Graduate Students
Longyun Guo
As the knowledge of detailed biochemical mechanisms grows, along with the fast development of high-throughput technologies which enable the quantification of metabolites, proteins and transcripts, it is now possible to integrate different sets of data using a systems biology approach to mechanistically understand a biological system. A mathematical model is a quantitative way to hypothesize a potential set of mechanisms to interpret the experimental observations. And once the model is proposed and validated, systematical aspects of the bio-network can be inferred, which is not easily measurable with experiments. Lignin biosynthesis in Arabidopsis is a perfect model system as each enzymatic step is well characterized, and lignin content is always an engineering target since its negative effect towards saccharification. A kinetic model of lignin biosynthesis will contribute to deeper understanding of underlying regulatory mechanisms, and help to provide a rational design for lignin biosynthesis manipulation.

My research is focused in the following areas:
  • Constructing a kinetic model of lignin biosynthesis in Arabidopsis to help understand the dynamic structure of the pathway.
  • Integrate RNA-seq data into the kinetic model to derive potential hierarchical regulations controlling the monolignol composition.
Shaunak (Rick) Ray
The phenylpropanoid pathway plays a major role in the biosynthesis of lignin and numerous secondary metabolites imperative to plant survival and vitality. Lignin biosynthesis, however, impedes the production of biofuel from lignocellulosic biomass. 2-phenylethanol is a highly used fragrance chemical that is naturally synthesized from the aromatic amino acid, L-phenylalanine which also serves as the primary substrate for lignin biosynthesis. It serves as an interesting concept of metabolic engineering of plants to be able to modulate the phenylpropanoid pathway in a way that lignin biosynthesis is reduced and 2-phenylethanol biosynthesis is increased allowing for higher yields of both biofuel and commodity chemicals. The use of kinetic modeling of the enzymatic reactions of the pathway serve as the basis for the prediction of fluxes and building a deeper understanding of the pathway control mechanisms.

My research is focused in the following areas:
  • Using analytical techniques based on chromatography and mass spectrometry for the detection of key metabolites in the biosynthesis of 2-phenylethanol
  • Generating a kinetic model using estimated parameters based on experimental data obtained from [13C6]-phenylalanine labeling studies in Arabidopsis
Nathaphon (Joel) Yu King Hing
The Calvin cycle, which is responsible for the fixation of carbon dioxide from the atmosphere, is an essential metabolic process common to all photosynthetic organisms. A kinetic model of the Calvin cycle can further improve our understanding of regulatory processes that occur within the cycle, help identify targets for metabolic engineering, and be used to optimize the rate of growth of photosynthetic organisms. Dynamic changes in Calvin cycle behavior caused by changes in light availability could be integrated into the kinetic model to predict steady states in a variety of light conditions.

My research is focused in the following areas:
  • Developing a kinetic model for the Calvin cycle in the cyanobacteria Synechocystis sp. PCC6803 that incorporates metabolic regulation by light
  • Analyzing metabolite profiles of cyanobacteria in different growth conditions using LC/MS and other techniques
Meng-Ling Shih
For plant volatile organic compounds (VOCs) to be released into the atmosphere, they must cross cellular membranes, the aqueous cell wall, and the cuticle. Simulations have previously demonstrated that VOCs may accumulate in the plasma membrane to levels that are likely detrimental to the cell if the emission of volatiles are driven solely by diffusion. Hence, we propose that there are biological mechanisms involved to lower the concentration of VOCs in cellular membranes. Lipid transfer proteins (LTPs) are a known mechanism for transportation of intracellular compounds through cell walls, and thus we propose a model for faciliated transport of VOCs via LTPs

My research is focused in the following areas:
  • Mass spectrometry analysis of LTP candidates incubated with VOCs to determine binding capacity
  • Experimental determination of enhanced transport of VOCs through phases in the presence of LTPs
  • Measurement of emission flux in transgenic Petunia hybrida with candidate LTP gene knockout and overexpres
Arnav Deshpande
Cancer cells are known to exhibit altered behavior which enables them to proliferate while sustaining themselves. The altered mechanisms that are characteristic of cancer cells are not well understood. Use of isotopic tracers and Metabolic Flux Analysis (MFA) have proven to be useful tools in showing altered fluxes through metabolic pathways and helped in better understanding how cancerous cells sustain themselves while also providing us with potential targets for drug and treatment development.

My research is focused in the following areas:
  • Using isotopic tracers and MFA to quantify fluxes in the glycolysis pathway in normal and cancerous cells.
  • Understand how cancer cells fight the high concentration of reactive oxygen species (ROS).
  • Using proteomics to measure the abundance of key metabolic enzymes and determine their redox status.

Undergraduate Students

  • Ryan Bing
  • Takashi Yokokura
Exchange Students

  Group Social

  • Spring 2016


Han Xiao Jiang (PhD): Amyris Biotechnologies

Hao Chen (PhD): Merck Inc.

Avantika Shastri (PhD): Sabic Innovative Plastics

Nannette Boyle (PhD): Assistant Professor, Colorado School of Mines

Sean Werner (PhD): Exxon Mobil

Neelanjan Sengupta (PhD): Becton Dickinson

Cameron Hill (MS): CalEnergy

John O'Grady (PhD): Perfinity Biosciences

Mattia R. Rastochak (BS): Exxon Mobil

Robin Wheeler (MS): uniQure

Rohit Jaini (PhD): Pfizer

Jeremiah Vue (MS): Lonza