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Laser-Assisted Single-Molecule Refolding, Rui Zhao 2011 Wayne State University

Laser-Assisted Single-Molecule Refolding, Rui Zhao

Wayne State University Dissertations

Non-coding RNAs must fold into precise secondary and tertiary structures in order to perform the biological functions. Due to the flexibility of RNA, the RNA folding energy landscape can be rugged and full of local minimum (kinetic trap). To provide a means to study kinetically trapped RNAs, we have developed a new technique combining single-molecule FRET detection with laser induced temperature jump. We have calibrated the magnitude of the temperature jump with 1˚C accuracy using gold micro-size sensor. The accuracy of temperature calibration was confirmed by close agreement between single-molecule and bulk DNA duplex melting experiments.

HIV 1 DIS RNAs …


Exciton Broadening In Polyaniline Chains During Ion Induced Hydrophobic Collapse And Aggregation, Louis R. Nemzer, Arthur Epstein 2011 Nova Southeastern University

Exciton Broadening In Polyaniline Chains During Ion Induced Hydrophobic Collapse And Aggregation, Louis R. Nemzer, Arthur Epstein

Louis R Nemzer

The ion-induced reprecipitation of the emeraldine base form of polyaniline from an aqueous-organic binary solution is a facile method for obtaining polymer nanoparticles and microscale clusters. The hydrophobic collapse and aggregation that accompanies the addition of various cosolutes induces changes in the peak wavelength and linewidth of the main exciton absorption. In particular, we find that the addition of ionic cosoutes leads to a redshifting and broadening of this spectroscopic feature, with divalent coions exhibiting an additional hypsochromic reversal at high concentrations. The denaturant urea, in contrast, causes a blueshift and line-narrowing at all concentrations. Using a quantitative Lorentz fit, …


Inhibition Of Calcium Oxalate Calculi By Ndga - A Spectroscopic Study, Preethi Dacha 2011 University of Texas at El Paso

Inhibition Of Calcium Oxalate Calculi By Ndga - A Spectroscopic Study, Preethi Dacha

Open Access Theses & Dissertations

Formation of calculi in urinary tract leads to kidney stones. This process is known as Urolithiasis. Some of the causes of urolithiasis are metabolic disorders, genetic factors, and anatomic abnormalities in the urinary system. Nowadays, urolithiasis is very common disease in population of all over the world. The present study strives to understand calcium oxalate calculi formation as well as its inhibition by using Nordihydroguaiaretic acid (NDGA), which is a chemical extract of the Larrea Tridentata bush, a plant that is traditionally employed in the El paso region as a natural treatment for kidney stones and bladder diseases. Thus, in …


A Cell Electrofusion Microfluidic Device Integrated With 3d Thin-Film Microelectrode Arrays, Ning Hu, Jun Yang, Shizhi Qian, Sang W. Joo, Xiaolin Zheng 2011 Old Dominion University

A Cell Electrofusion Microfluidic Device Integrated With 3d Thin-Film Microelectrode Arrays, Ning Hu, Jun Yang, Shizhi Qian, Sang W. Joo, Xiaolin Zheng

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device integrated with 3D thin film microelectrode arrays wrapped around serpentine-shaped microchannel walls has been designed, fabricated and tested for cell electrofusion. Each microelectrode array has 1015 discrete microelectrodes patterned on each side wall, and the adjacent microelectrodes are separated by coplanar dielectric channel wall. The device was tested to electrofuse K562 cells under a relatively low voltage. Under an AC electric field applied between the pair of the microelectrode arrays, cells are paired at the edge of each discrete microelectrode due to the induced positive dielectrophoresis. Subsequently, electric pulse signals are sequentially applied between the microelectrode arrays …


Physical Models Of Amyloid Fibril Assembly, Shannon Elizabeth Hill 2011 University of South Florida

Physical Models Of Amyloid Fibril Assembly, Shannon Elizabeth Hill

USF Tampa Graduate Theses and Dissertations

Formation of large fibers and plaques by amyloid proteins is recognized as the molecular hallmark of an increasing number of human disorders, including Parkinson's disease, Alzheimer's disease and even type II diabetes. The broader objective of my research is to unravel the basic mechanisms that initiate and regulate fibril formation by amyloidogenic proteins. This objective is significant because even basic aspects of how fibril formation proceeds from a soluble, monomeric protein to an insoluble amyloid fibril remain much debated. Furthermore, there is increasingly strong evidence suggesting that intermediates of the aggregation process, with properties distinct from those of mature fibrils, …


