Biochemistry, Biophysics, and Structural Biology Commons^™

The Terebridae And Teretoxins: Combining Phylogeny And Anatomy For Concerted Discovery Of Bioactive Compounds, Nicolas Puillandre, Mandë Holford

Publications and Research

The Conoidea superfamily, comprised of cone snails, terebrids, and turrids, is an exceptionally promising group for the discovery of natural peptide toxins. The potential of conoidean toxins has been realized with the distribution of the first Conus (cone snail) drug, Prialt (ziconotide), an analgesic used to alleviate chronic pain in HIV and cancer patients. Cone snail toxins (conotoxins) are highly variable, a consequence of a high mutation rate associated to duplication events and positive selection. As Conus and terebrids diverged in the early Paleocene, the toxins from terebrids (teretoxins) may demonstrate highly divergent and unique functionalities. Recent analyses of the …

Strategies For The Elimination Of Matrix Effects In The Lc-Ms/Ms Analysis Of The Lipophilic Toxins Okadaic Acid And Azaspiracid-1 In Molluscan Shellfish, Jane Kilcoyne, Elie Fux

Articles

Considerable efforts are being made worldwide to replace in vivo assays with instrumental methods of analysis for the monitoring of marine biotoxins in shellfish. Analysis of these compounds by the preferred technique of LC-MS/MS is challenged by matrix effects associated with shellfish tissue components. In methods validation, assessment of matrix interferences is imperative to ensure the accuracy of analytical results. We evaluated matrix interferences in the analysis of okadaic acid (OA) and azaspiracid 1 (AZA1) in mollucscan shellfish by using a conventional acidic method on electrospray triple stage quadrapole (TSQ) and hybrid quadrupole time of flight (QToF) instruments, with matrix …

Aromatic Acid Metabolites Of Escherichia Coli K-12 Can Induce The Marrab Operon, Lon Chubiz, Christopher Rao

Biology Department Faculty Works

MarR is a key regulator of the marRAB operon involved in antibiotic resistance and solvent stress tolerance in Escherichia coli. We show that two metabolic intermediates, 2,3-dihydroxybenzoate and anthranilate, involved in enterobactin and tryptophan biosynthesis, respectively, can activate marRAB transcription. We also found that a third intermediate involved in ubiquinone biosynthesis, 4-hydroxybenzoate, activates marRAB transcription in the absence of TolC. Of the three, however, only 2,3-dihydroxybenzoate directly binds MarR and affects its activity.

Specificity Determinants Of Arma, A Ribosomal Rna Methyltransferase That Confers Antibiotic Resistance, Tamara Zarubica

Theses and Dissertations

Bacterial resistance to 4,6-type aminoglycoside antibiotics, which target the 30S ribosomal subunit, has been traced to the arm/rmt family of rRNA methyltransferases. These plasmid-encoded enzymes transfer a methyl group from S-adenosylmethionine to N7 of the buried G1405 in the aminoglycoside binding site of 16S rRNA in the 30S ribosomal subunit. Neither 16S rRNA alone nor intact 70S ribosome is an efficient substrate for armA methyltransferase. To more fully characterize this family of enzymes, xiii we have investigated the substrate requirements of ArmA. We determined the Mg2+ dependence of ArmA activity and found that the enzyme could recognize both translationally active …

Axial Temperature Gradients In Gas Chromatography, Jesse Alberto Contreras

Theses and Dissertations

The easiest and most effective way to influence the separation process in gas chromatography (GC) is achieved by controlling the temperature of the chromatographic column. In conventional GC, the temperature along the length of the column is constant at any given time, T(t). In my research, I investigated the effects of temperature gradients on GC separations as a function of time and position, T(t,x), along the column. This separation mode is called thermal gradient GC (TGGC). The research reported in this dissertation highlights the fundamental principles of axial temperature gradients and the separation potential of the TGGC technique. These goals …

