From 2007.igem.org

Réunion le lendemain de la conférence Synthetic Biology 3.0

Contents 1 Présentations informelles des équipes 2 Recommendations de fonctionnement 3 The sites useful for you: 4 Documentation 5 Introduction to the Registry 5.1 Let us look at this procedure with some more details:

Présentations informelles des équipes

Equipes présentes:

• Paris
• Bologne
• Naples
• Glasgow
• Brown university
• Valencia
• Edimburgh
• Lubjana
• Lethbridge (Candada Alberta)
• St Petersbourg
• Ankara Turquie
• Mexico
• UC Berkeley (2 teams in the same lab and a high school team)
• Freiburg
• Imperial college

(personne de l'équipe de Zürich!)

Pas du tout de présentation des sujets, mais de la constitution des équipes, l’organisation, le financement etc...

Recommendations de fonctionnement

Utiliser le WIKI: use the WIKI as much as possible for the daily work. So let us also continue in english...

Do not hesitate to make changes on the registry and igem wikis; as well to comment on the other teams’ wikis. Your results will be presented on your iGEM wiki it is this page that will be evaluated. Startt immediately to work on, with this wiki, it a tool, and it will be your result. This year there will be less emphasis on the presentation at the jamboree ant much more weight at the wiki. Also, the wikis will be frozen about one week before the jamboree for evaluation. So it is better to be ready long term in advance.

Do not hesitate to communicate with the other teams. Use their wikis, use mails, communicate and exchange experience.

Work immediately with the registry. As soon as you have an idea of a part, look in the wiki if anything similar is already there. Begin the procedure for addihng a new part as soon as you are thinking about one ! Your entry will be stored in a special section of your team’s registry wiki: the sandbox, where you can work and play with it without committing if officially to the registry’s database.

The sandbox is accessible through our iGEM team’s wiki. When you login on the registry with your user name, you see the parts that are in your team’s sandbox. Just click and you can continue editing them. Parts in all the sandboxes of all the teams are searchable through the registry’s search function: they are not private and hidden. This is in order to help you if any other team is working on the same parts! This should not prevent you to add parts in the sandbox, even if your thoughts and investigations are in a very preliminary form! You can consult, correct, comment, contribute on the other teams’ wikis and parts ! And you can join efforts with other teams. When ready, you can choose to promote the part in the sandbox as regular registry parts.

Go and spend time with the iGEM websites in order to learn how to use them and gain experience from previous efforts. There are plenty of websites and it is a little bit confused. Randy and everybody elese agree and this should be improved in the future. A source of confusion is also that you may often be required to reenter your login several times. Login on the iGEM wiki and on the Registry wiki is not the same (altough the account and your user name and password is the same). It happens that the systems may ask you to login sometimes when you switch from one site to the other. Again, this should be improved in the future.

The sites useful for you:

The [http://igem2007.com igem2007.com] website

This is the public presentation site of this year’s competition. It will present results and general information. To you for the moment it can be seen as a portal for the to the other sites. In particular,

The igem2007 wiki

Here you can go on your team’s wiki page. Please update your personal information!

The http://partsregistry.org Registry and the Registry’s wiki]

There is here a subtelty since the two are accessible through the same interface. What you have to realize is that the Registry is a database: the database of BioBricks parts. And Randy introduced a protection on this database: it can not be changed by anyone at his own will. At the same time you have the Registry’s wiki: where the biobricks parts are documented and commented. Each part in the registry has an entry in the Registry’s database and in the registry’s wiki. When you call a part on the Registry’s website you see both kind of information: editable informations that you can change through the wiki and non editable information. Non editable information is for instance what you see when you click on “Hard information” in the navigation bar on the left that appears when viewing a part: it gives you the sequence, sequence that you are not allowed to directly change. Another non editable information is th “Physical information”, that gives you the reference of the well on the Biobricks microtiter plates, where the Biobrick is stored. The only way to know if you are viewing a registry’s database entry or an wiki’s is if an “edit” menu is available on the page !

Use of the Bibricks library (the microtiter plates): well all the microbiologist of you surely master the practice, however when you want to use a biobrick of the microtiter plates (the four plates we recevied cover 99% of the whole library), make a tiny hole in the cover, add water, pipette out a little bit, and to a culture over night of the plasmids to amplify a make our own reserve of the part! Do not use the microtiter plates as the reserve. Detailed protocols, dilutions etc... are somewhere in the documentation on the Registry wiki.

Further websites that may be useful to you: the igem2006.com website, and the igem2006 wiki (accessible for the previous site).

Documentation

New documentation and help has been added recently on the registry and the igem 2007 website (the website .com, not on the wiki). On the latter you can find new video podcast introducting you to practical igem work. In particular you can follow the same tutorial that the teachers have recevied during the workshop. You have also a video podcast on laboratory work. Randy suggest you to use podcasts and videos to docupment your wiki... think at it! (they can help you how to do it, just mail them). On the registry’s documentation and help page, the tutorial pages have also been improved.

