Biochemistry, Biophysics, and Structural Biology Commons^™

Mutations Of Adjacent Amino Acid Pairs Are Not Always Independent, Jyotsna Ramanan, Peter Revesz

CSE Conference and Workshop Papers

Evolutionary studies usually assume that the genetic mutations are independent of each other. This paper tests the independence hypothesis for genetic mutations with regard to protein coding regions. According to the new experimental results the independence assumption generally holds, but there are certain exceptions. In particular, the coding regions that represent two adjacent amino acids seem to change in ways that sometimes deviate significantly from the expected theoretical probability under the independence assumption.

Ionic Driven Embedment Of Hyaluronic Acid Coated Liposomes In Polyelectrolyte Multilayer Films For Local Therapeutic Delivery, Stephen L. Hayward, David M. Francis, Matthew J. Sis, Srivatsan Kidambi

Papers in Biomolecular Engineering

The ability to control the spatial distribution and temporal release of a therapeutic remains a central challenge for biomedical research. Here, we report the development and optimization of a novel substrate mediated therapeutic delivery system comprising of hyaluronic acid covalently functionalized liposomes (HALNPs) embedded into polyelectrolyte multilayer (PEM) platform via ionic stabilization. The PEM platform was constructed from sequential deposition of Poly-LLysine (PLL) and Poly(Sodium styrene sulfonate) (SPS) “(PLL/SPS)_4.5” followed by adsorption of anionic HALNPs. An adsorption affinity assay and saturation curve illustrated the preferential HALNP deposition density for precise therapeutic loading. (PLL/SPS)_2.5 capping layer on top …

A Multilaboratory Comparison Of Calibration Accuracy And The Performance Of External References In Analytical Ultracentrifugation, Huaying Zhao, Rodolfo Ghirlando, Carlos Alfonso, Fumio Arisaka, Ilan Attali, David L. Bain, Et Al. ..., Donald F. Becker, Peter Schuck

Department of Biochemistry: Faculty Publications

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy …

Investigations Into The Molecular Mechanisms Of Bacterial Pathogen-Host Interactions: Construction Of A Dual Plasmid System For Incorporation Of Unnatural Amino Acids Into Pseudomonas Syringae Pv. Tomato Dc3000, Scotty D. Raber

Department of Chemistry: Dissertations, Theses, and Student Research

A dual plasmid system for the incorporation of unnatural amino acids into plant pathogen, Pseudomonas syringae pv. tomato DC3000, has been designed. This invention is expected to allow (a) mutations of proteins synthesized by the bacterium, P. syringae pv. tomato DC3000, that can capture molecular targets, especially for such modified proteins secreted by the phytopathogen into the host plant cells of A. thaliana and S. lycopersicum, (b) expression of biological probes in the bacterial species to monitor changes in redox, nutritional, and other small molecule states over pre-, post- and in situ disease stages, and (c) secretion of such …

Effects Of Refuges On The Evolution Of Resistance To Transgenic Corn By The Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Jennifer Deitloff, Mike W. Dunbar, David A. Ingber, Bruce E. Hibbard, Aaron J. Gassmann

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

BACKGROUND: Diabrotica virgifera virgifera LeConte is a major pest of corn and causes over a billion dollars of economic loss annually through yield reductions and management costs. Corn producing toxins derived from Bacillus thuringiensis (Bt) has been developed to help manageD. v. virgifera.However, previous studies have demonstrated the ability of this species to evolve resistance to Bt toxins in both laboratory and field settings.

RESULTS: We used an experimental evolution approach to test the refuge strategies for delaying resistance of D. v. virgifera to corn producing Bt toxin Cry34/35Ab1. In the absence of refuges, D. v. virgifera developed resistance to …

Clique Topology Reveals Intrinsic Geometric Structure In Neural Correlations, Chad Giusti, Eva Pastalkova, Carina Curto, Vladimir Itskov

Department of Mathematics: Faculty Publications

Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonlinear monotone transformations. These features can be used to detect both random and geometric structure, and depend only on the relative ordering of matrix entries. We then analyzed the activity of pyramidal neurons in rat hippocampus, recorded while the animal was exploring a 2D environment, and confirmed that our method is able to detect geometric organization using …

Elasticity Of Differentiated And Undifferentiated Human Neuroblastoma Cells Characterized By Atomic Force Microscopy, Shijia Zhao, Alexander B. Stamm, Jeong Soon Lee, Alexei Gruverman, Jung Yul Lim, Linxia Gu

Department of Mechanical and Materials Engineering: Faculty Publications

Human neuroblastoma (SH-SY5Y) cells, with its ability to differentiate into neurons, have been widely used as the in vitro cell culture model for neuroscience research, especially in studying the pathogenesis of Parkinson’s disease (PD) and developing therapeutic strategies. Cellular elasticity could potentially serve as a biomarker to quantitatively distinguish undifferentiated and differentiated SH-SY5Y cells. The goal of this work is to characterize the retinoic acid (RA) induced alternations of elastic properties of SH-SY5Y cells using atomic force microscopy (AFM). The elasticity was measured at multiple points of a single cell. Results have shown that the differentiation of SH-SY5Y cell led …