Negative Dielectrophoretic Capture Of Bacterial Spores In Food Matrices, Mehti Koklu, Seungkyung Park, Suresh D. Pillai, Ali Beskok

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device with planar square electrodes is developed for capturing particles from high conductivity media using negative dielectrophoresis (n-DEP). Specifically, Bacillus subtilis and Clostridium sporogenes spores, and polystyrene particles are tested in NaCl solution (0.05 and 0.225 S/m), apple juice (0.225 S/m), and milk (0.525 S/m). Depending on the conductivity of the medium, the Joule heating produces electrothermal flow (ETF), which continuously circulates and transports the particles to the DEP capture sites. Combination of the ETF and n-DEP results in different particle capture efficiencies as a function of the conductivity. Utilizing 20 μm height DEP chambers, “almost complete” and …

Selection For Non-Amyloidogenic Mutants Of Islet Amyloid Polypeptide (Iapp) Identifies An Extended Region For Amyloidogenicity, Ayano Fox, Thibaut Snollaerts, Camille Errecart Casanova, Anastasia Calciano, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

The aggregation of the 37-residue polypeptide IAPP, as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of pancreatic β-islet cells in type II diabetes. While IAPP has been known to be the primary component of type II diabetes amyloid, the molecular interactions responsible for this aggregation have not been identified. To identify the aggregation-prone region(s), we constructed a library of randomly generated point mutants of IAPP. This mutant IAPP library was expressed in E. coli as genetic fusions to the reporter protein enhanced green fluorescent protein (EGFP). Because IAPP aggregates rapidly, both …

How To Be Successful In Exclusive Breastfeeding For Four To Six Months:Experiences Of Chinese Mothers In Ireland, Qianling Zhou

Other resources

No abstract provided.

Maternal Health Behaviours During Pregnancy And Associations With Infant Feeding Factors, Roslyn Tarrant, Katherine Younger, Margaret Sheridan-Pereira, John Kearney

Other resources

Maternal health behaviours during pregnancy and associations with postnatal infant feeding practices

Objectives: To examine modifiable maternal health behaviours during pregnancy, including folic acid use peri-conceptually, smoking and alcohol consumption patterns, and relate these factors to maternal postnatal infant feeding practices.

Materials and Methods: A prospective observational study involved the recruitment of 539 pregnant women from a Dublin maternity hospital. Following application of exclusion criteria, 450 mothers were followed up at 6 weeks and 6 months postpartum. Quantitative data on folic acid use, as well as mothers’ smoking and alcohol consumption patterns during pregnancy were collected from the antenatal questionnaire. …

Kinetic Characterization Of Salmonella Flik-Flhb Interactions Demonstrates Complexity Of The Type Iii Secretion Substrate-Specificity Switch, Daniel P. Morris, Eric D. Roush, J. Will Thompson, M. Arthur Moseley, James W. Murphy, Jonathan L. Mcmurry

Faculty Articles

The bacterial flagellum is a complex macromolecular machine consisting of more than 20000 proteins, most of which must be exported from the cell via a dedicated Type III secretion apparatus. At a defined point in flagellar morphogenesis, hook completion is sensed and the apparatus switches substrate specificity type from rod and hook proteins to filament ones. How the switch works is a subject of intense interest. FIiK and F1hBs play central roles. In the present study, two optical biosensing methods were used to characterize FIiK-F1hB interactions using wild-type and two variant FlhBs from mutants with severe flagellar structural defects. Binding …

Frataxin And Mitochondrial Fes Cluster Biogenesis, Timothy L. Stemmler, Emmanuel Lesuisse, Debumar Pain, Andrew Dancis

Biochemistry and Molecular Biology Faculty Publications

Friedreich’s ataxia is an inherited neurodegenerative disease caused by frataxin deficiency. Frataxin is a conserved mitochondrial protein that plays a role in Fe-S cluster assembly in mitochondria. Fe-S clusters are modular cofactors that perform essential functions throughout the cell. They are synthesized by a multi-step and multi-subunit mitochondrial machinery that includes a scaffold protein Isu for assembling a protein bound Fe-S cluster intermediate. Frataxin interacts with Isu, iron, and with the cysteine desulfurase Nfs1 that supplies sulfur, thus placing it at the center of mitochondrial Fe-S cluster biosynthesis.

