Medicine and Health Sciences Commons^™

Predicting Biomolecular Properties And Interactions Using Numerical, Statistical And Machine Learning Methods, Elyssa Sliheet

Mathematics Theses and Dissertations

We investigate machine learning and electrostatic methods to predict biophysical properties of proteins, such as solvation energy and protein ligand binding affinity, for the purpose of drug discovery/development. We focus on the Poisson-Boltzmann model and various high performance computing considerations such as parallelization schemes.

Imaging Nanoscale Plasma Membrane Dynamics Reveals Diversity In Clathrin-Coated Vesicle Formation, Tomasz Jacek Nawara

All ETDs from UAB

Clathrin-mediated endocytosis (CME) is an essential cellular process facilitating the internalization of a variety of cargo. Clathrin polymerization and changes in plasma membrane architecture and composition are necessary steps to mediate the formation of clathrin-coated vesicles (CCVs). However, simultaneous analysis of clathrin dynamics and membrane structure in living cells is challenging due to the limited axial resolution of fluorescence microscopes and the heterogeneity of CME. This has fueled conflicting models of vesicle assembly and obscured the roles of flat clathrin assemblies. Here we use Simultaneous Two-wavelength Axial Ratiometry (STAR) microscopy to bridge this critical knowledge gap by quantifying the nanoscale …

Investigating Bzip Recognition Of Dna Sequences Through A Knob-Socket Perspective, Aaron Tran

University of the Pacific Theses and Dissertations

To investigate whether higher order packing interactions confer protein-DNA specificity, a modified Knob-Socket (KS) model was used to analyze the interface of bZIP-DNA crystal structures. The KS analysis identified a nine-residue quadripartite recognition core consisting of four contiguous KS pockets P1, P2, N3, and N4 that each pack one of the four DNA half-site bases in the target sequence. Only one base per base pair packs, and these interactions are split across the DNA strands: the first two positive strand positions 1p and 2p pack into P1 and P2 while the last two negative strand positions 3n and 4n pack …

Modulation Of Kras Structure And Dynamics By Kras Ubiquitination And Membrane Depolarization, Vinay Nair

Dissertations & Theses (Open Access)

KRAS, a 21 kDa small GTPase protein, functions as a molecular switch playing a key role in regulating cell proliferation. Dysregulation of KRAS signaling by oncogenic mutations leads to uncontrolled cell proliferation, a hallmark of cancer cells. Attempts to therapeutically target oncogenic KRAS have led to limited success resulting in a need to identify new mechanisms to targeting KRAS. The interaction of KRAS with its regulators, effectors, and the membrane present one such avenue. In this study, we investigated how post-translational covalent and environmental modifications could modulate these interactions of KRAS. Using computational molecular dynamics simulations, nuclear magnetic resonance spectroscopy …

Abhd5 Induced Morphological Changes On Model Membrane Systems, Nasser S. Junedi

Honors College Theses

Proper regulation of neutral lipid storage (lipogenesis) and release (lipolysis) are critical molecular processes localized to an organelle called the Lipid Droplet (LD). The LD consists of a core with neutral lipids such as triacylglycerols (TAGs) and sterol esters surrounded by a phospholipid monolayer. Dysregulation of the processes localized to the LD are involved in the pathology of various diseases such as Neutral Lipid Storage Disease, diabetes, stroke and cancer. The non-enzymatic protein ABHD5 (α-β Hydrolase Domain-Containing Protein 5), is thought to play a key role in the process of lipolysis by forming homo-oligomers on the surface of the LD …

Simulation Of A Rat Muscle-Tendon Unit With Hill-Type Model Dynamics And The Study Of Viscoelasticity In A Collagen Molecule Via Molecular Dynamics, Veronica Siko

West Chester University Master’s Theses

The field of biological science has established that tendons transfer muscular forces to adjacent bones, but there is a dearth of information about the underlying physical principles of these interactions and how the property of viscoelasticity (displayed in tendons as a difference in mechanical response to stress with differing stretching rates) is encompassed in the collagen of tendons. This thesis details the results of concentric and eccentric contractions of the rat muscle-tendon unit (MTU) with and without viscoelasticity (concentric contraction requires active shortening of the muscle, while eccentric contraction requires active lengthening of the muscle) (Lovering & Brooks, 2014). Once …

Functional Analysis Of A Critical Glycine (Glycine 12) In Beta-Type Connexins Of Human Skin, Rasheed Bailey

Biology Theses

At least five beta-type connexins are expressed in various layers of the skin (Cx26, Cx30, Cx30.3, Cx31, and Cx32) and all include a glycine residue at position 12. Glycine12 (G12) is located about halfway through the cytoplasmic amino terminus and has been the focus of several studies related to connexin diseases and gap junction channel structure. The importance of this residue is evident in the severity and diversity of diseases associated with amino acid substitutions at G12 including hereditary forms of skin disease, deafness and neuropathy. This study uses bioinformatic analysis in combination with mutational analysis and electrophysiology to better …

