Airborne Fire Emission Factor Measurements, Robert J. Yokelson, T. Karl, Paulo Artaxo, Donald R. Blake, Ted J. Christian, David W. T. Griffith, Alex Guenther, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

The Tropical Forest and Fire Emissions Experiment (TROFFEE) used laboratory measurements followed by airborne and ground based field campaigns during the 2004 Amazon dry season to quantify the emissions from pristine tropical forest and several plantations as well as the emissions, fuel consumption, and fire ecology of tropical deforestation fires. The airborne campaign used an Embraer 110B aircraft outfitted with whole air sampling in canisters, mass-calibrated nephelometry, ozone by UV absorbance, Fourier transform infrared spectroscopy (FTIR), and proton-transfer mass spectrometry (PTR-MS) to measure PM(10), O(3), CO(2), CO, NO, NO(2), HONO, HCN, NH(3), OCS, DMS, CH(4), and up to 48 non-methane …

Beta-Lactamase: An Ideal Reporter System For Monitoring Gene Expression In Live Eukaryotic Cells, Sohail A. Qureshi

Department of Biological & Biomedical Sciences

To gain insightful information about the mechanisms through which genes are activated and repressed requires gene reporter systems that are sensitive, robust, and cost-effective. Although numerous reporter gene technologies are commercially available, none are as sophisticated and user-friendly as beta-lactamase (BLA) when it comes to studying gene expression in live cells. This article presents an overview of the BLA technology and describes how it can be exploited for studying rare events such as homologous recombination in somatic cells and be used to deliver any DNA sequence of choice anywhere within the genome.

To Establish Accurate Local Adult Reference Ranges For Routine Chemistries In A Large Diagnostic Clinical Biochemistry Laboratory In The Hse South Area, Barbara Kenneally

Theses

The objectives of this project were:

i. To establish adult reference ranges for routine chemistries quoted in the Clinical Biochemistry Department, Cork University Hospital (CUH), by using samples from blood donors at the local blood bank. 120 samples of blood from male blood donors and 120 samples from female blood donors were collected from the Irish Blood Transfusion Service (Cork). These samples were analysed for 21 routine chemistry analytes, using non-parametric statistics.

ii. To study the statistics of nineteen routine chemistries of the adult population served by the laboratory over a one- month period. Results were collected for each of …

The Effect Of 1,25-Dihydroxy Vitamin D3 On At1 Cell Receptor Expression In Human Iliac Artery Endothelial Cells (Hiaec), Jenny Thomas

Theses and Dissertations

The renin-angiotensin system (RAS) plays an important part in homeostasis through angiotensin IPs role as a vasoconstrictor. Defects in the renin angiotensin system can lead to hypertension, heart attack, and stroke (Weir, 1999). Studies have shown an inverse relationship between Vitamin D3 and blood pressure (Li et al., 2002). While studies have been performed on vitamin D's effect on renin expression, little is known about vitamin D's effect on the angiotensin II high-affinity type 1 (ATi) receptor. The hypothesis for this study was that human iliac artery endothelial cells (HIAEC) supplemented with 1,25-dihydroxy vitamin D3 will express less AT] receptor …

Pathways Of Anaerobic Carbon Cycling Across An Ombrotrophic–Minerotrophic Peatland Gradient, Jason K. Keller, Scott D. Bridgham

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatland soils represent globally significant stores of carbon, and understanding carbon cycling pathways in these ecosystems has important implications for global climate change. We measured aceticlastic and autotrophic methanogenesis, sulfate reduction, denitrification, and iron reduction in a bog, an intermediate fen, and a rich fen in the Upper Peninsula of Michigan for one growing season. In 3-d anaerobic incubations of slurried peat, denitrification and iron reduction were minor components of anaerobic carbon mineralization. Experiments using 14C-labeled methanogenic substrates showed that methanogenesis in these peatlands was primarily through the aceticlastic pathway, except early in the growing season in more ombrotrophic peatlands, …

Isolation, Characterization, And Degradation Of Bakuchiol From Psoralidium Tenuiflorum, Pei-Jan Hsu

Theses, Dissertations and Culminating Projects

Bioactivity guided fractionation of the EtOAc extract from Psoralidium tenuiflorum afforded the known compound bakuchiol as a racemic mixture. This compound was purified by liquid-liquid partitions and chromatographic techniques followed by characterization with ]H NMR, 13C NMR, and GCMS which agreed with previous literature. Previously, bakuchiol was reported from Psoralea corylirolia and Posoralea glandulosa in nature which are from the same family as P. tenuiflorum. This compound exhibited Staphylococcus epidermidis cytotoxicity.