Probing Molecules In Confined Space, Carissa Marie Vetromile 2011 University of South Florida

Probing Molecules In Confined Space, Carissa Marie Vetromile

USF Tampa Graduate Theses and Dissertations

Despite the plethora of information regarding cellular crowding and its importance on modulating protein function the effects of confinement on biological molecules are often overlooked when investigating their physiological function. Recently however, the encapsulation of biomolecules in solid state matrices (NafionTM, sol-gels, zirconium phosphate,etc.) has increased in importance as a method for examining protein conformation and dynamics in confined space as well as novel applications in biotechnology. Biotechnological applications include, but are not limited to, bioremediation, biosensors, biocatalysts, etc. In order to better utilize solid state materials as substrates for biological molecules an understanding of the effects of encapsulation on …


A Study Of Complex Systems: From Magnetic To Biological, Douglas Carroll Lovelady 2011 University of South Florida

A Study Of Complex Systems: From Magnetic To Biological, Douglas Carroll Lovelady

USF Tampa Graduate Theses and Dissertations

This work is a study of complex many-body systems with non-trivial interactions. Many such systems can be described with models that are much simpler than the real thing but which can still give good insight into the behavior of realistic systems. We take a look at two such systems. The first part looks at a model that elucidates the variety of magnetic phases observed in rare-earth heterostructures at low temperatures: the six-state clock model. We use an ANNNI-like model Hamiltonian that has a three dimensional parameter space and yields two-dimensional multiphase regions in this space. A low-temperature expansion of the …


Homologous And Heterologous Crystallin Protein Interactions As The Molecular Basis Of Inherited Cataract, Priya Ranjan Banerjee 2011 University at Albany, State University of New York

Homologous And Heterologous Crystallin Protein Interactions As The Molecular Basis Of Inherited Cataract, Priya Ranjan Banerjee

Legacy Theses & Dissertations (2009 - 2024)

Age-related cataract is the most common cause of blindness worldwide. Nearly fifty percent of Americans above the age of 75 are diagnosed with this disease (http://www.nei.nih.gov/eyedata/pbd_tables.asp), and surgical intervention is the sole method of treatment at present (http://www.nei.nih.gov/healthyvision/objective/cataracts.asp). In the developing world, even this treatment is not readily available. These are compelling reasons to search for better treatments to delay, prevent or arrest cataract formation. Recent evidence suggests that age-related cataracts also have a genetic component. Therefore, determining the mechanisms underlying genetic cataracts with a known association to a protein-mutation is one important strategy towards understanding the molecular basis for …


Conformation And Ion Transport Of Neuronal Uncoupling Proteins: Ucp2, Ucp4, And Ucp5, Tuan Hoang 2011 Wilfrid Laurier University

Conformation And Ion Transport Of Neuronal Uncoupling Proteins: Ucp2, Ucp4, And Ucp5, Tuan Hoang

Theses and Dissertations (Comprehensive)

Located in the inner mitochondrial membrane of brown adipose tissue, uncoupling protein -1 (UCP1) dissipates the proton electrochemical gradient, causing reduction in the rate of ATP synthesis, and generates heat by non-shivering thermogenesis. Three other UCP homologs (UCP2, UCP4 and UCP5), expressed in neurons, are suggested to have potential roles in the function and protection of the central nervous system (CNS). Up to date, structural information for UCPs still remains limited. Extensive biochemical studies on UCP2 have provided adequate evidence for its participation in proton and anion transport. So far, no functional studies in proteoliposome systems have been performed on …


Mechanisms Of Decreased Cholesterol Absorption Mediated By Phytosterols In The Intestinal Lumen, Andrew W. Brown 2011 University of Nebraska-Lincoln

Mechanisms Of Decreased Cholesterol Absorption Mediated By Phytosterols In The Intestinal Lumen, Andrew W. Brown

Department of Nutrition and Health Sciences: Dissertations, Theses, and Student Research

Phytosterols and their fatty acyl esters have been known for decades to lower LDL cholesterol, making them powerful nutraceuticals in lowering cardiovascular disease risk. The mechanisms by which phytosterols lower cholesterol, though, have been incompletely characterized. Three studies were executed to examine three aspects of cholesterol and phytosterol interactions in the intestinal lumen. In the first study, the ability of pancreatic cholesterol esterase to hydrolyze phytosterol esters was examined. Pancreatic cholesterol esterase hydrolyzed phytosterol esters, but the rate of hydrolysis proved sensitive to the structures of both the sterol and ester components. In the second study, cholesterol micellarization was challenged …


