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Other Biochemistry, Biophysics, and Structural Biology Commons™
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Articles 1 - 10 of 10
Full-Text Articles in Other Biochemistry, Biophysics, and Structural Biology
Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer
Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer
Doctoral Dissertations
The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including …
Elucidating Mechanisms Of Protein Aggregation In Alzheimer’S Disease Using Antibody-Based Strategies., Benjamin A. Colvin
Elucidating Mechanisms Of Protein Aggregation In Alzheimer’S Disease Using Antibody-Based Strategies., Benjamin A. Colvin
Dissertations
Alzheimer’s Disease (AD) is a devastating neurodegenerative disorder. There are two characteristic histopathological hallmarks in the brain: senile plaques and neurofibrillary tangles, composed of insoluble aggregates of the amyloids Amyloid-β (Aβ) and tau protein, respectively. These diagnostic markers, though distinctive, are not apparent effectors of AD pathology. Evidence has mounted suggesting smaller soluble aggregates (oligomers) of Aβ or tau are the true drivers of disease progression. This dissertation presents several amyloid biophysics projects. Aggregate biophysical parameters such as weight, shape, and conformation were measured using a range of methodologies, including Multiangle Light Scattering, Dynamic Light Scattering, UV-Circular Dichroism, UV-Fluorescence, Scanning …
Probing The Domain Architecture And Structural Dynamics Of Caspase-6 For Its Specific Regulation, Kevin Buadlart Dagbay
Probing The Domain Architecture And Structural Dynamics Of Caspase-6 For Its Specific Regulation, Kevin Buadlart Dagbay
Doctoral Dissertations
Caspases are cysteine aspartate proteases that direct programmed cell death in multicellular organisms. Activation of caspases is tightly regulated to secure maintenance of cellular homeostasis. The aberrant regulation of caspases can act as molecular triggers for a range of diseases from cancer to neurodegeneration. The detailed exploration of caspase structure, dynamics, function, and regulation is crucial to better understand and precisely control their cellular functions. This body of work specifically provides a multi-level understanding of the unique structural dynamics and regulation of caspase-6, the function of which is implicated in Alzheimer’s and Huntington’s diseases. A detailed map …
Disorder In Cysteine-Rich Granulin-3 And Its Implication In Alzheimer Disease, Gaurav Ghag
Disorder In Cysteine-Rich Granulin-3 And Its Implication In Alzheimer Disease, Gaurav Ghag
Dissertations
Granulins (GRNs) are a family of small, cysteine-rich proteins that are generated upon proteolytic cleavage of their precursor, progranulin (PGRN) during inflammation. All seven GRNs (1 – 7 or A – G) contain twelve conserved cysteines that form six intramolecular disulfide bonds, rendering this family of proteins unique. GRNs play multiple roles and are involved in a myriad of physiological as well as pathological processes. They are known to a play role in growth and embryonic development, wound healing, and signaling cascades as well as in tumorigenesis. They are also implicated in neurodegenerative diseases like frontotemporal dementia (FTD), Alzheimer disease …
Inquiry Into Perilipin-5a Expression In Triacylglycerol Rich Vs Normal Fed Mouse Tissue, Kobi Agyepong
Inquiry Into Perilipin-5a Expression In Triacylglycerol Rich Vs Normal Fed Mouse Tissue, Kobi Agyepong
Undergraduate Honors Thesis Projects
The steep rise in both childhood and adult obesity over the past three decades has moved to the forefront of public consciousness in recent years. This development has generated a marked increase in general health awareness and lifestyle changes for a vast number of individuals, most notably in the form of increased physical activity and diet alterations. The latter point is especially salient in a biochemical context, because of the myriad factors that can result in “fat accumulation”. Chief among these factors is the Perilipin 5A gene, (known as PLIN5A) which encodes the protein Perilipin 5A of the Perilipin family …
An Assessment Of Potential False Positive E.Coli Pyroprints In The Cplop Database, Skyler A. Gordon
An Assessment Of Potential False Positive E.Coli Pyroprints In The Cplop Database, Skyler A. Gordon
Master's Theses
The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as …
Modeling The Binding Of Neurotransmitter Transporter Inhibitors With Molecular Dynamics And Free Energy Calculations, Bernandie Jean
Modeling The Binding Of Neurotransmitter Transporter Inhibitors With Molecular Dynamics And Free Energy Calculations, Bernandie Jean
Electronic Theses and Dissertations
The monoamine transporter (MAT) proteins responsible for the reuptake of the neurotransmitter substrates, dopamine, serotonin, and norepinephrine, are drug targets for the treatment of psychiatric disorders including depression, anxiety, and attention deficit hyperactivity disorder. Small molecules that inhibit these proteins can serve as useful therapeutic agents. However, some dopamine transporter (DAT) inhibitors, such as cocaine and methamphetamine, are highly addictive and abusable. Efforts have been made to develop small molecules that will inhibit the transporters and elucidate specific binding site interactions. This work provides knowledge of molecular interactions associated with MAT inhibitors by offering an atomistic perspective that can guide …
Alpha-Synuclein: Insight Into The Hallmark Of Parkinson's Disease As A Target For Quantitative Molecular Diagnostics And Therapeutics, Baggio A. Evangelista
Alpha-Synuclein: Insight Into The Hallmark Of Parkinson's Disease As A Target For Quantitative Molecular Diagnostics And Therapeutics, Baggio A. Evangelista
Honors Undergraduate Theses
Parkinson’s disease (PD) is the second-most common neurodegenerative disease after Alzheimer’s disease. With 500,000 individuals currently living with Parkinson’s and nearly 60,000 new cases diagnosed each year, this disease causes significant financial burden on the healthcare system - amassing to annual expenditures totaling 200 billion dollars; predicted to increase through 2050. The disease phenotype is characterized by a combination of a resting tremor, bradykinesia, muscular rigidity, and depression due to dopaminergic neuronal death in the midbrain. The cause of the neurotoxicity has been largely discussed, with strong evidence suggesting that the protein, alpha-Synuclein, is a key factor. Under native conditions, …
Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera
Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera
Honors Undergraduate Theses
In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …
Methane Fluxes And Porewater Dissolved Organic Carbon Dynamics From Different Peatlands Types In The Pastaza-Marañon Basin Of The Peruvian Amazon., Jhon Del Aguila-Pasquel
Methane Fluxes And Porewater Dissolved Organic Carbon Dynamics From Different Peatlands Types In The Pastaza-Marañon Basin Of The Peruvian Amazon., Jhon Del Aguila-Pasquel
Dissertations, Master's Theses and Master's Reports
Relevant components of the carbon budget such as methane fluxes and porewater dissolved organic carbon (DOC) are poorly characterized in the Peruvian Pastaza Marañon basin (PMB). PMB is associated with a tropospheric hotspot for methane and therefore it may represent a significant methane source. We aimed to quantify the magnitude of CH4 fluxes and porewater DOC; and to determine their predictors across different peatland types in the PMB (open peatland, palm swamp, and pole forest). The study was conducted in two peatland sites covering the three main vegetation types in PMB. We collected gas and water samples using chamber-based …