Thermodynamic Modeling of Fluorescence In Situ Hybridization (FISH) for Environmental Applications
| Category | Publications |
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| Abstract | Fluorescence in situ hybridization (FISH) and microarray hybridization are two powerful methods for qualitative and quantitative analyses of microbial ecology in environmental samples. In general, both techniques rely on efficient but specific binding of DNA oligonucleotides (probes) to ribosomal RNA (rRNA) of target organisms. Probe design approaches in the past involved trial and error based experimental testing of sensitivity and specificity, and unsuccessful empirical characterization of presumed factors such as target accessibility. With the current and previous NSF grants, we have been developing and evaluating mathematical models of FISH for predicting the extent of probe/rRNA hybridizations. Based on the thermodynamics of nucleic acid interactions taking place during hybridizations, the models have helped us to successfully find out key factors in probe sensitivity and specificity. In theory, the same thermodynamic principles can be applied to microarray hybridizations, although necessity for some adjustments in modeling scheme and incorporation of additional parameters/variables is anticipated. In this IREE study, we collaborated with one of the pioneering groups in the application of microarrays for microbial ecological analyses, as an initial step towards modifying and using FISH models for the prediction of probe sensitivity and specificity in microarray hybridizations. For the most part, we learned the practice of environmental microarray techniques from our collaborators, and optimized experimental setup to reduce uncertainty, which was necessary for testing key variables related to models and underlying assumptions. Useful exchange of practical and theoretical knowledge helped in the determination of potential factors to be included during model modification, which is underway based on the experimental data produced. In addition, we established a connection to link our prospective website for FISH probe design, whose construction is a side task in our current NSF grant, to the well-known and widely used probe base website of our collaborators. |
| Contributor | Mourad Ouzzani
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| Bio | L. Safak Yilmaz received BS and MS in Civil Engineering from Bogazici University (Istanbul, Turkey) in 1998 and 2000. He did his Ph. D with Daniel R. Noguera in the Civil and Environmental Engineering department at University of Wisconsin Madison. His Ph. D. work involved the mechanistic models of Fluorescence In Situ Hybridization. After receiving his Ph.D. degree in 2006, he has held a postdoctoral appointment in the same lab. Daniel R. Noguera received the B.S. and M.S. degrees in Civil Engineering from the Universidad de Los Andes (Bogota, Colombia) in 1987 and 1989. He continued his graduate education at the University of Illinois at Urbana-Champaign, earning M.S. and Ph.D. degrees in Environmental Engineeering in 1991 and 1996, respectively. Following an 18 month postdoctoral appointment at Northwestern University, he joined the faculty in the Civil and Environmental Engineering Department at the University of Wisconsin - Madison as an Assistant Professor in 1997. More recently, he was promoted to Full Professor in 2005. His research program is in the general area of environmental biotechnology, with emphasis on biological aspects of water supply, wastewater treatment, and bioenergy production. |
| Sponsored By | NSF BES-0302618 |
| Cite this work | Researchers should cite this work as follows: L. Safak Yilmaz and Daniel R. Noguera, "Thermodynamic Modeling of Fluorescence In Situ Hybridization (FISH) for Environmental Applications", Trip report presented at the NSF IREE 2007 Grantees Conference, October 30 - November 1, 2007, Purdue University, West Lafayette, Indiana |
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