The Virginia SOL Eighth Grade Writing Test in Relationship to the National Commission on Writing Recommendations, Grade Configuration, Region, and Socioeconomic Status.

The purpose of this quantitative study was to examine Virginia Standards of Learning 8th grade writing assessments to determine if there was any association between school passing rates and the recommendations suggested by the 2003 National Commission on Writing to improve writing proficiency. This study further examined the possible differences in school passing rates that may exist due to the grade configuration of a school, the location of a school, the availability of a comprehensive writing plan, and the student percentage on free and reduced-price lunch. Data collection consisted of a self-administered survey sent to all 364 schools in Virginia that administered SOL writing assessments during the 2006-2007 school year./p\u3e This study showed no significant differences in 8th grade writing passing rates between schools with a comprehensive writing plan and those that do not. However, there was a significant difference in 8th grade teacher support for writing, division-administrative support for writing, and the understanding of writing scoring criteria in those schools with a comprehensive plan. There was little association between SOL writing scores and the implementation level of the 7 dimensions related to the National Commission on Writing recommendations. When controlling for socioeconomic status, there was no significant difference in writing scores. The addition of 4 multiple-choice questions to the SOL test two years ago without a change in the cut score necessary for a student to pass appears to have had a larger impact on the passing rates of schools than the variables included in this study

Subdiffusion in Membrane Permeation of Small Molecules

Citation: Chipot, C. and Comer, J. Subdiffusion in Membrane Permeation of Small Molecules. Sci. Rep. 6, 35913; doi: 10.1038/srep35913 (2016).Within the solubility–diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t0.7, in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids

Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives

Citation: Poblete, H., Miranda-Carvajal, I., & Comer, J. (2017). Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives. The Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.7b01130Understanding the interaction of carbon nanomaterials with proteins is essential for determining the potential effects of these materials on health and in the design of biotechnology based on them. Here we leverage explicit-solvent molecular simulation and multidimensional free-energy calculations to investigate how adsorption to carbon nanomaterial surfaces affects the conformational equilibrium of alanine dipeptide, a widely used model of protein backbone structure. We find that the two most favorable structures of alanine dipeptide on graphene (or large carbon nanotubes) correspond to the two amide linkages lying in the same plane, flat against the surface, rather than the nonplanar ?-helix-like and ?-sheet-like conformations that predominate in aqueous solution. On graphenic surfaces, the latter conformations are metastable and most often correspond to amide?? stacking of the N-terminal amide. The calculations highlight the key role of amide?? interactions in determining the conformational equilibrium. Lesser but significant contributions from hydrogen bonding to the high density interfacial water layer or to the hydroxy groups of hydroxylated graphene also define the most favorable conformations. This work should yield insight on the influence of carbon nanotubes, graphene, and their functionalized derivatives on protein structure

IUPUI Center for Health Geographics

poster abstractThe IUPUI Center for Health Geographics develops and supports research innovation through integration of geographic information science, medical informatics, community informatics, and public health. Our areas of research emphasis include geospatial technologies and standards for health surveillance, spatial and temporal contexts of health behaviors and health outcomes, and space-time models for investigating disease and mortality trends. Our poster highlights our collaborations, which include interdisciplinary partnerships with investigators in the fields of geographic information science, social science, clinical epidemiology, medical informatics, and health services research

Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation

Citation: Comer, J., Chen, R., Poblete, H., Vergara-Jaque, A., & Riviere, J. E. (2015). Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation. ACS Nano, 9(12), 11761–11774. https://doi.org/10.1021/acsnano.5b03592Computational techniques have the potential to accelerate the design and optimization of nanomaterials for applications such as drug delivery and contaminant removal; however, the success of such techniques requires reliable models of nanomaterial surfaces as well as accurate descriptions of their interactions with relevant solutes. In the present work, we evaluate the ability of selected models of naked and hydroxylated carbon nanotubes to predict adsorption equilibrium constants for about 30 small aromatic compounds with a variety of functional groups. The equilibrium constants determined using molecular dynamics coupled with free-energy calculation techniques are directly compared to those derived from experimental measurements. The calculations are highly predictive of the relative adsorption affinities of the compounds, with excellent correlation (r ? 0.9) between calculated and measured values of the logarithm of the adsorption equilibrium constant. Moreover, the agreement in absolute terms is also reasonable, with average errors of less than one decade. We also explore possible effects of surface loading, although we demonstrate that they are negligible for the experimental conditions considered. Given the degree of reliability demonstrated, we move on to employing the in silico techniques in the design of nanomaterials, using the optimization of adsorption affinity for the herbacide atrazine as an example. Our simulations suggest that, compared to other modifications of graphenic carbon, polyvinylpyrrolidone conjugation gives the highest affinity for atrazine—substantially greater than that of graphenic carbon alone—and may be useful as a nanomaterial for delivery or sequestration of atrazine

Self-Assembly of Amphiphilic Dendrimers: The Role of Generation and Alkyl Chain Length in siRNA Interaction