Clincial Translational Science Research Of The Functional Role Of Large Conductance Potassium Channels In Selective Destruction Of Triple Negative Breast Cancer Cells, Gina Sizemore

Graduate Theses, Dissertations, and Problem Reports

ABSTRACT

The preliminary background that puts this research into context is threefold; it is the aggressive nature of triple negative breast cancer (TNBC), the complexity surrounding its pathology, and the significant lack of targeted treatment for this disease. To clarify the focus of my research, I have concentrated on identifying a targeted treatment for TNBC. In the process, I have identified cycles of reciprocity between treatment, clinical diagnosis, staging, and pathology that will be addressed in smaller papers. However, the weight of this work is in the discovery of a novel target for triple negative breast cancer. The value of …

Giardia Lamblia Growth In Viscoelastic Fluids, Kelly Watanabe

CMC Senior Theses

Giardia lamblia is a single-celled protozoan parasite that when ingested, causes diarrheal disease and infects 33% of people in developing countries. Previous studies observe Giardia in water-like fluids, but Giardia's infectious environment consists of viscoelastic mucus in the small intestine. Therefore, Giardia was cultured in viscoelastic fluids, and its population growth was observed in vitro. To create shear-thinning viscoelastic fluids, 0.2% and 0.4% long-chain polyacrylamide (LCPAM) was added to cell culture media. Giardia was cultured in control media, 0.2% LCPAM, and 0.4% LCPAM, and population growth was quantitatively determined over time. Increasing LCPAM concentration resulted in a solution with …

Structure Based Drug Design Of High Affinity Kras Inhibitors, Michael Mccarthy

Dissertations & Theses (Open Access)

RAS, one of the most well characterized membrane-associated small GTPases, is a notorious oncogene with >15% of all tumors harboring RAS mutations. When RAS is mutated it becomes constitutively active sending cell growth, survival and proliferation into overdrive, which subsequently leads to cancer. Although, RAS has been aggressively targeted with drug design efforts for more than 30 years an FDA approved direct inhibitor has not yet been developed. There are three isoforms of RAS in cells; HRAS, NRAS and KRAS. We focused on KRAS since it is the most frequently mutated isoform in cancer. To identify novel non-covalent small molecules …

Fret-Based Investigations Of The Structure-Function Relationships In The Nmda Receptor, Drew M. Dolino

Dissertations & Theses (Open Access)

The N-methyl-D-aspartate (NMDA) receptor is one member of a class of proteins known as the ionotropic glutamate receptors. Ionotropic glutamate receptors mediate the majority of excitatory neurotransmission in the central nervous system, with the NMDA receptor standing out among these receptors for its requirement of a co-agonist, its magnesium-block-based coincidence detection, its slow kinetics, its calcium permeability, its allosteric modulation, and its especially important functional roles in synaptic plasticity, excitotoxicity, and more. In recent years, a wealth of structural information has come about describing endpoint structures to high resolution, but such structures are unable to fully resolve the movements …

Risperidone And Its Deconstructed Analogs: Functional Effects On The 5ht2ar, Sneha Shah

Theses and Dissertations

G protein-coupled receptors (GPCRs) are seven-transmembrane domain receptors that sense extracellular signal and activate intracellular signaling pathways. The serotonin 5HT2A receptor (or 2AR) is one of the GPCRs coupled to Gq proteins, activating PLC and hydrolyzing PIP2. This hydrolysis causes a diffusion of bound PIP2 away from the channel binding site resulting in G protein-gated inwardly rectifying K⁺ channel (GIRK) inhibition and a downstream stimulation of Ca²⁺ release from endoplasmic reticulum stores. Previous experiments have demonstrated that the serotonin 5HTA receptor is a target of serotonergic psychedelic drugs, such as LSD, and partially mediates the action of many …

Comparisons Of Three Analytical Techniques For Measuring Absolute And Relative Temperature Changes During Ultrasound Treatment, Michael G. Miller

Dissertations

Ultrasound is a thermal modality that utilizes acoustic energy to promote heating. While there are many factors that affect heating of body tissues, the effects of skinfold thickness and skin temperature upon ultrasound heating have not been studied extensively. In addition, while temperature typically follows a linear trend, past research typically uses ANOVA or regression analysis to examine this relationship; but these models examine the within-subject effects (time) and between effects (usually groups) at the group level, not the individual level. Therefore, the purposes of this study are to determine if skin temperature and skinfold thickness are predictors for intramuscular …

Rna-Dependent Selenocysteine Biosynthesis In Eukaryotes And Archaea, Sotiria Palioura

