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Frustrated Drift Of An Anchored Scroll-Wave Filament And The Geodesic Principle, Marcel Wellner, Christian W. Zemlin, Arkady M. Pertsov 2010 Old Dominion University

Frustrated Drift Of An Anchored Scroll-Wave Filament And The Geodesic Principle, Marcel Wellner, Christian W. Zemlin, Arkady M. Pertsov

Bioelectrics Publications

We investigate anchored scroll-wave filaments in an excitable medium whose diffusivity matrix, including its determinant, is spatially nonuniform. The study is motivated by cardiological applications where scroll-wave behavior in the presence of diffusivity gradients is believed to play an important role in the development of severe arrhythmias. A diffusivity gradient is expected to make the filament drift, unless drift is prevented ("frustrated") by anchoring to localized defects in the propagation medium. The resulting stationary filament is a geodesic curve, as demonstrated here in the case of a nonzero but constant gradient. That is, the diffusivity matrix has a determinant that ...


Purification And Properties Of Amycolatopsis Mediterranei Dsm 43304 Lipase And Its Potential In Flavour Ester Synthesis, Dharmendra Dheeman, Gary Henehan, Jesus Maria Frias 2010 Technological University Dublin

Purification And Properties Of Amycolatopsis Mediterranei Dsm 43304 Lipase And Its Potential In Flavour Ester Synthesis, Dharmendra Dheeman, Gary Henehan, Jesus Maria Frias

Articles

An extracellular thermostable lipase from Amycolatopsis mediterranei DSM 43304 has been purified to homogeneity using ammonium sulphate precipitation followed by anion exchange chromatography and hydrophobic interaction chromatography. This protocol resulted in 398 fold purification with 36% final recovery. The purified A. mediterranei DSM 43304 lipase (AML) has an apparent molecular mass of 33 kDa. The N-terminal sequence, AANPYERGPDPTTASIEATR, showed highest similarity to a lipase from Streptomyces exfoliatus. The values of and for p-nitrophenyl palmitate (p-NPP) under optimal temperature (60°C) and pH (8.0) conditions were 0.10 ± 0.01 mM and 2.53 ± 0.06 mmol/minmg ...


Evolution Of New Enzymatic Function By Structural Modulation Of Cysteine Reactivity In Pseudomonas Fluorescens Isocyanide Hydratase, Mahadevan Lakshminarasimhan, Peter Madzelan, Ruth Nan, Nicole Marie Milkovic, Mark A. Wilson 2010 University of Nebraska - Lincoln

Evolution Of New Enzymatic Function By Structural Modulation Of Cysteine Reactivity In Pseudomonas Fluorescens Isocyanide Hydratase, Mahadevan Lakshminarasimhan, Peter Madzelan, Ruth Nan, Nicole Marie Milkovic, Mark A. Wilson

Biochemistry -- Faculty Publications

Isocyanide (formerly isonitrile) hydratase (EC 4.2.1.103) is an enzyme of the DJ-1 superfamily that hydrates isocyanides to yield the corresponding N-formamide. In order to understand the structural basis for isocyanide hydratase (ICH) catalysis, we determined the crystal structures of wild-type and several site-directed mutants of Pseudomonas fluorescens ICH at resolutions ranging from 1.0 to 1.9 Å. We also developed a simple UV-visible spectrophotometric assay for ICH activity using 2-naphthyl isocyanide as a substrate. ICH contains a highly conserved cysteine residue (Cys101) that is required for catalysis and interacts with Asp17, Thr102, and an ordered ...


In Vivo Labeling Of A Model Β-Clam Protein With A Fluorescent Amino Acid, Mangayarkarasi Periasamy 2010 University of Massachusetts Amherst

In Vivo Labeling Of A Model Β-Clam Protein With A Fluorescent Amino Acid, Mangayarkarasi Periasamy

Masters Theses 1911 - February 2014

Proteins can be labeled with different tags to enable their structural and functional investigations. In addition, labeling proteins at specific sites helps in studying the conformational dynamics of these molecules. A plethora of methods is available to facilitate labeling, choice of which largely depends on the requirements and the anticipated end results. In general, the various labeling methods can be classified into four different classes based on the stage at which labeling is performed, namely post translational labeling, non-ribosomal synthesis, in vitro translation and in vivo translation. Interestingly all these techniques use different unnatural amino acids for this purpose.

Protein ...


