Exploring The Importance Of Single Nucleotide Polymorphisms Of Hspa9 In Dna Of Sarcoma Patients,
2013
University Of New Hampshire
Exploring The Importance Of Single Nucleotide Polymorphisms Of Hspa9 In Dna Of Sarcoma Patients, Christine M. Hebert
Honors Theses and Capstones
The aim of this project was to identify genetic variants that may influence the risk and progression of sarcoma through targeted genotyping of HSPA9 gene. It is important to look at genetic variants in DNA samples because if a variant is determined to be more likely than another, a screening for the particular variant can be done to identify a patient’s risk of sarcoma. The study population was sarcoma patients from the International Sarcoma Kindred Study. These patients had no mutations in p53 or MDM2. Genotyping data from the HapMap project (hapmap.org) for HSPA9 was used to identify the polymorphisms …
An Acid Catalyzed Reversible Ring-Opening/Ring-Closure Reaction Involving A Cyano-Rhodamine Spirolactam,
2013
University of South Carolina - Columbia
An Acid Catalyzed Reversible Ring-Opening/Ring-Closure Reaction Involving A Cyano-Rhodamine Spirolactam, H. Li, H. Guan, X. Duan, J. Hu, Guiren Wang, Qian Wang
Faculty Publications
Cyanamide was introduced into the rhodamine spirolactam framework to produce a colorless and non-fluorescent compound RBCN. It shows a reversible ring-opening/ring-closure process in response to the solution pH, which exhibits an “ON/OFF” switching in its fluorescence. Different from other rhodamine-type dyes, the ring-open form of RBCN is stable in protic solvents under neutral, near neutral and basic conditions, showing a pink color and very strong fluorescence. We also demonstrated the potential of RBCN in live cell imaging.
Executing And Teaching Science--The Breast Cancer Genetics And Technology-Rich Curriculum Professional Development Studies Of A Science Educator,
2013
University of South Carolina - Columbia
Executing And Teaching Science--The Breast Cancer Genetics And Technology-Rich Curriculum Professional Development Studies Of A Science Educator, Regina Evarn Wragg
Theses and Dissertations
This dissertation presents my explorations in both molecular biology and science education research. In study one, we determined the ADIPOQ and ADIPORI genotypes of 364 White and 148 Black BrCa patients and used dominant model univariate logistic regression analyses to determine individual SNP and haplotype associations with tumor or patient characteristics in a case-case comparison. We found twelve associations between individual SNPs and patient or tumor characteristics that impact BrCa prognosis. For example, the ADIPOQ rs1501299 C allele was associated with ER+ tumors (OR=4.73, p=0.001) among White women >50 years of age at their time of diagnosis. Also, the A …
Using Ammonium Pore Water Profiles To Assess Stoichiometry Of Deep Remineralization Processes In Methanogenic Continental Margin Sediments,
2013
Old Dominion University
Using Ammonium Pore Water Profiles To Assess Stoichiometry Of Deep Remineralization Processes In Methanogenic Continental Margin Sediments, David J. Burdige, Tomoko Komada
OES Faculty Publications
In many continental margin Sediments, a deep reaction zone exists which is separated from remineralization processes near the sediment surface. Here, methane diffuses upward to a depth where it is oxidized by downwardly diffusing sulfate. However, the methane sources that drive this anaerobic oxidation of methane (AOM) in the sulfate-methane transition zone (SMT) may vary among sites. In particular, these sources can be thought of as either (i) "internal" sources from in situ methanogenesis (regardless of where it occurs in the sediment column) that are ultimately coupled to organic matter deposition and burial, or (ii) "external" sources such as hydrocarbon …
The Influence Of Ubiquitin-Related Modifier Protein Urm1 On Prion Formation,
2013
Coastal Carolina University
The Influence Of Ubiquitin-Related Modifier Protein Urm1 On Prion Formation, Jacob Beaver
Bridges: A Journal of Student Research
