Generating New Type Ii Protein Models Using Cytochrome C,
2013
University of Northern Iowa
Generating New Type Ii Protein Models Using Cytochrome C, Lindsey M. Ludwig
Honors Program Theses
The purpose of this research was to create a simpler model of Type II proteins in order to study the ligand switch using cytochrome c (Figure 3). Cytochrome c was chosen because it is small, easy to work with, and relatively easy to mutate. It also already has a built-in mechanism for a ligand switch, making it the ideal candidate for this protein model. Mutating cytochrome c into a model Type II protein and learning more about how the ligand switch controls function may generate new insight into how the corresponding ligand switch works in more complex proteins.
Sequencing A Dna Polymerase Alpha Gene In Thermomyces Lanuginosus,
2013
University of Northern Iowa
Sequencing A Dna Polymerase Alpha Gene In Thermomyces Lanuginosus, Sonia Tien-Yang Han
Honors Program Theses
DNA polymerases are present in all living organisms and it is expected that there should be a reasonable degree of conservation, or similarity in how the polymerases function, between species. This makes the possibility of developing treatments using DNA polymerase more likely, as the treatment would not necessarily depend on using human DNA as the base material, which would be more expensive. However, this cannot be known unless there is a reasonable number of DNA sequences available from multiple species to analyze. This is a growing research, but the majority of sequences known are from mammals. Currently there is very …
An Investigation Of Alternative Oxidase Presence, Expression, And Regulation In The Moss Physcomitrella Patens,
2013
Wilfrid Laurier University
An Investigation Of Alternative Oxidase Presence, Expression, And Regulation In The Moss Physcomitrella Patens, Karina I. Neimanis
Theses and Dissertations (Comprehensive)
Alternative oxidase (AOX) is an inner mitochondrial membrane protein that introduces a branch point at ubiquinone within the respiratory electron transport system (ETS). The AOX protein bypasses two sites of proton translocation within the ETS and as a result the yield of ATP per oxygen consumed is significantly reduced. Although AOX appears to be energetically wasteful, recent studies have revealed that AOX has a wide taxonomic distribution. AOX multigene families, transcripts, protein levels, and enzymatic activity have been most thoroughly characterized in many angiosperm (flowering) plants. Given the data available for angiosperm AOXs, evidence of non-angiosperm AOXs in the primary …
Atp-Induced Changes In F-Actin Expression Via P2x7,
2013
University of Northern Iowa
Atp-Induced Changes In F-Actin Expression Via P2x7, Taylor Hircock
Honors Program Theses
The purpose of this research project was to study the effects that extracellular ATP has on F-actin levels in cells containing the P2X7 purinergic receptor. MAC-T cells which express the receptor were exposed to various levels of ATP and stained to undergo flow cytometry. In this case, F-actin was labeled with 488 phalloidin which was able to be detected by the flow cytometer. This was done in conjuction with controls to show how ATP exposure affected Factin levels. Based on these results, the cytoskeletal changes taking place in the cell in response to ATP were able to be measured and …
Expressed Sequence Tag For Dna Polymerase Alpha In Embryonic Chicken Brain,
2013
University of Northern Iowa
Expressed Sequence Tag For Dna Polymerase Alpha In Embryonic Chicken Brain, Rebecca Krewer
Honors Program Theses
Replicative DNA polymerases are enzymes located in the nuclei of cells. They have a role in the control of DNA synthesis in all cells, and problems with their function and control affect cell growth. One of these polymerases, DNA polymerase alpha ("pol α"), is a possible point of control for cell growth because it initiates DNA synthesis. The ability to selectively turn on or shut off this polymerase in cells could provide answers to problems ranging from cancer's unregulated growth to regeneration of tissues. However, control mechanisms for DNA pol α are not fully understood at this time. The central …
Combined Treatment With Mild Heat, Manothermosonication And Pulsed Electric Fields Reduces Microbial Growth In Milk.,
2013
Technological University Dublin
Combined Treatment With Mild Heat, Manothermosonication And Pulsed Electric Fields Reduces Microbial Growth In Milk., Rachel Halpin, O. Cregenzán-Alberti, P. Whyte, J.G Lyng, F. Noci
Articles