Citation: Marquez-Miranda, V., Araya-Duran, I., Camarada, M. B., Comer, J., Valencia-Gallegos, J. A., & Gonzalez-Nilo, F. D. (2016). Self-Assembly of Amphiphilic Dendrimers: The Role of Generation and Alkyl Chain Length in siRNA Interaction. Scientific Reports, 6, 15. https://doi.org/10.1038/srep29436An ideal nucleic-acid transfection system should combine the physical and chemical characteristics of cationic lipids and linear polymers to decrease cytotoxicity and uptake limitations. Previous research described new types of carriers termed amphiphilic dendrimers (ADs), which are based on polyamidoamine dendrimers (PAMAM). These ADs display the cell membrane affinity advantage of lipids and preserve the high affinity for DNA possessed by cationic dendrimers. These lipid/dendrimer hybrids consist of a low-generation, hydrophilic dendron (G2, G1, or G0) bonded to a hydrophobic tail. The G2-18C AD was reported to be an efficient siRNA vector with significant gene silencing. However, shorter tail ADs (G2-15C and G2-13C) and lower generation (G0 and G1) dendrimers failed as transfection carriers. To date, the self-assembly phenomenon of this class of amphiphilic dendrimers has not been molecularly explored using molecular simulation methods. To gain insight into these systems, the present study used coarse-grained molecular dynamics simulations to describe how ADs are able to self-assemble into an aggregate, and, specifically, how tail length and generation play a key role in this event. Finally, explanations are given for the better efficiency of G2/18-C as gene carrier in terms of binding of siRNA. This knowledge could be relevant for the design of novel, safer ADs with well-optimized affinity for siRNA

Comparative Functional Dynamics Studies on the Enzyme Nano-bio Interface

Citation: Thomas, S. E., Comer, J., Kim, M. J., Marroquin, S., Murthy, V., Ramani, M., … DeLong, R. K. (2018, August 8). Comparative functional dynamics studies on the enzyme nano-bio interface. https://doi.org/10.2147/IJN.S152222Comparative functional dynamics studies on the enzyme nano-bio interface Spencer E Thomas,1,2,* Jeffrey Comer,1,* Min Jung Kim,1 Shanna Marroquin,1 Vaibhav Murthy,1 Meghana Ramani,1 Tabetha Gaile Hopke,2 Jayden McCall,1 Seong-O Choi,1 Robert K DeLong1 1Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; 2Department of Biomedical Science, Missouri State University, Springfield, MO, USA *These authors contributed equally to this work Introduction: Biomedical applications of nanoparticles (NPs) as enzyme inhibitors have recently come to light. Oxides of metals native to the physiological environment (eg, Fe, Zn, Mg, etc.) are of particular interest—especially the functional consequences of their enzyme interaction. Materials and methods: Here, Fe2O3, zinc oxide (ZnO), magnesium oxide (MgO) and nickel oxide (NiO) NPs are compared to copper (Cu) and boron carbide (B4C) NPs. The functional impact of NP interaction to the model enzyme luciferase is determined by 2-dimensional fluorescence difference spectroscopy (2-D FDS) and 2-dimensional photoluminescence difference spectroscopy (2-D PLDS). By 2-D FDS analysis, the change in maximal intensity and in 2-D FDS area under the curve (AUC) is in the order Cu~B4C>ZnO>NiO>>Fe2O3>MgO. The induced changes in protein conformation are confirmed by tryptic digests and gel electrophoresis. Results: Analysis of possible trypsin cleavage sites suggest that cleavage mostly occurs in the range of residues 112–155 and 372–439, giving a major 45 kDa band. By 2-D PLDS, it is found that B4C NPs completely ablate bioluminescence, while Cu and Fe2O3 NPs yield a unique bimodal negative decay rate, -7.67×103 and -3.50×101 relative light units respectively. Cu NPs, in particular, give a remarkable 271% change in enzyme activity. Molecular dynamics simulations in water predicted that the surfaces of metal oxide NPs become capped with metal hydroxide groups under physiological conditions, while the surface of B4C becomes populated with boronic acid or borinic acid groups. These predictions are supported by the experimentally determined zeta potential. Thin layer chromatography patterns further support this conception of the NP surfaces, where stabilizing interactions were in the order ionic>polar>non-polar for the series tested. Conclusion: Overall the results suggest that B4C and Cu NP functional dynamics on enzyme biochemistry are unique and should be examined further for potential ramifications on other model, physiological or disease-relevant enzymes. Keywords: 2-dimensional fluorescence difference, 2-D FDS, AUC, corrected light intensity emitted, emission wavelength, excitation wavelength, wavelength of max intensity, RL

Spatial Integration of Community Data with Clinical Data in Support of Community Health Research and Practice

poster abstractThis poster will describe the recent integration of one of the nation’s largest health information exchanges, the Indiana Network for Patient Care developed by the Regenstrief Institute, with one of the nation’s most comprehensive community information system, the SAVI CIS developed by The Polis Center at IUPUI. Integrating community data that quantifies the social and physical environment with clinical data has great potential for supporting and advancing community health research and practice. Multi-sector collaboration on the development and evaluation of associated uses cases informed system integration is allowing spatially-aware research and practice to be more quickly realized

Hoosiers’ Health in a Changing Climate: A Report from the Indiana Climate Change Impacts Assessment

In the coming decades, Indiana’s changing climate will bring with it higher temperatures, longer heat waves, more extremely hot days and more frequent extreme storm events. Those changes will affect the health of Hoosiers in every part of the state. This report from the Indiana Climate Change Impacts Assessment (IN CCIA) describes historical and future climate-related health impacts that affect Hoosiers