Main Page

From GcatWiki
Jump to: navigation, search

This is our first attempt at GCAT Community Wiki.

This Wiki has been set up for the use of the GCAT community. The intent is that it be maintained by its users.

Please read the Guidelines for use.

Draft of Synthetic Biology Meeting Report

BUILDING BETTER SCENTISTS WITH SYNTHETIC BIOLOGY: A MEETING REPORT FROM THE GENOME CONSORTIUM FOR ACTIVE TEACHING (GCAT) WORKSHOP 2010

Synthetic biology can be defined as the application of engineering and mathematical principles to create novel biological devices and circuits. What separates synthetic biology from standard molecular biology is the development of standardized interchangeable DNA “parts” in similar fashion to how advances in engineering in the 19th century brought about standardized railroad gauges and screw threads. Through the use of this set of “parts”, laboratories around the world can easily exchange and combine biological constructs to develop novel “machines” for a variety of applications (Ferber et al., 2004, Purnick and Weiss, 2009), including medicinal chemistry (Martin et al., 2003, Tsuruta et al., 2009), genetic engineering (Hasty et. al., 2002, Sprinzak and Elowitz, 2005), and the creation of bacteria containing a completely-synthesized genome (Gibson et al., 2010). While synthetic biology can trace its roots to the world’s large research universities, over the last five years the field has emerged as an important area for interdisciplinary collaborations between science, technology, engineering, and mathematics (STEM) disciplines at primarily undergraduate institutions as well. Undergraduate student research has become an integral part of synthetic biology in large part because of the National Science Foundation (NSF)-sponsored undergraduate student research Jamboree in 2004 (Campbell, 2005) which evolved into the annual iGEM (International Genetically Engineered Machine) competition at MIT that attracts undergraduate student researchers from around the world to design biological devices that can address a wide range of biological, environmental and mathematical problems. (http://2010.igem.org/Main_Page). A common problem faced by primarily-undergraduate institutions is the lack of funding and material support needed to adequately expose students to modern molecular biology, including synthetic biology. To help alleviate this problem, the Genome Consortium for Active Teaching (GCAT) was founded in 2000 by Malcolm Campbell at Davidson College to act as a central clearinghouse both for the purchase and reading of microarrys and for information on how to execute genomics experiments at undergraduate institutions. In response to the evolution of molecular biology in the last decade, Campbell, along with Davidson colleague Laurie Heyer and collaborators Todd Eckdahl and Jeff Poet of Missouri Western State University, organized a Howard Hughes Medical Institute (HHMI)-sponsored GCAT workshop at Davidson in July of 2010 to further explore how to bring synthetic biology to the undergraduate classroom and laboratory and how faculty from multiple disciplines could work together to promote these programs. The workshop was attended by a biologist and non-biologist pair from 15 primarily undergraduate institutions with the goal that each pair could begin the mental preparations necessary to bring multidisciplinary synthetic biology activity to their respective institutions (See Figure 1 for the organizers and participants). MEETING THEMES AND EVENTS A number of themes appeared frequently throughout the workshop: ---Synthetic biology requires a new way of thinking for most scientists: to view problems through the lens of an engineer and consider issues of standardization, modularity, abstraction, and modeling and their applicability to the problem at hand. ---Synthetic biology is an excellent pedagogical and research tool to foster interdisciplinary work and learning. Successful interdisciplinary work requires everyone to work at frequent communication, to learn how to speak the language of each others disciplines, and to think about problems in novel ways. ---Synthetic biology is incredibly flexible: almost any scientific interest can be accommodated within the field, and this makes it relatively easy to find projects that require contributions from all members of a multidisciplinary team. This is important, because if any member of the team feels that their role in the overall project isn't important, the project ultimately won't work. ---This flexibility makes synthetic biology particularly accessible and stimulating for faculty and undergraduate students at small institutions: in most cases, individual faculty members are the sole representative of their academic speciality in his or her department, so having a way to leverage the interests, knowledge, and excitement of colleagues with whom there would normally be little to no communication provides a stimulating opportunity for new directions in research and teaching. Not only are