Two Dimensional NMR (HHCOSY and HETCOR) of bakuchiol indicated a disagreement with the previously described NMR structural assignment; a reassignment is described herein.

Long-term storage followed by attempted reisolation …

The Biophysical Analysis Of The Human Telomeric Repeat (Ttaggg)4 And Characterization Of Porphyrin Binding In Potassium Solutions, Cosimo Antonacci

Seton Hall University Dissertations and Theses (ETDs)

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Peroxisomes Contain A Specific Phytanoly-Coa/Pristanoyl-Coa Thioesterase Acting As A Novel Auxiliary Enzyme In Alpha-And Beta-Oxidation Of Methyl-Branched Fatty Acids In Mouse, Maria Westin, Mary Hunt, Stefan Alexson

Articles

Phytanic acid and pristanic acid are derived from phytol, which enter the body via the diet. Phytanic acid contains a methyl group in position three and therefore cannot undergo b-oxidation directly, but instead must first undergo a-oxidation to pristanic acid, which then enters b-oxidation. Both these pathways occur in peroxisomes, and in this study we have identified a novel peroxisomal acyl-CoA thioesterase, named ACOT6, which we show is specifically involved in phytanic acid and pristanic acid metabolism. Sequence analysis of ACOT6 revealed a putative peroxisomal targeting signal at the C-terminal end, and cellular localization experiments verified it as a peroxisomal …

Development Of An Immunoturbidimetric Particle Enhanced Assay For Detection Of C-Reactive Protein, Maria Nicholas

Theses

Background: C-reactive protein (CRP) is a well-known marker for inflammation. Recent studies have demonstrated that increases in CRP concentrations are associated with future coronary events in apparently healthy men and women. The requirement for assays, capable of testing CRP concentrations within the range 1-lOmg/l, is therefore great.

Methods: Two CRP assays were developed. The Sensitive assay is capable of measuring CRP concentrations as low as lmg/l for use as a potential cardiac marker test. The Normal assay can measure concentrations from 5-400mg/l for establishing levels of inflammation. Both assays developed are latex particle enhanced immunoturbidimetric assays designed for use on …

Mutations In Transmembrane Domains 1, 4 And 9 Of The Plasmodium Falciparum Chloroquine Resistance Transporter Alter Susceptibility To Chloroquine, Quinine And Quinidine, Roland A. Cooper, Kristan D. Lane, Bingbing Deng, Jianbing Mu, Jigar J. Patel, Thomas E. Wellems, Xinzhuan Su, Michael T. Ferdig

Biological Sciences Faculty Publications

Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT) can result in verapamil-reversible CQ resistance and altered susceptibility to other antimalarials. PfCRT contains 10 membrane-spanning domains and is found in the digestive vacuole (DV) membrane of intraerythrocytic parasites. The mechanism by which PfCRT mediates CQ resistance is unclear although it is associated with decreased accumulation of drug within the DV. On the permissive background of the P. falciparum 106/1(K76) parasite line, we used single-step drug selection to generate isogenic clones containing unique pfcrt point mutations that resulted in amino acid changes in PfCRT transmembrane domains 1 (C72R, K76N, K76I …

