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Dahp Oxime: A Transition State Mimic Inhibitor Of Dahp Synthase, Naresh Balachandran 2014 McMaster University

Dahp Oxime: A Transition State Mimic Inhibitor Of Dahp Synthase, Naresh Balachandran

Open Access Dissertations and Theses

The rise of bacterial infections and increase of antibiotic resistant bacteria has become a major problem in the treatment of bacterial infections. The use and overuse of antibiotics, and the inherent ability of bacteria to adapt to their environment, have lead to the emergence of strains that are resistant to all antibiotics. Ideally, new targets for antibacterial drug therapy would be essential to the virulence of most or all bacteria. That is, antibiotics exploiting these targets would have broad spectrum activity. 3-Deoxy-D-arabinoheptulosonate-7- phosphate (DAHP) synthase could be such a target. This enzyme catalyzes the condensation of erythrose 4-phosphate (E4P) and ...


A Characterization Of The Dynamic Interaction Between The Pro-Apoptotic Protein Bid And The Mitochondrial Outer Membrane, Aisha Shamas-Din Ms. 2014 McMaster University

A Characterization Of The Dynamic Interaction Between The Pro-Apoptotic Protein Bid And The Mitochondrial Outer Membrane, Aisha Shamas-Din Ms.

Open Access Dissertations and Theses

Bcl-2 family of proteins regulate apoptosis at the level of the mitochondrial outer membrane (MOM) through both protein-protein and protein-membrane interactions. While the role of the membrane as the “locus of action” has been recognized, the detailed molecular mechanisms and the consequences of the interactions of Bcl-2 family members with the membrane are yet to be fully understood. The findings presented here focus on the dynamic interactions of Bcl-2 proteins, most notably tBid with the MOM, and their functional significance on mitochondrial outer membrane permeabilization. We show that the activation of tBid is a multi-step process that is regulated by ...


Single Tube, Multiple Enzyme Reaction For Detection Of Uv And Oxidative Damage In Forensic Physiological Stains, Nicholas J. Eurek 2014 University of Nebraska - Lincoln

Single Tube, Multiple Enzyme Reaction For Detection Of Uv And Oxidative Damage In Forensic Physiological Stains, Nicholas J. Eurek

Theses and Dissertations in Biochemistry

For decades, the use of DNA as a biological tool has revolutionized forensic investigations. The primary use of this genetic evidence is for identification of a victim or suspect through short tandem repeat (STR) profiling. However, the usefulness of this evidence can be compromised through inhibition of PCR, damage to the DNA, or low copy number. Here, we investigate damage induced to DNA by environmental factors. UV light is known to damage DNA by the formation of cyclobutane pyrimidine dimers, 6-4 photoproducts, and strand breaks. These lesions can stall polymerase action or misincorporate bases during extension. Oxidative damage is also ...


Some Effects Of The Human Genome Project On The Erdős Collaboration Graph, Chris Fields 2014 Claremont Colleges

Some Effects Of The Human Genome Project On The Erdős Collaboration Graph, Chris Fields

Journal of Humanistic Mathematics

The Human Genome Project introduced large-scale collaborations involving dozens to hundreds of scientists into biology. It also created a pressing need to solve discrete mathematics problems involving tens of thousands of elements. In this paper, we use minimal path lengths in the Erdős Collaboration Graph between prominent individual researchers as a measure of the distance between disciplines, and we show that the Human Genome Project brought laboratory biology as a whole closer to mathematics. We also define a novel graph reduction method and a metric that emphasizes the robustness of collaborative connections between researchers; these can facilitate the analysis of ...


Rictor/Mtorc2 Loss In The Myf5 Lineage Reprograms Brown Fat Metabolism And Protects Mice Against Obesity And Metabolic Disease, Chien-Min Hung, Camila Martinez Calejman, Joan Sanchez-Gurmaches, Huawei Li, Clary B. Clish, Simone Hettmer, Amy J. Wagers, David A. Guertin 2014 University of Massachusetts Medical School

Rictor/Mtorc2 Loss In The Myf5 Lineage Reprograms Brown Fat Metabolism And Protects Mice Against Obesity And Metabolic Disease, Chien-Min Hung, Camila Martinez Calejman, Joan Sanchez-Gurmaches, Huawei Li, Clary B. Clish, Simone Hettmer, Amy J. Wagers, David A. Guertin

GSBS Student Publications

The in vivo functions of mechanistic target of rapamycin complex 2 (mTORC2) and the signaling mechanisms that control brown adipose tissue (BAT) fuel utilization and activity are not well understood. Here, by conditionally deleting Rictor in the Myf5 lineage, we provide in vivo evidence that mTORC2 is dispensable for skeletal muscle development and regeneration but essential for BAT growth. Furthermore, deleting Rictor in Myf5 precursors shifts BAT metabolism to a more oxidative and less lipogenic state and protects mice from obesity and metabolic disease at thermoneutrality. We additionally find that Rictor is required for brown adipocyte differentiation in vitro and ...


