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Articles 1 - 14 of 14

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi Reynolds, Pamela Sheaff Dec 2009

Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charged-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.


Computational Prediction Of The Agregated Structure Of Denatured Lysozyme, Pongsathorn Chotikasemsri Dec 2009

Computational Prediction Of The Agregated Structure Of Denatured Lysozyme, Pongsathorn Chotikasemsri

Masters Theses & Specialist Projects

Mis-folded proteins and their associated aggregates are a contributing factor in some human diseases. In this study we used the protein lysozyme as a model to define aggregation structures under denaturing conditions. Sasahara et al. (2007), Frare et al. (2009, 2006), and Rubin et al. (2008) observed conditions where heat denatured lysozyme formed fibril structures that were observed to be 8-17 nanometers in diameter under the electron microscope. Even though the crystal structure of lysozyme is known, the denatured form of this protein is still unknown. Therefore, we used Rosetta++ protein folding and blind docking software to create in silico ...


Signal Transduction Cross Talk Mediated By Jun N-Terminal Kinase-Interacting Protein And Insulin Receptor Substrate Scaffold Protein Complexes, Claire L. Standen, Norman J. Kennedy, Richard A. Flavell, Roger J. Davis Jul 2009

Signal Transduction Cross Talk Mediated By Jun N-Terminal Kinase-Interacting Protein And Insulin Receptor Substrate Scaffold Protein Complexes, Claire L. Standen, Norman J. Kennedy, Richard A. Flavell, Roger J. Davis

Open Access Articles

Scaffold proteins have been established as important mediators of signal transduction specificity. The insulin receptor substrate (IRS) proteins represent a critical group of scaffold proteins that are required for signal transduction by the insulin receptor, including the activation of phosphatidylinositol 3 kinase. The c-Jun NH(2)-terminal kinase (JNK)-interacting proteins (JIPs) represent a different group of scaffold molecules that are implicated in the regulation of the JNK. These two signaling pathways are functionally linked because JNK can phosphorylate IRS1 on the negative regulatory site Ser-307. Here we demonstrate the physical association of these signaling pathways using a proteomic approach ...


Nuclear Localization Of P38 Mapk In Response To Dna Damage, C. David Wood, Tina Thornton, Guadalupe Sabio, Roger J. Davis, Mercedes Rincon Jun 2009

Nuclear Localization Of P38 Mapk In Response To Dna Damage, C. David Wood, Tina Thornton, Guadalupe Sabio, Roger J. Davis, Mercedes Rincon

Davis Lab Publications

p38 MAP kinase (MAPK) is activated in response to environmental stress, cytokines and DNA damage, and mediates death, cell differentiation and cell cycle checkpoints. The intracellular localization of p38 MAPK upon activation remains unclear, and may depend on the stimulus. We show here that activation of p38 MAPK by stimuli that induce DNA double strand breaks (DSBs), but not other stimuli, leads to its nuclear translocation. In addition, naturally occurring DSBs generated through V(D)J recombination in immature thymocytes also promote nuclear accumulation of p38 MAPK. Nuclear translocation of p38 MAPK does not require its catalytic activity, but is ...


Mcl-1 Integrates The Opposing Actions Of Signaling Pathways That Mediate Survival And Apoptosis, Caroline Morel, Scott M. Carlson, Forest M. White, Roger J. Davis May 2009

Mcl-1 Integrates The Opposing Actions Of Signaling Pathways That Mediate Survival And Apoptosis, Caroline Morel, Scott M. Carlson, Forest M. White, Roger J. Davis

Open Access Articles

Mcl-1 is a member of the Bcl2-related protein family that is a critical mediator of cell survival. Exposure of cells to stress causes inhibition of Mcl-1 mRNA translation and rapid destruction of Mcl-1 protein by proteasomal degradation mediated by a phosphodegron created by glycogen synthase kinase 3 (GSK3) phosphorylation of Mcl-1. Here we demonstrate that prior phosphorylation of Mcl-1 by the c-Jun N-terminal protein kinase (JNK) is essential for Mcl-1 phosphorylation by GSK3. Stress-induced Mcl-1 degradation therefore requires the coordinated activity of JNK and GSK3. Together, these data establish that Mcl-1 functions as a site of signal integration between the ...


Effects Of Estrogen On Muscle Damage In Response To An Acute Resistance Exercise Protocol, Megan R. Wolf May 2009

Effects Of Estrogen On Muscle Damage In Response To An Acute Resistance Exercise Protocol, Megan R. Wolf

Honors Scholar Theses

Creatine Kinase (CK) is used as a measure of exercise-induced muscle membrane damage. During acute eccentric (muscle lengthening) exercise, muscle sarcolemma, sarcoplasmic reticulum, and Z-lines are damaged, thus causing muscle proteins and enzymes to leak into the interstitial fluid.

Strenuous eccentric exercise produces an elevation of oxygen free radicals, which further increases muscle damage. Muscle soreness and fatigue can be attributed to this membrane damage. Estradiol, however, may preserve membrane stability post-exercise (Brancaccio, Maffulli, & Limongelli, 2007; Carter, Dobridge, & Hackney, 2001; Tiidus, 2001). Because estradiol has a similar structure to Vitamin E, which is known to have antioxidant properties, and both are known to affect ...


Basics Of Sleep Guide, Charles Amlaner, Patrick Fuller Apr 2009

Basics Of Sleep Guide, Charles Amlaner, Patrick Fuller

Charles J. Amlaner

No abstract provided.