Yale Medicine Thesis Digital Library

Selenocysteine (Sec), the 21st genetically encoded amino acid, is the major metabolite of the micronutrient selenium. Sec is inserted into nascent proteins in response to a UGA codon. The substrate for ribosomal protein synthesis is selenocysteinyl-tRNASec. While the formation of Sec-tRNASec from seryl-tRNASec by a single bacterial enzyme selenocysteine synthase (SelA) has been well described, the mechanism of Sec-tRNASec formation in archaea and eukaryotes remained poorly understood. Herein, biochemical and genetic data provide evidence that, in contrast to bacteria, eukaryotes and archaea utilize a different route to Sec-tRNASec that requires the tRNASec-dependent conversion of O-phosphoserine (Sep) to Sec. In this …

Photochemical Delivery Of Bleomycin In Malignant Glioma Cells, Joseph William Blickenstaff Iii

UNLV Theses, Dissertations, Professional Papers, and Capstones

Despite continued efforts, glioblastoma multiforme (GBM) remains an incurable form of primary brain cancer. Surgical resection followed by radiation treatment and chemotherapy have been the most effective modalities in prolonging median survival time to 14 months. This research aims to study the response of two different cell culture models to a novel drug delivery method termed photochemical internalization (PCI). PCI is a technique to improve the utilization of macromolecules (e.g. the chemotherapeutic drug bleomycin) in site-specific cancer therapy. This concept is based on the use of specially designed photosensitizers (e.g. aluminum phthalocyanine disulfonate; AlPcS _2a ) which preferentially localize in …

Effects Of Diabetes And Aging On Posture And Acceleration Thresholds During Lateral Translations, Samantha Jean Richerson

Doctoral Dissertations

Research objectives. One source of falls in the elderly may be an inability to sufficiently adjust to transient postural perturbations or slips. Identifying useful predictors of fall potential, as well as factors that affect the ability of an individual to detect a movement of the standing support surface may provide insight into postural stability and methods to increase stability in elders. To do this, acceleration thresholds to short, precise, lateral platform translations and the resultant psychophysical responses of adults with early Type 2 diabetes to age-matched controls and young adults were measured.

Methods. Using an innovative SLIP-FALLS platform, …

Nmr Studies Of Acyl Chain-Protein Interactions, Mark Christian Oswood

Yale Medicine Thesis Digital Library

An approach employing heteronuclear NMR is presented for monitoring the interactions between long-chain fatty acids and proteins which are involved in their synthesis and intracellular transport. Two naturally occurring fatty acids, hexadecanoic (palmitic) and cis-9-10-methylene-hexadecanoic (MHA) acids were labeled using a biosynthetic scheme with 13C acetate as a source. The biosynthetic incorporation of 13C from a two carbon source resulted in sequential pairs of 13C atoms in the product. When combined with double quantum spectroscopy, a highly efficient suppression of natural abundance background resonances results. Proton-detected two and three-dimensional experiments which correlate double quantum carbon chemical shifts with proton shifts …

Characterization Of The Vasoactivity Of Tachykinins In Isolated Rat Kidney: Functional Studies And In Vitro Receptor Autoradiography, Yuejin Chen

Electronic Theses and Dissertations

Although tachykinins have potent vascular actions, their effect on renal resistance blood vessels is currently unknown. The vasoactive properties of tachykinins and related analogs were assessed in isolated perfused rat kidney. At a basal perfusion pressure (PP) of 75 $\pm$ 6 mm Hg (n = 5), bolus injections of substance P (SP) had no significant vasoactive effect. Following a sustained increase in baseline PP (134 $\pm$ 10 mm Hg) produced by phenylephrine (1 $\mu$M), SP evoked a dose-dependent increase in PP. The largest dose of SP increased PP by 60 $\pm$ 5 mm Hg. The vasoconstrictor response to SP was …

Basement Membrane Polarizes Epithelial Cells And Its Loss Can Result In Neoplastic Disorganization, Donald Elliot Ingber

Yale Medicine Thesis Digital Library

The studies described in this dissertation demonstrate that basement membrane may be required for maintenance of organized epithelial tissue architecture. The structural organization of normal rat pancreatic acinar epithelium is fully characterized in order to analyze its neoplastic disorganization within a pancreatic acinar cell tumor. Transmission electron microscopy and indirect immunofluorescence microscopy of frozen semithin tissue sections are utilized to localize different components of the plasmalemma, cytoskeleton, basement membrane and connective tissue. Normal acinar cells sit on a continuous basement membrane and display a polarized distribution of intracellular organelles, cytoskeletal elements, and distinct membrane domains while these organized cell relations …

Neutron Diffraction Analysis Of The Structure Of Rod Photoreceptor Membranes In Intact Retinas, Mark Jay Yeager

Yale Medicine Thesis Digital Library

No abstract provided.

Limited Fragmentation Of Specifically Labeled Rhodopsins, Jordan S. Pober

Yale Medicine Thesis Digital Library

No abstract provided.