Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course

By Dymond, Jessica S.; Scheifele, Lisa Z. et al. | Genetics, January 2009 | Go to article overview

Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course


Dymond, Jessica S., Scheifele, Lisa Z., Richardson, Sarah, Lee, Pablo, Chandrasegaran, Srinivasan, Bader, Joel S., Boeke, Jef D., Genetics


ABSTRACT

A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary research and is therefore an attractive addition to the undergraduate biology curriculum. This new discipline offers the promise of a deeper understanding of gene function, gene order, and chromosome structure through the de novo synthesis of genetic information, much as synthetic approaches informed organic chemistry. While considerable progress has been achieved in the synthesis of entire viral and prokaryotic genomes, fabrication of eukaryotic genomes requires synthesis on a scale that is orders of magnitude higher. These high-throughput but labor-intensive projects serve as an ideal way to introduce undergraduates to hands-on synthetic biology research. We are pursuing synthesis of Saccharomyces cerevisiae chromosomes in an undergraduate laboratory setting, the Build-a-Genome course, thereby exposing students to the engineering of biology on a genomewide scale while focusing on a limited region of the genome. A synthetic chromosome III sequence was designed, ordered from commercial suppliers in the form of oligonucleotides, and subsequently assembled by students into ~750-bp fragments. Once trained in assembly of such DNA "building blocks" by PCR, the students accomplish high-yield gene synthesis, becoming not only technically proficient but also constructively critical and capable of adapting their protocols as independent researchers. Regular "lab meeting" sessions help prepare them for future roles in laboratory science.

AN ongoing challenge to the design and maintenance of undergraduate biology curricula is the ability to incorporate new conceptual advances and technologies. Few curricula have been updated to reflect recent innovation and most are estimated to be out of date by approximately 2 decades (NATIONAL RESEARCH COUNCIL 2003). The advent of recombinant DNA technology .30 years ago enabled research to proceed at unparalleled rates (COHEN et al. 1973), and these concepts and techniques have been almost universally adopted in undergraduate molecular biology courses. More recently, innovations in engineering, computer science, and biotechnology have enabled biological research to enter the genomic era, yet undergraduate programs have been largely unable to keep pace with these developments. These delays become more inevitable and intractable as expansions in the scope of biological research are driven by the rapidity with which new technologies are being introduced; this technology-driven approach is difficult to reconcile with the dogmatic presentation of lecture material and the focus on memorization-based learning that have characterized traditional biology courses. To incorporate a genomic focus, undergraduate courses would be better served by an active learning orientation and an interdisciplinary foundation (NATIONAL RESEARCH COUNCIL 2003; ARES 2004; BIALEK and BOTSTEIN 2004; GROSS 2004). Many of these objectives could be achieved by the introduction of synthetic biology courses to the undergraduate curriculum.

Synthetic biology is a new discipline emerging in the scientific, social, and business arenas and is attracting national attention by promising advances in numerous areas, such as biofuel and pharmaceutical development, agriculture, and bioremediation. The field is best understood as the application of engineering principles to biological systems and is therefore inherently interdisciplinary, with a strong foundation in biology, engineering, computer science, and biotechnology. One focus of synthetic biologists is the deconstruction of biological systems into components that can be uncoupled from each other, abstracted into predictable forms, standardized so they are interchangeable, and then reassembled into new functional systems. …

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Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course
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