faculty forced out of intellectual comfort zones, but so are students: exposing students to other approaches and ways of thinking as part of a hands-on research experience will give students an unparalleled appreciation of the value and realities of interdisciplinary thinking, something which will be increasingly valuable to them in the future. ---Over several years and several batches of undergraduates, the organizers developed an overall set of goals for the projects they developed with their students: -Everyone (faculty and students) should learn new things. -Everyone should have fun. -The project should contribute to the knowledge base in synthetic biology. As mentioned more than once during the workshop, these goals are in listed in order of importance: if project participants are learning and enjoying what they're doing, then they’re succeeding. Based on the success that combined Davidson/Missouri Western teams have had at iGEM, it seems that their focus on the first two goals has enabled them to consistently achieve the third as well. The workshop started with discussions on the fundamental principles of synthetic biology, the suitability of synthetic biology for multidisciplinary research with undergraduate students, the connection and communication between biology and collaborating disciplines necessary for success, and the elements that make up a successful synthetic biology project. The discussions were followed by an introduction to the Biobrick™ standard assembly scheme at the foundation of synthetic biology and the Registry of Standard Biological Parts, a community resource maintained at MIT in which developed or developing parts are listed (http://partsregistry.org/Main_Page). To apply the lessons of the discussions, each pair of faculty worked with the Registry to conceive how to build a “lava lamp”: a DNA construct that would allow bacteria to fluoresce and float in response to stimulation. The organizers then gave presentations showcasing the exciting outcomes of the undergraduate synthetic biology research conducted collaboratively by Davidson College and Western Missouri State University, including an iGEM gold-medal winning project awarded for the development of a synthetic biology project that satisfied the team’s original biological and mathematical conception of the design. The workshop was broken up into biologist and non-biologist groups for a time in order to provide the opportunity for discussion between faculty from common disciplines. In these discussions, strategies for identifying areas of common interest and expertise from two different disciplines and developing successful interdisciplinary communication were emphasized. The ethical issues of designing synthetic biology systems were briefly discussed by both the whole group and in small sessions over lunch with the workshop organizers as well as bioethicists from Davidson. Given that this session happened to be held at the exact time that Congressional hearings on this precise subject were being held on Capitol Hill, the topic was especially relevant to the future of synthetic biology and will no doubt become more significant as the general public becomes more aware of the field. “Wet lab” time was also provided in which basic PCR and oliginucleotide assembly projects were performed in order to provide a taste of the workbench “nuts-and-bolts” of synthetic biology work. This portion of the meeting was especially valuable to the foundation of collaboration between faculty of different disciplines, since the biologist member of each pair was charged with explaining the principles and practice of the techniques to the non-biologist, and the non-biologist, in turn, provided context about how such techniques could possibly be used in the construction of a biological project that could also address their particular research interests. The remainder of the meeting was dedicated to the development of potential synthetic biology project ideas for undergraduate research and classroom purposes based on the interests and expertise of each faculty pair as well as the skills learned from the workshop. A diversity of projects were proposed that sought to develop sophisticated research experiences for undergraduates as well classroom laboratory experiences in which synthetic biology provided a foundation for an original research experience (see Powerpoint presentations of all of the proposals at http://www.bio.davidson.edu/projects/gcat/workshop_2010/workshop_2010_results.html) RESOURCES FOR THE DEVELOPMENT OF SYNTHETIC BIOLOGY PROJECTS In order to facilitate the transition between ongoing research and synthetic biology multidisciplinary research, a number of resources were presented at the meeting: ---GCAT Listserv: The GCAT Listserv (known as GCAT-L) is an email discussion list that connects faculty members who use (or are interested to use) genomic methods in their undergraduate courses. Messages sent to GCAT-L by any one of its subscribers are distributed to all of other