A Microfluidic Device For Impedance Spectroscopy, Ahmet Can Sabuncu 2011 Old Dominion University

A Microfluidic Device For Impedance Spectroscopy, Ahmet Can Sabuncu

Mechanical & Aerospace Engineering Theses & Dissertations

Recently, microfluidics has become a versatile tool to investigate cellular biology and to build novel biomedical devices. Dielectric spectroscopy, on the other hand, allows non-invasive probing of biological cells. Information on the cell membrane, cytoplasm, and nucleus can be obtained by dielectric spectroscopy provided that appropriate tools are used in specific frequency ranges. This dissertation includes fabrication, characterization, and testing of a simple microfluidic device to measure cell dielectric properties. The dielectric measurements are performed on human T-cell leukemia (Jurkat), mouse melanoma (B16), mouse hepatoma (Hepa), and human costal chondrocyte cells. Dielectric measurements consist of measuring the complex impedance of …


Tryptophan Anchored Peptides In Lipid Bilayer Membranes: Control Of Peptide Orientation And The Phase Behavior Of Cholesterol-Containing Ternary Lipid Mixtures, Johanna Maria Rankenberg 2010 University of Arkansas

Tryptophan Anchored Peptides In Lipid Bilayer Membranes: Control Of Peptide Orientation And The Phase Behavior Of Cholesterol-Containing Ternary Lipid Mixtures, Johanna Maria Rankenberg

Graduate Theses and Dissertations

Model WALP peptides and "next generation" WALP-derived hydrophobic model peptides were employed to discover principles that govern protein-lipid interactions in biological membranes.

Ternary cholesterol-containing lipid mixtures were examined in the presence of WALP peptides of different lengths (acetyl-GWW(LA)nLWWA-ethanolamide, with n between 3 and 8). Deuterium NMR spectra from labeled lipids reveal that WALP peptides may stabilize lipid ordered "raft" domains and therefore promote lipid phase separation, albeit to a minor extent. The results depend upon whether dioleolyl- or diphytanoyl-phosphatidylcholine is present as the fluid lipid component.

Several WALP peptides were modified to remove anchoring Trp residues from one …


Systematic Approach To Electrostatically Induced 2d Crystallization Of Nanoparticles At Liquid Interfaces, Sumit Kewalramani, Suntao Wang, Yuan Lin, Huong Giang Nguyen, Qian Wang, Masafumi Fukuto, Lin Yang 2010 Brookhaven National Laboratory, Upton, NY

Systematic Approach To Electrostatically Induced 2d Crystallization Of Nanoparticles At Liquid Interfaces, Sumit Kewalramani, Suntao Wang, Yuan Lin, Huong Giang Nguyen, Qian Wang, Masafumi Fukuto, Lin Yang

Faculty Publications

We report an experimental demonstration of a strategy for inducing two-dimensional (2D)crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situX-ray scattering measurements at the liquid–vapor interface. Theassembly was studied as a function of the solution …


Negative Dielectrophoretic Capture Of Bacterial Spores In Food Matrices, Mehti Koklu, Seungkyung Park, Suresh D. Pillai, Ali Beskok 2010 Old Dominion University

Negative Dielectrophoretic Capture Of Bacterial Spores In Food Matrices, Mehti Koklu, Seungkyung Park, Suresh D. Pillai, Ali Beskok

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device with planar square electrodes is developed for capturing particles from high conductivity media using negative dielectrophoresis (n-DEP). Specifically, Bacillus subtilis and Clostridium sporogenes spores, and polystyrene particles are tested in NaCl solution (0.05 and 0.225 S/m), apple juice (0.225 S/m), and milk (0.525 S/m). Depending on the conductivity of the medium, the Joule heating produces electrothermal flow (ETF), which continuously circulates and transports the particles to the DEP capture sites. Combination of the ETF and n-DEP results in different particle capture efficiencies as a function of the conductivity. Utilizing 20 μm height DEP chambers, “almost complete” and …


Experimental Investigation Of A Non-Thermal Atmospheric Pressure Plasma Jet, Asma Begum 2010 Old Dominion University

Experimental Investigation Of A Non-Thermal Atmospheric Pressure Plasma Jet, Asma Begum

Electrical & Computer Engineering Theses & Dissertations

The main objective of this dissertation is to understand the formation of the plasma jet from the plasma pencil, and the propagation of the plasma jet in the ambient atmosphere where the effect of the external electric field is almost zero. Before investigating the formation and propagation phenomenon of the plasma jet, common physical properties of plasma jets are determined by using the imaging technique and optical emission spectroscopy. The first goal of this dissertation is to establish the laminar helium gas flow channel through a plasma pencil.

