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Some Assembly Required Kit-Based Competitions Challenge Teams of Students to Learn Microbiology and Design Principles in the Context of Synthetic Biology

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Some Assembly Required Kit-Based Competitions Challenge Teams of Students to Learn Microbiology and Design Principles in the Context of Synthetic Biology Living Machines: Some Assembly Required Kit-based competitions challenge teams of students to learn microbiology and design principles in the context of synthetic biology Natalie Kuldell f you were a new student arriving at teams a common task, challenging them, for Massachusetts Institute of Technology example, to “design a machine that puts a round (MIT) in Cambridge during the early peg into a square hole” or to “build a mechani- I 1970s with an expressed interest in me- cal device that can roll down a 30° incline plane chanical engineering, you would have in 3 minutes.” With an explicit design challenge been advised to enroll in a class called “Intro- to meet, students no longer spent so much time duction to Design.” Students in this class were wondering what to build and, instead, could provided components such as wooden spools concentrate on designing and engineering spe- and metal rods, and were told to build a useful cific types of machines. The second change was device from these parts. to make each of these engineering assignments A teaching assistant from that era noted that competitive. Student teams engaged in sports- students taking that class spent little time engi- like battles to determine which team’s machine neering their machines because it took them so could perform with the greatest accuracy, con- long to decide what to build. When that teach- sistency, and precision. Not surprisingly, MIT ing assistant, Woodie Flowers, became an MIT students enjoyed measuring their success against professor and took over teaching that class, he others. made two big changes that had a major impact A generation later, other disciplines are em- on the students. The first was to assign all the bracing the notion of teaching through kit-based design competitions. A prime example is the annual FIRST Robotics Competition, Summary which was founded by Flowers of MIT and inventor Dean Kamen, president of DEKA • The impetus for a popular annual contest for Research & Development Corporation in students learning synthetic biology traces to an Manchester, N.H. Last year, for example, introductory course in engineering and design at more than 350 high school teams from five MIT. countries worked with kits having the same • The first chapter of iGEM involved a group of parts, each group striving to build the 16 undergraduate students at MIT in 2003 try- ing to make bacterial cells into a “living light- “best” robots within six weeks. Their ef- house” using standardized DNA “parts.” forts are judged regionally, with the local winners advancing to the finals, where the • The annual iGEM contest now includes stu- dents from four continents who compete re- teams match their robots against one an- gionally, with those winners gathering in No- other in a competitive atmosphere that ri- vember for a Jamboree. vals what happens at the Super Bowl or Natalie Kuldell is an • Formal educational modules at BioBuilder har- World Cup. This design competition engen- Instructor of Biolog- ness the iGEM approach for teaching engineer- ders not only palpable enthusiasm but last- ical Engineering at ing in the context of high school and college ing learning among the students who partic- the Massachusetts biology, an approach that may be adapted for ipate. Moreover, the event continues to Institute of Technol- teaching other scientific disciplines. grow, attracting more teams and younger ogy, Cambridge, students. Mass. Volume 7, Number 1, 2012 / Microbe Y 13 Tapping into Competitive tion. The project judged most impressive that Spirits to Teach Biology year was from the University of Texas (UT) at Biology is the new frontier where kit-based de- Austin. The UT team designed and built a strain sign competitions are generating keen enthusi- of E. coli that could serve as the pixels in a asm. Specifically, those contests are playing out photograph. in the field of biological engineering called syn- To reach this goal, the UT students fused a thetic biology. light-responsive sensor protein from cyanobac- Here, too, the impetus traces to MIT. In 2003, teria to the transmembrane protein from a two- several faculty members and researchers there, component signaling pathway (EnvZ/OmpR) including Drew Endy, now at Stanford Univer- that is native to E. coli. They transformed the sity, Tom Knight, now at Ginkgo BioWorks, gene for this fusion protein into a strain harbor- Gerald Sussman, and Randy Rettburg chal- ing an OmpR-regulated promoter that directed lenged a group of 16 students to build “a living transcription of a reporter gene, ␤-galactosi- lighthouse” from Escherichia coli bacteria, stip- dase, thereby assembling what they called their ulating that their goal was to make bacteria that “coliroid” strain. When grown in the dark, the emit