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- Autophagy (4)
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Articles 1 - 26 of 26
Full-Text Articles in Physical Sciences and Mathematics
Introducing An H113a Mutation Into Atg10 Y73q To Reduce Autophagic Activity And Understand The Effect Of Atg On Autophagosome Size And Number, Konrad L. Lautenschlager
Introducing An H113a Mutation Into Atg10 Y73q To Reduce Autophagic Activity And Understand The Effect Of Atg On Autophagosome Size And Number, Konrad L. Lautenschlager
Senior Honors Theses and Projects
Autophagy is an essential recycling process that occurs within eukaryotic cells, however, the individual functions of the current thirty-two known autophagic proteins are not yet entirely understood. At this time, it is known that the autophagic protein Atg7 works upstream of both Atg3 and Atg10. Atg3 is affected by Atg7 and allows for the attachment of Atg8 and the lipid PE which is part of the autophagosome membrane. The Atg10 pathway is also affected by Atg7 but attaches Atg12 to Atg5 which upregulates the function of Atg3 and ultimately Atg8 lipidation. These protein interactions are necessary for forming autophagosomes, large …
The Effect Of Autophagy Related Protein 10 And Its Mutants On Autophagic Activity, Sk Nadia Rahman Silvia
The Effect Of Autophagy Related Protein 10 And Its Mutants On Autophagic Activity, Sk Nadia Rahman Silvia
Senior Honors Theses and Projects
Autophagy is the cellular degradation process in which cellular contents are encapsulated by double-membrane vesicles, autophagosomes, and delivered to the vacuole to be degraded and recycled. This process is important for cell health and homeostasis. There are approximately 32 different autophagy-related proteins involved. Atg10 is an enzyme that may affect overall autophagic activity by changing autophagosome size and/or number. Our goal is to find mutants that cause a significant, partial loss in Atg10’s activity by mutating some residues near the active site and testing the functionality of these mutants by performing western blots and enzymatic assays. Here we show that …
Analysis Of The Role Of Sgs1p In Repair Of Double-Strand Dna Breaks In Saccharomyces Cerevisiae, Beth Wasserman
Analysis Of The Role Of Sgs1p In Repair Of Double-Strand Dna Breaks In Saccharomyces Cerevisiae, Beth Wasserman
Senior Honors Theses and Projects
Mis-repair of DNA double-stranded breaks (DSB) can result in genomic rearrangements and cancer. Sgs1p is a helicase that unwinds DNA for DSB repair. To better understand its role in break repair, I analyzed the frequency of various types of DSB repairs in yeast cells with the mutation sgs1-FD. Given this mutation disrupts an interaction between Sgs1p and a critical protein, Rad51p, I hypothesized mutant cells would have more error-prone repair than high fidelity canonical BIR repair. Genome sequence and chromosome size were examined in sgs1-FD yeast cells that underwent DSB repair. No difference was found in the frequency of …
An Investigation Of The Nature Of Plasminogen Activator Inhibitor Type-I (Pai-I) To Improve Upon Known Small Molecule Inhibitors, Justin A. Powers
An Investigation Of The Nature Of Plasminogen Activator Inhibitor Type-I (Pai-I) To Improve Upon Known Small Molecule Inhibitors, Justin A. Powers
Senior Honors Theses and Projects
Plasminogen activator inhibitor type-I (PAI-I ) is a serpin superfamily member protein that acts as the major inhibitor of tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA). At physiological levels, PAI-I plays an active role in regulating fibrinolysis, the process of normal blood clot degradation. Pathological levels of PAI-I have been linked to multiple health ailments: fibrosis, heart disease, cancer, and obesity. In recent years, PAI-1 has been the subject of targeted drug design. In this study, we identified a class of polyphenol compounds as the most capable of maintaining its inhibitory efficiency against vitronectin bound PAI-I in buffer …
Understanding The Role Of Atg7 And Atg14 In Autophagy, Ronith Chakraborty
Understanding The Role Of Atg7 And Atg14 In Autophagy, Ronith Chakraborty
Senior Honors Theses and Projects