In Vivo Imaging Of Transport And Biocompatibility Of Single Silver Nanoparticles In Early Development Of Zebrafish Embryos, Kerry J. Lee, Prakash D. Nallathamby, Lauren M. Browning, Christopher J. Osgood, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Real-time study of the transport and biocompatibility of nanomaterials in early embryonic development at single-nanoparticle resolution can offer new knowledge about the delivery and effects of nanomaterials in vivo, and provide new insights into molecular transport mechanisms in developing embryos. In this study, we directly characterized the transport of single silver nanoparticles into an in vivo model system (zebrafish embryos) and investigated their effects on early embryonic development at single-nanoparticle resolution in real time. We designed highly purified and stable (not aggregated and no photodecomposition) nanoparticles and developed single-nanoparticle optics and in vivo assays to enable the study. We …

Pldb, A Putative Phospholipase D Homologue, Mediates Quorum Sensing In Dictyostelium Discoideum Development, Yi Chen

Dissertations, Theses, and Capstone Projects

Quorum sensing, the ability to measure the local cell density, is required for animal cells to achieve proper cell growth, differentiation and development. However, because of the genetic intractability of mammalian cells, we study quorum sensing in the genetically pliable unicellular eukaryote Dictyostelium discoideum. D. discoideum cells live as individual cells under vegetative conditions. Starvation sets off development to a multicellular organism. But cells won't develop unless enough cells are under starvation conditions. Approximately 10⁵ cells are needed to form a fruiting body, the final stage of the development. When starved, cells are able to calculate the concentration …

A New Strategy For Assessing Selenoprotein Function: Sirna Knockdown/Knock-In Targeting The 3'-Utr, Min-Hyuk Yoo, Xue-Ming Xu, Anton A. Turanov, Bradley A. Carlson, Vadim N. Gladyshev, Dolph L. Hatfield

Department of Biochemistry: Faculty Publications

Selenocysteine insertion into protein in mammalian cells requires RNA elements in the 3'-untranslated regions (3'-UTRs) of selenoprotein genes. The occurrence of these conserved sequences should make selenoproteins particularly amenable for knockdown/knock-in strategies to examine selenoprotein functions. Herein, we utilized the 3'-UTR of various selenoproteins to knock down their expression using siRNAs and then knock in expression using constructs containing mutations within the target region. Thioredoxin reductase 1 (TR1) knockdown in a mouse kidney cell line resulted in the cells growing about 10% more slowly, being more sensitive to UV radiation, and having increased apoptosis in response to UV than control …

Mechanistic Studies Of The Long Chain Acyl-Coa Synthetase Faa1p From Saccharomyces Cerevisiae, Hong Li, Elaina M. Melton, Steven Quackenbush, Concetta C. Dirusso, Paul N. Black

Department of Biochemistry: Faculty Publications

Long chain acyl-CoA synthetase (ACSL; fatty acid CoA ligase: AMP forming; EC 6.2.1.3) catalyzes the formation of acyl-CoA through a process, which requires fatty acid, ATP and coenzymeA as substrates. In the yeast Saccharomyces cerevisiae the principal ACSL is Faa1p (encoded by the FAA1 gene). The preferred substrates for this enzyme are cis-monounsaturated long chain fatty acids. Our previous work has shown Faa1p is a principal component of a fatty acid transport/activation complex that also includes the fatty acid transport protein Fat1p. In the present work hexameric histidine tagged Faa1p was purified to homogeneity through a two-step process in the …

Evidence For A Pro-Oxidant Intermediate In The Assembly Of Cytochrome Oxidase, Oleh Khalimonchuk, Amanda Bird, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The hydrogen peroxide sensitivity of cells lacking two proteins,

Sco1 and Cox11, important in the assembly of cytochrome

c oxidase (CcO), is shown to arise from the transient accumulation

of a pro-oxidant heme A-Cox1 stalled intermediate. The

peroxide sensitivity of these cells is abrogated by a reduction in

either Cox1 expression or hemeAformation but exacerbated by

either enhanced Cox1 expression or heme A production arising

from overexpression of COX15. Sco1 and Cox11 are implicated

in the formation of the Cu_A and Cu_B sites of CcO, respectively.

