Biochemistry Commons^™

Millimeter-Scale Contact Printing Of Aqueous Solutions Using A Stamp Made Out Of Paper And Tape, Chao-Min Cheng, Aaron D. Mazzeo, Jinlong Gong, Andres W. Martinez, Scott T. Phillips, Nina Jain, George M. Whitesides

Chemistry and Biochemistry

This communication describes a simple method for printing aqueous solutions with millimeter-scale patterns on a variety of substrates using an easily fabricated, paper-based microfluidic device (a paper-based ―stamp‖) as a contact printing device. The device is made from inexpensive materials, and it is easily assembled by hand; this method is thus accessible to a wide range of laboratories and budgets. A single device was used to print over 2500 spots in less than three minutes at a density of 16 spots per square centimetre. This method provides a new tool to pattern biochemicals—reagents, antigens, proteins, and DNA—on planar substrates. The …

Trace Gas And Particle Emissions From Domestic And Industrial Biofuel Use And Garbage Burning In Central Mexico, Ted J. Christian, Robert Yokelson, B. Cardenas, L. T. Molina, G. Engling, S. C. Hsu

Chemistry and Biochemistry Faculty Publications

In central Mexico during the spring of 2007 we measured the initial emissions of 12 gases and the aerosol speciation for elemental and organic carbon (EC, OC), anhydrosugars, Cl(-), NO(3)(-), and 20 metals from 10 cooking fires, four garbage fires, three brick making kilns, three charcoal making kilns, and two crop residue fires. Global biofuel use has been estimated at over 2600 Tg/y. With several simple case studies we show that cooking fires can be a major, or the major, source of several gases and fine particles in developing countries. Insulated cook stoves with chimneys were earlier shown to reduce …

Laboratory Measurements Of Trace Gas Emissions From Biomass Burning Of Fuel Types From The Southeastern And Southwestern United States, I. R. Burling, Robert J. Yokelson, David W. T. Griffith, T. J. Johnson, P. Veres, J. M. Roberts, C. Warneke, S. P. Urbanski, J. Reardon, D. R. Weise, Wei Min Hao, J. De Gouw

Chemistry and Biochemistry Faculty Publications

Vegetation commonly managed by prescribed burning was collected from five southeastern and southwestern US military bases and burned under controlled conditions at the US Forest Service Fire Sciences Laboratory in Missoula, Montana. The smoke emissions were measured with a large suite of state-of-the-art instrumentation including an open-path Fourier transform infrared (OP-FTIR) spectrometer for measurement of gas-phase species. The OP-FTIR detected and quantified 19 gas-phase species in these fires: CO2, CO, CH4, C2H2, C2H4, C3H6, HCHO, HCOOH, CH3OH, CH3COOH, furan, H2O, NO, NO2, HONO, NH3, HCN, HCl, and SO2. Emission factors for these species are presented for each vegetation type burned. …

Evolution Of Trace Gases And Particles Emitted By A Chaparral Fire In California, S. K. Akagi, J. S. Craven, J. W. Taylor, G. R. Mcmeeking, Robert J. Yokelson, I. R. Burling, S. P. Urbanski, C. E. Wold, J. H. Seinfeld, H. Coe, M. J. Alvarado, D. R. Weise

Chemistry and Biochemistry Faculty Publications

Biomass burning (BB) is a major global source of trace gases and particles. Accurately representing the production and evolution of these emissions is an important goal for atmospheric chemical transport models. We measured a suite of gases and aerosols emitted from an 81 hectare prescribed fire in chaparral fuels on the central coast of California, US on 17 November 2009. We also measured physical and chemical changes that occurred in the isolated down-wind plume in the first similar to 4 h after emission. The measurements were carried out onboard a Twin Otter aircraft outfitted with an airborne Fourier transform infrared …

Automated Interpretation Of The Tandem Mass Spectra Of Peptides Using Artificial Neural Networks, Timothy Patrick Manning

Theses

The manual interpretation of mass spectra is a complex and time consuming task. The problem of manually interpreting this data is further exacerbated by the large numbers of mass spectra which can potentially be produced in a single proteoniics experiment. This shows the need for high throughput approaches to the interpretation of mass spectra. Existing automated approaches are however error prone due to the complexity of the task. Accordingly, this thesis discusses and evaluates the application of neural networks to improving the sensitivity, specificity and robustness of current approaches to the automated interpretation of such mass spectral data.