Autophagy is the process by which cytosolic components are trafficked to and degraded by the vacuole or lysosome. It plays a critical role in cellular health, aging, cancer, and neurodegenerative diseases. Atg7 and Atgl4 are enzymes required for the autophagic process in Saccharomyces cerevisiae. In this study, we hypothesized that Atg7 controls the size while Atg 14 controls the number of autophagosomes. Using western blotting, Pho8D.60 assay and transmission electron microscopy analysis, we found that Atg7 affects both the size and number of autophagosomes. In addition, we have created cells expressing various levels of Atgl4 using non-native promoters. In addition, …
Characterization Of The Histone Binding Properties Of The Epigenetic Reader Protein Uhrf2 To H3 In Phd Domain, Marisa Gilliam
Characterization Of The Histone Binding Properties Of The Epigenetic Reader Protein Uhrf2 To H3 In Phd Domain, Marisa Gilliam
Senior Honors Theses and Projects
Every cell contains the same genetic code, to have cell differentiation this genetic code needs to be regulated on what is expressed. The regulation of gene expression without altering the genetic code itself is known as epigenetics. An example of epigenetic regulation can be seen between the binding of UHRF2 and H3 histones. The purpose of this project is to determine ifD363 in UHRF2 is important for histone H3 binding. To do so, D363 was mutated to alanine, lysine or asparagine. The mutant protein was expressed, purified, and its ability to binding to H3 was tested by fluorescence polarization. Compared …
Analysis Of Oxidation Of Carbon Monoxide On Rh (110), Razan Tanbour
Analysis Of Oxidation Of Carbon Monoxide On Rh (110), Razan Tanbour
Senior Honors Theses and Projects
81% of all rhodium (Rh) is used in automobile catalytic converters. Consequently, researchers have dedicated a lot of effort into understanding the behavior of nonmetal oxides on a Rh surface. Using a computer simulation program, we have studied the absorption and oxidation of carbon monoxide (CO) on a terraced Rh surface (lattice) with a width of three and a height of 10000 using a mechanism that describes the behavior at low temperatures. Varying the reaction activation energies (rate constants), and the mobility of the CO, led to changes in the surface coverages of oxygen and CO. Specifically, increasing the activation …
Effects Of Yoga On The Motor Skills Of A Ten-Year-Old Male With Autism Spectrum Disorder, Amber Schmitt
Effects Of Yoga On The Motor Skills Of A Ten-Year-Old Male With Autism Spectrum Disorder, Amber Schmitt
Senior Honors Theses and Projects
Autism Spectrum Disorder (ASD} is a neurodevelopmental disorder that is typically diagnosed in childhood due to the presence of atypical development, social interactions, and repetitive stereotypical patterns of behavior. The purpose of the present study was to examine the effects of a yoga intervention on a ten-year-old male diagnosed with ASD. It was hypothesized that the yoga intervention on select instructed poses would increase both pose duration and pose performance and that the results would generalize to longer pose duration and better pose performance on non-instructed poses. Pre-intervention assessments of motor functioning were administered, including the Movement ABC, BOT-2, TGMD, …
Determining Atg11'S Binding Interactions Using A Yeast Two Hybrid System And Directed Mutagenesis, Jesse Smith
Determining Atg11'S Binding Interactions Using A Yeast Two Hybrid System And Directed Mutagenesis, Jesse Smith
Senior Honors Theses and Projects
Autophagy is a mechanism of intracellular degradation within eukaryotes. Because of its aid to a cells longevity, autophagy is believed to be important for the prevention of neurodegenerative diseases. Autophagy related protein 11 (Atg11) is a coiled-coil scaffolding protein required for selective autophagy in yeast. Atg11 is known to interact with Atg1, Atg20, and Atg29, in addition to connecting cargo molecules prApel -Atg19 to the phagophore assembly site. In addition to its many functions within yeast autophagy, Atg11 has two human homologs: Huntingtin protein and FIP200. This homology encourages us to gain a further understanding of Atg11's binding sites. In …
Understanding The Interface That Enables The Interaction Between Two Dopamine Receptor Subtypes Known As D1 And D2 Implicated In Depression, Adam Baraka
Senior Honors Theses and Projects
