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Dive into the research topics where Brent D. Foy is active.

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Featured researches published by Brent D. Foy.


FEMS Microbiology Ecology | 2011

OPTIMIZING THE ANALYSIS OF HUMAN INTESTINAL MICROBIOTA WITH PHYLOGENETIC MICROARRAY

Laura Rigsbee; Richard Agans; Brent D. Foy; Oleg Paliy

Phylogenetic microarrays present an attractive strategy to high-throughput interrogation of complex microbial communities. In this work, we present several approaches to optimize the analysis of intestinal microbiota with the recently developed Microbiota Array. First, we determined how 16S rDNA-specific PCR amplification influenced bacterial detection and the consistency of measured abundance values. Bacterial detection improved with an increase in the number of PCR amplification cycles, but 25 cycles were sufficient to achieve the maximum possible detection. A PCR-caused deviation in the measured abundance values was also observed. We also developed two mathematical algorithms that aimed to account for a predicted cross-hybridization of 16S rDNA fragments among different species, and to adjust the measured hybridization signal based on the number of 16S rRNA gene copies per species genome. The 16S rRNA gene copy adjustment indicated that the presence of members of the class Clostridia might be overestimated in some 16S rDNA-based studies. Finally, we show that the examination of total community RNA with phylogenetic microarray can provide estimates of the relative metabolic activity of individual community members. Complementary profiling of genomic DNA and total RNA isolated from the same sample presents an opportunity to assess population structure and activity in the same microbial community.


Bioinformatics | 2004

Tailored gene array databases: applications in mechanistic toxicology

Tatiana V. Karpinets; Brent D. Foy; John M. Frazier

MOTIVATION The development of an annotated global database suitable for a wide range of investigations is a challenging and labor-intensive task. Thus, the development of databases tailored for specific applications remains necessary. For example, in the field of toxicology, no annotated gene array databases are now available that may assist in the correlation of changes in gene activity to cellular functions and processes associated with the toxic response. RESULTS As an example of a tailored annotated database, an attempt was made to systematize available biological information on genes present on the Affymetrix Rat Toxicology U34 GeneChip, with a focus on how the gene products relate to liver cells and their response to chemical toxins. The information collected was imbedded in a local relational database to analyze data obtained in toxicological gene array experiments with hydrazine-exposed hepatocytes. The advantages and benefits of the tailored database in the biological interpretation of the results are demonstrated.


BMC Systems Biology | 2009

Stochastic simulation and analysis of biomolecular reaction networks.

John M. Frazier; Yaroslav Chushak; Brent D. Foy

BackgroundIn 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 recieved much attention. In order to investigate these issues, we employed a 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.ResultsSpecific 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.ConclusionThe 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.


Current Opinion in Biotechnology | 1995

Nuclear magnetic resonance analysis of cell metabolism.

Craig Zupke; Brent D. Foy

Nuclear magnetic resonance (NMR) continues to be a useful tool for the study of cellular metabolism. A variety of NMR techniques have been developed or newly applied to the analysis of cell systems. Many of these techniques are particularly useful for the analysis of immobilized cell bioreactors. The use of several NMR techniques has been an integral part of recent comprehensive metabolic studies. Novel computer-based models and methods have been developed which may make NMR study of metabolism more accessible and powerful.


Physics in Medicine and Biology | 2009

Local complex permittivity measurements of porcine skin tissue in the frequency range from 1 GHz to 15 GHz by evanescent microscopy

Richard A. Kleismit; Gregory Kozlowski; Brent D. Foy; Barbara E. Hull; Marian K. Kazimierczuk

The near-field evanescent microwave microscope is based on a coaxial transmission line resonator with a silver plated tungsten tip protruding through an end-wall aperture. The sensor is used to measure the local dielectric properties of porcine skin in the frequency range from 1 GHz to 15 GHz. The dielectric property of the skin within the near field of the tip frustrates the electric field and measurably changes the transmission lines resonant frequency and quality factor (Q). The shift of the resonators frequency and Q is measured as a function of tip-sample separation, and a quantitative relationship between the real and imaginary parts of the local dielectric constant using the method of images is established. The associated changes in quality factor image scans of subsurface tissue structure and dielectric properties of skin surface lesions are presented.