Novel Polymer Coupling Chemistry Based Upon Latent Cysteine-Like Residues And Thiazolidine Chemistry, Jospeh S. Carlson, Megan R. Hill, Taiga Young, Philip Costanzo

Chemistry and Biochemistry

Chain end functional polymers were prepared via reversible addition–fragmentation transfer (RAFT) polymerization techniques that were further chain extended with acrylonitrile. Under reducing conditions, latent cysteine-like residues were exposed at the chain ends. A variety of reduction conditions were explored and base polymers were then tethered together via thiazolidine chemistry.

Studies On Antidyslipidemic Effects Of Morinda Citrifolia (Noni) Fruit, Leaves And Root Extracts., Saf-Ur Rehman Mandukhail, Nauman Aziz, Anwar Gilani

Department of Biological & Biomedical Sciences

Background: The objective of present study was to provide the pharmacological basis for the medicinal use of Morinda citrifolia Linn in dyslipidemia using the aqueous-ethanolic extracts of its fruits (Mc.Cr.F), leaves (Mc.Cr.L) and roots (Mc.Cr.R). Results: Mc.Cr.F, Mc.Cr.L and Mc.Cr.R showed antidyslipidemic effects in both triton (WR-1339) and high fat diet-induced dyslipidemic rat models to variable extents. All three extracts caused reduction in total cholesterol and triglyceride levels in triton-induced dyslipidemia. In high fat diet-induced dyslipidemia all these extracts caused significant reduction in total cholesterol, triglyceride, low density lipoprotein-cholesterol (LDL-C), atherogenic index and TC/HDL ratio. Mc.Cr.R extract also caused increase …

Integrated Affinity Column Capillary Electrophoresis Microdevices For Biomarker Analysis, Weichun Yang

Theses and Dissertations

In this dissertation, microfluidic systems that integrate antibody-based sample preparation methods with electrophoretic separation are developed to analyze multiple biomarkers in a point-of-care setting. To form an affinity column, both monolith materials and wall-coated channels were explored. I successfully demonstrated that monolith columns can be prepared in microfluidic devices via photopolymerization. The selectivity of monolith columns was improved by immobilizing antibodies on the surface. These affinity columns can selectively enrich target analytes and reduce the signal of contaminant proteins up to 25,000 fold after immunoaffinity extraction. These results clearly demonstrate that microchip affinity monoliths can selectively concentrate and purify target …

Mechanisms Of Oxidant Generation By Catalase, Diane E. Heck, Michael Shakarjian, Hong-Duck Kim, Jeffrey Laskin, Anna M. Vetrano

NYMC Faculty Publications

The enzyme catalase converts solar radiation into reactive oxidant species (ROS). In this study, we report that several bacterial catalases (hydroperoxidases, HP), including Escherichia coli HP-I and HP-II also generate reactive oxidants in response to ultraviolet B light (UVB). HP-I and HP-II are identical except for the presence of NADPH. We found that only one of the catalases, HPI, produces oxidants in response to UVB light, indicating a potential role for the nucleotide in ROS production. This prompts us to speculate that NADPH may act as a cofactor regulating ROS generation by mammalian catalases. Structural analysis of the NADPH domains …

The Marine Sponge Metabolite Mycothiazole: A Novel Prototype Mitochondrial Complex I Inhibitor., J Brian Morgan, Fakhri Mahdi, Yang Liu, Veena Coothankandaswamy, Mika B. Jekabsons, Tyler A. Johnson, Koneni V. Sashidhara, Phillip Crews, Dale G. Nagle, Yu-Dong Zhou