The dopamine receptor subtypes known as DI and D2 have been shown to form a heteromer complex, which is thought to lead to the disruption of a multitude of signaling pathways within the brain. As a result, this has been proposed to lead to diseased states such as Alzheimer's and depression. In previous studies, it has been shown that the use of synthetic peptides corresponding to the surface interface of the interactions (specifically in the third intracellular loop of D2 interface) within the complex have served to compete against the formation of the heteromer. Through in vitro biochemical techniques such …
Expression And Purification Of Atg11: A Protein Involved In The Organization Of Autophagy, Carson Zois
Expression And Purification Of Atg11: A Protein Involved In The Organization Of Autophagy, Carson Zois
Senior Honors Theses and Projects
Autophagy is a physiological process for the degradation of internal cell components to promote cell survival. This process allows the cell to maintain homeostasis, recycle damaged cellular components and helps protect against disease. Autophagy can be selective or non-selective. Non-selective, or bulk, autophagy occurs during times of cellular starvation and results in non-specific degradation of cytoplasmic materials. Selective autophagy targets specific components within the cytoplasm for degradation, and is always active. In both forms of autophagy, components are degraded when a double-membraned structure, called the autophagosome, encapsulates the target cargo and is then recruited to the lysosome in mammalian cells, …
Analysis Of Variable Regions In Feline Leukemia Virus Envelope Sequences, Brianna Sohl
Analysis Of Variable Regions In Feline Leukemia Virus Envelope Sequences, Brianna Sohl
Senior Honors Theses and Projects
Feline Leukemia Virus (FeLV) is a retrovirus that affects domesticated cats and other species in the Felis genus. There are three major subtypes, each characterized by unique disease progression and proviral sequences. FeLV-A is weakly pathogenic, -B has been associated with tumors, and -C causes severe anemia. Proviral sequences were amplified using PCR with FeL V-specific and adapter-specific primers. The method of primer walking has yielded consensus sequences for several fragments of 1,000-3,000 base pairs of proviral DNA. Sequences for ten different clones of the provirus envelope region from a FeL V positive blood sample were compared to known sequences …
Investigation Of Atg11 And Its Interaction With Ypt1 In Autophagy, Hayley Cawthon
Investigation Of Atg11 And Its Interaction With Ypt1 In Autophagy, Hayley Cawthon
Senior Honors Theses and Projects
Autophagy is a cellular process conserved in eukaryotes that involves the trafficking of intracellular material from the cytosol to the vacuole/lysosome. This material is wrapped in a double membraned vesicle called an autophagosome, which ls constructed at the pre-autophagosomal structure. Many proteins are Involved In autophagy, one of them being Atgll. This protein is crucial in the selective autophagy pathway, and is responsible for proper formation of the pre-autophagosomal structure as well as recruiting the material intended for degradation to the autophagosome. Atgl 1 interacts with many other autophagy proteins, but it Is unknown whether it interacts with these binding …
Short Chain Fatty Acid Production By Probiotic Organisms In The Gastrointestinal Tract, Elyssa Rautiola
Short Chain Fatty Acid Production By Probiotic Organisms In The Gastrointestinal Tract, Elyssa Rautiola
Senior Honors Theses and Projects
Interest in determining the mechanism by which pro biotic bacteria in the gastrointestinal tract produce short chain fatty acids (SCFA) has increased over the past few years. This study uses gas chromatography and mass spectrometry to characterize lactate production in aerobic test tube cultures, aerobic bioreactor cultures, and anaerobic bioreactor cultures. To collect anaerobic bioreactor samples, a novel in vitro anaerobic model was developed. The pH and colony forming units of each bacterial sample was also measured in order to understand the correlation between lactate production and bacterial growth. The purpose of this study was to analyze production of SCFA …
Synthesis Of 1-Pyrenyldiazomethane For Derivatization Of Short-Chain Fatty Acids, Mary E. Kalvaitis
Synthesis Of 1-Pyrenyldiazomethane For Derivatization Of Short-Chain Fatty Acids, Mary E. Kalvaitis