Interconversion Of The Specificities Of Human Lysosomal Enzymes, Ivan B. Tomasic 2010 University of Massachusetts Amherst

Interconversion Of The Specificities Of Human Lysosomal Enzymes, Ivan B. Tomasic

Masters Theses 1911 - February 2014

Fabry disease (FD) is an X-linked recessive lysosomal storage disorder (LSD) known to affect approximately 1 in every 40,000 males, and a smaller number of females. FD results from a deficiency of functional α-galactosidase (α-GAL), which leads to the accumulation of terminally α-galactosylated substrates in the lysosome. The predominant treatment is Enzyme Replacement Therapy (ERT), requiring the regular infusion of recombinant human α-GAL. More than half of individuals receiving ERT experience a range of adverse infusion reactions, and it has been reported that as many as 88% of patients receiving ERT develop neutralizing IgG antibodies against the drug.

In ...


Anti-Diabetic Potentials Of Phenolic Enriched Chilean Potato And Select Herbs Of Apiaceae And Lamiaceae Families, Fahad Saleem 2010 University of Massachusetts Amherst

Anti-Diabetic Potentials Of Phenolic Enriched Chilean Potato And Select Herbs Of Apiaceae And Lamiaceae Families, Fahad Saleem

Masters Theses 1911 - February 2014

The incidence of diabetes mellitus and cardiovascular diseases is increasing at a worrisome rate globally. Diabetes mellitus is known to occur due to high blood glucose levels, caused by defects in insulin levels. Adult on-set type II diabetes, which is closely associated with obesity, is reported to be 90-95% of all diabetic cases and linked to diet and lifestyle factors. A large population of the developed and developing countries is now being effected by this epidemic. Natural sources of phenolic antioxidants and inhibitors of digestive enzymes from food sources have potential for low cost dietary management of type II diabetes ...


Morphological Changes And Immunohistochemical Expression Of Rage And Its Ligands In The Sciatic Nerve Of Hyperglycemic Pig (Sus Scrofa), Judyta K. Juranek, Alexey Aleshin, Eileen M. Rattigan, Lynne Johnson, Wu Qu, Fei Song, Radha Ananthakrishnan, Nosirudeen Quadri, Shi Du Yan, Ravichandran Ramasamy, Ann Marie Schmidt, Matthew S. Geddis 2010 Columbia University

Morphological Changes And Immunohistochemical Expression Of Rage And Its Ligands In The Sciatic Nerve Of Hyperglycemic Pig (Sus Scrofa), Judyta K. Juranek, Alexey Aleshin, Eileen M. Rattigan, Lynne Johnson, Wu Qu, Fei Song, Radha Ananthakrishnan, Nosirudeen Quadri, Shi Du Yan, Ravichandran Ramasamy, Ann Marie Schmidt, Matthew S. Geddis

Publications and Research

The aim of our project was to study the effect of streptozotocin (STZ)—induced hyperglycemia on sciatic nerve morphology, blood plasma markers and immunohistochemical expression of RAGE (the Receptor for Advanced Glycation End-products), and its ligands—S100B and Carboxymethyl Lysine (CML)-advanced glycation endproduct (AGE) in the laboratory pig. Six months after STZ—injections, blood plasma measurements, morphometric analysis of sciatic nerve fiber density, immunofluorescent distribution of potential molecular neuropathy contributors, ELISA measurement of plasma AGE level and HPLC analysis of sciatic nerve levels of one of the pre-AGE and the glycolysis intermediate products—methyl-glyoxal (MG) were performed. The results ...


Influence Of Cultivation Conditions On The Production Of A Thermostable Extracellular Lipase From Amycolatopsis Mediterranei Dsm 43304, Dharmdendra Dheeman, Jesus Maria Frias, Gary Henehan 2010 Technological University Dublin

Influence Of Cultivation Conditions On The Production Of A Thermostable Extracellular Lipase From Amycolatopsis Mediterranei Dsm 43304, Dharmdendra Dheeman, Jesus Maria Frias, Gary Henehan

Articles

Among several lipase producing actinomycete strains screened, Amycolatopsis mediterranei DSM 43304 was found to produce a thermostable, extracellular lipase. Culture condition and nutrient source modification studies involving carbon sources, nitrogen sources, incubation temperature and medium pH were carried out. Lipase activity of 1.37 ± 0.103 IU/ml of culture medium was obtained in 96 h at 28 °C and pH 7.5 using linseed oil and fructose as carbon sources and a combination of phytone peptone and yeast extract (5:1) as nitrogen sources. In optimal culture conditions the lipase activity was enhanced 12-fold with a 2-fold increase in ...


