Unit 2: Road to iGEM

This unit guides you through starting a team, brainstorming for topics, paper reading, parts designing and ordering, lab experiments, results analyzing, wiki, poster and presentation preparation and finally, going to the iGEM Jamboree.

How to start an iGEM team

(How to build an iGEM team, iGEM Paris Bettencourt, https://youtu.be/Y58rhJoHzWM)

Recruiting team members

There are mainly six kinds of people you need to hunt for. The six types of members are specialised in different areas

The Bosses, Primary and Secondary PIs, adults in charge

Principal investigators (PIs) are individuals in a position of authority who are responsible for the team. So simply call them the Bosses. The Bossed are not very engaged to the team’s project but their signatures can be everything to the team. This includes the official team registration, the team poster, certifying the safety form, payment of the team’s fees, and any other official aspect of the team. The Bosses provide guidance and support throughout the season, including assistance with fundraising, lab support, and help with school bureaucracy and regulations. The Bosses should plan on accompanying the team to the Giant Jamboree. The Bosses serve as the official points of contact for iGEM Headquarters; the Bosses must be able to receive emails / phone calls from iGEM HQ, and respond promptly. Each team must have at least two Bosses (primary and secondary). In a high school setting, the Primary PI is most likely the biology teacher in charge; Secondary PI would be biology lab tech or another less involved biology teacher.

The Bookworms, Students rich in knowledge and idea

This group of student initiate the project. They look for unsolved problems in daily life and research on the topic. Broad science and engineering background is required so that they can link knowledge of different aspects together to tackle one single problem. Long hours of frustrating online research and literature review is demanded. Using their background knowledge and some newly collected information from the Internet, these students select the best research topic from the brainstorm and then start working on them. Their main job is to outline the goals of the project and design the details of the project and the BioBrick parts. After outlining the project, they need to design the experiments to test their ideas. But to a practical level, this is where the Lab geeks come into picture and help the Bookworms to design wet lab experiments. With the Lab geeks providing practical procedures and experiment results, the Bookworms usually take up the workload of writing the full scientific report, providing content for the wiki page.

The Lab geeks, Organised and flexible students who ace lab work

This type of student execute and verify the ideas from the Bookworms by practically doing wet lab experiments. They advise the Bookworms with their practical experience when designing the experiments. While doing experiment, they are in charge of the modification of in lab work and possibly in project design. The Lab geeks must be well-organised to work in the lab, so that they come out of the lab in one piece. Maintaining a good record of their lab work is also essential for them. The Lab geeks may find themselves involving in material ordering too. A good iGEM team also needs a lot of facilitators to help run different projects smoothly. The Lab geeks should have solid science knowledge background and is versatille to carry out different aspects of work, from the logistics of the team to the experiments.

The Tech nerds, student(s) who know everything about programming

The Tech nerds need to know at least how to create a webpage using HTML and CSS. They are responsible for the creation of the team’s wiki page, for the display of progress and results (wiki page is discussed in later units). They also provide technical support for the team whenever needed, for example the sharing of resources on drive, producing high quality and good-looking presentation documents, or even designing softwares for the team and iGEM. Besides, if the team need any custom programs to facilitate their research, Tech nerds are also responsible for it.

The iGEM experts, one who knows iGEM back to front

This person/ group of people need to be very familiar with every iGEM process and requirements. These students are in charge of monitoring the progress of the team, checking if the team is fulfilling medal requirements. Students without strong biology background is also suitable. They might not be the expert in all professional knowledge, but they should have some background knowledge of the synthetic biology too. They are also responsible for the extremely important sections of iGEM, such as human practice and public engagement. (will be discussed in next unit)

The “Dorothies”, born to be an administrator

A team member who takes care of all other team members. Dorothies needs to book the flight tickets, hotel and university admission talks. The Dorothies will plan for the whole iGEM Boston trip, including search for sightseeing locations and taking us there, taking us grocery shopping. A lot of times, the Dorothies are mistaken to be the teachers in charge when visiting university and science museum. As the facilitator between the team and other team and iGEM HQ, the Dorothies help contact iGEM HQ when anything goes wrong.

Team registration

Below are the steps the register a team.

Create a new account for your team PI, or use an existing account of the team PI
Create a new team here: http://igem.org/New_Team.cgi
Pay the registration fee
Create user accounts for team members and add them into the team

For non-high-school teams, your team PI will have a team membership code for members to join the team directly. Students have to enter the code while joining a team in http://igem.org/Join_Team.cgi.

For high school teams, students have to fill out consent forms and send to iGEM to add members into the team. Details of consent form will be discussed in later sections.

Forms to fill in

The deadline of the below forms vary each year, check the iGEM website for the latest deadline.