Senior Honors Theses and Projects
Use of I-pyrenyldiazomethane (PDAM) for derivatizing short-chain fatty acids (SCFA) is a successful way to analyze complex SCF A samples quickly and with minimal sample preparation. The costs associated with ordering PDAM from a commercial source can be high, typically more than $300 not including shipping costs. This project developed a simple two-step synthesis procedure that can be used in undergraduate chemistry laboratories. We found that the PDAM produced by this procedure is pure enough to use for our derivatization needs without further purification. This synthesis can be used to further explore the use of PDAM for fast and simple …
A Comparative Analysis Of The Electronic And Structural Characteristics Of Polyphenolic Inhibitors Of Pai-1, Patrick Spoutz
A Comparative Analysis Of The Electronic And Structural Characteristics Of Polyphenolic Inhibitors Of Pai-1, Patrick Spoutz
Senior Honors Theses and Projects
Polyphenolic compounds containing two gallate groups have been shown to be effective inhibitors of Plasminogen Activator Inhibitor-1 (PAI-1). In this work we use Density Functional calculations to examine energetically-accessible configurations of two digallate compounds exhibiting disparate inhibitory activity toward PAI-1. In addition, we examine the partial charges of potentially acidic protons and the relative stability of the respective conjugate bases of a select group of PAI-1 inhibitors. This analysis was carried out to determine whether such characteristics can be used to distinguish between effective and less effective inhibitors. An examination of the stable configurations of CDE-008 and CDE-056 indicates that …
Computational Studies Of Stereochemical Effects In The Synthesis Of Sugar Mimics, Louis Anthony Lello
Computational Studies Of Stereochemical Effects In The Synthesis Of Sugar Mimics, Louis Anthony Lello
Senior Honors Theses and Projects
Density Functional methods are used to model the tandem aza-Cope rearrangement – Mannich cyclization reaction leading to substituted acylpyrrolidines. The ultimate goal is to determine optimum reaction conditions that maximize stereoselectivity, as only one set of stereoisomers is pharmacologically active. Three aspects of the reaction are investigated. First, we determine the relative size of three rotational barriers in the interconversion of two iminium cation stereoisomers that are precursors to the aza-Cope rearrangement. The lowest energy pathway for the interconversion is identified, as well as the relative stability of the two stereoisomers for two different substituents: diphenyl and methyl. Activation barriers …
Resolution Modeling Of Length Tuning In Gas Chromatography, James P. Grinias
Resolution Modeling Of Length Tuning In Gas Chromatography, James P. Grinias
Senior Honors Theses and Projects
Tunable selectivity provides a relatively simple and inexpensive way to manipulate peak positions and gain resolution in chromatographic separations. Length tuning utilizes two columns of different polarities connected in series. Selectivity is manipulated by changing the relative lengths of the two columns. However, a direct correlation is not seen between relative length and effective contribution due to gas compression effects. Rather, a direct correlation is observed between the carrier gas transport time through a segment of column (relative to the total carrier gas transport time) and the effective contribution of that segment. This relationship has been used to predict retention …
A Density Functional Study Of The Relative Stability Of Intermediates In A Mcmurry Coupling Reaction, Andrew Jozef Livingston
A Density Functional Study Of The Relative Stability Of Intermediates In A Mcmurry Coupling Reaction, Andrew Jozef Livingston
Senior Honors Theses and Projects
Reductive cyclization via McMurry coupling is a common way to form pyrrolizidine rings. In this work we investigate the titanium-catalyzed McMurry coupling reaction leading to a pyrrolizidine alkaloid using density functional methods. Specifically, we compare the relative energies of all possible pinacolate intermediates at the UB3LYP/6-31G level of theory. The most stable intermediate is found to be the one resulting from C-O bond insertion in the ester group. The McMurry product is not predicted to form.