Synthesis And Evaluation Of Azetidinone Analogues Of Combretastatin A-4 As Tubulin Targeting Agents, Niamh O'Boyle, Miriam Carr, Lisa M. Greene, Orla Bergin, Seema M. Nathwani, Thomas McCabe, David G. Lloyd, Daniela M. Zisterer, Mary J. Meegan 2010 Technological University Dublin

Synthesis And Evaluation Of Azetidinone Analogues Of Combretastatin A-4 As Tubulin Targeting Agents, Niamh O'Boyle, Miriam Carr, Lisa M. Greene, Orla Bergin, Seema M. Nathwani, Thomas Mccabe, David G. Lloyd, Daniela M. Zisterer, Mary J. Meegan

Articles

The synthesis and antiproliferative activity of a new series of rigid analogues of combretastatin A-4 are described which contain the 1,4-diaryl-2-azetidinone (β-lactam) ring system in place of the usual ethylene bridge present in the natural combretastatin stilbene products. These novel compounds are also substituted at position 3 of the β-lactam ring with an aryl ring. A number of analogues showed potent nanomolar activity in human MCF-7 and MDA-MB-231 breast cancer cell lines, displayed in vitro inhibition of tubulin polymerization and did not cause significant cytotoxicity in normal murine breast epithelial cells. 4-(4-Methoxyaryl)-substituted compound 32, 4-(3-hydroxy-4-methoxyaryl)-substituted ...


Genetic Connections Between Neurological Disorders And Cholesterol Metabolism, Ingemar Bjorkhem, Valerio Leoni, Steve Meaney 2010 Karolinska Institute

Genetic Connections Between Neurological Disorders And Cholesterol Metabolism, Ingemar Bjorkhem, Valerio Leoni, Steve Meaney

Articles

Cholesterol is an essential component of both the peripheral and central nervous systems of mammals. Over the last decade, evidence has accumulated that disturbances in cholesterol metabolism are associated with the development of various neurological conditions. In addition to genetically defined defects in cholesterol synthesis, which will be covered in another review in this Thematic Series, defects in cholesterol metabolism (cerebrotendinous xanthomatosis) and intracellular transport (Niemann Pick Syndrome) lead to neurological disease. A subform of hereditary spastic paresis (type SPG5) and Huntington's disease are neurological diseases with mutations in genes that are of importance for cholesterol metabolism. Neurodegeneration is ...


Biochemical Characterization Of The Human Mediator Complex, Yuefeng Gao 2010 University of Colorado at Boulder

Biochemical Characterization Of The Human Mediator Complex, Yuefeng Gao

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

RNA polymerase II coordinates with a wide range of factors and catalyzes DNA transcription to synthesize mRNA. One critical step of transcription initiation is the interaction between the Mediator complex and the carboxy-terminal domain (CTD) of the largest subunit of human RNA polymerase II that consists of 52 repeats of the general consensus sequence YSPTSPS. This Mediator-Pol II CTD interaction is believed to be important in transcriptional regulation, RNA processing and chromatin remodeling. Therefore, elucidating the mechanism of this interaction is crucial for understanding gene expression and developing potential clinical applications. Our lab used a chemical crosslinking method in order ...


From Regulation To Pathogenesis: Employing Fluorescent Tools To Study Calcium, Janet Elaine McCombs 2010 University of Colorado at Boulder

From Regulation To Pathogenesis: Employing Fluorescent Tools To Study Calcium, Janet Elaine Mccombs

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Ca2+ is a ubiquitous and highly regulated signaling second messenger in cells, involved in a number of processes and pathways. Due to the complexity of Ca2+ signaling and its organization within a cell, it is inherently difficult to study. A number of fluorescent tools have been developed throughout the years in order to overcome these complications. Such probes allow for imaging of rapid Ca2+ transients in real-time at the single cell level, enabling the separation of the spatio-temporal aspects of Ca2+ signals. As Ca2+ is essential to cellular regulation and function, it is unsurprising Ca ...


Analysis Of B-Rafv600e Regulated Micrornas And Proteins In Melanoma, Kasey Lyn Couts 2010 University of Colorado at Boulder

Analysis Of B-Rafv600e Regulated Micrornas And Proteins In Melanoma, Kasey Lyn Couts

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Genome sequencing studies have identified oncogenic B-Raf mutations in over 70% of all sporadic melanomas. The B-RafV600E mutation leads to elevated kinase activity and constitutive activation of the mitogen-activated protein (MAP) kinase signaling pathway, which supports a variety of oncogenic functions critical to melanoma formation and progression. Metastatic melanomas are highly resistant to conventional chemotherapeutic treatments, and pharmacological inhibitors of B-RafV600E have been incompletely effective in pre-clinical studies. Understanding the global molecular responses to constitutive MAP kinase signaling in melanomas would allow the development of more effective therapeutics.

Manipulation of microRNA (miRNA) expression is emerging as an important molecular mechanism ...