Natural Sciences and Mathematics | Faculty Scholarship

A natural product chemistry-based approach was applied to discover small-molecule inhibitors of hypoxia-inducible factor-1 (HIF-1). A Petrosaspongia mycofijiensis marine sponge extract yielded mycothiazole (1), a solid tumor selective compound with no known mechanism for its cell line-dependent cytotoxic activity. Compound 1 inhibited hypoxic HIF-1 signaling in tumor cells (IC(50) 1nM) that correlated with the suppression of hypoxia-stimulated tumor angiogenesis in vitro. However, 1 exhibited pronounced neurotoxicity in vitro. Mechanistic studies revealed that 1 selectively suppresses mitochondrial respiration at complex I (NADH-ubiquinone oxidoreductase). Unlike rotenone, MPP(+), annonaceous acetogenins, piericidin A, and other complex I inhibitors, mycothiazole is a mixed polyketide/peptide-derived compound …

Synthesis And Characterization Of An Oligothiophene-Ruthenium Complex And Synthesis And Optical Properties Of Oligothiophene-Ruthenium Complexes Bound To Cdse Nanoparticles, Nathan A. Bair

Theses and Dissertations

Oligothiophenes are of increasing interest in organic based electronic devices in part due to their high electron and hole mobilities. In an organic photovoltaic (OPV) device, the electronic properties of oligothiophenes make them advantageous as charge transfer junctions. To serve as charge transfer junctions, oligothiophenes must be functionalized to bind to the donor and acceptor parts of the device. The donor and acceptor parts are different materials and the synthesis of asymmetric oligothiophenes is of great interest. Previous researchers in our lab synthesized four asymmetric oligothiophenes, two with two thiophene subunits and two with four. Each set of oligothiophenes contained …

Bilinear Programming And Protein Structure Alignment, J. Cain, D. Kamenetsky, N. Lavine

Mathematical Sciences Technical Reports (MSTR)

Proteins are a primary functional component of organic life, and understanding their function is integral to many areas of research in biochemistry. The three-dimensional structure of a protein largely determines this function. Protein structure alignment compares the structure of a protein with known function to that of a protein with unknown function. A protein’s three-dimensional structure can be transformed through a smooth piecewise-linear sigmoid function to a real symmetric contact matrix that represents the functional significance of certain parts of the protein. We address the protein alignment problem as a minimization of the 2-norm difference of two proteins’ contact matrices. …

Synthesis, Kinetic And Photocatalytic Studies Of Porphyrin-Ruthenium-Oxo Complexes, Yan Huang

Masters Theses & Specialist Projects

Macrocyclic ligand-complexed transition metal-oxo intermediates are the active oxidizing species in a variety of important biological and catalytic oxidation reactions. Many transition metal catalysts have been designed to mimic the predominant oxidation catalysts in Nature, namely the cytochrome P450 enzymes. Ruthenium porphyrin complexes have been the center of the research and have successfully been utilized, as catalysts, in major oxidation reactions such as the hydroxylation of alkanes. This study focuses on kinetic and photocatalytic studies of oxidation reactions with wellcharacterized high-valent ruthenium-oxo porphyrin complexes.
The trans-dioxoruthenium(VI) porphyrins have been among the best characterized metal-oxo intermediates and their involvement as …

Exploring Zirconia As A Column Packing Material, Tushar Ghugare

Masters Theses & Specialist Projects

Zirconia is one of the most promising column packing materials for High Performance Liquid Chromatography (HPLC). The perfect HPLC support material should be energetically homogenous, have a high surface area on which different chemical species can reversibly attach and be physically and chemically stable over a wide range of pH, temperature and solvent conditions. Most existing supports do not have all of these properties. This project is also focused on a proteomics study. Zirconia, hafnium oxide and titanium oxide which are some of the more promising materials currently available, can be used for the separation and analysis of phosphorylated proteins. …