Detecting A-Series Ganglioside Expression Profile Changes During Microglial Activation, 2018 The University of Western Ontario
Detecting A-Series Ganglioside Expression Profile Changes During Microglial Activation, Mona M. Alshaikh
Electronic Thesis and Dissertation Repository
With aging, our brains become more susceptible to disease and injury. Different regions of the brain have differing levels of vulnerability to stress and injury, and this brain region-dependent variability to vulnerability could be partly explained by the existence of glycosphingolipids within the cell’s plasma membrane called gangliosides. Gangliosides are expressed predominantly within the brain and play various roles within the central nervous system including neural repair, cell survival, and neurodegeneration. Our laboratory has demonstrated that gangliosides can shift their composition from GM1 back to GM2 and GM3 following stroke in mice and rats indicating a role for simple gangliosides …
Reversible Heparin Molecules And Methods Of Making And Using The Same, 2018 Chapel Hill , NC
Reversible Heparin Molecules And Methods Of Making And Using The Same, Jian Liu, Yongmei Xu, Robert J. Linhardt, Edward Harris
Department of Biochemistry: Faculty Publications
Methods and systems for synthesizing heparin compounds are provided . The chemoenzymatic synthesis of structurally homogeneous low molecular weight heparins that have a reversible anticoagulant activity is provided . Also disclosed are heparin compounds having anticoagulant activity , including a binding affinity to antithrombin and an anti - Xa activity , but no detectable anti - lla activity . Additionally , provided are synthetic , low - molecular weight heparin com pounds with reversible anticoagulant activity , where the anticoagulant activity is reversible by protamine.
Department Of Chemistry And Biochemistry 23rd Departmental Symposium In Conjunction With The Petersheim Academic Exposition, 2018 Seton Hall University
Department Of Chemistry And Biochemistry 23rd Departmental Symposium In Conjunction With The Petersheim Academic Exposition, Seton Hall University
Petersheim Academic Exposition
No abstract provided.
Preparation And Characterization Of A Small Library Of Thermally-Labile End-Caps For Variable-Temperature Triggering Of Self-Immolative Polymers, 2018 University of Windsor
Preparation And Characterization Of A Small Library Of Thermally-Labile End-Caps For Variable-Temperature Triggering Of Self-Immolative Polymers, S. Maryamdokht Taimoory, S. Iraj Sadraei, Rose Anne Fayoumi, Sarah Nasri, Matthew Revington, John F. Trant
Chemistry and Biochemistry Publications
The reaction between furans and maleimides has increasingly become a method of interest as its reversibility makes it a useful tool for applications ranging from self-healing materials, to self-immolative polymers, to hydrogels for cell culture and for the preparation of bone repair. However, most of these applications have relied on simple monosubstituted furans and simple maleimides and have not extensively evaluated the potential thermal variability inherent in the process that is achievable through simple substrate modification. A small library of cycloadducts suitable for the above applications was prepared, and the temperature dependence of the retro-Diels-Alder processes was determined through in …
Role Of Protein Charge Density On Hepatitis B Virus Capsid Formation, 2018 The University of Akron
Role Of Protein Charge Density On Hepatitis B Virus Capsid Formation, Xinyu Sun, Dong Li, Zhaoshuai Wang, Panchao Yin, Rundong Hu, Rundong Hu, Hui Li, Qiao Liu, Yunyi Gao, Baiping Ren, Jie Zheng, Yinan Wei, Tianbo Liu
Chemistry Faculty Publications
