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Peng Y.,University of Southern Mississippi | Maxwell A.S.,University of Southern Mississippi | Barker N.D.,Badger Technical Services LLC | Laird J.G.,U.S. Army | And 4 more authors.
BMC Bioinformatics | Year: 2014

Background: While next-generation sequencing (NGS) technologies are rapidly advancing, an area that lags behind is the development of efficient and user-friendly tools for preliminary analysis of massive NGS data. As an effort to fill this gap to keep up with the fast pace of technological advancement and to accelerate data-to-results turnaround, we developed a novel software package named SeqAssist ("Sequencing Assistant" or SA). Results: SeqAssist takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data. It consists of three separate workflows: (1) the SA_RunStats workflow generates basic statistics about an NGS dataset, including numbers of raw, cleaned, redundant and unique reads, redundancy rate, and a list of unique sequences with length and read count; (2) the SA_Run2Ref workflow estimates the breadth, depth and evenness of genome-wide coverage of the NGS dataset at a nucleotide resolution; and (3) the SA_Run2Run workflow compares two NGS datasets to determine the redundancy (overlapping rate) between the two NGS runs. Statistics produced by SeqAssist or derived from SeqAssist output files are designed to inform the user: whether, what percentage, how many times and how evenly a genomic locus (i.e., gene, scaffold, chromosome or genome) is covered by sequencing reads, how redundant the sequencing reads are in a single run or between two runs. These statistics can guide the user in evaluating the quality of a DNA library prepared for RNA-Seq or genome (re-)sequencing and in deciding the number of sequencing runs required for the library. We have tested SeqAssist using a synthetic dataset and demonstrated its main features using multiple NGS datasets generated from genome re-sequencing experiments. Conclusions: SeqAssist is a useful and informative tool that can serve as a valuable "assistant" to a broad range of investigators who conduct genome re-sequencing, RNA-Seq, or de novo genome sequencing and assembly experiments. © 2014 Peng et al.; licensee BioMed Central Ltd.

Scott A.M.,U.S. Army | Gorb L.,Badger Technical Services LLC | Burns E.A.,Badger Technical Services LLC | Yashkin S.N.,Samara State Technical University | And 2 more authors.
Journal of Physical Chemistry C | Year: 2014

The adsorption of high nitrogen compounds (HNCs) on the selected adsorption sites of carbonaceous materials from the gas phase has been investigated by ab initio quantum chemical methods at the density functional level applying both periodic and cluster approaches with M06-2X and BLYP functionals including dispersion forces (BLYP-D2). Among the possible structures of the adsorption complexes, the most stable systems possess nitrogen-containing heterocycles in a parallel orientation toward the modeled carbon surface. The adsorption enthalpies, calculated using the rigid rotor-harmonic oscillator approach (RRHO), were in good agreement with available experimental data. This approach was shown to provide sufficiently accurate adsorption enthalpies from the gas phase for the HNC-carbon systems. The vibrational, rotational, and translation contributions to the adsorption entropy were also analyzed by the approach extended beyond the RRHO scheme. The effects of anharmonic vibrations and internal rotations of the adsorbate on the adsorption sites of the modeled carbon surface were estimated. The Gibbs free energies calculated using the RRHO approach were adjusted to take into account the heterogeneity of the carbon surfaces and underestimation of the adsorption enthalpies at the BLYP-D2(PBC) level. The corrected Gibbs free energy values of adsorption are negative for all of the investigated HNC-carbon systems, and they agree well with available experimental data. This suggests an effective adsorption of selected high nitrogen compounds on carbonaceous materials from the gas phase at 298.15 K. Partition coefficients for distribution of high nitrogen compounds on modeled carbon surfaces were also predicted in good agreement with the experimental results. © 2014 American Chemical Society.

Scott A.M.,U.S. Army | Burns E.A.,Badger Technical Services LLC | Hill F.C.,U.S. Army
Journal of Molecular Modeling | Year: 2014

The adsorption of nitrogen-containing compounds (NCCs) including 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 3-nitro-1,2,4-triazol-5-one (NTO) on kaolinite surfaces was investigated. The M06-2X and M06-2X-D3 density functionals were applied with the cluster approximation. Several different positions of NCCs relative to the adsorption sites of kaolinite were examined, including NCCs in perpendicular and parallel orientation toward both surface models of kaolinite. The binding between the target molecules and kaolinite surfaces was analyzed and bond energies were calculated applying the atoms in molecules (AIM) method. All NCCs were found to prefer a parallel orientation toward both kaolinite surfaces, and were bound more strongly to the octahedral than to the tetrahedral site. TNT exhibited the strongest interaction with the octahedral surface and DNAN with the tetrahedral surface of kaolinite. Hydrogen bonding was shown to be the dominant non-covalent interaction for NCCs interacting with the octahedral surface of kaolinite with a small stabilizing effect of dispersion interactions. In the case of adsorption on the tetrahedral surface, kaolonite-NCC binding was shown to be governed by the balance between hydrogen bonds and dispersion forces. The presence of water as a solvent leads to a significant decrease in the adsorption strength for all studied NCCs interacting with both kaolinite surfaces. © Springer-Verlag 2014.