Consent Form

High school teams have to send the filled out consent forms to iGEM in order to add their team members into the team. Every team members need to get their parent’s agreement to join the competition. Besides, for every school participating in the team, the principal need to fill out a consent form too. The forms can be downloaded from the iGEM wiki of that year. After all forms are filled, the hard copy must be sent to iGEM HQ.

Safety Check In Form

Not every team need to submit the safety check in form. Only teams which plan to use organisms or parts outside of the whitelist need to submit the form. The form submissions will be review by iGEM safety experts, evaluating the risks of using that organism or part and will assist the team in handling those organisms or parts. Check the iGEM website for the latest version of the whitelist.

Safety Form

To ensure safety, iGEM requires all team to submit a safety form. It helps iGEM access the possible risks of your project. In the safety form, you maybe asked below topics:

Overall plan of your project
Possible risks identification
Risk awareness

Judging Form

The judging form is very important as it tells the judges what to expect. In the form, you will tell iGEM and the judges what prize are you aiming form. For example, if you are aiming to get the “Best part collection” prize, you have to fill in the parts’ code in the form, so that judges can evaluate those parts.

Brainstorming for topic

At this stage the whole team is involved in trying to find a suitable topic. A lot of problems are out there, even ones that involves energy, can be a great iGEM topic, so be creative and don’t hesitate to try out new ideas! You can also think of improving a previous idea. A good iGEM topic should have these following qualities.

Firstly, it should be a practical and possible to be done in your own level. Even Though it is possible for us to borrow universities lab and equipment, you should still check whether the idea is simply an imagination and its difficulty level. If the project is way too complex, the time distribution and manpower distribution should be better organized. You might want to consider simplifying the project a bit.

Next up, you should make sure the idea is safe and ethically sound. This is very important as one of the core values of iGEM is to promote the biosafety and ethics of the field. It is not acceptable to carry out any experiments or handle potentially hazardous projects as it may cause harm to the environment and personnel handling it.

Another important thing to notice is that you should make sure that your idea is somehow better than other current approaches. The iGEM also focus on the project being economical and it would be best to show that your idea of using synthetic biology approach is better than the current approach of such issue.

Lastly, you should make sure that your project has a significance to your local community. The judges love to see ideas that originate from small, real life stories. Being down to earth helps the project connects with the local community and will be easier to carry out human practice and public engagement part.

With these limitations being said, you should not be afraid of exploring weird and interesting topic. Being curious and creative is always very important.

Literature review

Doing literature review is a very crucial step as it provides background knowledge and gives insight to possible problems that will be encountered. It should start once the topic is confirmed and the whole team should be involved, as this process is very time-consuming and might be very difficult to find suitable paper. It can be a very demanding and frustrating job as you will have no idea what you are reading at the beginning. Everyone goes through this phase of reading 10 extra papers just to understand that one original paper.

As you gain experience and knowledge, the reading will become much easier and faster. If you encounter some new concepts and vocabulary, it is best to look them up immediately and jot them down in a notebook. This would greatly help you to build a larger scientific vocabulary bank. The following table shows you some open access and free tools in doing a literature review.

NCBI (The National Center for Biotechnology Information)

An extensive database on all biological fields. It is a very useful tool in finidning papers and sequence of DNA. Other functions related to literature review includes PubMed (Biomedical resources), Gene (info about that gene), Protein(info about the protein)

https://www.ncbi.nlm.nih.gov/

PLOS

A site to find different scientific journals. Can be sorted in subjects.

https://www.plos.org/

Uniprot

Uniprot is an excellent tool if you want to learn more about a certain protein. Amino acid sequence and other information can be obtained through this site.

http://www.uniprot.org/

iGEM wiki

What a better way to understand the part by visiting the original team site. This may give you a much more in depth understanding of the part and experience of handling it.

When you read a paper, it is important to employ certain tactics to speed up your reading. So here are a few tactics you can use. Firstly, read the summary very carefully and grasp the idea of what the author wanted to achieve. To save time, you can skip the Materials and Methods (M&M) section, but you should never skip diagrams, charts and captions. Another key section you should focus is the discussion of the result as it gives you the results of the experiment and it may give you some heads up for possible errors.

Project design

Once you have confirmed the topic and have an idea of what your team wants to accomplish, you should dig deep into the problem to be tackled. Find out 1-3 specific goals that you want to achieve.

You should then research for any existing solutions that achieve those goals. If they are successfully achieved by previous iGEM teams, you are not advised to continue with that idea unless you are confident in surpassing their outcomes. In most cases, the problem is solved in physics, chemistry or biochemistry ways. In these cases, you have to try to solve the problem with synthetic biology and genetic engineering.

