Biochemistry Commons^™

Effect Of Temperature And Oxygen Levels On Lactate Production In Palaemonetes Pugio, Robin Schofield, Teresa Mika, Carl Reiber

Festival of Communities: UG Symposium (Posters)

Oxygen delivery rates must keep pace with the increased metabolic rate observed in poikilothermic animals exposed to increased temperature if aerobic metabolism is to be maintained. Physical failure of the oxygen delivery system to meet these demands may be a mechanism of cardiac failure in crustaceans at temperature extremes. As part of the determination of the effect of temperature on the cardio-respiratory system, we are measuring whole animal lactate levels in grass shrimp acclimated to 20°C over temperature ranges in normoxic and hyperoxic conditions. Lactate levels are measured as an indicator of a switch from aerobic to anaerobic metabolism. Animals …

Dicarbonyldichloridobis(Trimethylphosphane)Iron(Ii)–Carbonyldichloridotris(Trimethylphosphane)Iron(Ii)–Tetrahydrofuran (1/1/2), Nigam Rath, Meghan Stouffer, Matthew Janssen, John Bleeke

Chemistry & Biochemistry Faculty Works

The asymmetric unit of the title crystal, [FeCl2(C3H9P)3(CO)]·[FeCl2(C3H9P)2(CO)2]·2C4H8O, contains half mol­ecules of the two closely related FeII complexes lying on mirror planes and a tetra­hydro­furan solvent mol­ecule, one C atom of which is disordered over two sets of sites with site occupancy factors 0.633 (9) and 0.367 (9). In both FeII complex mol­ecules, a distorted octa­hedral coordination geometry has been observed around the Fe atoms. Weak intermolecular C-H...O inter­actions are observed in the crystal structure.

Determining The Composition Of The Dwelling Tubes Of Antarctic Pterobranchs, Lukasz J. Sewera

Honors Projects

Pterobranchs are a group of marine invertebrates within the Hemichordata, which share characteristics with both chordates and echinoderms.  Pterobranchs live in colonies of secreted tubes, coenicia, which are composed of a gelatinous material of unknown composition.  Visually, the tubes appear similar to the tunic of tunicates, a group of invertebrates within the Chordata. The nonproteinaceous tunic of tunicates is composed of cellulose, which is unusual.  The goal of this study was to determine the composition of the pterobranch coenicium. Some aspects of pterobranch phylogeny are still unclear even after multiple molecular and morphological studies.  Identification of any new shared characteristics …

Activation Of Multiple Apoptotic Pathways In Human Nasopharyngeal Carcinoma Cells By The Prenylated Isoflavone, Osajin, Tsung-Teng Huang, Fu-Guo Liu, Chia-Fong Wei, Chia-Chen Lu, Chang-Chieh Chen, Hung-Chi Lin, David M. Ojcius, Hsin-Chih Lai

All Dugoni School of Dentistry Faculty Articles

Osajin is a prenylated isoflavone showing antitumor activity in different tumor cell lines. The underlying mechanism of osajin-induced cancer cell death is not clearly understood. In the present study, the mechanisms of osajin-induced cell death of human nasopharyngeal carcinoma (NPC) cells were explored. Osajin was found to significantly induce apoptosis of NPC cells in a dose- and time-dependent manner. Multiple molecular effects were observed during osajin treatment including a significant loss of mitochondrial transmembrane potential, release of cytochrome c into the cytosol, enhanced expression of Fas ligand (FasL), suppression of glucose-regulated protein 78 kDa (GRP78), and activation of caspases-9, -8, …

Analysis Of Critical Amino Acid Residues In Unc-45 Necessary For Its Interaction With Myosin Using Site-Directed Mutagenesis, Amanda H. Nolan

Undergraduate Research Conference

UNC-45 is an important protein for muscle contraction and heart formation. The UNC-45 protein is a chaperone for the myosin heavy chain head, and UNC-45 only binds to the UCS domain of the myosin head. In our research for the interaction of myosin and UNC-45. The mutation was accomplished using the multiple sequence alignment method and site-directed mutagenesis. The mutations were generated in UNC-45 of Mus musculus (mouse), and the specific amino acids that were mutated were: L741A and L860F. The mutant proteins were sequenced and over-expressed for analysis.