Qualitative Thm-Gc-Ms Analysis Of Proteins And Amino Acids In Rock Painting Binders, Melissa Doolin
Qualitative Thm-Gc-Ms Analysis Of Proteins And Amino Acids In Rock Painting Binders, Melissa Doolin
Senior Honors Theses and Projects
A vital step to radiocarbon dating rock paintings involves the characterization of organic material in the paint. Using THM-GC-MS we have created a library of mass spectrometric data on possible organic binders, to compare to authentic paint samples. To reduce interference from contaminants and the mineral background, we are developing a simple purification technique to extract proteins and carbohydrates from these samples. Separating the organics can greatly enhance our results for GC-MS identification and subsequent radiocarbon analysis by accelerator mass spectroscopy.
Isolation And Analysis Of Cyanobacterial Dna, Tiffany Crosby
Isolation And Analysis Of Cyanobacterial Dna, Tiffany Crosby
Senior Honors Theses and Projects
Cyanobacteria are a phylum of bacteria that possess a diverse number of biological characteristics. One of the evolutionary innovations of the cyanobacteria are its ability to perform oxygenating photosynthesis, which all cyanobacteria are able to perform. It is believed that a form of metabolism became the dominant method for producting fixed carbon from carbon dioxide (CO2) at around 3.5 billion years ago. Instead of using hydrogen sulfide, whose generated waste products were difficult to eliminate, the photosynthetic cyanobacteria used water as their hydrogen source (1). Many cyanobacteria are also capable of fixing atmospheric nitrogen (2). Cyanobacteria are present …
Synthesis Of An Aza-Cope Rearrangement - Mannich Cyclization Precursor From L-Proline, Patricia T. Sinawe
Synthesis Of An Aza-Cope Rearrangement - Mannich Cyclization Precursor From L-Proline, Patricia T. Sinawe
Senior Honors Theses and Projects
No abstract provided.
Lipid Metabolism In A549 And 9hte Cells Quantitation Of Lipid Peroxidation, Elizabeth Quintus
Lipid Metabolism In A549 And 9hte Cells Quantitation Of Lipid Peroxidation, Elizabeth Quintus
Senior Honors Theses and Projects
No abstract provided.
Synthesis And Analysis Of An Α-Amylase Inhibitor And An Antimicrobial Peptide, Brahmlin Kaur Sethi
Synthesis And Analysis Of An Α-Amylase Inhibitor And An Antimicrobial Peptide, Brahmlin Kaur Sethi
Senior Honors Theses and Projects
Abstract 1: α-Amylase is an important enzyme in the body responsible for hydrolyzing many polysaccharides such as dietary starch. Inhibition of this enzyme could be extremely beneficial in diabetic patients because it could lower the glucose levels in the blood. Our objective is to synthesize a small analog of a natural α-amylase inhibitor, Tendamistat. This molecule has 15-22 residue segment that are critical for its activity. The peptide was synthesized, cleaved, purified, analyzed, and an enzyme assay was run. Michaelis Menton and Lineweaver-Burk plots were constructed to determine the Vmax, Km, and Ki for each …
Development Of An Upper Level Undergraduate Research Based Laboratory: The Purification, Analysis, And Dinetic Study Of Cytochrome B5, Mary Mcphail
Senior Honors Theses and Projects
The purpose of this project was to develop an upper level undergraduate biochemistry laboratory (CHEM 453) based upon a novel research project, designed to replace an existing instructional laboratory that employs ‘cookbook’ exercises. Methods for the expression, purification, spectral analysis of structural integrity, and electron transfer capability of rabbit cyt b5 were adapted from published work done by Dr. Lucy Waskell of the University of Michigan and Dr. Mansuy of the University of Paris. In our hands, rabbit liver cyt b5 expressed in E. coli was purified to 45% specific content of the theoretical content. Additionally, 37 nmol …
Synthesis Of Pyrrolidines And Pyrrolizidines Using The Aza-Cope Rearrangement Mannich Cyclization Under Microwave Conditions, Amanda Schalk
Synthesis Of Pyrrolidines And Pyrrolizidines Using The Aza-Cope Rearrangement Mannich Cyclization Under Microwave Conditions, Amanda Schalk
Senior Honors Theses and Projects
No abstract provided.