It is best if the biological machine tackles the same problem more efficiently in time and cost than the existing methods. After you have a better solution, you need to start designing your own composite parts in order to achieve your goals. Please refer to the next unit about part design. You may find the gene of interest in many places. You can also order your designed composite parts from many biotechnology company. For our usual practice, please reference to the next section.

Part ordering

After you have designed your parts, you are highly recommended to order the parts from IDT. However, as IDT provides a lot of difference service regarding DNA synthesis. Our most used service is the gBlocks Gene Fragments and Custom gene synthesis. Note that IDT has sponsored each team with 20 kb of free gBlocks Gene Fragments (in 2018), so make good use of it.

gBlocks Gene Fragments allows for a rapid and free DNA fragment synthesis on your demand. However the length of the gBlocks Gene Fragments is limited to 3000 bp or lower. If your part (gene of interest) and the pSB1C3 plasmid backbone together is less than 3000 bp, you should use this service. Don't forget to add the iGEM prefix and suffix to the part that you ordered. This method of ordering is already iGEM compatible as the backbone is pSB1C3, the iGEM standard vactor.

Link: http://sg.idtdna.com/pages/products/.../gblocks-gene-fragments

Another service that we commonly use from IDT is the Custom gene synthesis, which is excellent for synthesizing parts that are not applicable in using the gBlocks service. The Custom gene synthesis allows you to synthesize a DNA sequence according to your demand and shipit in an IDT Best-fit vectors ( with various selective marker available). This allows the user to transform the plasmid directly and carry on with their assays. Remember to add the add the iGEM prefix and suffix to the part that you ordered so that it can be reassembled into other plasmid backbones (pSB1C3). However, the plasmid order from this not iGEM compatible as the plasmid backbone is not pSB1C3. Therefore, prior to the submission of parts, it is necessary to clone the gene into the pSB1C3 backbone via restriction digestion and ligation.

Link: https://eu.idtdna.com/pages/products/.../custom-gene-synthesis

The detailed procedure of using IDT will be discussed later.

Wet lab

Phase 1 - Cloning

Flowchart of the cloning process

Once you have received the parts from IDT, you can begin the cloning process. Please watch this video on how to handle the gBlock fragments:

However, this step is advised to be carried out in the collaborated university laboratory as they have access to essential equipment and can provide better experience. Like ordering, the process of cloning is different for products plasmid of gBlocks Gene Fragments and Custom gene synthesis.

For product plasmids of gBlocks synthesis (iGEM backbone pSB1C3 included), it is ready to be transformed directly into the cell. After transformation, you should streak some of the cells out into another plate. This batch of cell should then go through plasmid preparation (mini-prep) to extract their plasmid for sequencing by BGI. This is crucial as it checks whether the sequence that was shipped is correct. The plasmid contained in these cells are also ready to be submitted to iGEM as the plasmid backbone is the iGEM shipping backbone pSB1C3. The remaining cells can be used in the Wet Lab phase 2: assays.

If the plasmid is ordered from the Custom gene synthesis, it would be pre-assembled in a vector (IDT Best-fit vector). If you wish to carry out assays, this plasmid is already ready to be directly transformed into cells. Remember to use the appropriate antibiotic as the selective marker for transformation. Various assays can then be carried out. You should also mini-prep to extract the plasmid for sequencing. For submission of the part, you are required to clone this part into a standard iGEM backbone pSB1C3 by restriction digestion and ligation. PCR and gel electrophoresis is recommended after the ligation to ensure the cloning is done successfully.

Cloning is one of the most difficult steps in the road to iGEM as it is very time-consuming and encountering technical difficulties is very common in this stage. Most high school labs has very limited abilities in cloning so we often collaborate with other teams to cope with technical difficulties. It is highly recommended to have a Wet Lab log book to keep track of all the cloning procedures and result as this would help the troubleshooting process immensely.

Phase 2 - Assay and Test

Once the cloning procedure and various measures of checking (Run gel and sequencing) is done, you can begin the assay phase. Just like the cloning phase , the assay and test phase is also one of the most difficult steps. As the assay required for different project is different, it is not possible to provide a guide to exactly what you should do. However, there are some general reminders and tips:

Firstly, you should have a clear idea of how to test the part since the project design phase. Finding the right equipment and Laboratory to carry out the experiments can sometimes be very challenging and in a worst case scenario, you might not be allowed to test the parts as it may not be safe. To prevent such situations happen, you are advised to think about every aspect of the testing phase during the project design phase. Do not leave developing the assays until the very last minute as it often requires some major modifications. Experiments too dangerous(eg.pathogenic substances and blood) or that requires too complex equipment (eg. HPLC) are not recommended to be carried out.