Prions are infectious proteins that are autocatalyzing (formed by altering a regular protein into the structurally different prion form), and are associated with many neurodegenerative diseases such as Alzheimer's, Parkinson's, Huntington's, and Bovine Spongiform encephalopathy (or Mad Cow disease). This experiment tested the effect of three different plasmids—pH317, pER62, and pMP46—on prion formation in both wild-type and Urm1 deletion mutants in the yeast Saccharomyces cerevisiae. The proposed hypothesis was over-expression of the Ure2 prion forming protein would increase the frequency of prion formation, as well as yield less sustainable prion amyloids (or prion aggregations) that are easier to cure. Another …
Bioinformatic And Functional Analysis Of 1-Aminocyclopropane-1-Carboxylate (Acc)- Deaminase Homologues In Strains Of Sinorhizobium,
2013
Hamline University
Bioinformatic And Functional Analysis Of 1-Aminocyclopropane-1-Carboxylate (Acc)- Deaminase Homologues In Strains Of Sinorhizobium, Alyssa L. Renn
Departmental Honors Projects
Nitrogen fixing bacteria like Sinorhiziobia have the ability to convert nitrogen gas into ammonia, allowing its incorporation into proteins and other biological molecules. These organisms form a symbiosis with legume plants such as peas, soybeans, and alfalfa. The symbiotic relationship between Sinorhizobia and legumes requires of the function of many proteins; one is 1- aminocyclopropane-1-carboxylic acid (ACC)-deaminase. Bacteria containing ACC-deaminase enzymes are more effective in nodulation due to their ability to lower the concentration of ethylene and bypass the plant defense systems. Upon examination of the complete DNA sequence of forty-eight Sinorhiziobia strains from different geographical locations, eighteen sequences similar …
Relationship Of Cross-Linking Potential To Mechanism Of Cell Death,
2013
Colby College
Relationship Of Cross-Linking Potential To Mechanism Of Cell Death, Adam N. Spierer
Honors Theses
Mechlorethamine (HN2), a nitrogen derivative of mustard gas, was the first synthetic anti-tumor chemotherapeutic because it forms covalent cross-links between strands of duplex DNA. HN2 represents a class of bifunctional alkylating agents that are both chemotherapeutic and carcinogenic: diepoxybutane (DEB), the active form of the pro-drug treosulfan, and epichlorohydrin (ECH), a structural hybrid of HN2 and DEB, also form covalent cross-links between DNA. While HN2 and DEB are clinically used as anti-tumor chemotherapeutics, ECH is a structural hybrid of these two compounds not used in a clinical setting. Accordingly, we aimed to understand the relationship between the cross-linking potential of …
The Genetic Engineering Of Motor Proteins,
2013
University at Albany, State University of New York
The Genetic Engineering Of Motor Proteins, Rachael M. Hartz
Legacy Theses & Dissertations (2009 - 2024)
Molecular motors are a remarkable feature within living organisms that are responsible for directional mechanical motion, which is driven by adenosine triphosphate (ATP) hydrolysis. Actin-binding molecular motors are of specific interest in the field of nanotechnology as filamentous actin is capable of carrying cargo, such as quantum dots, while it is translocated along a motor coated surface. The binding regions of motor proteins, which are known to interact with actin, such as Myosin, have been thoroughly examined and identified. Rapid genetic engineering of the ATP-hydrolyzing enzyme, adenosine kinase, to incorporate these binding regions is possible through the use of site- …
2'-O-Methyl Substitutions In The Yeast Telomerase Pseudoknot And Their Effects On Telomerase Activity,
2013
University at Albany, State University of New York
2'-O-Methyl Substitutions In The Yeast Telomerase Pseudoknot And Their Effects On Telomerase Activity, Katelyn Mae Jasper
Legacy Theses & Dissertations (2009 - 2024)
Telomerase is a ribonucleoprotein (RNP) complex that synthesizes telomeric repeats at the ends of linear chromosomes to form the DNA–protein complexes known as telomeres. Telomeres protect the ends of chromosomes from degradation during replication due to the end-replication problem. When replication occurs, gaps are created at the beginning of the lagging and leading strands that result in the loss of a small amount of DNA at every replication cycle. By adding thousands of copies of telomeric repeats, the repeats are lost in the replication process and not precious genetic information. The telomerase RNA varies drastically among different species both in …