subscribers. Information on how to subscribe and use GCAT-L is posted at http://www.bio.davidson.edu/projects/gcat/GCAT-L.html ---Wiggio/Wiki: To facilitate communication between collaborators on different campuses, Wiggio.com is an online toolkit that is freely available on the Internet that allows file sharing and editing, management of group calendars, posting of links, setting up conference calls, online chat, and sending text, voice and email messages to group members. Group members can define how each is informed about upcoming group activity. The toolkit can be accessed at http://wiggio.com. In addition, the GCAT community Wiki has been setup for use by the GCAT community and is maintained by its users; it can be accessed at http://gcat.davidson.edu/GcatWiki/index.php/Main_Page. ---GCAT Mini-Registry: A mini-registry was provided to workshop participants that contained ten parts that are present in the Registry of Standard Biological Parts. The parts include promoters, Ribosome Binding Sites (RBS), Double Terminators, Red Fluorescent Protein (RFP) and Green Fluorescent Protein (GFP). ---GCATalog: This catalog, developed by Bill Hatfield at Davidson along with Laurie Heyer and Malcolm Campbell, is freely available and is optimized for use in synthetic biology applications. Using this web-based catalog, synthetic biology users can generate a publically-accessible freezer inventory that allows the synthetic biology community to share commonly used BioBricks™ as well as other biological constructs. (http://gcat.davidson.edu/GCATalog/) ---Open WetWare: In order to promote sharing of unpublished work and protocols between scientists engaged in biological engineering, an open WetWare page was created (http://openwetware.org/wiki/Main_Page). This page has information related to labs working in synthetic biology, course and teaching resources, protocols, and a continually-updated blog. Another related website highlighted as a repository of synthetic biology tools was that of Drew Endy’s laboratory in the Department of Bioengineering at Stanford University (http://openwetware.org/wiki/Endy_Lab). This Open WetWare- linked laboratory website has information on ongoing research, publications and detailed descriptions of projects and tools generated. WORKSHOP ASSESSMENT To gauge the effectiveness of the workshop in providing the resources and creative sparks necessary for developing synthetic biology projects in the classrooms and laboratories of its participants, thorough pre- and post-assessment surveys were conducted. The pre-assessment was administered online approximately one month before the workshop and the post-assessment was administered with pen and paper on the final day of the meeting. The questions on the two surveys compared the participants’ pre- and post- workshop perceptions of synthetic biology as a distinct field, as an area for multi-disciplinary collaboration, and as a viable option for their classroom and research programs. The results of the survey comparison revealed a general feeling of excitement and improved understanding about synthetic biology (Figure 2), with the vast majority agreeing with the comment from one participant who stated that “I now feel confident that I understand the basic ins and outs of synthetic biology—what it is and isn’t—as well as how I can implement projects in this area with my students.” Interestingly, although 75% of workshop attendees had previous experience in basic molecular biology laboratory work, data analysis, and experimental design, only 25% had ever engaged in a previous multidisciplinary collaboration. This trend was reflected in the post-assessment of the meeting as well, as many felt that the forging of collaborative projects that satisfy the intellectual curiosities of faculty from disparate disciplines stood as the most significant challenge for the successful implementation of synthetic biology projects. Several participants noted that the meeting was, in the words of one attendee, “important to meet and establish a network of colleagues,” and it was evident to meeting participants that the establishment of collaborations between different disciplines and between different institutions of all sizes will contribute greatly towards the successful implementation of synthetic biology projects that expose students to the collaborative and multidisciplinary nature of modern scientific research. Indeed, the establishment of multidisciplinary collaborations engendered by this workshop reflects the need for academics from different disciplines to join forces to share ideas and resources in their educational endeavors as obstacles including scarcity of individual college resources and increased competition for research funding threaten to curtail the development of scientific educational opportunities for students (Dodson et al., 2010). INCORPORATING SYNTHETIC BIOLOGY IN RESEARCH Research in synthetic biology is an excellent way to bridge the STEM disciplines in a way that is accessible to