In recent years, there has been considerable interest in non-thermal milk processing. The objective of the present study was to assess the efficacy of two non-thermal technologies (manothermosonication; MTS, and pulsed electric fields; PEF) in comparison to thermal pasteurisation, by assessing the microbial levels of each of these milk samples post-processing. Homogenised milk was subjected to MTS (frequency; 20 kHz, amplitude; 27.9 μm, pressure; 225 kPa) at two temperatures (37 °C or 55 °C), before being immediately treated with PEF (electric field strength; 32 kV/cm, pulse width; 10 μs, frequency; 320 Hz). Thermal pasteurisation (72 °C, 20 s) was included …
(R)-Β-Lysine Modified Elongation Factor P Functions In Translation Elongation,
2012
The Ohio State University
(R)-Β-Lysine Modified Elongation Factor P Functions In Translation Elongation, Tammy J. Bullwinkle, S. Betty Zou, Andrei Rajkovic, Steven J. Hersch, Sara Elgamal, Nathaniel Robinson, David Smil, Yuri Bolshan, William Wiley Navarre, Michael Ibba
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Post-translational modification of bacterial elongation factor P (EF-P) with (R)-β-lysine at a conserved lysine residue activates the protein in vivo and increases puromycin reactivity of the ribosome in vitro. The additional hydroxylation of EF-P at the same lysine residue by the YfcM protein has also recently been described. The roles of modified and unmodified EF-P during different steps in translation, and how this correlates to its physiological role in the cell, have recently been linked to the synthesis of polyproline stretches in proteins. Polysome analysis indicated that EF-P functions in translation elongation, rather than initiation as proposed previously. This was …
Polyphenoloxidase And Perioxidase Activity During Open Air Ripening Storage Of Pineapple (Ananas Comosus L.), Mango (Mangifera Indica) And Papaya (Carica Papaya) Fruits Grown In Dar Es Salaam, Tanzania,
2012
Chemistry Department, University of Dar es Salaam, P. O. Box 35061 Dar es Salaam, Tanzania
Polyphenoloxidase And Perioxidase Activity During Open Air Ripening Storage Of Pineapple (Ananas Comosus L.), Mango (Mangifera Indica) And Papaya (Carica Papaya) Fruits Grown In Dar Es Salaam, Tanzania, Oc Othman
Tanzania Journal of Science
Polyphenoloxidase (PPO) and perioxidase (POD), the enzymes responsible for causing browning and change in texture and flavor of fruits and vegetables, were extracted and measured in harvested mature pineapple (Ananas comosus L.), mango (Mangifera indica) (Viringe and Dodo varieties) and papaya (Carica papaya) fruits during off vine, open air, room temperature ripening storage. The initial (at harvest) average PPO activity values in Δ Optical Density (OD) per minute per cm3 of enzyme solution were 0.00074, 0.00083 and 0.0010 for early, mid and late season pineapple fruits respectively. The initial average PPO activity values in ΔOD/min/ cm3 of enzyme solution were …
Morc2 Signaling Integrates Phosphorylation-Dependent, Atpase-Coupled Chromatin Remodeling During The Dna Damage Response,
2012
George Washington University
Morc2 Signaling Integrates Phosphorylation-Dependent, Atpase-Coupled Chromatin Remodeling During The Dna Damage Response, Da-Qiang Li, Sujit S. Nair, Kazufumi Ohshiro, Anupam Kumar, Vasudha S. Nair, Suresh B. Pakala, Sirigiri Divijendra Natha Reddy, Rajendra P. Gajula, Jeyanthy Eswaran, L. Aravind, Rakesh Kumar
Biochemistry and Molecular Medicine Faculty Publications
Chromatin dynamics play a central role in maintaining genome integrity, but how this is achieved remains largely unknown. Here, we report that microrchidia CW-type zinc finger 2 (MORC2), an uncharacterized protein with a derived PHD finger domain and a conserved GHKL-type ATPase module, is a physiological substrate of p21-activated kinase 1 (PAK1), an important integrator of extracellular signals and nuclear processes. Following DNA damage, MORC2 is phosphorylated on serine 739 in a PAK1-dependent manner, and phosphorylated MORC2 regulates its DNA-dependent ATPase activity to facilitate chromatin remodeling. Moreover, MORC2 associates with chromatin and promotes gamma-H2AX induction in a PAK1 phosphorylation-dependent manner. …
A Comparison Of Boltzmann And Gibbs Definitions Of Microcanonical Entropy For Small Systems,
2012
Brigham Young University
A Comparison Of Boltzmann And Gibbs Definitions Of Microcanonical Entropy For Small Systems, Randall B. Shirts
Faculty Publications
Two different definitions of entropy, S= klnW, in the microcanonical ensemble have been competing for over 100 years. The Boltzmann/Planck definition is that W is the number of states accessible to the system at its energy E (also called the surface entropy). The Gibbs/Hertz definition is that W is the number of states of the system up to the energy E (also called the volume entropy). These two definitions agree for large systems but differ by terms of order N-1 for small systems, where N is the number of particles in the system. For three analytical …
