User:Juedwang

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Before this, I studied physics at McGill University in Canada.
Before this, I studied physics at McGill University in Canada.
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== Research ==
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  All organisms possess mechanisms to faithfully replicate their DNA.  Replication is highly regulated to minimize errors that could lead to cell death or tumorigenesis.  How do cells avoid mistakes during DNA replication?  How is DNA replication coordinated with cellular processes such as growth and division?  How is replication responsive to external cues such as nutrient availability?  These are important unresolved questions which we will address using the bacterium Bacillus subtilis.
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My research interest is to systematically investigate how cells regulate elongation of DNA replication.  Regulation of elongation is a less studied process than regulation of initiation of DNA replication, but it could have significant impact on the maintenance of genomic integrity.
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  B. subtilis displays relative simpler mode of replication comparing to eukaryotes, and is convenient for genetic, genomic, quantitative and systematic analyses.  Understanding universal principles of regulating DNA replication helps us to understand causes for genetic diseases and cancerMore importantly, the replication machine of B. subtilis is closely related to many microbial pathogens but is dramatically different from eukaryotes.  Studying how B. subtilis replicates helps us to find ways to produce useful antimicrobial drugs that target DNA replication of these pathogens.
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By profiling DNA replication in the gram-positive bacterium Bacillus subtilis on a genomic scale, I have characterized a nutrient dependent checkpoint that inhibits the elongation of DNA replication. This elongation control does not appear to require cis-acting DNA elements or replication roadblocks, but is throughout the chromosome.  I plan to investigate the mechanisms and the impact of elongation control on regulating the cell cycle and preventing disruptions of replication.  I will combine classical genetics, biochemistry, and global profiling of replication to study replication in a quantitative manner and analyze the results computationally. The experimental methods developed could also be useful to study the regulation of DNA replication in other organisms.
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[[Image:arrayforks.jpg]]
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1. Characterize a pathway that regulates replication elongation.  I have found a novel mechanism for nutritional regulation of DNA replication.  Upon starvation, the small nucleotide ppGpp rapidly and directly inhibits B. subtilis primase.  We will combine genetics and biochemistry to illustrate the molecular mechanism of this inhibition.
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2. Evaluate the contribution of regulating replication elongation to maintaining genomic stability Replication arrest caused by adverse situations often leads to replication fork collapse.  I found that ppGpp-mediated replication arrest does not lead to such disruption, suggesting that ppGpp could be part of a checkpoint pathway that monitors nutrient availability and regulates replication. This regulation might help to minimize disruption to replication forks.  We will monitor the survival, mutation, and DNA damage response of cells when this control is abolished.
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3. Investigate the state of arrested replication forks in the middle of a chromosome and the events that lead to replication restartWe will use fluorescence microscopy to visualize the cellular localization of various replication and repair proteins.  To characterize the binding of these proteins to the chromosome, we will conduct ChIP-Chip analysis (chromosome immunoprecipitation-microarrays).
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4. Explore how replication shapes genomic organizationIn B. subtilis, transcription of the majority of genes (75%) co-orients with replication.  I monitored replication of B. subtilis mutants with re-arranged genomes, and found that head-on transcription impedes replication, while co-orientation of transcription minimizes this impediment. We will use evolutionary and genetic approaches to further examine the nature of the selective pressure to co-orient replication with transcription.

Revision as of 00:09, 12 September 2006

Bio

Personal

Hi.. my name is Jade. I am a postdoctoral associate in the Grossman Lab at MIT.

Education

I went to grad school in San Francisco. I worked in the Weissman Lab in UCSF. My graduate work is described here.

Before this, I studied physics at McGill University in Canada.

  All organisms possess mechanisms to faithfully replicate their DNA.  Replication is highly regulated to minimize errors that could lead to cell death or tumorigenesis.  How do cells avoid mistakes during DNA replication?  How is DNA replication coordinated with cellular processes such as growth and division?  How is replication responsive to external cues such as nutrient availability?  These are important unresolved questions which we will address using the bacterium Bacillus subtilis.
  B. subtilis displays relative simpler mode of replication comparing to eukaryotes, and is convenient for genetic, genomic, quantitative and systematic analyses.  Understanding universal principles of regulating DNA replication helps us to understand causes for genetic diseases and cancer.  More importantly, the replication machine of B. subtilis is closely related to many microbial pathogens but is dramatically different from eukaryotes.  Studying how B. subtilis replicates helps us to find ways to produce useful antimicrobial drugs that target DNA replication of these pathogens.

Image:Arrayforks.jpg 1. Characterize a pathway that regulates replication elongation. I have found a novel mechanism for nutritional regulation of DNA replication. Upon starvation, the small nucleotide ppGpp rapidly and directly inhibits B. subtilis primase. We will combine genetics and biochemistry to illustrate the molecular mechanism of this inhibition. 2. Evaluate the contribution of regulating replication elongation to maintaining genomic stability Replication arrest caused by adverse situations often leads to replication fork collapse. I found that ppGpp-mediated replication arrest does not lead to such disruption, suggesting that ppGpp could be part of a checkpoint pathway that monitors nutrient availability and regulates replication. This regulation might help to minimize disruption to replication forks. We will monitor the survival, mutation, and DNA damage response of cells when this control is abolished. 3. Investigate the state of arrested replication forks in the middle of a chromosome and the events that lead to replication restart. We will use fluorescence microscopy to visualize the cellular localization of various replication and repair proteins. To characterize the binding of these proteins to the chromosome, we will conduct ChIP-Chip analysis (chromosome immunoprecipitation-microarrays). 4. Explore how replication shapes genomic organization. In B. subtilis, transcription of the majority of genes (75%) co-orients with replication. I monitored replication of B. subtilis mutants with re-arranged genomes, and found that head-on transcription impedes replication, while co-orientation of transcription minimizes this impediment. We will use evolutionary and genetic approaches to further examine the nature of the selective pressure to co-orient replication with transcription.

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