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In recent years, several stochastic simulation algorithms have been developed to generate Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks. However, the effects of various stochastic simulation and data analysis conditions on the observed dynamics of complex biomolecular reaction networks have not received much attention. In order to investigate these issues, we employed a software package developed in out group, called Biomolecular Network Simulator (BNS), to simulate and analyze the behavior of such systems. The behavior of a hypothetical two gene in vitro transcription-translation reaction network is investigated using the Gillespie exact stochastic algorithm to illustrate some of the factors that influence the analysis and interpretation of these data. Results: Specific issues affecting the analysis and interpretation of simulation data are investigated including: (1) the effect of time interval on data presentation and time-weighted averaging of molecule numbers, (2) effect of time averaging interval on reaction rate analysis, (3) effect of number of simulations on precision of model predictions, and (4) implications of stochastic simulations on optimization procedures. Conclusion: The two main factors affecting the analysis of stochastic simulations are: (1) the selection of time intervals to compute or average state variables and (2) the number of simulations generated to evaluate the system behavior., Published in BMC Systems Biology, v3:64, 2009. Prepared in collaboration with Telemedicine and Advanced Technology Research Center, U. S. Army Medical Research and Materiel Command, Fort Detrick, MD. Sponsored in part by AFOSR.

The purpose of this effort was to utilize cadmium, a known toxicant of environmental and occupational concern, to develop an understanding of the relationships between chemical kinetics (rates of chemical movement into the body) and cellular dynamics (cellular response to chemical entering the cells) in order to predict early target organ toxicity and refine/validate a biologically-based kinetic model. This effort involved three studies. The first measured cadmium kinetics over 24 hours in male Fischer 344 rats dosed intravenously with 0.0, 0.5, 1.0, 2.0 or 3.0 mg/kg Cd. Serum liver enzymes and histology were also monitored to determine the extent of hepatic damage. The second evaluated metallothionein (MT) mRNA regulation in these rats in response to the Cd toxicity. MT isoforms I and II were found to be separately regulated. In the third, male F344 rat hepatocytes were isolated and exposed to Cd in vitro at doses of 0 microM, 5 microM, 10 microM and 15 microM. MT mRNA expression in these hepatocytes was not similar to the in vivo response.

In the last few decades, scientists have learned how to manipulate the basic components of life, how to design biomolecular networks, how to evolve biomolecules with unique characteristics and how to direct and control cellular processes at the molecular level. Using this knowledge as a foundation, it is theoretically possible to conceive of designing biological constructs, which we refer to as cell-like entities (CLEs), that use custom engineered biological machinery to accomplish specified tasks. The practical challenge is: Can we fabricate biological constructs for specific purposes using the same principles and components found in natural biological systems? For example, can CLEs be designed to detect very low levels of specific chemicals and fluoresce to indicate their presence; can they be designed to synthesize functional chemicals on demand, or can they use engineered metabolic pathways to detoxify environmental pollutants? The building of CLEs that could accomplish these goals would result in fundamental breakthroughs in exploiting our understanding of cellular control systems and biochemical information processing. The concept of the CLE is based on understanding how the biochemical reactions network that we call a living cell functions, how is it controlled and what are the key processes and components that will provide unique functions when integrated. The goal is not to create a living organism, but to create a biological construct that utilizes the essence of living systems to provide a wide array of solutions to current technological and medical challenges., Prepared in cooperation with Wright State Univ. and URES, Inc., Dayton, OH.

Cell biology studies involving genomics, proteomics and metabolomics technologies generate large quantities of data. Unfortunately, today's research environment is encumbered by inefficient access to this vital data. Information searches are hampered by disparities on both technical and conceptual levels between individual data sources. The current trend is for data sources to exist as a series of isolated computational silos, providing a depth of data in a narrow field of research. The Acero Genomics Knowledge Platform (GKP) is an enterprise solution that offers fully integrated data-representation across diverse scientific data types and sources. The DataCap data collection module (a part of the Air Force Genomics, Proteomics, Bioinformatics System (AFGPB) application is one module of a series of modules that operate on top of the Acero Platform. The purpose of the DataCap is to provide the individual researcher with the ability to collect experimental data in an integrated format compatible with the Acero GKP. This technical report covers the architecture, the design and the operation of the DataCap in its Phase I configuration., Prepared in collaboration with Air Force Research Lab (AFRL), Human Effectiveness Directorate, Wright-Patterson AFB, OH.

