Biochemistry, Biophysics, and Structural Biology Commons^™

Inhibition Of Proprotein Convertase Ski-1 Blocks Transcription Of Key Extracellular Matrix Genes Regulating Osteoblastic Mineralization, Jeff P. Gorski, Nichole T. Huffman, Sridar Chittur, Ronald J. Midura, Claudine Black, Julia Oxford, Nabil G. Seidah

Biomedical Research Institute Publications and Presentations

Mineralization, a characteristic phenotypic property of osteoblastic lineage cells, was blocked by AEBSF and dec-RRLL-cmk, inhibitors of SKI-1 (site 1; subtilisin kexin like-1) protease. Since SKI-1 is required for activation of SREBP and CREB/ATF family transcription factors, we tested the effect of these inhibitors on gene expression. AEBSF decreased expression of 140 genes by 1.5- to 3.0-fold including Phex, Dmp1, COL1A1, COL11A1 and fibronectin. Direct comparison of AEBSF and dec-RRLL-cmk, a more specific SKI-1 inhibitor, demonstrated that expression of Phex, Dmp1, COL11A1 and fibronectin was reduced by both while COL1A2 and HMGCS1 were reduced …

Loose Ligands And Available Iron In The Ocean, Ronald Benner

Faculty Publications

No abstract provided.

Dynamic Glucoregulation And Mammalian-Like Responses To Metabolic And Developmental Disruption In Zebrafish, Agata Jurczyk, Nicole M. Roy, Rabia Bajwa, Philipp Gut, Kathryn Lipson, Chaoxing Yang, Laurence Covassin, Waldemar J. Racki, Aldo A. Rossini, Nancy Phillips, Didier Y. R. Stainier, Dale L. Greiner, Michael A. Brehm, Rita Bortell, Philip Diiorio

Biology Faculty Publications

Zebrafish embryos are emerging as models of glucose metabolism. However, patterns of endogenous glucose levels, and the role of the islet in glucoregulation, are unknown. We measured absolute glucose levels in zebrafish and mouse embryos, and demonstrate similar, dynamic glucose fluctuations in both species. Further, we show that chemical and genetic perturbations elicit mammalian-like glycemic responses in zebrafish embryos. We show that glucose is undetectable in early zebrafish and mouse embryos, but increases in parallel with pancreatic islet formation in both species. In zebrafish, increasing glucose is associated with activation of gluconeogenic phosphoenolpyruvate carboxykinase1 (pck1) transcription. Non-hepatic Pck1 protein is …

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 …

Novel Copper Loaded Core-Shell Silica Nanoparticles With Improved Copper Bioavailability Synthesis, Characterization And Study Of Antibacterial Properties, Pavithra Maniprasad

Electronic Theses and Dissertations

A novel core-shell silica based antimicrobial nanoparticle was synthesized. The Stöber silica shell has been engineered to accommodate copper. Synthesis of the core-shell Cu-silica nanoparticle (C-S CuSiNP) involves preparation of base-hydrolyzed Stöber silica “seed” particles first, followed by the acid-catalyzed seeded growth of the Cu-silica shell layer around the core. Scanning electron microscopy and transmission electron microscopy showed monodispersed, spherical shaped nanoparticles with smooth surface morphology. Characterization of particle size distribution in solution by the Dynamic Light Scattering (DLS) technique was fairly consistent with the electron microscopy results. Loading of Cu to nanoparticles was confirmed by the SEM-Energy Dispersive X-Ray …

A Solid Phase Assay For Topoisomerase I Interfacial Poisons And Catalytic Inhibitors, Vidusha Cyril

Electronic Theses and Dissertations

We report a mechanism based screening technique to rapidly identify eukaryotic topoisomerase I targeting agents. The method is based on genetic tagging of topoisomerase I to immobilize the enzyme on a solid surface in a microtiter well format. DNA is added to the wells and retained DNA is detected by Picogreen fluorescence. Compounds that result in an increase in Picogreen staining represent potential topoisomerase interfacial poisons while those that reduce fluorescence report catalytic inhibitors; therefore, the solid phase assay represents a „bimodal‟ readout that reveals mechanisms of action. The method has been demonstrated to work with known interfacial poisons and …

Performance Screening Of Chemostat Adapted Recombinant Zymomonas Mobilis Strains, Deirdre M. Beard, Nancy Dowe

STAR Program Research Presentations

Corn stover biomass can be pretreaed and hydrolyzed into soluble sugars to be fermented by microorganisms to ethanol. NREL has developed a recombinant bacteria Zymomonas mobilis 8b that metabolizes both five and six carbon sugars. During pretreatment, toxic inhibitors such as furfural and acetate are produced. NREL has made an attempt to adapt two sub-strains of Z. mobilis 8b to acetate and furfural by using a chemostat method. During the chemostat process, cultures were frozen back in glycerol and saved. In this study, those frozen cultures were revived and analyzed for performance in environments with varying concentrations of furfural and …

