My Research
Research interest: Genome scale
pathway reconstruction by microarray expression profiling: from simple
yeast to complex zebrafish model.
Zebrafish has been a great animal model for developmental and
large-scale forward genetics research. The relative simpleness of
animal care and accessibility to the embryonic development also make
zebrafish a potentially good systems biology model. The latest
technological developments and findings from unicellular organisms like
yeast can be first tested on this simpler multicellular vertebrate
before investigating on more complex organisms like rodents or
primates. Or complex problems from higher animals can be investigated
on simpler zebrafish and yeast models in order to obtain further
fundamental insights. I believe zebrafish is going to be an important
bridge for these models of different complexities. My current research
interest is to conduct genomics researches on zebrafish and yeast, and
hope to build up the foundations of using zebrafish as the bridge model
for
functional genomics research.
Zebrafish project
More to come...
Yeast project
The following is the description of Cavalieri's group research interest
(http://www.cgr.harvard.edu/fellows/Current_Fellows/current_fellows.html).
I am currently studying the yeast adaptation to acetic acid stress.
"We are investigating how genetic diversity is created and maintained,
and affects the behavior of populations in laboratory and natural
settings. We have used DNA microarrays to examine genetic diversity in
populations of budding yeast isolated from natural wine fermentations
and natural environments. We are also developing genomic approaches to
map phenotypic traits in yeasts other than the standard lab strain,
S288c. In particular, we are studying the yeasts’ adaptation to toxic
agents, such as acetic acid and ethanol, present in the natural
environments in which yeast evolved and produced by the yeasts
themselves to out-compete other microorganisms. We believe that
mechanisms that evolved in wine yeasts to resist osmotic, high-ethanol
and acetic acid stress are conserved in the mechanisms that mammalian
cells use to resist small molecules and chemotherapeutic agents.
We have also developed a method to use real-time PCR to follow tagged
strains during wine fermentation, and to determine the relative
abundance of strains marked with different tags. Using these new
methods we are examining strain fitness, population dynamics and rates
of genetic change during fermentation and growth in YPD, and the extent
of divergence and isolation between natural yeast populations.
Combining these experiments with expression analyses should allow us to
map the genetic control networks associated with fitness and growth in
different environments, and under different stresses. In this
connection, we have developed a new bioinformatics tool, Pathway Processor,
which allows us to project whole-genome expression results onto
metabolic networks, connecting expression variation with metabolic
phenotypes and helping us to reconstruct genetic regulatory networks."
last updated: 2 Feb 2004
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