Small Molecule Perturbation Of The Tlr4/Md-2 Interaction, Joshua A. Stahl 2010 University of Colorado at Boulder

Small Molecule Perturbation Of The Tlr4/Md-2 Interaction, Joshua A. Stahl

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Opioid-induced glial cell activation has accumulated great interest over the past several years. Recent evidence suggests that glia are activated by opioids and that the activation of glial cells is linked to suppression in analgesia, leading to the development of opioid tolerance and dependence. Current study shows that opioid-induced glial activation is regulated by Toll-Like receptor-4(TLR4), a membrane spanning receptor that functions in complex with Myeloid differentiation factor-2 (MD-2). Interestingly TLR4 receptors are solely expressed by glia within the central nervous system (CNS), suggesting development of small molecules to improve opioid-based pain management therapies through the inhibition of the ...


Rna Processing Events Affecting C. Elegans Operons: A Computational And Mutational Analysis, Mary Ann Allen 2010 University of Colorado at Boulder

Rna Processing Events Affecting C. Elegans Operons: A Computational And Mutational Analysis, Mary Ann Allen

Molecular, Cellular, and Developmental Biology Graduate Theses & Dissertations

In C. elegans, the combined actions of trans-splicing, 3’ end formation and inhibition of transcription termination by RNA polymerase II (Pol II) are necessary to generate monocistronic transcripts from primary polycistronic transcripts. However, how these processes are regulated to create functional monocistronic units out of polycistronic transcripts is poorly understood.

From a global perspective, certain transcripts are trans-spliced to either SL1, SL2 or both. The genes encoding SL1 trans-spliced transcripts have longer distances between the trans-splice site and the nearest upstream gene, and also have evidence of promoters adjacent to the trans-splice sites. The converse is true for genes encoding ...


Small Rna-Amino Acid Interactions And Implications For The Origin Of Translation, Rebecca Marie Turk 2010 University of Colorado at Boulder

Small Rna-Amino Acid Interactions And Implications For The Origin Of Translation, Rebecca Marie Turk

Molecular, Cellular, and Developmental Biology Graduate Theses & Dissertations

Ribonucleic acid (RNA) has the ability to store and transfer genetic information, and also to catalyze chemical reactions. This observation has led to the RNA world hypothesis, which states that there was likely a time in early evolution (before DNA and proteins) in which RNA carried out both these functions. In particular, RNA may have played an important role in the origin of protein (peptide) synthesis, or translation. While modern protein synthesis requires protein catalysis or stabilization at each of the relevant chemical steps, RNA is the functional heart of the ribosome. There must have been a mechanism in place ...


Cationic Antimicrobial Peptides And Their Mode Of Action: A Genomics Approach For A Better Understanding, Eileen Colie Spindler 2010 University of Colorado at Boulder

Cationic Antimicrobial Peptides And Their Mode Of Action: A Genomics Approach For A Better Understanding, Eileen Colie Spindler

Molecular, Cellular, and Developmental Biology Graduate Theses & Dissertations

Antimicrobial peptides (AMPs) produced from naturally occurring peptides have recently become a focus for drug design. These synthetic derivatives are relatively small (6-12 amino acids), potent, not easily resisted, and active against a broad-range of pathogens; making such compounds particularly attractive as platforms for the development of novel antimicrobials. However, the mode of action of these synthetic peptides, as well as many naturally occurring peptides, remains largely uncharacterized. This lack of understanding, and more specifically the absence of detailed knowledge of the complexity of AMP mode(s) of action, continues to limit our capabilities for taking full advantage of these ...


Sorting Of Drosophila Small Silencing Rnas Partitions Microrna* Strands Into The Rna Interference Pathway, Megha Ghildiyal, Jia Xu, Herve Seitz, Zhiping Weng, Phillip D. Zamore 2010 University of Massachusetts Medical School

Sorting Of Drosophila Small Silencing Rnas Partitions Microrna* Strands Into The Rna Interference Pathway, Megha Ghildiyal, Jia Xu, Herve Seitz, Zhiping Weng, Phillip D. Zamore

GSBS Student Publications

In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character-as is found in small interfering RNAs (siRNAs)-directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. Here, we show that while most Drosophila miRNAs are bound to Ago1, miRNA* strands accumulate bound to Ago2. Like siRNA loading, efficient ...


Explorations In Homeoviscous Adaptation And Mass Spectral Analysis Of Membrane Lipids, Michael Douglas Timmons 2010 University of Kentucky

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 ...


15N Solid-State Nmr Detection Of Flavin Perturbation By H-Bonding In Models And Enzyme Active Sites, Dongtao Cui 2010 University of Kentucky

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 ...


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