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

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.A N 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 Few curricula have been updated to reflect recent innovation and most are estimated to be out of date by approximately 2 decades (National Research Council 2003).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 1 These authors contributed equally to this work.

“Perfect” designer chromosome V and behavior of a ring derivative

“…All synV building blocks (BBs),~750-bp primary DNA segments, and minichunks-~2-to 4-kb secondary DNA segments-were built, starting with oligonucleotides, and sequence-verified by students of the "Build-A-Genome (BAG) China" course offered at Tianjin University (TJU) (23). Sixty-one students were organized into five groups to build the synthetic DNA for synV (536,024 bp) in~4 months (figs.…”

“…S2A). Three colonies with full length PCR product were sequenced and the right colonies were stored after sequence aligned with the reference sequence by using Serial Cloner software (7,23).…”

Developing data literacy competencies to enhance faculty collaborations

“…Further evidence of the benefits of incorporating bioinformatics resources within undergraduate information or data literacy instruction to enhance student understanding of molecular processes has been reported by a number of recent studies (Badotti et al, 2013;Dymond et al, 2009;Weisman, 2010;Wightman & Hark, 2012). Best practices for implementing similar programs have been delineated (Badotti et al, 2013;Bednarski et al, 2005;Miskowski, Howard, Abler, & Grunwald, 2007;Via et al, 2011;Weisman, 2010), while others have discussed the programmatic role librarians can provide in supporting molecular biologists as they navigate the myriad data resources (MacMullen & Denn, 2005).…”

The impact of synthetic biology in chemical engineering—Educational issues

“…In this context, the sooner a student embraces synthetic biology with all its uncertainties and real world connotations the better and a full undergraduate course may be the way to achieve this and may appeal to the maverick soul who can appreciate the challenges inherent in the discipline. Dymond et al, (2009) described undergraduate teaching in synthetic biology at Johns Hopkins University from a geneticist's point of view.…”