students. The research is well-suited for undergraduate involvement as evidenced by the increasing number of teams competing at iGEM (129 teams registered for 2010 as of July versus 112 teams in 2009 and 84 in 2008). While the majority of these teams are from research universities, primarily undergraduate institutions such as Davidson College and Missouri Western State University have been successful at the competition and have also published some of their work in peer-reviewed journals (Haynes et al., 2008, Jordan et al., 2009). Also, many undergraduate institutions are well-positioned to pursue projects in synthetic biology since only basic computer and molecular biology resources are needed and the necessary reagents are relatively inexpensive. While iGEM participation allows access to the entire library of available BioBricks™, participation in this program may be cost-prohibitive for many institutions. The GCAT community currently exploring strategies to address this issue but notes that in the meantime it is relatively simple to construct plasmids using BioBrick™ strategies. There are a number of approaches that may be taken to develop research programs in synthetic biology, which range from student-generated, self-contained summer research projects to long-term, faculty-designed projects designed for student involvement over a number of years. To develop bona fide interdisciplinary projects, it is important to create the time and space for the idea generation. If possible, GCAT suggests attending iGEM as an observer to see first-hand the wide range of approaches to synthetic biology. Closer to home, exploring previous iGEM projects online and the resources GCAT has to offer on synthetic biology can also provide a good jumping-off point. Also, a successful interdisciplinary synthetic biology collaboration is dependent on communication by scheduling regular meetings between partners. The Davidson/Missouri Western team achieves this by holding weekly biology/math colloquia with interested students via Wiggio.com that connects the campuses as mentioned above. Over time, the professors and students gain an appreciation for the interconnectedness of different disciplines and, importantly, have fun in the process. INCORPORATING SYNTHETIC BIOLOGY IN THE CLASSROOM The presentations and exercises from the workshop sparked many conversations about ways to use this material in the classroom. The accessibility of parts and the willingness of the synthetic biology community to share knowledge and, potentially, resources with beginners have most participants preparing lab experiences for the coming academic year and beyond. Brainstorming about ways to make a bacterial “lava lamp” got most of the workshop participants excited to think of the variety of tasks that bacteria can be induced to perform. The designing of a long-term classroom project with a long-range engineering goal in mind could be a very good way to enlist the creative talents of your students. Whether or not it ever got built, contemplating the feasibility of such a project is very likely to elicit significant student buy-in to synthetic biology concepts. Once the students have taken mental ownership of the overall picture and seized upon a long-term goal, there are innumerable things to try, from straightforward to Byzantine. For example, one might examine whether the dose response of an inducible promoter is linear by creating a promoter + ribosome binding site + GFP plasmid and measuring fluorescence as a function of inducer concentration. Cis-trans effects could be examined by using two plasmids, one carrying kanamycin resistance as well as one structure of interest and one with ampicillin resistance and the other structure. Other variables could include bacterial strain, ribosome binding site, distance between the various components, promoters, etc. Much new learning could occur with the available building blocks, or the students could create new ones to test their pet ideas. It seems that the only limitation is the imagination of the student. Any new creations could be entered into the Registry of Standard Biological Parts and the GCATalog for sharing with the community at large. SUMMARY Synthetic biology is a newly-emerging field, in which costs are relatively low and the value of student input can be high. It rewards tackling the sort of interdisciplinary problems that are increasingly important for our students' professional futures but are often difficult to undertake from our traditional disciplinary towers. Undergraduate students have shown both interest and ability in pursuing this research, as the results of 5 years of iGEM jamborees amply testify to their success in this endeavor. The organizers are considering the possibility of offering additional faculty workshops in future; if they do, the participants of the 2010 meeting believe that there cannot be a more focused, effective, and fun introduction to synthetic biology for those who want to explore this exciting new field.