Several neural …

The Roles Of Rhle And Hfq In Srna-Dependent Gene Regulation, Abeykoon Jayalath Iresha Sandeepanie Rathnayake

Wayne State University Theses

THE ROLES OF RHLE AND HFQ IN SRNA-DEPENDENT GENE REGULATION

by

ABEYKOON JAYALATH IRESHA SANDEEPANIE RATHNAYAKE

DECEMBER 2010

Advisor: Dr. Andrew Feig

Major: Chemistry

Degree: Master of Science

Bacteria are adapted to live in diverse environmental conditions. Thus, they show excellent tolerance and response to extreme environmental conditions caused by low or high temperatures, high salinity, reactive oxygen species or high nutrient concentrations. sRNAs have been identified and characterized as cis-acting or trans-acting post-transcriptional regulators in diverse cellular processes including virulence and adaptation to environmental stress (11,12,14,15). Interactions of sRNAs and target mRNAs result in translational repression, translational activation or/and …

Elucidating The Structure Of Protein Aggregates By Raman Spectroscopy, Ludmila A. Popova

Legacy Theses & Dissertations (2009 - 2024)

The structures and properties of amyloid fibrils are of considerable interest due to their associations with numerous neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease and transmissible spongiform encephalopaties (prion diseases). Understanding fibrillogenesis at a molecular level requires detailed structural characterization of amyloid fibrils. However amyloid fibrils are difficult objects to study due to their non-crystalline and insoluble nature. These properties make the application of classical tools of structural biology, such as X-Ray crystallography and solution Nuclear Magnetic Resonance spectroscopy, impractical for structural characterization of protein fibrils.

15N Solid-State Nmr Detection Of Flavin Perturbation By H-Bonding In Models And Enzyme Active Sites, Dongtao Cui

University of Kentucky Doctoral Dissertations

Massey and Hemmerich proposed that the different reactivities displayed by different flavoenzymes could be achieved as a result of dominance of different flavin ring resonance structures in different binding sites. Thus, the FMN cofactor would engage in different reactions when it had different electronic structures. To test this proposal and understand how different protein sites could produce different flavin electronic structures, we are developing solid-state NMR as a means of characterizing the electronic state of the flavin ring, via the ¹⁵N chemical shift tensors of the ring N atoms. These provide information on the frontier orbitals. We propose that …

Amino Acid Transport In Thermophiles: Characterization Of An Arginine-Binding Protein In Thermotoga Maritima, Matthew S. Luchansky, Bryan S. Der, Sabato D'Auria, Gabriella Pocsfalvi, Luisa Iozzion, Daniela Marasco, Jonathan D. Dattelbaum

Chemistry Faculty Publications

Members of the periplasmic binding protein superfamily are involved in the selective passage of ligands through bacterial cell membranes. The hyperthermophilic eubacterium Thermotoga maritima was found to encode a highly stable and specific periplasmic arginine-binding protein (TM0593). Following signal sequence removal and overexpression in Escherichia coli, TM0593 was purified by thermoprecipitation and affinity chromatography. The ultra-stable protein with a monomeric molecular weight of 27.7 kDa was found to exist as both a homodimer and homotrimer at appreciable concentrations even under strongly denaturing conditions, with an estimated transition temperature of 116 °C. Its multimeric structure may provide further evidence of …