The respective wild-type genes suppress the peroxide sensitivities

of sco1∆ …

Coa1 Links The Mss51 Post-Translational Function To Cox1 Cofactor Insertion In Cytochrome C Oxidase Assembly, Fabien Pierrel, Megan L. Bestwick, Paul A. Cobine, Oleh Khalimonchuk, Julia A. Cricco, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The assembly of cytochrome c oxidase (CcO) in yeast mitochondria is shown to be dependent on a new assembly factor designated Coa1 that associates with the mitochondrial inner membrane. Translation of the mitochondrial-encoded subunits of CcO occurs normally in coa1Δ cells, but these subunits fail to accumulate. The respiratory defect in coa1Δ cells is suppressed by high-copy MSS51, MDJ1 and COX10. Mss51 functions in Cox1 translation and elongation, whereas Cox10 participates in the biosynthesis of heme a, a key cofactor of CcO. Respiration in coa1Δ and shy1Δ cells is enhanced when Mss51 and …

Dna Multiplex Hybridization On Microarrays And Thermodynamic Stability In Solution: A Direct Comparison, Daniel J. Fish, M. Todd Horne, Greg P. Brewood, Jim P. Goodarzi, Saba Alemayehu, Ashwini Bhandiwad, Robert P. Searles, Albert S. Benight

Chemistry Faculty Publications and Presentations

Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH degrees , DeltaS degrees and DeltaG degrees of melting transitions in solution were evaluated directly using differential scanning calorimetry. Quantitative comparison with results from 63 multiplex microarray hybridization experiments provided a linear relationship for perfect match and most mismatch duplexes. Examination of outliers suggests that both duplex length and relative position of tandem mismatches could be important factors contributing to …

The Application Of Electrospray Ionization Coupled To Ultrahigh Resolution Mass Spectrometry For The Molecular Characterization Of Natural Organic Matter, Rachel L. Sleighter, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Mass spectrometry has recently played a key role in the understanding of natural organic matter (NOM) by providing molecular-level details about its composition. NOM, a complex assemblage of organic molecules present in natural waters and soils/sediments, has the ability to bind and transport anthropogenic materials. An improved understanding of its composition is crucial in order to understand how pollutants interact with NOM and how NOM cycles through global carbon cycles. In the past, low-resolution (> 3000) mass analyzers have offered some insights into the structure of NOM, but emerging ultrahigh resolution (> 200000) techniques such as electrospray ionization (ESI) coupled …

A Peroxisomal Acyltransferase In Mouse Identifies A Novel Pathway For Taurine Conjugation Of Fatty Acids., Sarah-Jayne Reilly, Eithne O'Shea, O'Byrne James, Stefan Alexson, Mary Hunt

Articles

A wide variety of endogenous carboxylic acids and xenobiotics are conjugated with amino acids, before excretion in urine or bile. The conjugation of carboxylic acids and bile acids with taurine and glycine has been widely characterized and de-novo synthesized bile acids are conjugated to either glycine or taurine in peroxisomes. Peroxisomes are also involved in the oxidation of several other lipid molecules, such as very long chain acyl-CoAs, branched chain acyl-CoAs and prostaglandins. In this study we have now identified a novel peroxisomal enzyme called acyl-CoA:amino acid N-acyltransferase (ACNAT1). Recombinantly expressed ACNAT1 acts as an acyltransferase that efficiently conjugates very …

Functional Association Between Three Archaeal Aminoacyl-Trna Synthetases, Mette Praetorius-Ibba, Corinne D. Hausmann, Molly Paras, Theresa E. Rogers, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacyl-tRNA synthetases (aaRSs) are responsible for attaching amino acids to their cognate tRNAs during protein synthesis. In eukaryotes aaRSs are commonly found in multi-enzyme complexes, although the role of these complexes is still not completely clear. Associations between aaRSs have also been reported in archaea, including a complex between prolyl-(ProRS) and leucyl-tRNA synthetases (LeuRS) in Methanothermobacter thermautotrophicus that enhances tRNA^Pro aminoacylation. Yeast two-hybrid screens suggested that lysyl-tRNA synthetase (LysRS) also associates with LeuRS in M. thermautotrophicus. Co-purification experiments confirmed that LeuRS, LysRS, and ProRS associate in cell-free extracts. LeuRS bound LysRS and ProRS with a comparable K_{D …}