WORKS CITED

Campbell M.A. (2005). Meeting Report: Synthetic Biology Jamboree for Undergraduates. Cell Biol Educ 4: 19-23.

Dodson MV, Guan LL, Fernyhough ME, Mir PS, Bucci L, McFarland DC, Novakofski J, Reecy JM, Ajuwon KM, Thompson DP, Hausman GJ, Benson M, Bergen WG, Jiang Z. (2010). Perspectives on the formation of an interdisciplinary research team. Biochem Biophys Res Commun. 391(2): 1155-7.

Ferber, D. (2004). Microbes made to order. Science 303, 158 -161.

Gibson D.G., Glass J.I., Lartigue C., Noskov V.N., Chuang R., Algire M. A., Benders G.A., Montague M.G., Ma L., Moodie M.M., Merryman C., Vashee S., Krishnakumar R., Assad-Garcia N., Andrews-Pfannkoch C., Denisova E.A., Young L., Qi Z., Segall-Shapiro T.H., Calvey C.H., Parmar P.P., Hutchison III C.A., Smith H.O., and Venter J.C. (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329 (5987), 52

Hasty, J., McMillen, D., and Collins, J.J. (2002). Engineered gene circuits. Nature 240, 224 -230.

Haynes KA, Broderick ML, Brown AD, Butner TL , Dickson JO, Harden WL, Heard LH, Jessen EL, Malloy KJ, Ogden BJ, Rosemond S, Simpson S, Zwack E, Campbell AM, Eckdahl TT, Heyer LJ, Poet JL (2008 ). Engineering bacteria to solve the Burnt Pancake Problem. J. Biol. Eng 2: 1-12.

Jordan B, Acker K, Adefuye O, Crowley ST, DeLoache W, Dickson JO, Heard L, Martens AT, Morton N, Ritter M, Shoecraft A, Treece J, Unzicker M, Valencia A, Waters M, Campbell AM, Heyer LJ, Jeffrey L. Poet JL Todd T. Eckdahl TT. (2009). Solving a Hamiltonian Path Problem with a Bacterial Computer. J. Biol. Eng. 3:11

Martin V.J., Pitera D.J., Withers S.T., Newman J.D. and Keasling J.D. (2003). Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21,796–802

Purnick P.E.M. and Weiss R. (2009). The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410-422

Sprinzak D., and Elowitz M.B. (2009). Reconstruction of genetic circuits. Nature 438, 443-448.

Tsuruta H., Paddon C.J., Eng D., Lenihan J.R., Horning T., Anthony L.C., Regentin R., Keasling J.D., Renninger N.S., and Newman J.D. (2009). High-Level Production of Amorpha-4,11-Diene, a Precursor of the Antimalarial Agent Artemisinin, in Escherichia coli. PLoS ONE 4(2): e4489.


Figure 1-- GCAT Synthetic Biology Workshop participants, organizers, and HHMI representatives. Top row (left to right): Laurie Heyer, Jeff Poet, Jeff Matocha, Nathan Reyna (back), Malcolm Campbell, Qiang Shi, Kathy Ogata; second row: Nighat P Kokan, Robert M. Jonas, Santiago Toledo, Vidya Chandrasekaran, Valerie Burke, Yixin Yang, Andrea Holgado, Anil L. Pereira; third row: Todd Eckdahl, Susmita Acharya, Consuelo Alvarez, Paul F. Hemler, Michael J. Wolyniak, Libby Shoop, Paul Overvoorde, Nathan Reyna, Matthew Tuthill, Carl Salter, Chris Jones, Robert Morris, Tom Twardowski, Joyce Stamm, Talitha Washington; Last Row: all participants, Theresa Grana, Leo Lee, Jodi Schwarz, Teresa A. Garrett.

Figure 2—Comparison of pre-assessment and post-assessment of the GCAT workshop by its participants.