Amino Acid Transport In Thermophiles: Characterization Of An Arginine-Binding Protein In Thermotoga Maritima. 2. Molecular Organization And Structural Stability, Andrea Scirè, Anna Marabotti, Maria Staiano, Luisa Iozzion, Matthew S. Luchansky, Bryan S. Der, Jonathan D. Dattelbaum, Fabio Tanfani, Sabato D'Auria

Chemistry Faculty Publications

ABC transport systems provide selective passage of metabolites across cell membranes and typically require the presence of a soluble binding protein with high specificity to a specific ligand. In addition to their primary role in nutrient gathering, the binding proteins associated with bacterial transport systems have been studied for their potential to serve as design scaffolds for the development of fluorescent protein biosensors. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the physicochemical properties of a hyperthermophilic binding protein from Thermotoga maritima. We demonstrated preferential binding for the polar amino acid arginine …

The Thermal Characteristic Of Imipenem Encapsulated In Low And High Molecular Weight Of Polyethylene Glycol., Abdul Aziz Ismail

Student Works (2010-2019)

Microencapsulation technique is widely used in pharmaceutical industries to control the release of a drug. Biodegradable polymer such as Polyethylene glycol (PEG) is frequently used as encapsulation material. This study has tried to produce microencapsulation product of Imipenem antibiotics in Polyethylene Glycol.Commercially available product called Tienam® was used as a major source of Imipenem. We used freeze-drying method to produce the microencapsulation products. The successful of producing of this product is confirmed by the yellowish appearance of the product whereby it shows the colour properties of Tienam® Thermal analysis using Differential Scanning Calorimeter (DSC) was used to characterize pure materials …

Studies Of Antioxidant Activity Of Bioactive Compounds Derived From Ardisia Crispa., Hassan Mahmood Kzar Jindal

Student Works (2010-2019)

In recent times, researches have focused on medicinal plants in order to extract natural and low cost antioxidants that can help protect the human body against oxidative stress, and replace the synthetic additives that might be carcinogenic. In present study, the crude extracts of leaves and fruits from Ardisia crispa were investigated for their chemical constituents and antioxidant activity. Preliminary phytochemical screening of the crude extracts via TLC analysis revealed the presence of several secondary compounds mainly, terpenoids and phenolic compounds in addition to alkaloids and saponins. HPLC analysis showed the possibility of presence of gallic acid in the fruits …

Dielectrophoretic Choking Phenomenon In A Converging-Diverging Microchannel, Ye Ai, Shizhi Qian, Sheng Liu, Sang W. Joo

Mechanical & Aerospace Engineering Faculty Publications

Experiments show that particles smaller than the throat size of converging-diverging microchannels can sometimes be trapped near the throat. This critical phenomenon is associated with the negative dc dielectrophoresis arising from nonuniform electric fields in the microchannels. A finite-element model, accounting for the particle-fluid-electric field interactions, is employed to investigate the conditions for this dielectrophoretic (DEP) choking in a converging-diverging microchannel for the first time. It is shown quantitatively that the DEP choking occurs for high nonuniformity of electric fields, high ratio of particle size to throat size, and high ratio of particle's zeta potential to that of microchannel. © …

Biochemical Characterization Of Human Mismatch Recognition Proteins Mutsα And Mutsβ, Lei Tian

University of Kentucky Doctoral Dissertations

The integrity of an organism's genome depends on the fidelity of DNA replication and the efficiency of DNA repair. The DNA mismatch repair (MMR) system, which is highly conserved from prokaryotes to eukaryotes, plays an important role in maintaining genome stability by correcting base-base mismatches and insertion/deletion (ID) mispairs generated during DNA replication and other DNA transactions. Mismatch recognition is a critical step in MMR. Two mismatch recognition proteins, MutSα (MSH2-MSH6 heterodimer) and MutSβ (MSH2-MSH3 heterodimer), have been identified in eukaryotic cells. MutSα and MutSβ have partially overlapping functions, with MutSα recognizing primarily base-base mismatches and 1-2 nt ID mispairs …