Introduction to the Registry

A whole iGEMsummer project in one hour...

So let us take an example. Inspired by the miint senting E. coli projet of last year MIT team you want to synthetize a vanilla parfumed E. coli. Let us play the game how to produce vanilla parfume. This example should be the same as in the tutorial online, and in the video podcast. Go and check also there! In summary:

• search the registry with keywords of what you’re interested in
• look in the literature for reference of the compound (google, pubmed, etc..)
• get sequence in Genbank
• add a part in your registry sandbox
• document your entry as much as possible (accession number, references, description of use,...)
• include links with other registry entries that you make use (especially for compound parts)

Let us look at this procedure with some more details:

Always start with looking in the registry.

The search function on the registry makes a google search on the registry website. You can search with keyword “vanilla”. Ok, not many responses. Extend with a whole google search, vanilla, vanilla protein, vanilla production,... you can find that in fact you need a protein called vanillin, to get vanilla. Back to the registry, let us search for “vanillin”. Yesy! There is a part documented for “vanilin”. It is from last year Valencia team! Oh, it does not produce vanillin, it docks vanilla! Well this is great. If we synthetize a vanillin producing bacteria, we gained an intercellular communication system!

How to synthetize vanilin? Some research is required. Let us go to pubmed, type vanilin. YES ! There is an article on vanilin production. Read the paper... vanilin production requires two genes fcs and ech.

We need to do parts for the production of the two associated proteins.

Get the sequence of the genes. We are lucky, in the methods’ section of the paper there is a direct link to the Genebank entries.

Go to gene bank, and get the coding sequence in FASTA format (select display FASTA in the menu)

Return to the Registry and let us start to ... add a part. This will be a basic part, DNA sequence, not a composite element. So we choose add a basic part. On the entry form select your team (you do not have any other choice but you have to select, this function is for other users). You will se a range of biobricks reference numbers that has been attributed to our team (we have 1000 numbers, if you plan to enter more than thousand parts you can, just contact Randy). So choose a new number for you new part and proceed:

• give a name
• select the part’s type, here it is a coding region, cds. You can otherwise select other types, e.g. terminators, promoters,...
• describe your part short
• describe your part long (this is a wiki, so you can add here figures, draswings images in the usual wiki’s way).

Attention: you are required to put text in all the fields, even if for the moment you have nothing to write. Paste the sequence you copied from genebank (without header). Here you paste you core sequence, not the biobrick’s sequence. That is you do not include in the sequence any biobricks prefix and suffix.

When all this is done and validated, the systems indicated if the sequence biobricksz compatible, that is it shows the possible conflicts with restriction’s enzymes cutting sites, that should be corrected before promoting the part to the registry database.

At any moment you can stop, and come back later. You come back to your part that is stored in your team’s sandbox through the registry wiki: browse parts by team, ann select your team. You see all the parts in your sandbox. Choose the one you are working on.

For instance something we can do now is: add a feature. That is we will enter in the system the description of some features on the DNA sequence we just stored. Here we will simply describe it as coding sedquence, and we do not have more features to add. Somewhere on the part description find out the menu “feature” and complete the form telling that the sites from 1 to the last one of your sequence correspond to a coding region. This region will be highlighted with a nice color code for a cds.

Now that we have the coding region we can use it to build a vanilin production device. We can decide to engineer a device that generates vanilin as response to some some signal. This device will thus be a composite part for which we need a promoter, a ribosome binding sequence, the coding region we just included as a part and a terminator. We can go to the Registry, in the “part by type” section and choose some adequate parts by reading the descriptions. Get note of the registry reference number of these elements (they have a format BBa_xxxxxxxxx).

Start adding a new part part (again this will be going in your sandbox). But this time you are entering a composite part. Choose accordingly: add a composite part. The procedure is the same as for a basic part, but you now have a “subpart” entry in the form where you must write one after the other in the right order as they would be on your plasmid and with a space character in between each, the reference numbers of the biobricks you are using in your composite biobrick (forget the biobrick prefix in the format, eg. do not enter BBa_180001 as reference, but 180001). Submit. Your new composite biobrick will then be shown with the nice graphical icons of each compound!

If you now want to know how to build your composite part from the existing biobick: use the registry. Visualize each part (click on it) and in the navigation bar on the left select “physical information”. This will show you the location on the Biobircks microtiter plates of the well containing the plasmids with the corresponding biobricks.

Last thing: you want to build a new composite part. Maybe there are parts that already contain a subset of your design in their own structure. On the wiki you can do a subpart search. In subpart search, paste the reference of your new composite part under development, it will automatically search the wiiki of any composite subparts of your parts that may already exist. If there are any , they could help in our assembly.