Expansin Synergy With Cellulases: Development Of A Transgenic Maize System For Expansin Production And Evaluation Of Synergistic Activity On Lignocellulosic Substrates,
2012
Arkansas State University
Expansin Synergy With Cellulases: Development Of A Transgenic Maize System For Expansin Production And Evaluation Of Synergistic Activity On Lignocellulosic Substrates, Sangwoong Yoon
Student Theses and Dissertations
One of the greatest barriers to produce biofuels from lignocellulosic material is efficient cellulose depolymerization by cellulase activity. Expansin is a protein that is active in cell wall expansion in growing regions of most plants. Because of this unique activity, expansin synergistic activity with cellulase is believed to lower the depolymerization barrier. Over-expression of expansin in the maize production system is designed to produce sufficient protein 1) to study its physiological effects, and 2) to assess its ability to serve as an industrial enzyme for applications, particularly in biomass conversion. Transgenic lines of maize that express the cucumber expansin gene …
Cloning, Expression, And Characterization Of Ara H 3, A Major Peanut Allergen,
2012
University of New Orleans
Cloning, Expression, And Characterization Of Ara H 3, A Major Peanut Allergen, Cathryn E. Garvey
LSU New Orleans Theses and Dissertations
Abstract There are eight foods that contribute to food allergies in the western world and peanut is the most common. Currently, there are no medical treatments that can cure an individual of food allergy, so avoidance of the allergic food is the only option. In the United States, there are three immunodominant allergic proteins accountable for patient sensitization to peanut, Arachis hypogea 1, 2, and 3 (Ara h 1, Ara h 2, Ara h 3). Therefore, research into why peanuts are more allergic than other foods that have homologous proteins is critical and may be obtained by studying the structural …
Crystal Structures And Kinetics Of Monofunctional Proline
Dehydrogenase Provide Insight Into Substrate Recognition And
Conformational Changes Associated With Flavin Reduction And
Product Release,
2012
University of Missouri-Columbia
Crystal Structures And Kinetics Of Monofunctional Proline Dehydrogenase Provide Insight Into Substrate Recognition And Conformational Changes Associated With Flavin Reduction And Product Release, Min Luo, Benjamin W. Arentson, Dhiraj Srivastava, Donald F. Becker, John J. Tanner
Department of Biochemistry: Faculty Publications
Proline dehydrogenase catalyzes the FAD-dependent oxidation of proline to Δ1- pyrroline-5- carboxylate, which is the first step of proline catabolism. Here, we report the structures of proline dehydrogenase from Deinococcus radiodurans in the oxidized state complexed with the proline analog L-tetrahydrofuroic acid and in the reduced state with the proline site vacant. The analog binds against the si face of the FAD isoalloxazine and is protected from bulk solvent by the α8 helix and the β1-α1 loop. The FAD ribityl chain adopts two conformations in the E-S complex, which is unprecedented for flavoenzymes. One of the conformations is novel for …
Microfluidic Devices With Integrated Sample Preparation For Improved Analysis Of Protein Biomarkers,
2012
Brigham Young University - Provo
Microfluidic Devices With Integrated Sample Preparation For Improved Analysis Of Protein Biomarkers, Pamela Nsang Nge
Theses and Dissertations
Biomarkers present a non-invasive means of detecting cancer because they can be obtained from body fluids. They can also be used for prognosis and assessing response to treatment. To limit interferences it is essential to pretreat biological samples before analysis. Sample preparation methods include extraction of analyte from an unsuitable matrix, purification, concentration or dilution and labeling. The many advantages offered by microfluidics include portability, speed, automation and integration. Because of the difficulties encountered in integrating this step in microfluidic devices most sample preparation methods are often carried out off-chip. In the fabrication of micro-total analysis systems it is important …
Selection Of Trna Charging Quality Control Mechanisms That Increase Mistranslation Of The Genetic Code,
2012
The Ohio State University
Selection Of Trna Charging Quality Control Mechanisms That Increase Mistranslation Of The Genetic Code, Srujana S. Yadavalli, Michael Ibba
