From Keaslingwiki
The Keasling Lab combines the development and application of synthetic biology tools with a comprehensive understanding of microbial physiology to tackle challenging high-impact problems. We aim to provide lasting solutions in such areas as environmental biotechnology, renewable energy, and biosynthetic production of theurapeutic molecules.
| Synthetic biology is the redesign of biological systems and their parts for useful and practical purposes. We are able to leverage the power and vastness of biological systems to answer problems for which nature has yet to find a solution. Although fragments to many of the solutions we seek already exist in nature, they are incomplete on their own. We must not only identify and augment these components, but also create and evolve new components; all of which are combined in the construction of a single host to provide an integrative solution.
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Genome-wide monitoring of microbial cells is hardly a new area of research. Many research groups have used two-dimensional gels to analyze the response of microorganisms to perturbations of metabolism or genetic content. While they were able to observe and later characterize the induction of several genes (by the appearance or disappearance of spots on 2-D protein gels), the analysis was tedious and difficult. The discovery of Magic Spot (ppGppp) has led to a number of metabolite profiling studies in which several phosphorylated metabolites were separated by 2-D thin-layer chromatography (TLC) and the most prominent spots analyzed. Again, it was relatively simple to see changes in the various spots on the TLC during changes in the cell’s genome or its environment, but it was more challenging to identify those spots. More recently, DNA arrays have been used to study changes in gene expression in Escherichia coli in response to environmental stimuli. The use of DNA arrays has significantly improved and eased analysis of the genetically modified strains and non-model organisms, because one can readily associate the changes in the intensity of a particular spot on the array with the regulation of a particular gene. Improved methods for protein profiling have made proteomics a useful technology for studying the effect of a genetic change (whether deletion of a gene, expression of heterologous genes / evolved variants or physiological profiling of non-model organisms). Similar technologies are only now becoming available for profiling of a large fraction of the metabolite content of the cell.
However, to date, there have been few or no studies that use transcript, protein, and metabolite profiling together to obtain a more complete understanding of a microbial strain. By monitoring and comparing all three profiles simultaneously, we have gained critical insights into the significance of changes (or the lack thereof) in gene expression. The parallel analysis of these complimentary cellular aspects, also enable a high though-put and less expensive investigation into the overall physiology of the microbe.
The microorganisms being studied in our group are: E. coli, B. subtilis, Desulfovibrio vulgaris Hildenborough, Shewanella oneidensis MR1 and Saccharomyces cerevisiae.
Bioremediation, the treatment of environmental contaminants via biological systems, is an important focus of the laboratory. For the effective and economical use of bioremediation, it is important that we understand the mechanisms of biodegradation and bioaccumulation. Ideally, naturally existing bioremediation processes may be utilized, but these processes must be understood before their potential can be harnessed. Specifically, it is important to determine which factors limit the remediation, and may thus be stimulated, and it is critical to understand the end results of stimulating biological pathways (for example, which byproducts will be produced). We have employed a number of high-throughput techniques to explore the metabolic pathways of bioremediation-relevant model organisms. When natural processes to remediate an environment do not exist or cannot be stimulated, novel pathways may be engineered to accomplish the cleanup task.