Secondly, you should look at various standard test method regarding your test. In order for your test to be representable, it would be best to use the standard test method if it is available to you. If it does not completely suits your requirement, you may want to consider modifying it to your needs. If there is no current test method for it, it is acceptable to create your own, but make sure that it is a scientific and fair test.

Thirdly, keeping a good lab record is essential in doing any wet lab work, and this obviously applies to the assay and testing phase too. You need to record the details of each procedure, modification, calculation applied to each experiment. Keeping a precise and systematic lab record will help you figure out where the errors come from and helps medicate with human error. this will help the troubleshooting process immensely.

Fourthly, make good use of control experiments(both positive and negative control) can help you sort out the error. This is one of the most basic techniques in science (together with fair test) but it is still extremely important to help explain errors. A good set of control should indicate certain key factors that may affect the experiment, and give insight to what may have actually went wrong, ultimately helping the troubleshooting process.

Assay and test phase may be the most frustrating times of the whole journey to iGEM, but do not give up, but it is also one of the most rewarding and memorable phases. So brace yourself and get ready to start doing lab.

Part Documentation

iGEM requires teams to document each of their registered parts. The documentation of a part is basically describing the design of the part and how the part functions. You need to include information clearly in order to help people understand how your construct works. As iGEM is an open database, the ultimate goal is to let others use your part in their own projects.

On this page, you would like to talk about the importance of the encoded gene in your project (1). In the above case, the chemical pathway from phenylalanine to cinnamaldehyde is shown to illustrate the action of 4CL gene. You may also want to include assays on your construct to explain how the part function practically (2). In the above example, the results of cinnamaldehyde volatile test is presented in graphical method in order to infer that cinnamaldehyde has properties that we expected.

Poster, Presentations and Wiki

The poster, presentation and wiki are all of the mark-bearing items. Therefore teams must complete these items. Of course you would want to make these items as presentable as possible.

Poster of Team Heidelberg 2015

Before the real presentation session in the Giant Jamboree, your team need to produce a powerpoint for it. This powerpoint presentation is extremely crucial-- you have been working on your project for one year or two. This half an hour is all the time you get to showcase your achievements. Would you want to screw up your presentation and waste all your time and effort? Below are some guidelines and suggestions for your team to perform well in the presentation. You are suggested to cover 7 slides in every 5 minutes. Since you will speak for 20-25 minutes on stage, prepare a minimum of 28 slides. Your powerpoint should be eye catching, easy to read and have a simple design. Use graphics to aid your explanation whenever possible. Never attempt to pack a huge amount of information in one slide. It is appropriate to make some, not too many, jokes in the presentation.

You should include the following in your presentation:

Inspiration to your project
Background knowledge on your topic
Introduce your constructs
Explain in detail how each basic part and composite part works
Explain the design of assays
Present the experiments results orderly, preferably in graphs or tables
Pose further investigation
Difficulties faced in the project and improvements to be made
Introduce what have you done to meet the requirements for Human practice, Public engagement, Collaboration and Interlab.

At the end of the above presentation slides, prepare some extra slides for the Q&A session. You can treat these slides as supplementary information. There is no limitation for the number of these slides, most of them will not be used at the end of the day but it is always best to prepare for everything. Predict the question asked by judges. According to your predictions, produce slides containing pieces of extra information (e.g. reference article, very detailed chemical pathways, error calculations, failed attempts…) to aid your response.

Wiki is the record of the progress and description of your accomplishments. The contents and design of wiki will be discussed in detail in Unit 7.

Giant Jamboree (updated to 2018)

The Giant Jamboree is held annually in Boston in late-October to early-November, usually lasting 4-5 days. It is the climax of iGEM. Registered teams from around the world gather in Boston to present their projects. Before the official start of Jamboree are Registration, Audio/ visual check and Poster Set Up sessions.

The Opening Ceremony notes the start of the Jamboree. Teams may choose time slots for their presentation. In general, a total of 3 teams of same category present in each session. Each team holds the stage for 30 minutes, 25 minutes for presentation and 5 minutes for responding to questions from the judge panel.

Aside from Presentation sessions, there is a Poster session every evening where judges may visit the teams poster area and ask some questions about anything about the project. Both the Presentation and Poster session are mark bearing sessions. The atmosphere of Poster session is not as serious as presentation session. However, members who did not present in the presentation session are more likely to be challenged by judges. Therefore, every member should be ready for questions. Even if you are not an expert on every area in your project who can explain all the details, at least you should know how the project work on a whole. The non-marking bearing sessions include the opening and closing ceremonies, seminars, workshops, talks and social events. Be prepared for a party scene in Giant Jamboree. You will find yourself in a party thrown by biology enthusiasts. To get the most out of the competition, try to engage in conversations between iGEMers and share your ideas freely. Hope you find your place in the Jamboree.

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