Structure-Activity Relationship Of 2,3-Benzodiazepin-4-Ones As Noncompetitive Ampa Receptor Antagonists,
2013
University at Albany, State University of New York
Structure-Activity Relationship Of 2,3-Benzodiazepin-4-Ones As Noncompetitive Ampa Receptor Antagonists, Mohammad Shaban Qneibi
Legacy Theses & Dissertations (2009 - 2024)
2,3-Benzodiazepin-4-one (BDZ-11) derivatives are a special group of 2,3-benzodiazepine compounds. These compounds have been previously synthesized as AMPA receptor inhibitors, and they are also potential drugs for the treatment of various neurological diseases involving excessive AMPA receptor activity. AMPA receptors are a subtype of glutamate ion channel proteins and are responsible for the majority of excitatory neurotransmission in the mammalian central nervous system. Specifically, they are critically involved in neuronal development and brain activities, including learning and memory. Overstimulation of AMPA receptors is associated with some neurological diseases such as ALS, stroke and Alzheimer's disease. Despite the fact that hundreds …
Characterizing The Effects Of Glutaraldehyde On The Ryanodine Receptor Calcium Release Channel,
2013
University at Albany, State University of New York
Characterizing The Effects Of Glutaraldehyde On The Ryanodine Receptor Calcium Release Channel, Joshua Dov Strauss
Legacy Theses & Dissertations (2009 - 2024)
Ryanodine receptors (RyR) are large intracellular calcium release channels, which
New Tools To Study Amyloid Fibrils And Intrinsically Disordered Proteins In Vitro And In Vivo,
2013
University at Albany, State University of New York
New Tools To Study Amyloid Fibrils And Intrinsically Disordered Proteins In Vitro And In Vivo, Jacqueline D. Washington
Legacy Theses & Dissertations (2009 - 2024)
Amyloid fibrils are β-sheet-rich protein aggregates commonly found in the organs and tissues of patients with various amyloid-associated diseases. The structure of insulin fibrils was characterized by deep ultraviolet resonance Raman and Nuclear Magnetic Resonance spectroscopy combined with hydrogen-deuterium exchange. Our new approach of combining NMR and Raman spectroscopy with molecular dynamic simulations for characterizing amyloid fibrils provided exclusive knowledge about fibril structure at amino acid residue resolution.
Y-Family Dna Polymerases : Mechanism Of Single-Base Deletion And Effect Of Pcna Interaction,
2013
University at Albany, State University of New York
Y-Family Dna Polymerases : Mechanism Of Single-Base Deletion And Effect Of Pcna Interaction, Yifeng Wu
Legacy Theses & Dissertations (2009 - 2024)
Translesional synthesis (TLS) by specialized Y-family DNA polymerases is a DNA damage tolerance pathway to bypass DNA lesions that have not been repaired by other DNA repair mechanisms. Despite their valuable lesion bypass ability, the Y-family DNA polymerases display a much lower fidelity upon replicating undamaged DNA. Their activity therefore needs to be well regulated in the cell. In our first project, we examined how an archaeal Y-family DNA polymerase, Dpo4, makes single-base deletions during replication. Dpo4 belongs to the DinB subfamily which is known to make single-base deletions. Although previous studies suggested that it uses a dNTP-stabilized misalignment mechanism, …
Structural Biology Of The Receptor For Advanced Glycation End Products (Rage),
2013
University at Albany, State University of New York
Structural Biology Of The Receptor For Advanced Glycation End Products (Rage), Jing Xue
Legacy Theses & Dissertations (2009 - 2024)
The receptor for advanced glycated end products (RAGE), due to its location in the major histocompatibility complex class III (MHC III) region, suggests its involvement in immune responses. Because RAGE has been linked to complications of diabetes and chronic inflammation, the severity of Alzheimer's disease and cancer, it's significant to understanding the biological mechanism of signal transduction of RAGE.