Calmodulation Meta-Analysis: Predicting Calmodulin Binding Via Canonical Motif Clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, William R. Kobertz 2014 University of Massachusetts Medical School

Calmodulation Meta-Analysis: Predicting Calmodulin Binding Via Canonical Motif Clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, William R. Kobertz

Biochemistry and Molecular Pharmacology Publications and Presentations

The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM-peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator ...


Developing Crosslinking Constructs Of Protein Kinase R, Prisma E. Lopez 2014 University of Connecticut

Developing Crosslinking Constructs Of Protein Kinase R, Prisma E. Lopez

Honors Scholar Theses

Protein Kinase R (PKR) is a key component of the innate immune antiviral response. PKR is activated upon binding to dsRNA. However, recent studies have shown that PKR can also bind to and become activated by duplex RNAs containing complex secondary structure. The mechanism of PKR binding and activation by these RNAs is currently not known. The approach taken here to determine the mechanism of PKR binding by these RNAs is through the development of PKR constructs that are capable of covalently binding to RNAs. Constructs were created by site-specific incorporation of an unnatural, photoactivatable amino acid within PKR. These ...


Hive-Hexagon: High-Performance, Parallelized Sequence Alignment For Next-Generation Sequencing Data Analysis, Luis Santana-Quintero, Hayley Dingerdissen, Jean Thierry-Mieg, Raja Mazumder, Vahan Simonyan 2014 Himmelfarb Health Sciences Library, The George Washington University

Hive-Hexagon: High-Performance, Parallelized Sequence Alignment For Next-Generation Sequencing Data Analysis, Luis Santana-Quintero, Hayley Dingerdissen, Jean Thierry-Mieg, Raja Mazumder, Vahan Simonyan

Biochemistry and Molecular Medicine Faculty Publications

Due to the size of Next-Generation Sequencing data, the computational challenge of sequence alignment has been vast. Inexact alignments can take up to 90% of total CPU time in bioinformatics pipelines. High-performance Integrated Virtual Environment (HIVE), a cloud-based environment optimized for storage and analysis of extra-large data, presents an algorithmic solution: the HIVE-hexagon DNA sequence aligner. HIVE-hexagon implements novel approaches to exploit both characteristics of sequence space and CPU, RAM and Input/Output (I/O) architecture to quickly compute accurate alignments. Key components of HIVE-hexagon include non-redundification and sorting of sequences; floating diagonals of linearized dynamic programming matrices; and consideration ...


Characterizing The Response Of Multidrug-Resistant Klebsiella Pneumoniae Species To The Application Of A Phage Cocktail, Steven Liu 2014 California Polytechnic State University

Characterizing The Response Of Multidrug-Resistant Klebsiella Pneumoniae Species To The Application Of A Phage Cocktail, Steven Liu

Symposium

Project Summary: The application of bacteriophages to treat bacterial infections is known as phage therapy, which takes advantage of bacteriophage’s natural ability to infect and lyse bacterial hosts. Phages have been shaped by billions of years of evolution to be highly specialized deliverers of bactericidal agents to the cytoplasm of their target bacteria. Ever since discovery of bacteriophages in 1915, phage therapy was recognized as a potentially powerful tool for eliminating bacterial infections. The effectiveness of phage therapy can be increased by creating a mixture of multiple phages to target a wider variety of bacterial strains. Furthermore, phage therapy ...


A Framework For Application Of Metabolic Modeling In Yeast To Predict The Effects Of Nssnv In Human Orthologs, Hayley Dingerdissen, Daniel S. Weaver, Peter D. Karp, Yang Pan, Vahan Simonyan, Raja Mazumder 2014 Himmelfarb Health Sciences Library, The George Washington University

A Framework For Application Of Metabolic Modeling In Yeast To Predict The Effects Of Nssnv In Human Orthologs, Hayley Dingerdissen, Daniel S. Weaver, Peter D. Karp, Yang Pan, Vahan Simonyan, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

Background

We have previously suggested a method for proteome wide analysis of variation at functional residues wherein we identified the set of all human genes with nonsynonymous single nucleotide variation (nsSNV) in the active site residue of the corresponding proteins. 34 of these proteins were shown to have a 1:1:1 enzyme:pathway:reaction relationship, making these proteins ideal candidates for laboratory validation through creation and observation of specific yeast active site knock-outs and downstream targeted metabolomics experiments. Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from ...