Y27632, A Rho-Activated Kinase Inhibitor, Normalizes Dysregulation In Alpha1-Adrenergic Receptor-Induced Contraction Of Lyon Hypertensive Rat Artery Smooth Muscle., Maria Regina Freitas, Masumi Eto, Jason A Kirkbride, Christa Schott, Jean Sassard, Jean-Claude Stoclet Mar 2009

Y27632, A Rho-Activated Kinase Inhibitor, Normalizes Dysregulation In Alpha1-Adrenergic Receptor-Induced Contraction Of Lyon Hypertensive Rat Artery Smooth Muscle., Maria Regina Freitas, Masumi Eto, Jason A Kirkbride, Christa Schott, Jean Sassard, Jean-Claude Stoclet

Department of Molecular Physiology and Biophysics Faculty Papers

RhoA-activated kinase (ROK) is involved in the disorders of smooth muscle contraction found in hypertension model animals and patients. We examined whether the alpha1-adrenergic receptor agonist-induced ROK signal is perturbed in resistance small mesentery artery (SMA) of Lyon genetically hypertensive (LH) rats, using a ROK antagonist, Y27632. Smooth muscle strips of SMA and aorta were isolated from LH and Lyon normotensive (LN) rats. After Ca(2+)-depletion and pre-treatment with phenylephrine (PE), smooth muscle contraction was induced by serial additions of CaCl(2). In LH SMA Ca(2+) permeated cells to a lesser extent as compared with LN SMA, while ...


Western Corn Rootworm (Diabrotica Virgifera Virgifera Leconte) Population Dynamics, Lance J. Meinke, Thomas W. Sappington, David W. Onstad, Thomas Guillemaud, Nicholas J. Miller, Judit Komáromi, Nora Levay, Lorenzo Furlan, József Kiss, Ferenc Toth Feb 2009

Western Corn Rootworm (Diabrotica Virgifera Virgifera Leconte) Population Dynamics, Lance J. Meinke, Thomas W. Sappington, David W. Onstad, Thomas Guillemaud, Nicholas J. Miller, Judit Komáromi, Nora Levay, Lorenzo Furlan, József Kiss, Ferenc Toth

Entomology Publications

The western corn rootworm Diabrotica virgifera virgifera LeConte is a major insect pest of field maize, Zea mays L. Larvae can cause substantial injury by feeding on maize roots. Larval feeding may destroy individual roots or root nodes, and reduce plant growth, stability, and yield. Costs associated with managing corn rootworms in continuous maize are annually one of the largest expenditures for insect management in the United States Corn Belt. Even though D. virgifera virgifera has been studied intensively for over 50 years, there is renewed interest in the biology, ecology, and genetics of this species because of its ability ...


Further Progress On Lateral Flow Estimation Using Speckle Size Variation With Scan Direction, Tiantian Xu, Gregory R. Bashford Jan 2009

Further Progress On Lateral Flow Estimation Using Speckle Size Variation With Scan Direction, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional blood flow velocity measurement using ultrasound is capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these Doppler-based methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. In this paper, we report additional data on a new method recently introduced. This method estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to the blood reflectors (typically ...


Resolving The Lateral Component Of Blood Flow Velocity Based On Ultrasound Speckle Size Change With Scan Direction And Speed, Tiantian Xu, Greg R. Bashford Jan 2009

Resolving The Lateral Component Of Blood Flow Velocity Based On Ultrasound Speckle Size Change With Scan Direction And Speed, Tiantian Xu, Greg R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional blood flow velocity measurement using ultrasound is capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these Doppler-based methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. In this paper, we introduce a method which estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to the blood reflectors (typically red blood cells) stretches (i.e., is ...


Single Molecule Diffusion Coefficient Estimation By Image Analysis Of Simulated Ccd Images To Aid High-Throughput Screening, Pengfei Song, Lloyd M. Davis, Greg Bashford Jan 2009

Single Molecule Diffusion Coefficient Estimation By Image Analysis Of Simulated Ccd Images To Aid High-Throughput Screening, Pengfei Song, Lloyd M. Davis, Greg Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Extension of one-dimensional signal analysis to two-dimensional image analysis could accelerate conventional methods of high-throughput screening in the discovery of new pharmaceutical agents. This work describes a first step taken towards this goal – the evaluation of image-analysis based estimation strategies of the diffusion coefficient of a single molecule transported within a microfabricated flowcell. A computer simulation of single-molecule imaging by a charge-coupled device (CCD) camera is used to determine if it is possible to distinguish three different types of molecules with different diffusion coefficients. The Gaussian fitting algorithm finds the variance of the transverse trajectory, which increases linearly with the ...


Optimal Thresholds Of Feature Tracking For Blood Velocity And Tissue Motion Estimation, Tiantian Xu, Gregory R. Bashford Jan 2009

Optimal Thresholds Of Feature Tracking For Blood Velocity And Tissue Motion Estimation, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Feature tracking is an algorithm for estimating blood flow velocity and tissue motion using pulse-echo ultrasound. In contrast to cross-correlation speckle-tracking techniques, feature tracking identifies features at discrete locations and corresponds them from frame to frame. Prior studies have demonstrated that feature-tracking estimates exhibit lower variance than those obtained by the conventional autocorrelation method and require less computational complexity than either speckle tracking or autocorrelation. To date, not much attention has been paid to the process by which trackable features (normally local maxima) are selected from the set of all available features. In the selection process, it is desired to ...


The Evolution Of Sleep, Charles Amlaner, John Lesku, Niels Rattenborg Dec 2008

The Evolution Of Sleep, Charles Amlaner, John Lesku, Niels Rattenborg

Charles J. Amlaner

No abstract provided.