Rice: Unconventional Wisdom
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Metabolic Engineering and Synthetic & Systems Biology Laboratory

Yandi Dharmadi


Yandi DharmadiEducation

B.S., Chemical Engineering, Iowa State University, 1999
M.S., Chemical Engineering, Iowa State University, 2002
Ph.D., Chemical Engineering, Rice University, 2006 (expected)

Project Description

The main objective of the project is to study the fundamental cellular response of E. coli in the presence of multiple sugars as carbon sources, as part of the larger goal of utilizing bacteria as biocatalysts to produce valuable bio-based products from plant biomass. We are currently evaluating sugar consumption and cell growth characteristics of several E. coli catabolite repression mutants. Further insights gained through the use of oligonucleotide microarrays in monitoring gene expression profiles will be essential for uncovering the underlying cellular mechanisms of sugar utilization.  

In a microarray experiment, a labeled cDNA fragment will hybridize to its complementary oligonucleotide sequence on the array. We are using molecular dynamics simulation at the mesoscopic level to study the hybridization process, and non-specific hybridization in particular. Oligonucleotides for microarrays are currently designed through bioinformatics search to identify the most unique sequence in the genome. The molecular simulations approach can potentially be useful as validation tool for design purposes.  

We routinely use HPLC to monitor extracellular components of cell cultures during growth. In a chromatogram, peak resolution is essential to be able to quantify the individual components. In order to achieve the best peak resolution, we have developed a computer program to identify the optimum operating conditions, based on an empirical retention model obtained using statistical experimental design. We also invented a better global chromatographic resolution function and a novel, more robust optimum search algorithm for the optimization program. More information about the program.


Recent Publications

Dharmadi, Y., and Gonzalez, R. (2004). Computer-assisted optimization of HPLC separation for simultaneous quantification of substrates and products in E. coli fermentations. In preparation for J. Microbiol. Methods .

Dharmadi, Y., and Gonzalez, R. (2004). A better global resolution function and a novel iterative stochastic search method for optimization of HPLC separation. J. Chromatogr. A . (Under Revision).

Gonzalez, R. and Dharmadi. Y. (2004). DNA microarrays: experimental Issues, data Analysis, and application to bacterial systems. Biotechnol. Prog. 20 (5): 1309-1324.

Dharmadi, Y., Q. Chang, and C.E. Glatz. (2003). Recovery of enzyme byproducts from potential plant hosts for recombinant protein production. Enzyme Microb. Technol., 33 , 596-605.


Contact Information

C124 Abercombie
Rice University
Houston, TX, 77005
Phone 713-348-2933
yandi@rice.edu