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 …

Haemato-Biochemical Changes In Natural Cases Of Canine Babesiosis, Showkat Ahmad Shah, Naresh Kumar Sood, Srinivasa Rao Tumati

Biochemistry Collection

Incidence of severe anemia due to babesiosis in dogs resulting in death in a short time of illness is on the increase in Punjab, during last few decades due to introduction of exotic breeds like Grey Hound, German shepherd, Doberman, Labrador and others. In the present study the hematological and biochemical changes in blood samples obtained from 4 dogs naturally infected with Babesia were evaluated. The dogs were presented to the Department of Veterinary Clinical Services Complex, GADVASU, Ludhiana from August 2008 to April 2009. The evaluation included Hemoglobin (Hb), Red Blood Cell count (RBC), Packed Cell Volume (PCV), Mean …

Biochemical Methane Potential Of Different Organic Wastes And Energy Crops From Estonia, M. Luna-Derisco, A. Normak, K. Orupõld

Biochemistry Collection

The biochemical methane potential (BMP) of different Estonian substrates as alternative sources for biogas production was studied. For this purpose, the BMP test was carried out in batch mode at mesophilic temperature (36°C). Substrates were divided into 2 groups: agricultural substrates (silage, hay, cattle and pig slurry) and food industry residues (milk, brewery and cereal industry residues). Methane yields obtained were between 286–319 L kgVS^-1 for silage and hay, 238–317 L kgVS^-1 for animal slurry and 272–714 L kgVS^-1 for agro-industrial wastes. The highest methane yield was obtained from sour cream (714 L kgVS^-1), the …

Effect Of Dietary Antibacterial Peptide And Zinc-Methionine On Performance And Serum Biochemical Parameters In Piglets, J. H. Wang, C. C. Wu, J. Feng

Biochemistry Collection

The objective of this study was to evaluate the effect of dietary supplementation of antibacterial peptide and zinc methionine on performance and some serum biochemical parameters of weaned piglets. Rongchang male piglets (28 days of age, initial weight 8.4 ± 0.65 kg) were used. All piglets were randomly allotted to four diets including the control group, the antibacterial peptide (AP) group containing 10 mg antibacterial peptide/kg diet, the zinc methionine (Zn-Met) group with 1 200 zinc methionine/kg diet (equal to 200 mg Zn²⁺/kg diet), the zinc methionine/antibacterial peptide (Zn/AP) group containing 10 mg antibacterial peptide and 1 200 …

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 …

Acute Synaptic Activity Causes Differential Mirna Expression In The Drosophila Melanogaster Larval Central Nervous System, Robert Ian Sand

Electronic Theses and Dissertations

The primary goal of this thesis was to determine if spaced synaptic stimulation induced the differential expression of microRNAs (miRNAs) in the Drosophila melanogaster central nervous system (CNS). Prior to attaining this goal, we needed to identify and validate a spaced stimulation paradigm that could induce the formation of new synaptic growth at a model synapse, the larval neuromuscular junction (NMJ). Both Channelrhodopsin- and high potassium-based stimulation paradigms adapted from (Ataman, et al. 2008) were tested. Once validation of these paradigms was complete, we sought to characterize the miRNA expression profile of the larval CNS by miRNA array. Following attainment …

The Fire Inventory From Ncar (Finn): A High Resolution Global Model To Estimate The Emissions From Open Burning, C. Wiedinmyer, S. K. Akagi, Robert J. Yokelson, L. K. Emmons, J. A. Al-Saadi, J. J. Orlando, A. J. Soja

Chemistry and Biochemistry Faculty Publications

The Fire INventory from NCAR version 1.0 (FINNv1) provides daily, 1 km resolution, global estimates of the trace gas and particle emissions from open burning of biomass, which includes wildfire, agricultural fires, and prescribed burning and does not include biofuel use and trash burning. Emission factors used in the calculations have been updated with recent data, particularly for the non-methane organic compounds (NMOC). The resulting global annual NMOC emission estimates are as much as a factor of 5 greater than some prior estimates. Chemical speciation profiles, necessary to allocate the total NMOC emission estimates to lumped species for use by …

Emission Factors For Open And Domestic Biomass Burning For Use In Atmospheric Models, S. K. Akagi, Robert J. Yokelson, C. Wiedinmyer, M. Alvarado, J. S. Reid, T. Karl, J. D. Crounse, P. O. Wennberg

Chemistry and Biochemistry Faculty Publications

Biomass burning (BB) is the second largest source of trace gases and the largest source of primary fine carbonaceous particles in the global troposphere. Many recent BB studies have provided new emission factor (EF) measurements. This is especially true for non-methane organic compounds (NMOC), which influence secondary organic aerosol (SOA) and ozone formation. New EF should improve regional to global BB emissions estimates and therefore, the input for atmospheric models. In this work we present an up-to-date, comprehensive tabulation of EF for known pyrogenic species based on measurements made in smoke that has cooled to ambient temperature, but not yet …