The role of electrostatic interactions in the viral capsid assembly process was studied by comparing the assembly process of a truncated hepatitis B virus capsid protein Cp149 with its mutant protein D2N/D4N, which has the same conformational structure but four fewer charges per dimer. The capsid protein self-assembly was investigated under a wide range of protein surface charge densities by changing the protein concentration, buffer pH, and solution ionic strength. Lowering the protein charge density favored the capsid formation. However, lowering charge beyond a certain point resulted in capsid aggregation and precipitation. Interestingly, both the wild-type and D2N/D4N mutant displayed …
Conformational Arrangements Of Ubch7-Ubiquitin With Ospg And Parkin, 2018 The University of Western Ontario
Conformational Arrangements Of Ubch7-Ubiquitin With Ospg And Parkin, Tara E. C. Condos
Electronic Thesis and Dissertation Repository
The E2-ubiquitin conjugate is a key regulator of ubiquitination and is therefore an important component of cellular homeostasis. Disruptions to proper E2-ubiquitin functioning have implications in diseases such as shigellosis and Parkinson’s disease discussed here. E2-ubiquitin conjugates like UbcH7-ubiquitin are extremely dynamic and can adopt multiple conformations in solution or bound to target proteins. However, the conformational arrangements that UbcH7-ubiquitin adopts while free in solution, bound to the shigellosis-associated kinase OspG or to the Parkinson’s disease-related E3 ligase parkin are unknown. Also unknown, is a mechanistic explanation for how UbcH7-ubiquitin interactions with OspG and parkin are associated with disease. Here, …
Effect Of Mutation Of Cvn7 Conservon Genes Sco6796 And Sco6798 Of Streptomyces Coelicolor., 2018 Otterbein University
Effect Of Mutation Of Cvn7 Conservon Genes Sco6796 And Sco6798 Of Streptomyces Coelicolor., Caroline Fulmer
Undergraduate Distinction Papers
Abstract
Streptomyces coelicolor is a gram-positive Actinobacterium. It is a filamentous soil organism that performs complex multicellular development. Its physiological and morphological differentiation produces active secondary metabolite antibiotics that have pharmaceutical applications. Studies of S. coelicolor show that cyclic di-GMP proteins regulate physiological and morphological development. S. coelicolor has 13 copies of an operon that are collectively named “conservon” because they are highly conserved. The operons are named cvn1-13 and genes in each operon are denoted cvnA-D. RNA-Seq data of a cyclic di-GMP phosphodiesterase double mutant showed differential expression between wild type and many of the operons in the …
Identifying Rmda Protein Interactions In Streptomyces Using A Bacterial Two-Hybrid System, 2018 Otterbein University
Identifying Rmda Protein Interactions In Streptomyces Using A Bacterial Two-Hybrid System, Rachel Nguyen
Undergraduate Distinction Papers
Streptomyces is a genus of the phylum actinobacteria most commonly found as soil bacteria and used as a major source of antibiotics. RmdA and RmdB are phosphodiesterases that break down the ubiquitous second messenger cyclic-di-GMP which determines colony morphology and development of Streptomyces. The objective of this research is to identify whether RmdA will have interactions with itself using the Bacterial Adenylate Cyclase Two-Hybrid (BACTH) System. Each gene was fused into one of two BACTH vectors that encode a different domain of a single protein (T18 and T25) and then cotransformed into the BACTH indicator strain. The transformants were …
Dna Binding Kinetics Of Large Antiviral Hairpin Polyamides, 2018 University of Missouri, St. Louis
Dna Binding Kinetics Of Large Antiviral Hairpin Polyamides, Jacquelyn Niederschulte
Dissertations
While vaccines exist for the some of the most problematic strains of human papillomavirus (HPV), a double stranded DNA virus, there is currently no cure. HPV remains one of the most commonly sexually transmitted infections and is responsible for virtually all cervical cancers and genital warts. Natural products Distamycin A and netropsin have inspired the hairpin Nmethylpyrrole (Py)/N-methylimidazole (Im) polyamides (PAs) studied here. The larger hairpin PAs, designed to bind to sites of 10 or more DNA bp, have been shown to be effective antivirals against oncogenic HPV strains 16, 18, and 31, while smaller hairpin PAs are not. Despite …