Molecular Biochemical Study Of The Cataract-Associated Mutants In Human Gammad-Crystallin,
2013
University at Albany, State University of New York
Molecular Biochemical Study Of The Cataract-Associated Mutants In Human Gammad-Crystallin, Cindy Yeung
Legacy Theses & Dissertations (2009 - 2024)
Cataract is a vision impairment disease that leads to light scattering and opacity of the eye lens. It is recognized as the most prevalent cause of blindness. Most cataracts occur due to aging, but those that occur in childhood or in young adults are typically of genetic origin. In the young (developing) eye, post–surgical complications such as glaucoma are common after cataract surgery. Hence there is a great need to develop non-surgical intervention strategies for the treatment of cataract. Here, two cataract-associated mutants of human γD-crystallin (HGD): i) Arg76 to Ser (R76S) and ii) a truncation mutation at Trp156 (W156X …
The Sxrna Platform : Biophysical Characterization Of Trans-Acting Rna Switches For Gene Expression Control,
2013
University at Albany, State University of New York
The Sxrna Platform : Biophysical Characterization Of Trans-Acting Rna Switches For Gene Expression Control, Christine Bazinet
Legacy Theses & Dissertations (2009 - 2024)
In the past decade, microRNAs (miRNAs) have become a hot topic in biochemical research. These very short ~ 22 nucleotide strands of RNA have been recognized as a functional RNA group and found to play a key role in mediating gene regulation along with RNA-binding proteins (RBPs). For example, by binding to the histone stem-loop (HSL) region of the target mRNA, normally in the 3'- untranslated region (UTR), gene expression can either be activated or deactivated for up or down regulation of the gene product. The majority of miRNAs have been found to down regulate gene expression upon binding to …
Protein Structures Under Physiological Conditions,
2013
University at Albany, State University of New York
Protein Structures Under Physiological Conditions, Karl Michael Bertrand
Legacy Theses & Dissertations (2009 - 2024)
My research focused on the evaluation of protein structures and protein dynamics inside eukaryotic cells under physiological conditions. The primary analyses of my research involved the use of in-cell Nuclear Magnetic Resonance spectroscopy using Heteronuclear Single Quantum Coherence experiments. This allowed me to visualize protein structures at an atomic resolution level, as well as, study the interactions of these proteins with small molecules.
Mutational Analysis Of An Rna Aptamer,
2013
University at Albany, State University of New York
Mutational Analysis Of An Rna Aptamer, Deblina Biswas
Legacy Theses & Dissertations (2009 - 2024)
Aptamers are oligonucleotide molecules (DNA or RNA) that are selected against specific target proteins, nucleic acids or small molecules by using the well established technique of SELEX (Systemic Evolution of Ligands by Exponential Enrichment). Their ability to bind with high affinity and specificity has opened up a wide arena of scientific applications. Aptamers have been shown to have many potential therapeutic and bioanalytical contributions such as in the treatment of diseases like cancer, cardiovascular and other major ailments. The aim of this dissertation is to study and analyze double transversion involving 4 bases in a RNA aptamer molecule: MinB4-au-flipS clamp …
(S)-Trifluoroselenomethionine : A New Non-Natural Amino Acid With Enhanced Methioninase-Induced Cytotoxicity Toward Human Colon Cancer Cells,
2013
University at Albany, State University of New York
(S)-Trifluoroselenomethionine : A New Non-Natural Amino Acid With Enhanced Methioninase-Induced Cytotoxicity Toward Human Colon Cancer Cells, Stephene Nathele Lodge
Legacy Theses & Dissertations (2009 - 2024)
Abstract
Rna Interference Of Ctla4 In Human Leukaemia T Cells,
2013
Technological University Dublin
Rna Interference Of Ctla4 In Human Leukaemia T Cells, Ralitsa Vassileva
Doctoral
The activation of naive T cells is essential for the initiation of the adaptive immunity. One promising approach to overcome immunological tolerance involves augmenting endogenous T cell-mediated immunity by interrupting the T cell down-regulatory pathways. In this project a gene therapy delivery system to overexpress small interfering RNA was used to silence the inhibitory signals induced by CTLA4. A small hairpin RNA duplex designed to silence expression of CTLA4 was successfully cloned into a plasmid. A stably transfected T cell line that is expressing constitutively the CTLA4 siRNA has been developed as a model to understand the role of CTLA4 …
