My research interest is to apply modern technology to solving interesting biological problems. Some of the technologies that I have worked on includes high-throughput genomics technologies, optical imaging, and micro/nanofabrication. These are some powerful tools that can measure or analyze biological systems from a whole system scale down to a single molecule inside a single cell. By analyzing data from genome-wide experiments, we can decipher the behavior of a biological system through its network interactions. By studying the behavior of single molecules within a cell, we can gain understanding of the molecular mechanisms of how each macromolecule function. Combining these approaches can give us a fundamental and global understanding of biology. Listed below is a summary of my past research projects:
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Project: Development of a library of terminator parts for synthetic genetic circuits
2010-present Postdoctoral Scholar, Dr. Christopher Voigt’s Laboratory, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA.
Transcriptional terminators are essential parts for preventing crosstalk in synthetic genetic circuits. I am characterizing a library of more than a hundred natural and synthetic prokaryotic intrinsic terminators. Using a test construct with green fluorescent protein (GFP) and red fluorescent protein (RFP) separated by the terminator of interest controlled by an inducible promoter, the termination efficiencies of the terminators can be measured by the ratio of RFP to GFP fluorescence. I am measuring mRNA and protein levels using quantitative real-time PCR and flow cytometry. The data collected are used to derive a biophysical model that predicts the termination efficiency from DNA sequence.
Related publication:
- Chen Y-J, Ma EJ and Voigt CA, .”Characterization and biophysical modeling of bacterial terminators for synthetic biology.” (in preparation).
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Project: DNA Sequencing by Denaturation
2004-2009 Graduate and Postdoctoral Researcher, Genomics and Systems Biotechnology Laboratory (PI: Dr. Xiaohua Huang), Department of Bioengineering, University of California, San Diego, La Jolla, CA.
Genome sequencing technologies are in high demand for applications such as genome-wide association studies, cancer research, and personalized medicine. However, traditional technology requires hundreds of millions of dollars and several months to sequence one mammalian genome. To lower the cost and time, I developed a new DNA sequencing method called sequencing by denaturation (SBD).
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In SBD, the sequencing of hundreds of millions of template is performed on a surface in parallel. First, a Sanger sequencing reaction is performed on templates immobilized on a surface to generate a ladder of DNA fragments randomly terminated by fluorescently-labeled dideoxyribonucleotides. These fragments are sequentially denatured and the process is monitored by measuring the change in fluorescence intensities from the surface. By analyzing the denaturation profiles, the base sequences of the templates can be determined in a massive parallel manner.
Using thermodynamic principles, I simulated the SBD process and developed a base-calling algorithm to decode the sequences from the fluorescence intensity profiles. These simulations demonstrate that up to 20 bases from a DNA molecule can be sequenced by SBD within a moderate error rate. |
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Experimentally, we constructed an instrument which integrates fluorescence imaging, temperature control, and fluidics onto a single device through a custom-made biochemical reaction chamber. This system was used to demonstrate the proof of concept for SBD by measuring the denaturation curves of 6 fluorescently-labeled oligonucleotides hybridized to a common template on the surface. The correctly distinguished melting temperatures demonstrate that SBD can be used to sequence at least 6 bases.
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In summary, the theoretical and experimental proof of principle for SBD has been demonstrated. With my calculations, SBD has the potential to lower the cost of sequencing a human genome to $1000 since it decreases the reagent volume for sequencing one genome into the amount for one single reaction. This method can be useful for genome re-sequencing, gene expression profiling and genotyping.
Related publication:
- Chen Y-J, Roller EE, and Huang X, ”DNA sequencing by denaturation: Experimental proof of concept with an integrated fluidics device.” Lab on a Chip, 10: 1153-1159, 2010. (Abstract). Featured in Highlights in Chemical Biology: .”DNA sequencing on a chip.”, 3, 2010. (Article)
- Chen Y-J, and Huang, X, “DNA sequencing by denaturation: Principle and thermodynamic simulations.” Analytical Biochemistry, 384: 170-179, 2009. (Abstract)
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Project: Validation of a Physical Network Model by Microarray Experiments
2003 Graduate Rotation Student, Integrative Network Biology Laboratory (PI: Trey Ideker), Department of Bioengineering, University of California, San Diego, La Jolla, CA.
A physical network combining protein-protein interaction with gene expression data was constructed to provide a more comprehensive understanding of the yeast model system. These resulted in the prediction of a few pathways that are the most active in yeast. I conducted gene expression microarray experiments to validate the predictions.
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Project: High-aspect-ratio Sub-diffraction-limit Objects Fabricated with Two-photon-absorption Photopolymerization
2001-2002 Undergraduate Researcher, Joint Laboratory of Optical Sciences and Ultrafast Technology (PI: Jyhpyng Wang & Chau-Hwang Lee), Institute of Atomic and Molecular Sciences, Academia Sinica, Taiwan.
High-aspect-ratio objects are important elements in microelectromechanical systems (MEMS). These objects are difficult to fabricate with photolithography methods in the submicron and smaller scales. Two-photon-absorption photopolymerization offers the capability of fabricating three-dimensional sub-diffraction-limit devices because only the tightly focused region will be polymerized.
Using a femtosecond pulse laser, I exposed and developed an array of rod and grating patterns in the photoresist SU-8. These rods and gratings with heights of 2 to 5 µm are in the size range of 200 to 400 nm, which is less than the 800 nm wavelength of the exposed laser. This method produces patterns that cannot be fabricated using contact printing and is faster than fabricating submicron patterns using an electron beam.
  
Related publications:
- Chen Y-J , Chen Y-C, Lee C-H, and Wang J, “High-aspect-ratio sub-diffraction-limit objects fabricated with two-photon-absorption photopolymerization.” Proceedings of Conference on Lasers and Electro-Optics , 1: 252-253, Long Beach, California, 2002. (Abstract)
- Chen Y-J , Chen Y-C, Lin H-W, Lee C-H, Wang J, “Sub-wavelength Three-dimentional Objects Fabricated with Two-photon-absorption Photopolymerization.” Proceedings of Optics and Photonics, Taiwan , 2001. (Abstract)
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Project: How Proteins Go into the Nucleus – the determination of the nuclear localization signal of the transcription factor SF1
1997-1998 Researcher, Dr. Bon-chu Chung’s Laboratory, Institute of Molecular Biology, Academia Sinica, Taiwan.
SF1 is a transcription factor which functions in the nucleus of a cell. However, like other proteins, it is translated in the cytoplasm. Therefore, it is important to determine the nuclear localization signal (NLS) that directs the protein into the nucleus for function.
By designing several truncated protein sequences and cloning them with a green fluorescence protein (GFP) tag, I determined which peptide sequence can direct the transfected clone to fluorescence in the nucleus. By identification and alignment of this NLS to other NLS of proteins in the same super-family, I suggested a potential mechanism for these proteins to enter the nucleus, which is essential for the proper function of these transcription factors.
Related publication:
- Li L-A, Chiang F-L, Chen J-C, Hsu N-C, Chen Y-J, Chung B-c, "Function of steroidogenic factor 1 domains in nuclear localization, transactivation, and interaction with transcription factor TFIIB and c-Jun." Molecular Endocrinololgy 13: 1588-1598, 1999. (Abstract)
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