Practical Approach To Bioinformatics, Nigel Yarlett, Melissa Grigione

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Computational Investigation Of The Bioactive Selenium Compounds Ebselen And Selenious Acid, Sonia Antony

Chemistry & Biochemistry Theses & Dissertations

Selenium, a toxic element, is required in trace quantities for the proper functioning of biological systems. The experimental mechanistic study of the reactions of ebselen and selenious acid is difficult due to complexity of the reaction mixtures and the presence of short-lived intermediates. Computational modeling of the reactivity of these species can give us an insight into their mechanisms, but the process is complicated by proton exchanges associated with the mechanistic steps. In gas phase modeling, this may be corrected to a certain level using the solvent assisted proton exchange (SAPE) method. SAPE is a modeling technique that mimics solvent …

Bioinformatics, Thermodynamics And Kinetics Analysis Of An All Alpha Helical Protein With A Gree-Key Topology, Hai Li

Chemistry & Biochemistry Theses & Dissertations

Computational and experimental studies focusing on the role of conserved residues for folding and stability is an active and promising area of research. To further expand our understanding we present the results of a bioinformatics analysis of the death domain superfamily. The death domain superfamily fold consists of six α-helices arranged in a Greek-key topology, which is shared by the all β-sheet immunoglobulin and mixed α/β-plait superfamilies. Our sequence and structural studies have identified a group of conserved hydrophobic residues and corresponding long-range interactions, which we propose are important in the formation and stabilization of the hydrophobic core and native …

Organometallic Iron(Iii)-Salophene Exerts Cytotoxic Properties In Neuroblastoma Cells Via Mapk Activation And Ros Generation, Kyu Kwang Kim, Rakesh K. Singh, Robert M. Strongin, Richard G. Moore, Laurent Brard, Thilo S. Lange

Chemistry Faculty Publications and Presentations

The objective of the present study was to investigate the specific effects of Iron(III)-salophene (Fe-SP) on viability, morphology, proliferation, cell cycle progression, ROS generation and pro-apoptotic MAPK activation in neuroblastoma (NB) cells. A NCI-DTP cancer screen revealed that Fe-SP displayed high toxicity against cell lines of different tumor origin but not tumor type-specificity. In a viability screen Fe-SP exhibited high cytotoxicity against all three NB cell lines tested. The compound caused cell cycle arrest in G1 phase, suppression of cells progressing through S phase, morphological changes, disruption of the mitochondrial membrane depolarization potential, induction of apoptotic markers as well as …

Structural Study Of Mcry2: A Circadian Rhythm Regulator, Brenda L. Rodarte^, Gustavo A. Avila, Adrian S. Enriquez, Nicolas D. Silva, Tiffany H. Blankenship, Erquan Eric Zhang*, Chuan Xiao*

COURI Symposium Abstracts, Spring 2011

A circadian clock is a 24 hour biological rhythm that regulates physiological, psychological and behavioral processes in living organisms. Understanding the regulation mechanism of such circadian rhythms can have great impact in certain diseases such as sleeping disorders and cancers. There are many genes regulating circadian rhythms in different species. Cryptochromes (CRY) are photosensory receptors mediating light regulation of growth and development in certain species. Mouse cryptochrome protein mCRY2 has been found to encode a blue light photoreceptor and is important for mice circadian rhythm. The main goal of the project is to determine the atomic structure of mCRY2, via …

Enzymatic Characterization Of An Endolysin Mediated By Chaperonin In Bacteriophage Phi El, Diana A. Tafoya^, Nadia Herrera, Sudheer Molugu, Zachariah Hildenbrand, Maxim V. Filchikov, Vadim V. Mesyanzhinov, Konstantin A. Miroshnikov, Ricardo A. Bernal*

COURI Symposium Abstracts, Spring 2011

Bacteriophage phi-EL is a virus that attacks the human pathogen Pseudomonas aeruginosa. One of the gene products from phi-EL is a putative endolysin. Endolysin is an enzyme produced during gene expression in the lytic cycle of the bacteriophage. Its function is to digest the peptidoglycan layer of the host cell wall, thereby releasing the newly formed virions. In order to confirm the identity of this putative endolysin, the gene product was transformed into competent E. coli cells, expressed to high levels and purified to high homogeneity using nickel affinity and size exclusion chromatography. The peptidoglycan-hydrolyzing activity of the protein …

Human Endogenous Sodium Pump Inhibitors Measurement, Source, Synthesis And Regulation, Jie Ma

Theses and Dissertations

The sodium pump (SP or Na+,K+-ATPase) is a membrane embedded protein complex that pumps 3 sodium ions out and 2 potassium ions into the cell per cycle and in so doing creates a cell membrane electrochemical potential. The membrane potential is critical for any functional cell. In the vasculature, reduction in the voltage potential causes vascular smooth muscle contraction and a narrowing of blood vessels (vasoconstriction) which can lead to increased blood pressure (hypertension). Substantial research over the past several decades has provided a vast amount of research on SP inhibitors, sometimes called endogenous digitalis-like factors (EDLF). Increased levels of …

