Andrew Yao

Research Associate

Personal Education

M.S. University of California – Davis, Biochemistry, Molecular, Cellular, Developmental Biology
B.S. University of California – Davis, Biomedical Engineering

Research Interests/Projects

My primary research interest involves characterizing transcriptional networks in diseases. To accelerate such research, better technologies are required to be able to decode complex regulatory pathways. One of these technologies, chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq), has allowed many scientists an unparalleled view of regulatory networks, especially in the bacterial and archaeal domains of life. Improving on the ChIP-seq technology, and/or developing new technologies with similar scope are my main research goals.

I also enjoy the fascinating and ever expanding field of synthetic biology. I’m particularly interested in discovering and testing new ways of putting DNA together and using non-transcriptional regulatory mechanisms to improve and create novel circuits.

Current Project(s)

ChIP-seq in Halobacterium salinarum NRC-1 – ChIP-seq allows for the genome-wide mapping of transcription factor binding sites. This technology allows us to obtain a broad picture of an organisms response to certain stimuli to eventually link a stimulus and phenotypic output(s). The use of this technology is limited mainly by the large required input of chromatin, and the multiple column/bead based purifications that bias the sample. Improvements in these two areas will allow for greater resolution of data and open the technology to many other interesting model organisms or cell lines.

Past Projects

Development of a universal haloarchaeal defined media – GCMS is currently the best technology to discover the diversity of metabolites in living organisms. However, to be able to measure changes in metabolite levels within a cell, one most be able to set a known baseline for metabolite concentrations. For that reason, having a defined media in which our model organisms and potentially other members of the haloarchaeal clade is essential. This project entails finding a non-specific haloarchaeal defined media by inducing single dropouts of its components. By analyzing growth data in response to those drop outs we hope to be able to find a “perfect” universal defined media.

Gas vesicle biogenesis in Halobacterium salinarum NRC-1 – NRC-1 is one of the best studied model archaeal organisms. Much literature exists on NRC-1’s ability to express gas vesicles. We are looking into how the expression of gas vesicles affects the ability to measure cell density with traditional light spectroscopy and also studying the complex response network of this process to multiple stimuli.

Andrew Yao

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