Interactions Of Eukaryotic Translation Initiation Factors And 3' Untranslated Region Of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study Of Equilibrium Binding, Kinetics And Thermodynamics, Bidisha Banerjee 2014 The Graduate Center, CUNY

Interactions Of Eukaryotic Translation Initiation Factors And 3' Untranslated Region Of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study Of Equilibrium Binding, Kinetics And Thermodynamics, Bidisha Banerjee

Dissertations and Theses, 2014-Present

Eukaryotic initiation factor (eIF) 4F binding to mRNA is the first committed step in cap-dependent protein synthesis. Barley Yellow Dwarf Virus (BYDV) employs a cap-independent mechanism of translation initiation which is mediated by a structural element BTE (BYDV translation element) located in the 3’ UTR of its mRNA. eIF4F bound the BTE and a translational inactive mutant with high affinity; thus questioning the role of eIF4F in translation of BYDV. To examine the effects of eIF4F in BYDV translation initiation, BTE mutants with widely different in vitro translation efficiencies ranging from 5-164% compared to WT were studied. Using fluorescence anisotropy ...


Recruitment Of The Ribosomal 40s Subunit To The 3'Untranslated Region Of A Viral Mrna, Via The Eif4 Complex, Facilitates Cap-Independent Translation., Sohani Das Sharma 2014 The Graduate Center, CUNY

Recruitment Of The Ribosomal 40s Subunit To The 3'Untranslated Region Of A Viral Mrna, Via The Eif4 Complex, Facilitates Cap-Independent Translation., Sohani Das Sharma

Dissertations and Theses, 2014-Present

Translation of uncapped plant viral RNAs can be facilitated by either an internal ribosomal entry site (IRES) in the 5' untranslated region (UTR) or a cap-independent translation element (CITE) in the 3' UTR. Barley yellow dwarf virus (BYDV) mRNA, which lacks both cap and poly(A) tail, has a translation element (3'BTE) in its 3' UTR that is essential for efficient translation initiation at the 5'-proximal AUG. This mechanism requires binding of the eukaryotic initiation factor 4G (eIF4G) subunit of the heterodimer eIF4F to the 3'BTE and base pairing between the 3'BTE and the 5' UTR ...


The Evolution Of Respiratory O2/No Reductases: An Out-Of-The-Phylogenetic-Box Perspective, Anne-Lise Ducluzeau, Barbara Schoepp-Cothenet, Robert van Lis, Frauke Baymann, Michael J. Russell, Wilfgang Nitschke 2014 University of Nebraska - Lincoln

The Evolution Of Respiratory O2/No Reductases: An Out-Of-The-Phylogenetic-Box Perspective, Anne-Lise Ducluzeau, Barbara Schoepp-Cothenet, Robert Van Lis, Frauke Baymann, Michael J. Russell, Wilfgang Nitschke

Biochemistry -- Faculty Publications

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O2-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O2 in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O2-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O2-levels on life is the evolutionary ...


The Effect Of Tuning Cold Plasma Composition On Glioblastoma Cell Viability, Xiaoqian Cheng, Jonathan H. Sherman, William Murphy, Edward Ratovitski, Jerome Canady, Michael Keidar 2014 Himmelfarb Health Sciences Library, The George Washington University

The Effect Of Tuning Cold Plasma Composition On Glioblastoma Cell Viability, Xiaoqian Cheng, Jonathan H. Sherman, William Murphy, Edward Ratovitski, Jerome Canady, Michael Keidar

Biochemistry and Molecular Medicine Faculty Publications

Previous research in cold atmospheric plasma (CAP) and cancer cell interaction has repeatedly proven that the cold plasma induced cell death. It is postulated that the reactive oxygen species (ROS) and reactive nitrogen species (RNS) play a major role in the CAP cancer therapy. In this paper, we seek to determine a mechanism of CAP therapy on glioblastoma cells (U87) through an understanding of the composition of the plasma, including treatment time, voltage, flow-rate and plasma-gas composition. In order to determine the threshold of plasma treatment on U87, normal human astrocytes (E6/E7) were used as the comparison cell line ...


Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina 2014 Seton Hall University

Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina

Seton Hall University Dissertations and Theses (ETDs)

The cancer epidemic continues to afflict millions of humans world-wide each year and despite a renewed hope with the development of new and improved forms of therapy, a cure for cancer remains an elusive goal. This is partly related to the rise of resilient forms of tumors that have evolved with resistance towards conventional chemotherapy and radiation treatments. Moreover, these non-specific therapeutic regimens are highly toxic, leading to severe immunosuppressive effects which poisons the body and compromises the road towards remission. In an effort to mitigate these limitations, cancer-targeting approaches are currently experiencing a renaissance in the translation of new ...