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Mistranslation can follow two events during protein synthesis: production of non-cognate amino acid:transfer RNA (tRNA) pairs by aminoacyl-tRNA synthetases (aaRSs) and inaccurate selection of aminoacyl-tRNAs by the ribosome. Many aaRSs actively edit non-cognate amino acids, but editing mechanisms are not evolutionarily conserved, and their physiological significance remains unclear. To address the connection between aaRSs and mistranslation, the evolutionary divergence of tyrosine editing by phenylalanyl-tRNA synthetase (PheRS) was used as a model. Certain PheRSs are naturally error prone, most notably a Mycoplasma example that displayed a low level of specificity consistent with elevated mistranslation of the proteome. Mycoplasma PheRS was found …
Spatial Patterns Of Mercury In Atmospheric Deposition, Soils And Lake Biota In The Adirondack Park, New York,
2012
Syracuse University
Spatial Patterns Of Mercury In Atmospheric Deposition, Soils And Lake Biota In The Adirondack Park, New York, Xue Yu
Civil and Environmental Engineering - Dissertations
Mercury (Hg), as a trace element cycling in the environment, poses a serious health threat to both humans and wildlife due to its toxicity. Atmospheric deposition is the main source of Hg to most remote environments. The Adirondack Park in New York State of the United States receives moderate Hg deposition, and is a region characterized by relatively high concentrations of Hg in the terrestrial and especially aquatic biota. It is important to understand the mechanisms that contribute to the sensitivity of this region to Hg inputs. In my research, studies of the spatial patterns of Hg in atmospheric deposition, …
Molecular Mechanisms Regulating Neonatal Oocyte Survival And Primordial Follicle Formation In The Mouse Ovary,
2012
Syracuse University
Molecular Mechanisms Regulating Neonatal Oocyte Survival And Primordial Follicle Formation In The Mouse Ovary, Robin L. Jones
Biology - Dissertations
In mammals, formation of the primordial follicle is a complex process involving the breakdown of germ cell cysts, where oocytes must separate from each other and subsequently become surrounded by somatic cells. As cysts separate, a large number of germ cells are lost by apoptosis, however the mechanisms by which cyst breakdown and germ cell death occur are not well understood. We first hypothesized that two anti-apoptotic regulators from the BCL2 family of proteins, BCL2 and MCL1, may be responsible for regulating neonatal oocyte survival. To elucidate the effects of BCL2 in the neonatal ovary, we examined ovaries of both …
Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions,
2012
University of Nevada, Las Vegas
Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller
Life Sciences Faculty Research
Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …
Immunoproteomics: The Key To Discovery Of New Vaccine Antigens Against Bacterial Respiratory Infections,
2012
Intsitute of Technology Tallaght
Immunoproteomics: The Key To Discovery Of New Vaccine Antigens Against Bacterial Respiratory Infections, Ruth Dennehy, Siobhan Mcclean
Articles
The increase in antibiotic resistance and the shortage of new antimicrobials to prevent difficult bacterial infections underlines the importance of prophylactic therapies to prevent infection by bacterial pathogens. Vaccination has reduced the incidence of many serious diseases, including respiratory bacterial infections. However, there are many pathogens for which no vaccine is available and some vaccines are not effective among all age groups or among immunocompromised individuals. Immunoproteomics is a powerful technique which has been used to identify potential vaccine candidates to protect against pathogenic bacteria. The combination of proteomics with the detection of immunoreactive antigens using serum highlights immunogenic proteins …
Knockout Of The 15 Kda Selenoprotein Protects Against
Chemically-Induced Aberrant Crypt Formation In Mice,
2012
Towson University
Knockout Of The 15 Kda Selenoprotein Protects Against Chemically-Induced Aberrant Crypt Formation In Mice, Petra A. Tsuji, Bradley A. Carlson, Salvador Naranjo-Suarez, Min-Hyuk Yoo, Xue-Ming Xu, Dmitri E. Fomenko, Vadim Gladyshev, Dolph L. Hatfield, Cindy D. Davis
Department of Biochemistry: Faculty Publications
Evidence suggests that selenium has cancer preventive properties that are largely mediated through selenoproteins. Our previous observations demonstrated that targeted down-regulation of the 15 kDa selenoprotein (Sep15) in murine colon cancer cells resulted in the reversal of the cancer phenotype. The present study investigated the effect of Sep15 knockout in mice using a chemically-induced colon cancer model. Homozygous Sep15 knockout mice, and wild type littermate controls were given four weekly subcutaneous injections of azoxymethane (10 mg/kg). Sep15 knockout mice developed significantly (pGBP-1 in humans has been associated with a highly significant, increased five-year survival rate in colorectal cancer patients. In …