Explorations In Homeoviscous Adaptation And Mass Spectral Analysis Of Membrane Lipids, Michael Douglas Timmons

University of Kentucky Doctoral Dissertations

The focus of this dissertation is centered on the mass spectral analysis of lipids and changes occurring in keeping with the concept of homeoviscous adaptation [1]. Homeoviscous adaptation is the process of modification of membrane lipids in response to environmental stimuli [1]. Dissertation investigations applied this concept to prokaryotic and eukaryotic organisms, and expanded the perception of environmental factors from exogenous organic solvents to intracellular environment.

The field of lipidomics deals with the analysis of phospholipid and fatty acid components of membranes the changes that occur due to environmental stimuli and their biological significance [2-6]. The high sensitivity of mass …

In Vivo Oxidative Stress In Alzheimer Disease Brain And A Mouse Model Thereof: Effects Of Lipid Asymmetry And The Single Methionine Residue Of Amyloid-Β Peptide, Miranda Lu Bader Lange

University of Kentucky Doctoral Dissertations

Studies presented in this dissertation were conducted to gain more insight into the role of phospholipid asymmetry and amyloid-β (Aβ)-induced oxidative stress in brain of subjects with amnestic mild cognitive impairment (aMCI) and Alzheimer disease (AD). AD is a largely sporadic, age-associated neurodegenerative disorder clinically characterized by the vast, progressive loss of memory and cognition commonly in populations over the age of ~65 years, with the exception of those with familial AD, which develop AD symptoms as early as ~30 years-old. Neuropathologically, both AD and FAD can be characterized by synapse and neuronal cell loss in conjunction with accumulation of …

Progress Toward The Total Synthesis Of Lyconadin A, Yu Zhang

Theses and Dissertations

Lyconadin A is a pentacyclic Lycopodium alkaloid isolated from the club moss Lycopodium complanatum with antitumor properties. We have developed a novel 7-exo/6-exo acyl radical cascade cyclization as a method of making the bicyclo[5.4.0]undecane ring system of lyconadin A. The model products are trans-fused ring systems, while a cis-fused ring system is needed in lyconadin A. We have discovered a method to convert the trans-fused model cascade cyclization product into the desired cis isomer. Based on Donohoe's pyridone synthesis, we developed a method for the construction of 5-alkyl and 3,5-dialkyl-6-carbomethoxy-2-pyridones, the former of which …

Subcutaneous Administration Of Tc007 Reduces Disease Severity In An Animal Model Of Sma, Virginia B. Mattis, Marina Y. Fosso, Cheng-Wei Tom Chang, Christian L. Lorson

Chemistry and Biochemistry Faculty Publications

Background Spinal Muscular Atrophy (SMA) is the leading genetic cause of infantile death. It is caused by the loss of functional Survival Motor Neuron 1 (SMN1). There is a nearly identical copy gene, SMN2, but it is unable to rescue from disease due to an alternative splicing event that excises a necessary exon (exon 7) from the majority of SMN2-derived transcripts. While SMNΔ7 protein has severely reduced functionality, the exon 7 sequences may not be specifically required for all activities. Therefore, aminoglycoside antibiotics previously shown to suppress stop codon recognition and promote translation read-through have been examined to increase the …

Synthesis And Evaluation Of N6,5'-Bis-Ureido-5'-Amino-5'-Deoxyadenosine Derivatives: Novel Nucleosides With Antiproliferative And Protein Kinase Binding Activities, Marcelio Oliveira

Theses and Dissertations

A new series of N6,5'-bis-ureido-5'-amino-5'-deoxyadenosine derivatives was prepared and evaluated for anticancer activities using the NCI 60 panel of human cancers. Certain of the derivatives showed promising activities (low micromolar GI50's) against several of the representative cancers. These included cell lines from the following general cell types in the NCI 60: Leukemia, Breast, Central Nervous System, Non-Small Cell Lung, Ovarian, Prostate, Renal, and Colon cancers. Select compounds were also screened for their affinities for protein kinases. The synthesis of the compounds was straightforward and involved N6 acylation with arylisocyanates, preceded by activation and nucleophilic substitution of the 5'-position to give …