Super Collision Energy Transfer Studies In Single Collisions Between Vibrationally Hot Benzene Like Molecules And Ground State Bath Molecules: The Effect Of Physical Properties Of Donor And Bath Molecules On Super Collision Energy Transfer, Kilyoung Kim

Theses and Dissertations

This research is focused on single-collision energy transfer events between highly vibrationally excited benzene-like donor molecules and small bath molecules, CO2 and N2O in the vibrational ground level. Measuring how much energy is transferred from donors to bath molecules was accomplished by probing bath molecules scattered into specific-rotational states using a tunable Δv=0.0003 cm-1 solid state diode laser. The normalized energy transfer probability distribution function, P(E,E'), determined from energy gain information, is very useful in comparing collisional energy transfer efficiency between various collision systems. P(E,E') is also used to investigate the effects of donor and bath physical properties on collisional …

A Novel Use Of Digoxin Immune Fab Fragment In Identification And Isolation Of An Endogenous Digitalis-Like Factor Found In Preeclampsia, Moana Lee Hopoate-Sitake

Theses and Dissertations

The mechanisms mediating the hypertension of preeclampsia (PE) are unclear. Endogenous digitalis-like factors (EDLFs) are specific sodium pump (SP) inhibitors implicated in essential and experimental hypertension, but they have not been fully explored in the setting of PE. This study uses a digoxin antibody Fab fragment to address the question of whether such factors are present and increased in PE, to investigate a possible treatment of PE, and to isolate and characterize all EDLFs present in PE. Sera and placenta from women with PE did show a significant increase in SP inhibition in comparison to women with normal pregnancy and …

Surface Modification, Fabrication, And Characterization Of Silicon, Polymer, And Nanotube Composite Materials, Lei Pei

Theses and Dissertations

In my research, I have performed many characterization and fabrication experiments that are based on tools of analytical chemistry, materials chemistry, and surface science. My research projects are as follows. (1) Fabrication of transparent polymer templates for nanostructured amorphous silicon photovoltaics was done using low-cost nanoimprint lithography of polydimethylsiloxane. This approach provides a test bed for absorption studies in nanostructured film geometries and should result in improved light capturing designs in thin-film solar cells. Nanopatterned polymer films were characterized by scanning electron microscopy and optical measurements. (2) A straightforward method for fabricating freely suspended, thin, carbon nanotube (CNT) membranes infiltrated …

Two Rotary Motors In F-Atp Synthase Are Elastically Coupled By A Flexible Rotor And A Stiff Stator Stalk., André Wächter, Yumin Bi, Stanley D Dunn, Brian D Cain, Hendrik Sielaff, Frank Wintermann, Siegfried Engelbrecht, Wolfgang Junge

Biochemistry Publications

ATP is synthesized by ATP synthase (F(O)F(1)-ATPase). Its rotary electromotor (F(O)) translocates protons (in some organisms sodium cations) and generates torque to drive the rotary chemical generator (F(1)). Elastic power transmission between F(O) and F(1) is essential for smoothing the cooperation of these stepping motors, thereby increasing their kinetic efficiency. A particularly compliant elastic domain is located on the central rotor (c(10-15)/ε/γ), right between the two sites of torque generation and consumption. The hinge on the active lever on subunit β adds further compliance. It is under contention whether or not the peripheral stalk (and the "stator" as a whole) …

Quantifying The Energetic Contributions Of Desolvation And Π-Electron Density During Translesion Dna Synthesis, Edward A. Motea, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

This report examines the molecular mechanism by which high-fidelity DNA polymerases select nucleotides during the replication of an abasic site, a non-instructional DNA lesion. This was accomplished by synthesizing several unique 5-substituted indolyl 2′-deoxyribose triphosphates and defining their kinetic parameters for incorporation opposite an abasic site to interrogate the contributions of π-electron density and solvation energies. In general, the Kd, app values for hydrophobic non-natural nucleotides are ∼10-fold lower than those measured for isosteric hydrophilic analogs. In addition, kpol values for nucleotides that contain less π-electron densities are slower than isosteric analogs possessing higher degrees of π-electron density. The differences …

Formation And Stability Of Atmospherically Relevant Isoprene-Derived Organosulfates And Organonitrates, Adam I. Darer, Neil C. Cole-Filipiak, Alison E. O'Connor, Matthew J. Elrod

