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Research Projects
My hybrid position (wet-lab & bioinformatics) at Zacharewski
laboratory involved three projects.
1) Working for Edward Dere
on AhR signaling pathway related experiments, which included
compound specific QRT-PCR verification for SAhMR(Selective AhR
Mediated Responses) on TCDD & ICZ treated Hepa1c1c7 cells
and Hepa1c1c7 C4 Mutants (Arnt defective/deficient) Hepatoma
cell line study with ICZ & BNF.
• SAhMR: gene expressions for two genes (Il1r1& Tnni3)
in question were verified by QRT-PCR.
• The purpose of the study on Hepa1c1c7 C4 mutants was
to verify if the gene expression response following ICZ (indole-[3,2,-b]-carbazole)
or BNF (beta-naphthoflavone) administration are mediated through
AhR pathway. This was done by extracting RNA from the harvested
cells at time points 4 hrs and 12 hrs for 5 replicates (treated
& harvested by Marcel,
previous co-op student). Microarray experiment was then performed
on 4 replicates to look at the gene expression.
2) Working under the supervision of Josh
Kwekel on searching of estrogen responsive (ER) genes through
literature and adding them on microarray slides for mouse, rat
and human.
3) Working for Lyle Burgoon
on developing a support vector machine (SVM) to detect lesions
in histology slides. This project has been divided into two
major applications. One, which makes a model file after training
the SVM and second, which reads in the model file(s) and predicts
the lesions. The applications are coded in Java using libSVM
and other java libraries.
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