The Identification And Characterization Of A Putative Chromosome Segregation Gene In Streptomyces Coelicolor, 2018 Otterbein University
The Identification And Characterization Of A Putative Chromosome Segregation Gene In Streptomyces Coelicolor, Sean Kirk
Undergraduate Distinction Papers
Streptomyces coelicolor is a soil bacterium that is a model for bacterial development. It is a filamentous, sporulating bacterium known to produce many medically utilized antibiotics. The goal of this research was to examine several developmental mutants and characterize novel genes of interest. Previously generated random transposon insertion mutants were analyzed using visual and microscopic phenotyping. Mutants of interest were further pursued and each transposon disruption site was identified by Inverse PCR and DNA sequencing. One of the novel genes is suspected to be involved in DNA segregation and codes for a putative membrane protein. Staining with propidium iodide was …
Constitutive Expression Of Thioglucoside Glucohydrolase 1 (Tgg1) Decreases Intercellular Trafficking In Arabidopsis Thaliana, 2018 University of Tennessee, Knoxville
Constitutive Expression Of Thioglucoside Glucohydrolase 1 (Tgg1) Decreases Intercellular Trafficking In Arabidopsis Thaliana, Alessandro Francesco Sarno
EURēCA: Exhibition of Undergraduate Research and Creative Achievement
Plasmodesmata (PD) are pores that traverse plant cell walls, providing a route for intercellular trafficking of essential metabolites, nutrients, and signaling molecules between adjacent plant cells, thereby aiding communication. The increased size exclusion limit 2 (ise2) mutant of Arabidopsis thaliana has an increased abundance of branched PD, as well as a greater flux of intercellular trafficking. A search for proteins that interact with ISE2 identified THIOGLUCOSIDE GLUCOHYDROLASE 2 (a myrosinase). A. thaliana also encodes a second, closely-related myrosinase, TGG1. Myrosinases are enzymes that catalyze the hydrolysis of glucosinolates, a type of secondary metabolite that are amino acid derivatives. The breakdown …
Phase Diagram Of Water Confined By Graphene, 2018 Columbia University
Phase Diagram Of Water Confined By Graphene, Zhenghan Gao, Nicolas Giovambattista, Ozgur Sahin
Publications and Research
The behavior of water confined at the nanoscale plays a fundamental role in biological processes and technological applications, including protein folding, translocation of water across membranes, and filtration and desalination. Remarkably, nanoscale confinement drastically alters the properties of water. Using molecular dynamics simulations, we determine the phase diagram of water confined by graphene sheets in slab geometry, at T = 300 K and for a wide range of pressures. We find that, depending on the confining dimension D and density σ, water can exist in liquid and vapor phases, or crystallize into monolayer and bilayer square ices, as observed in …
A Multisession, Undergraduate Molecular Biology Lab Experiment Using Green Fluorescent Protein Including Subcloning And Color Changing Mutagenesis, 2018 St. Cloud State University
A Multisession, Undergraduate Molecular Biology Lab Experiment Using Green Fluorescent Protein Including Subcloning And Color Changing Mutagenesis, Nathan S. Winter
Chemistry Faculty Publications
This paper describes a series of experiments involving handling and manipulating the DNA coding for Green Fluorescent Protein (GFP) including the subcloning of this gene, and mutating the DNA so that Cyan Fluorescent Protein (CFP) or Blue Fluorescent protein (BFP) are expressed. The primers needed for the PCR based subcloning of GFP are presented, as are those needed to mutate the GFP to either CFP or BFP.