Faculty & Staff Scholarship

Isoprene is the precursor for number of alcohol, organosulfate, and organonitrate species observed in ambient secondary organic aerosol (SOA). Recent laboratory and field work has suggested that isoprene-derived epoxides may be crucial intermediates that can explain the existence of these compounds in SOA. To confirm this hypothesis, the specific hydroxy epoxides observed in gas phase isoprene photooxidation experiments (as well as several other related species) were synthesized and the bulk phase aqueous reactions of these species in the presence of sulfate and nitrate were studied via nuclear magnetic resonance (NMR) techniques. The results indicate that both primary and tertiary organosulfates …

Sphingolipids In The Root Play An Important Role In Regulating The Leaf Ionome In Arabidopsis Thaliana, Dai-Yin Chao, Kenneth Gable, Ming Chen, Ivan Baxter, Charles R. Dietrich, Edgar B. Cahoon, Mary Lou Guerinot, Brett Lahner, Shiyu Lu, Jennifer E. Markham, Joe Morrissey, Gongshe Han, Sita Gupta, Jeffrey M. Harmon, Jan G. Jaworski, Teresa M. Dunn, David E. Salt

Department of Biochemistry: Faculty Publications

Sphingolipid synthesis is initiated by condensation of Ser with palmitoyl-CoA producing 3-ketodihydrosphinganine (3-KDS), which is reduced by a 3-KDS reductase to dihydrosphinganine. Ser palmitoyltransferase is essential for plant viability. Arabidopsis thaliana contains two genes (At3g06060/TSC10A and At5g19200/TSC10B) encoding proteins with significant similarity to the yeast 3-KDS reductase, Tsc10p. Heterologous expression in yeast of either Arabidopsis gene restored 3-KDS reductase activity to the yeast tsc10D mutant, confirming both as bona fide 3-KDS reductase genes. Consistent with sphingolipids having essential functions in plants, double mutant progeny lacking both genes were not recovered from crosses of single tsc10A and tsc10B …

Development Of Monolithic Stationary Phases For Cation-Exchange Capillary Liquid Chromatography Of Peptides And Proteins, Xin Chen

Theses and Dissertations

This dissertation focuses on the preparation of polymeric monolithic capillaries for ion exchange chromatography of peptides and proteins, since polymeric monoliths have shown promise for providing improved protein separations. Characteristics of monolithic columns include low back pressure, simplicity of fabrication and biocompatibility. Preparation of strong and weak cation-exchange monolithic stationary phases in 75 μm I.D. capillaries by direct in situ copolymerization was achieved using various functional monomers including sulfopropyl methacrylate, phosphoric acid 2-hydroxyethyl methacrylate, bis[2-(methacryloyloxy)ethyl] phosphate and 2-carboxyethyl acrylate with polyethylene glycol diacrylate and other PEG materials. The resulting monoliths provided excellent ion exchange capillary LC of peptides and proteins …

Decreased Stability And Increased Formation Of Soluble Aggregates By Immature Superoxide Dismutase Do Not Account For Disease Severity In Als., Kenrick A Vassall, Helen R Stubbs, Heather A Primmer, Ming Sze Tong, Sarah M Sullivan, Ryan Sobering, Saipraveen Srinivasan, Lee-Ann K Briere, Stanley D Dunn, Wilfredo Colón, Elizabeth M Meiering

Biochemistry Publications

Protein aggregation is a hallmark of many diseases, including amyotrophic lateral sclerosis (ALS), where aggregation of Cu/Zn superoxide dismutase (SOD1) is implicated in causing neurodegeneration. Recent studies have suggested that destabilization and aggregation of the most immature form of SOD1, the disulfide-reduced, unmetallated (apo) protein is particularly important in causing ALS. We report herein in depth analyses of the effects of chemically and structurally diverse ALS-associated mutations on the stability and aggregation of reduced apo SOD1. In contrast with previous studies, we find that various reduced apo SOD1 mutants undergo highly reversible thermal denaturation with little aggregation, enabling quantitative thermodynamic …

Loose Ligands And Available Iron In The Ocean, Ronald Benner

Faculty Publications

No abstract provided.