Pore Size Characterization Of Monolithic Capillary Columns Using Capillary Flow Porometry, Yan Fang

Theses and Dissertations

A simple capillary flow porometer (CFP) was assembled for pore structure characterization of monolithic capillary liquid chromatography columns based on ASTM standard F316-86. Determination of differential pressures and flow rates through dry and wet samples provided the necessary information to determine the through-pore throat diameter, bubble point pore diameter, mean flow pore diameter, and pore distribution. Unlike measurements in bulk using traditional techniques to provide indirect information about the pore properties of monolithic columns, monoliths can be characterized in their original chromatographic forms with this system. The performance of the new CFP was first evaluated by characterizing the pore size …

Gas Phase Chiral Recognition, Characterization Of Porous Polymer Monolith Nanospray Ionization, And The Negative Mode Crafti Method Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Nannan Fang

Theses and Dissertations

Our group has been studying chiral recognition in gas phase using mass spectrometry for more than 10 years. We are interested in gas phase studies of fundamental interactions because the gas phase avoids complications and masking effects that may arise upon solvation. Therefore, the results of gas phase experiments can be directly compared with those of high-level computational studies. In chapter 2, I studied the roles of hydrogen bonding and pi stacking in gas phase chiral recognition between aromatic crown molecules and aromatic amines. High affinity between host and guest doesn't necessarily result in better recognition. If the affinity is …

Theoretical Studies Of 2,3 -Sigmatropic Rearrangements Of Allylic Selenoxides And Selenimides, Craig A. Bayse, Sonia Antony

Chemistry & Biochemistry Faculty Publications

Density-functional theory is used to model the endo and exo transition states for [2,3]-sigmatropic rearrangement of allylic aryl-selenoxides and -selenimides. The endo transition state is generally preferred for selenoxides if there is no substitution at the 2 position of the allyl group. Based upon the relative energies of the endo and exo transition states, enantioselectivity of rearrangements is expected to be greatest for molecules with substitutions at the 1- or (E)-3- position of the allyl group. Ortho substitution of a nitro group on the ancillary selenoxide phenyl ring reduces the activation barriers, increases the difference between the endo and exo …

Total Synthesis Of (-)-Acutumine, Fang Li

Theses and Dissertations

Acutumine is a tetracyclic alkaloid isolated from the Asian vine Menispermum dauricum with selective T-cell cytotoxicity and antiamnestic properties. We have developed a total synthetic route to this congested alkaloid, during which we also found a novel, stereoselective radical-crossover reaction that combines an intramolecular radical conjugate addition with a subsequent enolate hydroxylation. Key features of this synthesis also include a reagent-controlled diastereoselective ketone allylation, an anionic oxy-Cope rearrangement to form a congested quaternary sterocenter, a pyridine-mediated selective ozonolysis, and a Lewis acid promoted Michael-type cyclization.

Development Of Biocompatible Polymer Monoliths For The Analysis Of Proteins And Peptides, Yun Li

Theses and Dissertations

Biocompatibility is an important issue for the development of chromatographic stationary phases for the analysis of biomolecules (including proteins and peptides). A biocompatible stationary phase material is a material that resists nonspecific adsorption of biomolecules and does not interact with them in a way that would alter or destroy their structures or biochemical functions. The monolithic column format is a good alternative to typical spherical particle packed columns for capillary liquid chromatography of biomacromolecules. Several novel anion-exchange polymer monoliths for the analysis of proteins were synthesized for improved biocompatibility. Two novel polymeric monoliths were prepared in a single step by …

Real-Time Virus Analysis Via Image Charge Detection Surface Induced Dissociation Tandem Mass Spectrometry, Seth T. Call