This report documents a comparative study on the performance of five commercially available programs that perform a total of eight different computational methods for the estimation of the logarithm of the octanol-water partition coefficient (log P). The choice of the programs for employment was based on cost and the need for a comparison of the fragment-based and nonfragment-based methodologies. A database of 150 compounds, for which the log P value is accurately known, has been accumulated and the bank of programs utilized to give eight estimated values for the log P of each compound. Each of the eight sets of 150 data points has been evaluated on the basis of the square of the correlation coefficient, and the slope and intercept of the linear best-fit line as calculated by Microsoft? Excel 97 when the data is plotted against the corresponding experimental values. This report compares the performance of the eight different computational methods, with respect to specific structural characteristics, based on the above graphical parameters. This study also found that the accuracy and precision of each of the methods is dependent on the hydrophobicity and structural classification of the compound(s) under scrutiny.

New chemicals developed for the use by the Air Force must undergo evaluation to determine if these chemicals will be detrimental to the health of Air Force personnel. Chemical safety assessment is a costly and time consuming process. This report is a description of recommended procedures for toxicity testing of new chemicals. A strategy for the progressive and logical development of toxicology data that are needed for health hazard characterization, and ultimately for risk assessment is presented. The overall cost and time requirements of the proposed testing strategy are provided. The relationship between the amount of toxicity testing conducted and the level of confidence in the toxicity classification of new chemical is emphasized., Prepared in cooperation with Toxicology/Regulatory Services, Inc., Charlottesville, VA.

The interaction of exogenous chemicals (xenobiotics) with endogenous biomolecules can modulate the kinetics of that chemical in biological systems. The purpose of this report is to provide a fundamental understanding of the underlying mathematical and experimental principles involved in describing these interactions. The theoretical basis of the interaction of xenobiotics with binding sites located on endogenous molecules are discussed in the context of the following scenarios: (i) interaction between a single chemical and a single class of binding sites, (il) interaction between a single chemical and multiple classes of binding sites, (iii) interactions between multiple chemicals and a single class of binding sites. Each of these situations is analyzed in the context of the reaction mechanisms involved and the mathematical description of those reactions. Experimental approaches to evaluating the basic mechanisms of binding and estimation of binding parameters using titration experiments and inhibition experiments are described. Practical instructions are provided for the conduct and interpretation of these experiments. The relationship between theoretical considerations and practical experimental consequences are highlighted.

The objective of this report is to describe a generic biologically-based kinetic (BBK) model to simulate the kinetics of water soluble - lipid insoluble chemicals (log Po/w < 0) in the isolated perfused rat liver (IPRL) system. Such a model should have sufficient flexibility to allow for the inclusion of various physiological and biochemical processes into the description of the kinetics of chemicals that fall into this physical-chemical category. The following kinetic processes are incorporated into this model: (1) transport across cellular membranes, both at the sinusoidal-hepatocyte interface and the hepatocyte-biliary canalicular interface, (2) protein binding, both in perfusion medium and intracellular compartments of the liver, and (3) metabolism of the chemical in liver. The initial modeling efforts resulted in the development of a robust BBK model, named BBKM-IPRLR, that allows for the investigation of the effects of these kinetic process on the behavior of water soluble chemicals in the IPRL system. The generic model is used to demonstrate the effect of various kinetic processes on the observable state variables. Interactions between various kinetic processes are also demonstrated.

The overall objective of this research program is to develop new approaches to predict the systemic toxicokinetics of chemicals utilizing in vitro experimental model systems and biologically-based kinetic (BBK) models. The focus of the proposed research is to test the hypothesis that in vitro measurements of membrane transport parameters in hepatic membrane vesicles are predictive of hepatic transport in vivo. Although this study is focused on transport processes in one particular organ, i.e. hepatic transport processes, these processes are a major controlling factor in determining systemic kinetics of many chemicals, particularly those which do not satisfy the 'perfusion limited' condition usually assumed in many current PBPK models.