Synthesis And Optical Properties Of Four Oligothiophene-Ruthenium Complexes And Synthesis Of A Bidentate Ligand For C-F Bond Activation, Joseph S. Bair

Theses and Dissertations

Photovoltaic cells and fluorescence sensing are two important areas of research in chemistry. The combination of photon-activated electron donors with electron acceptors provides a strong platform for the study of optical devices. A series of four oligothiophene-ruthenium complexes has been synthesized. Variation in oligothiophene length and bipyridine substitution allowed comparison of these variables on electronic properties. The longer oligothiophenes display lower energy absorption and emission compared to the shorter ones. Aromatic conjugation appears more complete with para-, rather than meta-, substitution. Oligothiophenes and Ru(bpy)32+ are highly fluorescent individually, but fluorescence is quenched when connected. Bonds of carbon to fluorine are …

Development Of Polymer Monoliths For The Analysis Of Peptides And Proteins, Binghe Gu

Theses and Dissertations

Several novel polymer monoliths for the analysis of peptides and proteins were synthesized using polyethylene glycol diacrylate (PEGDA) as crosslinker. Photo-initiated copolymerization of polyethylene glycol methyl ether acrylate and PEGDA yielded an inert monolith that could be used for size exclusion liquid chromatography of peptides and proteins. This macroscopically uniform monolith did not shrink or swell in either water or tetrahydrofuran. More importantly, it was found to resist adsorption of both acidic and basic proteins in aqueous buffer without any organic solvent additives. A strong cation-exchange polymer monolith was synthesized by copolymerization of 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPS) and PEGDA. A ternary …

Ammonium And Ergosterol Production And Chitinolytic Enzyme Activities Of Urban And Rural Isolates Of Two Common Decomposer Fungi, Hai Li

All-Inclusive List of Electronic Theses and Dissertations

Increased temperature in urban areas compared to rural areas is known as the urban heat island (UHi) effect. The effects of UHI on ecosystem processes can indicate the potential effects of global warming on processes such as organic matter decomposition and nutrient cycling, etc. It was reported that the urban isolates of two fungal species ( Chrysosporium pannorum and Trichoderma koningii) appeared to have adapted to higher temperatures in urban oak forest compared to rural isolates. Since these fungi decompose chitin, releasing ammonium, the apparent adaptation of these fungi to higher temperatures is probably due to increased chitinolytic enzyme activity …

Development Of Methods For The Study Of Phosphoproteins, Zhaoyuan Chen

Theses and Dissertations

Characterization of phosphoproteins-including detection, identification of phosphoproteins and identification of phosphorylation sites-is mostly done with radiolabeling and proteomic techniques. Three main topics related to phosphoprotein characterization are included in this dissertation. First, large-scale characterization of the CHO (Chinese hamster ovary) cell phosphoproteome was done using two dimensional gel electrophoresis (2DE) separation, visualization of phosphoproteins by radiolabeling or a phosphoprotein specific dye, followed by MALDI-TOF identification. Because radiolabeling of phosphoproteins is very sensitive and straightforward to quantify, such analysis can give a clear picture of the relative phosphosphorylation of proteins present in a sample. But there are also limitations to this …

Capillary Electrophoresis Of Proteins With Selective On-Line Affinity Monoliths, Jenny Marcela Armenta Blanco

Theses and Dissertations

The analysis of proteins in biological fluids by capillary electrophoresis (CE) is of interest in clinical chemistry. However, due to low analyte concentrations and poor concentration limits of detection (CLOD), protein analysis by this technique is frequently challenging. Coupling preconcentration techniques with CE greatly improves the CLOD. An on-line preconcentration-CE method that can selectively preconcentrate any protein for which an antibody is available would be very useful for the analysis of low abundance proteins and would establish CE as a major tool in biomarker discovery. To accomplish this, an on-line protein G monolithic preconcentrator CE system for enrichment and separation …