Theses and Dissertations

This thesis reports on the development of a novel mass spectrometer combining image charge detection with surface induced dissociation for real-time analysis of intact viruses. Protonated viruses produced using electrospray are accelerated and subsequently impact on a solid surface. Capsid peptides released during the impact are analyzed using time-of-flight mass spectrometry. Image charge detection is used to measure the mass and charge states of structurally intact, electrosprayed viruses prior to impact. Since virus capsids are composed of loosely-bound proteins, collision of viruses with surfaces at moderate impact energies could release intact proteins. The masses and numbers of different protein types …

Design And Characterization Of A Human Exposure Chamber And Inversion Episodes In Salt Lake City, Utah In January/February Of 2009, Roman Yuri Kuprov

Theses and Dissertations

Research on health effects of particulate matter (PM) has been a very active area in the last two decades. One plausible mechanism by which exposure to PM affects human health includes modification of autonomic endothelium function. Decreased endothelium activity causes heightened risks of cardiovascular disease. A human exposure chamber designed to conduct experiments to quantify diminished function of endothelium from short term exposure to PM is described. The chamber consists of two stages for containment and pre-treatment of PM and exposure of human subjects. Concentrations of CO, CO2, NO, NO2, O3, and PM2.5, are monitored and controlled in the exposure …

Geometric Build-Up Solutions For Protein Determination Via Distance Geometry, Robert Tucker Davis

Masters Theses & Specialist Projects

Proteins carry out an almost innumerable amount of biological processes that are absolutely necessary to life and as a result proteins and their structures are very often the objects of study in research. As such, this thesis will begin with a description of protein function and structure, followed by brief discussions of the two major experimental structure determination methods. Another problem that often arises in molecular modeling is referred to as the Molecular Distance Geometry Problem (MDGP). This problem seeks to find coordinates for the atoms of a protein or molecule when given only a set of pair-wise distances between …

The Study Of Variations In The Properties Of Biodiesel On Addition Of Antioxidants, Hiranmayee Kandala

Masters Theses & Specialist Projects

This research studies variations in biodiesel upon addition of different concentrations of antioxidant and petrodiesel additives. Oxidation onset temperature, oxidation induction time, oxidative stability, thermal stability, crystallization onset temperature and moisture retention properties of the biodiesel, with and without antioxidants have been studied. Antioxidants like BHT, BHA, PrG, Vit E and Vit C were added to the biodiesel during the study. These samples were analyzed using the PDSC, TGA, DSC and TGA-SA instrumentation.

The results of this research show an improvement in the OOT, OIT and Oxidative stability of biodiesel with the addition of antioxidants and by blending the biodiesel …

Synthesis And Characterization Of Bis-Phosphine Complexes With Transition Metals, Alicia L. Mcdaniel

Masters Theses & Specialist Projects

Extractants and extraction methodologies play a vital role in many industrial processes, from the concentration of precious metals from ores to the separation of longlived nuclei from radioactive waste as well as the removal of heavy metals from soils and water for remediation. The vast majority of extractants rely on the use of nitrogen, oxygen, sulfur or selenium as Lewis base donor atoms to form coordination complexes with the metal ions of interest. These extractants often make use of the chelate effect and/or the macrocyclic effect in order to form stable complexes. Some of the best known types of chelate …

A Top-Down Proteomic Approach For The Discovery Of Novel Serum Biomarkers Of Pregnancy-Related Disease, Karen Merrell

Theses and Dissertations

The serum fraction of blood is an ideal material in which to search for novel biomarkers for disease. It is easily obtained through relatively non-invasive means, routinely collected, and a rich treasure-trove of information about the health of an individual. Cells react to signal molecules, take up nutrients, and release waste products, fragments that are the result of proteolysis, and other molecules out into the bloodstream. If these components are unique to the cells in question, that part of the complex mixture that is the blood stream can potentially characterize the health of the tissue or organ those cells are …