Tsendra O.,Jackson State University | Tsendra O.,Ukrainian Academy of Sciences | Scott A.M.,U.S. Army | Gorb L.,Badger Technical Services LLC | And 6 more authors.
Journal of Physical Chemistry C | Year: 2014

A cluster approach extended to the ONIOM methodology has been applied using several density functionals and Møller-Plesset perturbation theory (MP2) to simulate the adsorption of selected nitrogen-containing compounds [NCCs, 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 3-nitro-1,2,4-triazole-5-one (NTO)] on the hydroxyated (100) surface of α-quartz. The structural properties were calculated using the M06-2X functional and 6-31G(d,p) basis set. The M06-2X-D3, PBE-D3, and MP2 methods were used to calculate the adsorption energies. Results have been compared with the data from other studies of adsorption of compounds of similar nature on silica. Effect of deformation of the silica surface and adsorbates on the binding energy values was also studied. The atoms in molecules (AIM) analysis was employed to characterize the adsorbate-adsorbent binding and to calculate the bond energies. The silica surface shows different sorption affinity toward the chemicals considered depending on their electronic structure. All target NCCs are physisorbed on the modeled silica surface. Adsorption occurs due to the formation of multiple hydrogen bonds between the functional groups of NCCs and surface silanol groups. Parallel orientation of NCCs interacting with the silica surface was found to be favorable when compared with perpendicularly oriented NCCs. NTO was found to be the most strongly adsorbed on the silica surface among all of the considered compounds. Dispersion correction was shown to play an important role in the DFT calculations of the adsorption energies of silica-NCC systems. © 2014 American Chemical Society.

Golius A.,Jackson State University | Gorb L.,Badger Technical Services LLC | Michalkova Scott A.,U.S. Army | Hill F.C.,U.S. Army | Leszczynski J.,Jackson State University
Structural Chemistry | Year: 2015

This study focuses on elucidating the stable forms of a new energetic material that is a member of the class of insensitive munitions (IM), 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO), including its tautomers, and anions. The geometry and properties of all compounds were calculated using density functional theory (M06-2X) and MP2 quantum chemical approaches. Calculations were carried out in the gas phase and in aqueous solution. Chemical stability of these compounds was evaluated in terms of the Gibbs free energy change. Two different solvation models were applied (CPCM and PCM). Calculations showed that overall differences in the results obtained using these two solvation models are negligible for all compounds considered. All possible NTO tautomers were examined and the results are in good agreement with previous studies performed in the gas phase. The stability order was revealed to be slightly dependent on the method applied. In order to estimate acidic properties of NTO, anions of several NTO tautomers were analyzed. In addition, pK a values were calculated using different approaches. As compared with available experimental data it was found that the conductor-like screening model for real solvents approach leads to more accurate estimation of the pK a value than the CPCM and PCM approaches. The pK a value calculated using PCM and CPCM data showed large errors; however, it was proven that the pattern of deprotonation energy was correctly estimated. © 2015 Springer Science+Business Media New York.

Hill F.C.,U.S. Army | Sviatenko L.K.,Jackson State University | Sviatenko L.K.,Kirovohrad State Pedagogical University | Gorb L.,Badger Technical Services LLC | And 5 more authors.
Chemosphere | Year: 2012

The nitroaromatic compounds 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT) and 2,4-dinitroanisole (DNAN) are potential environmental contaminants and their transformations under a variety of environmental conditions are consequently of great interest. One possible method to safely degrade these nitrocompounds is alkaline hydrolysis. A mechanism of the initial stages of this reaction was investigated computationally. Simulations of UV-VIS and NMR spectra for this mechanism were also produced. The results obtained were compared to available experimental data on the alkaline hydrolysis of TNT and suggest that the formation of Meisenheimer complexes and an anion of TNT are potential first-step intermediates in the reaction path. As the reaction proceeds, computational results indicate that polynegative complexes dominate the degradation pathway, followed by cycles of carbon chain opening and breaking. A second possible pathway was identified that leads to polymeric products through Janovsky complex formation. Results from this study indicate that the order of increasing resistance to alkaline hydrolysis is TNT, DNT and DNAN. © 2012 Elsevier Ltd.

Omelchenko I.V.,Ukrainian Academy of Sciences | Shishkin O.V.,Ukrainian Academy of Sciences | Shishkin O.V.,University of Kharkiv | Gorb L.,Badger Technical Services LLC | And 3 more authors.
Structural Chemistry | Year: 2012

Geometrical parameters, aromaticity, and conformational flexibility of the set of polysubstituted benzenes with different number and position of nitro and amino groups were calculated at the MP2/cc-pvdz level of theory. The key factor for structural and energetic changes has been identified. This is related to the presence of nitro and amino groups in vicinal positions that forms strong intramolecular resonance-assisted hydrogen bonds with a binding energy of 7-14 kcal/mol. Increasing number of such bonds facilitates a cooperative effect, inducing notable changes in molecular geometry (particularly increasing bond alternation within H 2N-C-C-NO 2 fragment and planarization of amino group), drastic increasing of conformational flexibility and decreasing of aromaticity. In spite of well-known π-electron effects of nitro and amino substituents, influence of their push-pull interaction through aromatic moiety is negligible compared to the effect of the hydrogen bonding. That results in great difference of the ortho-isomers as compared to meta-and para-isomers. © 2012 Springer Science+Business Media, LLC.