Transmembrane Domains Of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association In Vitro, 2018 University of Kentucky
Transmembrane Domains Of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association In Vitro, Stacy R. Webb, Stacy E. Smith, Michael G. Fried, Rebecca Ellis Dutch
Molecular and Cellular Biochemistry Faculty Publications
Enveloped viruses require viral fusion proteins to promote fusion of the viral envelope with a target cell membrane. To drive fusion, these proteins undergo large conformational changes that must occur at the right place and at the right time. Understanding the elements which control the stability of the prefusion state and the initiation of conformational changes is key to understanding the function of these important proteins. The construction of mutations in the fusion protein transmembrane domains (TMDs) or the replacement of these domains with lipid anchors has implicated the TMD in the fusion process. However, the structural and molecular details …
Shaping Light In Backward-Wave Nonlinear Hyperbolic Metamaterials, 2018 University of Missouri-St. Louis
Shaping Light In Backward-Wave Nonlinear Hyperbolic Metamaterials, Thomas George, Alexander Popov, Sergey Myslivets, Vitaly Slabko, Victor Tkachenko
Chemistry & Biochemistry Faculty Works
Backward electromagnetic waves are extraordinary waves with contra-directed phase velocity and energy flux. Unusual properties of the coherent nonlinear optical coupling of the phase-matched ordinary and backward electromagnetic waves with contra-directed energy fluxes are described that enable greatly-enhanced frequency and propagation direction conversion, parametrical amplification, as well as control of shape of the light pulses. Extraordinary transient processes that emerge in such metamaterials in pulsed regimes are described. The results of the numerical simulation of particular plasmonic metamaterials with hyperbolic dispersion are presented, which prove the possibility to match phases of such coupled guided ordinary and backward electromagnetic waves. Particular …
Site-Directed Mutagenesis Of Malate Dehydrogenase: A Class Project, 2018 Olivet Nazarene University
Site-Directed Mutagenesis Of Malate Dehydrogenase: A Class Project, Bruce J. Heyen, Chesley Rowlett, Jon Zatorski, Ryan Burch, Emily Veach, Andy Gemmaka
Scholar Week 2016 - present
Malate dehydrogenase (MDH) is an important enzyme in an organism’s metabolic pathways. MDH is found in almost all living cells and catalyzes the conversion of malate to oxaloacetate which also involves nicotinamide dehydrogenase (NAD) as a coenzyme. A method to study how an enzyme operates is to alter one of its amino acids and compare the activity of the enzyme before and after the mutation. As a class project in Advanced Biochemistry during the spring semester of 2018, we are working as a team to propose and carry out a point-based mutation on MDH.
Effect Of An Arginine-To-Isoleucine Active Site Mutation On Escherichia Coli Malate Dehydrogenase Enzymatic Activity, 2018 Olivet Nazarene University
Effect Of An Arginine-To-Isoleucine Active Site Mutation On Escherichia Coli Malate Dehydrogenase Enzymatic Activity, Jon Zatorski, Bruce J. Heyen
Scholar Week 2016 - present
Citric acid cycle enzymes function in an environment with numerous substrate analogues and therefore contain active site residue organizations that confer high substrate specificity. Extensive research into the catalytic mechanism of Escherichia coli malate dehydrogenase (eMDH) has identified arginine81 as being crucial to catalysis. In this investigation, an engineered eMDH having an Ile81 rather than an Arg81 (R81I) was isolated using a hexahistadine (His6) tag. Enzymatic activity of the R81I mutant with respect to malate, lactate, and pyruvate was explored. The R81I mutant did show significant activity toward malate, but did not show significant activity toward lactate or pyruvate. Investigations …
Synthesis And Incorporation Of 1,2-Alkanolamine-Functionalized Lysine As A Non-Canonical Amino Acid Into Gfp, 2018 Olivet Nazarene University
Synthesis And Incorporation Of 1,2-Alkanolamine-Functionalized Lysine As A Non-Canonical Amino Acid Into Gfp, Chesley M. Rowlett
Scholar Week 2016 - present
Synthesis of specific post translational modifications in proteins can be difficult but achievable via genetic code expansion techniques. An attempt has been made to synthesize and incorporate D-cThrK into green fluorescent protein (GFP) at an amber mutation site in Escherichia coli via the coordination of pyrrolysyl- tRNA synthetase and its cognate tRNApyl. The incorporation of this non-canonical amino acid and potential chemical transformations following it allow the synthesis of proteins with post translational lysine modifications, making a variety of basic and biotechnological applications available.
The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, 2018 Olivet Nazarene University
The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, Micah Forshee
Scholar Week 2016 - present
The microbiome is a dynamic community that can positively and negatively influence host health. Lactobacillus reuteri is a probiotic that has received much attention for its ability to inhibit pathogens such as Salmonella Typhimurium, Escherichia coli, and Clostridium difficile. It does so by its unique ability to metabolize glycerol into the antimicrobial compound 3-HPA, which is commonly referred to as reuterin. The ability to secrete reuterin is dependent not only on glycerol availability but also the concentration of glucose. In fact, there appears to be a “goldilocks” ratio between glucose and glycerol as either too much or too …
Shaping Light In Backward-Wave Nonlinear Hyperbolic Metamaterials, 2018 University of Missouri-St. Louis