Investigating The Role Of Retinoblastoma Protein And Transforming Growth Factor-Beta In Growth Inhibition, Mehdi Amiri 2014 Western University

Investigating The Role Of Retinoblastoma Protein And Transforming Growth Factor-Beta In Growth Inhibition, Mehdi Amiri

University of Western Ontario - Electronic Thesis and Dissertation Repository

The Retinoblastoma protein (pRB) is a key regulator of cell proliferation in the G1 phase of the cell cycle. The LxCxE binding cleft is a highly conserved region of pRB. Using a knock-in mouse model, called Rb1∆L, with disrupted pRB and LxCxE interactions, our lab has shown that epithelial cells from Rb1∆L/∆L mice do not respond to TGF-β1 mediated growth arrest. Using shRNAs to deplete the expression of components of LxCxE motif containing complexes, data showed that SAP18 is not involved in TGF-β1 mediated growth arrest. However, depletion of SAP30 and MTA2 compromised TGF-β1 mediated growth arrest ...


The Global Cancer Genomics Consortium's Third Annual Symposium: From Oncogenomics To Cancer Care, Luis Costa, Sandra Casimiro, Sudeep Gupta, Stefan Knapp, M. Radhakrishna Pillai, Mazakazu Toi, Rajendra Badwe, Maria Carmo-Fonesca, Rakesh Kumar 2014 Himmelfarb Health Sciences Library, The George Washington University

The Global Cancer Genomics Consortium's Third Annual Symposium: From Oncogenomics To Cancer Care, Luis Costa, Sandra Casimiro, Sudeep Gupta, Stefan Knapp, M. Radhakrishna Pillai, Mazakazu Toi, Rajendra Badwe, Maria Carmo-Fonesca, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

The Global Cancer Genomics Consortium (GCGC) is a cohesive network of oncologists, cancer biologists and structural and genomics experts residing in six institutions from Lisbon, United Kingdom, Japan, India, and United States. The team is using its combined resources and infrastructures to address carefully selected, shared, burning questions in cancer medicine. The Third Annual Symposium was organized by the Institute of Molecular Medicine, Lisbon Medical School, Lisbon, Portugal, from September 18 to 20, 2013. To highlight the benefits and limitations of recent advances in cancer genomics, the meeting focused on how to better translate our gains in oncogenomics to cancer ...


The Mechanism Of Small Rna Biogenesis, Degradation, And Function In Arabidopsis, Meng Xie 2014 University of Nebraska - Lincoln

The Mechanism Of Small Rna Biogenesis, Degradation, And Function In Arabidopsis, Meng Xie

Dissertations and Theses in Biological Sciences

Eukaryotic small RNAs play important roles in many biological processes through sequence-specific RNA silencing. In plants, there are mainly two small RNAs triggering gene silencing: microRNAs (miRNAs) and small interfering RNAs (siRNAs). The biogenesis and precise regulation of small RNA abundance are crucial for plant growth, development, genomic stability, and the resistance to both abiotic and biotic stresses. In this study, we used Arabidopsis thaliana, the model plant, to study the mechanism of RNA-directed DNA methylation (RdDM), in which siRNAs can trigger DNA methylation and gene silencing. In addition, we investigated the mechanism of miRNA biogenesis and degradation. For RdDM ...


Mutagenesis Of 8-Oxoguanine Adjacent To An Abasic Site In Escherichia Coli Cells Proficient Or Deficient In Dna Polymerase Iv, Savas T. Tsikis 2014 University of Connecticut

Mutagenesis Of 8-Oxoguanine Adjacent To An Abasic Site In Escherichia Coli Cells Proficient Or Deficient In Dna Polymerase Iv, Savas T. Tsikis

Honors Scholar Theses

It is well established that clustered DNA damages or multiply damaged sites (MDS) are the result of ionizing radiation and that they are characterized by an enhanced mutagenic potential. As a model MDS, we have evaluated the mutagenic and cytotoxic properties of the ubiquitous oxidative DNA damage 8-oxoguanine (G8-oxo) adjacent to the abasic site lesion (Z) using a single stranded M13mp7L2 vector. The recombinant DNA was used to transform wild type E. coli strains and strains deficient in the translesion DNA polymerase of the Y-family, DNA polymerase IV, in the presence or absence of SOS induction. The percent survival ...


Aminoglycoside-Induced Sensitization Of Cancer Cells And Development Of Carbohydrate-Containing Drugs, Michael F. Cuccarese 2014 Northeastern University

Aminoglycoside-Induced Sensitization Of Cancer Cells And Development Of Carbohydrate-Containing Drugs, Michael F. Cuccarese

Chemistry Dissertations

Modern drug discovery requires that synthesis of compounds with unique structures and properties is performed in concert with in-depth research on the biological event being targeted. The synergy of these two components of drug discovery generates the meaningful data necessary for a hypothesis-driven approach toward novel therapeutics. Herein, research is presented that pertains both to the study of biological activity, as well as the development of novel synthetic methods.

While the bactericidal effects of aminoglycosides are well understood, their therapeutic potential in human cells is emerging. Herein, a novel use of this class of compounds in cancer therapy is described ...


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