light predictably and reliably. coliroid cells transcribe more of the lacZ gene, During January at MIT, classes are suspended turning an indicator in the media black. In the for several weeks for a session called IAP, Inde- light, LacZ transcription drops, allowing the pendent Activities Period. During the 2003 in- yellow media to show. The students displayed a dependent session, that group of 16 students photograph in which the cells spell out “hello struggled to complete the living lighthouse proj- world” at the 2004 Jamboree. A report describ- ect, working with a limited budget against a ing their experiments appeared the next year in tight deadline. Seeking shortcuts or other ploys Nature. that would accelerate their progress, they fig- The iGEM program continues to grow each ured out a scheme to make the sharing of useful year. In 2010, 130 teams from 26 countries snippets of DNA more efficient. They found participated. In 2011, iGEM grew further, hold- that, by standardizing DNA segments into ing three preliminary competitions to determine “parts,” it became easier to assemble them into which teams from the Americas, Europe, and increasingly more complex genetic programs. Asia would progress to the final Jamboree, held That winter session project from 2003 later in November. Other plans call for extending this was turned into an annual contest, called the competition to teams from high schools. Thus, International Genetically Engineered Machines iGEM increasingly resembles FIRST Robotics, (iGEM) competition. Held each summer, the with both programs encouraging teams from main goal of iGEM is to build “biological sys- colleges and high schools to design machines tems from standardized (DNA) parts.” from kits and for those teams to compete against Unlike the MIT Introduction to Design class one another. or the FIRST Robotics Competition, however, no single design challenge unifies the work of the iGEM teams, and they do not pit their biological Kits for Making Robots Differ from machines against one another. Instead, students Those for Engineering Cells from the participating schools work on their Although the outlines of the iGEM and FIRST own campuses during the summer months, and Robotics competition are alike, there are critical then come to MIT in the fall to celebrate their differences between the kits used for building engineered cells at a “Jamboree.” Projects are robots and those used to engineer living cells. compared based on their ability to “impress the For instance, a student in mechanical engineer- judges”—a subjective measure, but one that spurs ing has no trouble distinguishing wooden spools the teams to work diligently on their projects. from metal rods, even if those parts are mixed together in a single package. By contrast, iGEM The iGEM Synthetic Biology students typically work with identical-looking Competitions Keep Growing flecks of freeze-dried DNA, making it trivially By 2004, five U.S. teams were invited to partic- easy to begin a summer-long project with the ipate in the iGEM synthetic biology competi- wrong stock of DNA. 14 Y Microbe / Volume 7, Number 1, 2012 Kuldell: Hands-on Teaching of Synthetic Biology, and a Stint as a Professional Dancer Natalie Kuldell worked summers sachusetts Institute of Technology cell and developmental biology at at the National Institutes of (MIT) in Cambridge and a visit- Harvard University in 1994. She Health (NIH) while in high ing scientist at nearby Harvard was a postdoctoral fellow at Har- school, and it proved transforma- Medical School. Her research fo- vard Medical School from 1994 tive. “It seemed so great to be able cuses on understanding the con- to 1997. to head into the lab every day,” trol of gene expression in eukary- Kuldell spent a year between she says, crediting her mentors, otic cells. Working with Fred college and graduate school as a NIH biochemists Alan Peterkof- Winston at Harvard, she exam- professional dancer in Boston, sky and Marshall Nirenberg, for ines artificial gene expression sys- performing with several compa- inspiring her. “I was hooked, and tems in cells of Saccharomyces nies, including the Performing I knew at age 16 that their job was cerevisiae. Arts Ensemble and the Kelly Don- the one I wanted. Since they stud- Kuldell also serves as associate ovan Dancers. “I continued to ied chemistry in college, rather director of education and training dance, but in a diminished role in than biology, that’s what I did, at SynBERC, a multi-university the company, through graduate knowing full well that I’d go to program in synthetic biology, and school, through becoming a mom, graduate school in the life sci- directs BioBuilder.org, an inter- and through my academic transi- ences, as they did.” active website that features syn- tions,” she says. “I still dance ev- The experience also helped her thetic biology learning materials, ery week. I continue to feel con- to realize the importance of some of them animated narra- nected to the wonderful dance hands-on learning, an approach tives. She also set up an educa- community here in Boston, even she now takes when teaching.
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