Sviatenko L.K.,Jackson State University | Sviatenko L.K.,Kirovohrad Volodymyr Vynnychenko State Pedagogical University | Gorb L.,Badger Technical Services Inc. | Hill F.C.,U.S. Army | Leszczynski J.,Jackson State University
Journal of Computational Chemistry | Year: 2013

A number of density functionals was utilized to predict gas-phase adiabatic ionization potentials (IPs) for nitrogen-rich heterocyclic compounds. Various solvation models were applied to the calculation of difference in free energies of solvation of oxidized and reduced forms of heterocyclic compounds in acetonitrile (AN) for correct reproduction of their standard oxidation potentials. We developed generally applicable protocols that could successfully predict the gas-phase adiabatic ionization potentials of nitrogen-rich heterocyclic compounds and their standard oxidation potentials in AN. This approach is supported by a MPW1K/6-31+G(d) level of theory which uses SMD(UA0) approximation for estimation of solvation energy of neutral molecules and PCM(UA0) model for ionized ones. The mean absolute derivation (MAD) and root mean square error (RMSE) of the current theoretical models for IP are equal to 0.22 V and 0.26, respectively, and for oxidation potentials MAD = 0.13 V and RMSE = 0.17. © 2013 Wiley Periodicals, Inc.

Yang Y.,University of Southern Mississippi | Maxwell A.,University of Southern Mississippi | Zhang X.,Nanjing University | Wang N.,University of Southern Mississippi | And 3 more authors.
BMC Bioinformatics | Year: 2013

Background: Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of action. From a risk assessment perspective, alterations in biological pathways are a rich resource for setting toxicant thresholds, which may be more sensitive and mechanism-informed than traditional toxicity endpoints. Here we developed a novel differential networks (DNs) approach to connect pathway perturbation with toxicity threshold setting. Methods: Our DNs approach consists of 6 steps: time-series gene expression data collection, identification of altered genes, gene interaction network reconstruction, differential edge inference, mapping of genes with differential edges to pathways, and establishment of causal relationships between chemical concentration and perturbed pathways. A one-sample Gaussian process model and a linear regression model were used to identify genes that exhibited significant profile changes across an entire time course and between treatments, respectively. Interaction networks of differentially expressed (DE) genes were reconstructed for different treatments using a state space model and then compared to infer differential edges/interactions. DE genes possessing differential edges were mapped to biological pathways in databases such as KEGG pathways. Results: Using the DNs approach, we analyzed a time-series Escherichia coli live cell gene expression dataset consisting of 4 treatments (control, 10, 100, 1000 mg/L naphthenic acids, NAs) and 18 time points. Through comparison of reconstructed networks and construction of differential networks, 80 genes were identified as DE genes with a significant number of differential edges, and 22 KEGG pathways were altered in a concentration-dependent manner. Some of these pathways were perturbed to a degree as high as 70% even at the lowest exposure concentration, implying a high sensitivity of our DNs approach. Conclusions: Findings from this proof-of-concept study suggest that our approach has a great potential in providing a novel and sensitive tool for threshold setting in chemical risk assessment. In future work, we plan to analyze more time-series datasets with a full spectrum of concentrations and sufficient replications per treatment. The pathway alteration-derived thresholds will also be compared with those derived from apical endpoints such as cell growth rate. © 2013 Yang et al; licensee BioMed Central Ltd.

Michalkova A.,Jackson State University | Gorb L.,Badger Technical Services LLC | Hill F.,U.S. Army | Leszczynski J.,Jackson State University | Leszczynski J.,U.S. Army
Journal of Physical Chemistry A | Year: 2011

This study presents new insight into the prediction of partitioning of organic compounds between a carbon surface (soot) and water, and it also sheds light on the sluggish desorption of interacting molecules from activated and nonactivated carbon surfaces. This paper provides details about the structure and interactions of benzene, polycyclic aromatic hydrocarbons, and aromatic nitrocompounds with a carbon surface modeled by coronene using a density functional theory approach along with the M05-2X functional. The adsorption was studied in vacuum and from water solution. The molecules studied are physisorbed on the carbon surface. While the intermolecular interactions of benzene and hydrocarbons are governed by dispersion forces, nitrocompounds are adsorbed also due to quite strong electrostatic interactions with all types of carbon surfaces. On the basis of these results, we conclude that the method of prediction presented in this study allows one to approach the experimental level of accuracy in predicting thermodynamic parameters of adsorption on a carbon surface from the gas phase. The empirical modification of the polarized continuum model leads also to a quantitative agreement with the experimental data for the Gibbs free energy values of the adsorption from water solution. © 2011 American Chemical Society.

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