Anion Activation Site Of Insulin-Degrading Enzyme, Nicholas Noinaj, Eun Suk Song, Sonia Bhasin, Benjamin J. Alper, Walter K. Schmidt, Louis B. Hersh, David W. Rodgers

Chemistry & Physics Faculty Publications

Insulin-degrading enzyme (IDE) (insulysin) is a zinc metallopeptidase that metabolizes several bioactive peptides, including insulin and the amyloid β peptide. IDE is an unusual metallopeptidase in that it is allosterically activated by both small peptides and anions, such as ATP. Here, we report that the ATP-binding site is located on a portion of the substrate binding chamber wall arising largely from domain 4 of the four-domain IDE. Two variants having residues in this site mutated, IDE^{K898A,K899A,S901A} and IDE^R429S, both show greatly decreased activation by the polyphosphate anions ATP and PPP_i. IDE^{K898A,K899A,S901A} is also deficient …

Caffeine Metabolism And Cytochrome P450 Enzyme Mrna Expression Levels Of Genetically Diverse Inbred Mouse Strains, Neal Addicott, Michael Malfatti, Gabriela G. Loots

STAR Program Research Presentations

Cytochrome P450 (CYP) enzymes activate or eliminate medications and other xenobiotics, and Caffeine has been used as an indicator of activity for some CYPs. The natural genetic variation in the human population for caffeine metabolizing CYPs does not yet have an established animal model for comparison, but the natural variation in inbred mouse strains presents an attractive starting point. The project gave four different strains of mice a 40mg/kg dose of caffeine and sampled blood and liver tissue after 30 minutes. Samples were analyzed using High Performance Liquid Chromatography (HPLC), reverse transcription PCR (rtPCR), and quantitative PCR (qPCR). The DBA/2J …

The Prevalence Of Canine Leishmania Infantum Infection In Western China Detected By Pcr And Serological Tests, Jun-Yun Wang, Yu Ha, Chun-Hua Gao, Yong Wang, Yue-Tao Yang, Hai-Tang Chen

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Canine leishmaniasis (CanL) is endemic in western China, resulting in important public health problem. It is essential to evaluate the prevalence of canine Leishmania infantum infection for designing control policy. In the present study we report for the first time prevalence of Leishmania infection in dogs living in Jiuzhaigou County (Sichuan Provence, China), which is not only an important endemic area of CanL but also a tourism scenic spot, detected by PCR, ELISA and dipstick test. The results could provide key information for designing control programs against canine and human leishmaniasis. In addition, the complete sequence of the …

A New Noncovalent Force: Comparison Of P∙∙∙N Interaction With Hydrogen And Halogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When PH(3) is paired with NH(3), the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom. Quantum calculations indicate that this attraction is due in part to the transfer of electron density from the lone pair of the N atom to the σ(∗) antibond of a P-H covalent bond. Unlike a H-bond, the pertinent hydrogen is oriented about 180° away from, instead of toward, the N, and the N lone pair overlaps with the lobe of the P-H σ(∗) orbital that is closest to the P. In …

A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers

Faculty Publications, Chemistry

A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning …

Novel Application Of Query-Based Qualitative Predictors For Characterization Of Solvent Accessible Residues In Conjunction With Protein Sequence Homology. Proceedings Of The 22nd International Workshop On Database And Expert Systems Applications, D Rose, R Nepal, S Gholizadeh, R Mishra, R Lau, Brooke Lustig

Faculty Publications, Chemistry

No abstract provided.

Microfluidic Paper-Based Analytical Devices: From Pocket To Paper-Based Elisa, Andres W. Martinez

Chemistry and Biochemistry

Microfluidic paper-based analytical devices (microPADs) began as a simple idea with an ambitious goal. The idea was to make microfluidic devices out of paper instead of plastic or glass. The goal was to develop low-cost and portable paper-based diagnostic devices to improve healthcare in developing countries. Over the past 6 years, many developments have been made in the emerging field of paper-based microfluidic devices. Reviewing the development of these devices in the Whitesides group at Harvard University (Cambridge, MA, USA) can provide some insight into the future of the field and encourage scientists from a variety of backgrounds to contribute …

Better Biomolecule Thermodynamics From Kinetics, Kiran Girdhar, Gregory Scott, Yann R. Chemla, Martin Gruebele

Chemistry and Biochemistry

Protein stability is measured by denaturation: When solvent conditions are changed (e.g., temperature, denaturant concentration, or pH) the protein population switches between thermodynamic states. The resulting denaturation curves have baselines. If the baselines are steep, nonlinear, or incomplete, it becomes difficult to characterize protein denaturation. Baselines arise because the chromophore probing denaturation is sensitive to solvent conditions, or because the thermodynamic states evolve structurally when solvent conditions are changed, or because the barriers are very low (downhill folding). Kinetics can largely eliminate such baselines: Relaxation of chromophores, or within thermodynamic states, is much faster than the transition over activation …