Bioinformatics | 2011

Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays

Oleg Paliy; Brent D. Foy

MOTIVATION Many current studies of complex microbial communities rely on the isolation of community genomic DNA, amplification of 16S ribosomal RNA genes (rDNA) and subsequent examination of community structure through interrogation of the amplified 16S rDNA pool by high-throughput sequencing, phylogenetic microarrays or quantitative PCR. RESULTS Here we describe the development of a mathematical model aimed to simulate multitemplate amplification of 16S ribosomal DNA sample and subsequent detection of these amplified 16S rDNA species by phylogenetic microarray. Using parameters estimated from the experimental results obtained in the analysis of intestinal microbial communities with Microbiota Array, we show that both species detection and the accuracy of species abundance estimates depended heavily on the number of PCR cycles used to amplify 16S rDNA. Both parameters initially improved with each additional PCR cycle and reached optimum between 15 and 20 cycles of amplification. The use of more than 20 cycles of PCR amplification and/or more than 50 ng of starting genomic DNA template was, however, detrimental to both the fraction of detected community members and the accuracy of abundance estimates. Overall, the outcomes of the model simulations matched well available experimental data. Our simulations also showed that species detection and the accuracy of abundance measurements correlated positively with the higher sample-wide PCR amplification rate, lower template-to-template PCR bias and lower number of species in the interrogated community. The developed model can be easily modified to simulate other multitemplate DNA mixtures as well as other microarray designs and PCR amplification protocols.


ieee international conference on high performance computing data and analytics | 2007

Stochastic Simulations of Cellular Biological Processes

Yaroslav Chushak; Brent D. Foy; John M. Frazier

At the functional level, all biological processes in cells can be represented as a series of biochemical reactions that are stochastic in nature. We have developed a software package called biomolecular network simulator (BNS) that uses a stochastic approach to model and simulate complex biomolecular reaction networks. Two simulation algorithms-the exact Gillespie stochastic simulation algorithm and the approximate adaptive tau-leaping algorithm-are implemented for generating Monte Carlo trajectories that describe the evolution of a system of biochemical reactions. The software uses a combination of MATLAB and C-coded functions and is parallelized with the message passing interface (MPT) library to run on multiprocessor architectures.


Toxicology Mechanisms and Methods | 2003

Incorporation of Protein-Binding Kinetics and Carrier-Mediated Membrane Transport into a Model of Chemical Kinetics in the Isolated Perfused Rat Liver

Brent D. Foy; John M. Frazier

Nonlinear processes present difficult problems in extrapolating toxicological kinetics from one dose or species to another. A model that includes the details of these processes will aid in identifying those conditions under which a linear extrapolation is not valid. Previously, a kinetic model of the perfused rat liver system was presented that included the effects of equilibrium protein binding, diffusion-based and saturable membrane transport, metabolism, and biliary excretion. This model has been extended here to account for two complex processes. First, the kinetics of chemical association and dissociation from binding sites in various compartments are explicitly included to allow for the possibility that the binding of the compound is not in equilibrium. Second, mediated transport via a simple four-state carrier in the membrane has been included at both the sinusoidal and biliary membranes of the liver cell. This enables inclusion of carrier-specific transport processes (such as selective transport against a concentration gradient) in modeling the kinetics in perfused rat liver experiments. Simulations demonstrating the effects of each of these processes on observable state variables have been conducted. Physiological conditions that elicit nonlinear behavior have been identified.


Biochimica et Biophysica Acta | 2002

Kinetic analyses of liver phosphatidylcholine and phosphatidylethanolamine biosynthesis using 13C NMR spectroscopy

Nicholas V. Reo; Mehdi Adinehzadeh; Brent D. Foy


Carcinogenesis | 2005

Tumorigenesis: the adaptation of mammalian cells to sustained stress environment by epigenetic alterations and succeeding matched mutations

Tatiana V. Karpinets; Brent D. Foy

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Oleg Paliy

Wright State University

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Joseph Blake

Wright State University

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