Synthetic Biology Workshop, Davidson, July 2010


Morris: In Eric's section, I think he meant devices instead of devises, and in Andrea and Anil's section #8 I think the Endy lab is at Stanford, not Sanford. This is my first ever effort at group paper writing using a wiki, so please bear with me. I do not envy Consuelo and Michael's job of giving this one voice, and look forward to seeing the more nearly finished product.

Anil: Morris, thanks for pointing out the typo. I have corrected it. Dear All, I made the following notes on the Birds of a Feather Meeting – Non Biologists. Please include any content as you see fit.

A question was raised regarding the level of mathematics used in synthetic biology as evidenced in some of the projects presented during the workshop. Would mathematicians find the level of math challenging enough to be drawn to the field? It was felt that that even though many mathematicians may not find the mathematics challenging enough, the focus of applying mathematics is in modeling the biological processes involved. This provides a way to compare those results that are predicted, to those that are observed. The mathematical models can be used to predict possible outcomes of a proposed approach and also verify its feasibility before beginning any implementation work. It was also felt that mathematicians might want to know what they could contribute. For example, they could contribute by modeling a diffusion process.

The challenges of inter-departmental collaborations within and across universities were discussed. Since most departments have their own way of approaching things, faculty members who are attempting collaboration might get frustrated with possible impediments. Departments must make changes to foster collaboration. Also, institutional changes must be made as a result of faculty members conducting collaborative research. For example, faculty members on tenure committees must learn that it is quite common for collaborative research papers to have many authors. This does not diminish the contribution of one or more of the authors. Also, the names of authors on papers are ordered differently depending on the field.

The challenges of cross-disciplinary collaboration where the experience level of faculty members in their respective fields might vary, was also discussed. Faculty members who are more experienced in their fields might be frustrated with the lack of adequate explanation provided by their colleagues. For example, a chemistry professor did not receive an adequate response from the junior colleague to a query regarding polymerization.

The issue of how much time non-tenured faculty members must spend with their students for research as opposed to tenured faculty members was discussed. It was felt that while tenured faculty members might have the luxury of attempting new research and yet be unsuccessful, tenure track faculty members might be adversely affected by failure. Pragmatism in choice of research topics and time management was advised.

It was felt that one of the concerns for potential collaborators in the field could be: what constitutes service to the synthetic biology research community? Such faculty members can be informed that contributing parts to the community counts as service to the community. Other concerns could be: how does one become part of the community? How does one contribute to or access shared resources? How can one teach non-biology majors basic concepts in biology? When does one introduce these concepts? How can one better communicate with Biologists? The importance of maintaining a glossary of key abbreviations and their explanations (for example, ds DNA) was discussed. Such a glossary must be readily available to future synthetic biology workshop participants and collaborating non-biologists. It was also felt that some pre workshop material and preparation might help the non-biologists. The instructors explained that they felt a common language could be developed through the interaction of the biologist and non-biologist pairing in the workshop, where the biologist can introduce his/her colleague to basic concepts in biology. Participants agreed that this approach was quite helpful.

Halomicrobium mukohataei Genome Fall 2009


Halorhabdus utahensis Genome


Missouri Western/Davidson iGEM2010


Missouri Western/Davidson iGEM2009


Davidson/Missouri Western iGEM2008


MAGIC Tool Development


Nova Southeastern University


== Davidson College== Small liberal arts college near Charlotte, NC. A. Malcolm Campbell and Laurie J. Heyer GCAT faculty

Next School Here





Please see documentation on customizing the interface and the User's Guide for usage and configuration help.

GCAT Main Page

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - bacterial communication with light.

http://parts.mit.edu/igem07/index.php/Cambridge - they talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Tokyo_Tech - They say, “Bistability and cell-cell communication are necessary to realize our model of ‘Balanced differentiation’.”

Retrieved from "https://gcat.davidson.edu/GcatWiki/index.php?title=Main_Page&oldid=11682"