The formation position, formation time, and the criterion of the plasma jet …


Is The Curvature Of The Flagellum Involved In The Apparent Cooperativity Of The Dynein Arms Along The "9+2" Axoneme?, Christian Cibert, Andrei Ludu 2010 Université Paris 6

Is The Curvature Of The Flagellum Involved In The Apparent Cooperativity Of The Dynein Arms Along The "9+2" Axoneme?, Christian Cibert, Andrei Ludu

Andrei Ludu

In a recent study [Cibert, 2008. Journal of Theoretical Biology, 253, 74-89], by assuming that the walls of microtubules are involved in cyclic compression/dilation equilibriums as a consequence of their cyclic curvature of the axoneme, it was proposed that local adjustments of spatial frequencies of both dynein arms and beta-tubulin monomers facing series create propagation of joint probability waves of interaction (JPI) between these two necessary partners. Modeling the occurrence of these interactions along the entire length of an axoneme between each outer doublet pair (without programming any cooperative dialog between the molecular complexes) and the cyclic attachment of two …


Dynamics Of The Toc Gtpases: Modulation By Nucleotides And Transit Peptides Reveal A Mechanism For Chloroplast Protein Import, Lovett Evan Reddick 2010 University of Tennessee - Knoxville

Dynamics Of The Toc Gtpases: Modulation By Nucleotides And Transit Peptides Reveal A Mechanism For Chloroplast Protein Import, Lovett Evan Reddick

Doctoral Dissertations

The chloroplast is the green organelle in the plant cell responsible for harvesting energy from sunlight and converting it into sugars and ATP. Origins of this organelle can be traced back to an endosymbiotic event in which a primitive eukaryotic cell capable of oxidative phosphorylation engulfed a free-living cyanobacterium capable of photosynthetic respiration (1). Immediately following this event the details are not clear, however what is known is that over the course of evolution, the engulfed cyanobacteria relinquished approximately 97% of its protein coding sequences to the host cell nucleus, thus making the newly formed chloroplast reliant on its host …


Coupling Into Waveguide Evanescent Modes With Applications In Electron Paramagnetic Resonance, Jason Walter Sidabras 2010 Marquette University

Coupling Into Waveguide Evanescent Modes With Applications In Electron Paramagnetic Resonance, Jason Walter Sidabras

Master's Theses (2009 -)

The use of analytical and numerical techniques in solving the coupling of evanescent modes in a microwave waveguide through slots can be optimized to create a uniform magnetic field excitation on axis within a waveguide. This work has direct applications in Electron Paramagnetic Resonance (EPR) where a 100~kHz time-varying magnetic field is incident on a sample contained in a microwave cavity. Typical cavity designs do not take into consideration the uniformity of the 100~kHz field modulation and assume it to be uniform enough over the sample region from quasi-static principles. This work shows otherwise and uses Ansoft (Pittsburgh, PA) High …


Conformational Change And Topological Stability Of Proteins, Jeffrey Andrew Tibbitt 2010 Old Dominion University

Conformational Change And Topological Stability Of Proteins, Jeffrey Andrew Tibbitt

Chemistry & Biochemistry Theses & Dissertations

The conformation and topology of a protein changes when stabilizing forces are absent, but the mechanisms by which these changes occur remains elusive. This dissertation aims to broaden the understandings. On the conformational level, the M20 loop conformers of E. coli dihydrofolate reductase are interrogated to identify factors responsible for their stability as well as to determine how one conformer might change into another. Molecular dynamics is used to simulate the open, closed and occluded conformers (observed in X-ray crystal structures) under a series of different single ligand conditions. Analysis shows that all open conformers move to a similar new …


A Comparison Of Three Computer-Based Methods Used To Determine Emg Signal Amplitude, Doug Renshaw 2010 University of Texas of the Permian Basin

A Comparison Of Three Computer-Based Methods Used To Determine Emg Signal Amplitude, Doug Renshaw

Doug Renshaw

No abstract provided.


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