Team:BIOTEC Dresden/Scratch

From 2009.igem.org

1st may 2009

  1. recruiting more group leaders and post docs as instructors. we made a list of people we

are gonna talk to. please feel free to suggest any names you can think of.

  1. Arranging funds.. companies we can talk to.. sponsorship details etc..
  1. also made a list of people from MPI that we must speak to.
  1. getting lab space.. and some consumables to start the work.
  1. getting our own home page.
  1. also we decided to have a iGEM meeting every week.. and an unanimous desicion was made

to have it on tuesday at 17:15 every week. everyone related to iGEM is expected to attend. And we will circulate a mail regarding what will be discussed in the meeting a few days/1 day in advance.

cheers divya

12th may

so today tomek, priyanka and i, we met up with Michael Alvers from Transinsight. he might make a small contribution of which he will inform us on friday... also he offered to be a business advisor.he will advice us on approaching companies, which is what we need at the moment.

also he offered to provide us with a new software they are marketing.. called kalaimo.. its like a improvised version of imaris.. so if v do any particle tracking.. it will be very useful.

also he said he will spread the word.. about our igem team.. n talk to people he knows or thinks might be interested.

19th may

Today we divided the team into 3 groups, and assigned jobs to each group. these are the things that need to be done.. apart from the labwork..

it was decided that parallel work will improve efficiency ��

Group 1: Reading Deepika, stanley, arnab

until next week this group will work on a presentation content which will be used for funding etc, and also improvise on the current presentation.

Group 2: wiki Priyanka, Anja

until next week this group will brain storm and come up with concepts and ideas for the wiki page, also look at previous years wiki entries.


Group 3: funding Tomek, Daniel, Divya.

until next week we intend to get appointments and speak to 5 companies at least, and also some people at the MPI.

experimental work: anja and deepika have already started their part. the biobricks kit has arrived. so v have to get the lab space to keep our stuff.

Also there is a new advisor v have.. ilaria (phd student from schwille lab)

Missing 26th may ???/

2nd june The meeting today had a very low turnout

funding: we sent mails to all the companies whom we had contacted in leipzig.. haven’t got a reply from any.. so we intend to wait this week.. and make calls by monday.. also the ones that are in Biotec we will go to them personally on thursday.. stanley and I will be going to some of them.. it would be great if 1 or 2 more join.. we were working on the proposal with Ilaria during the meeting.. and it will be ready tomo..

we couldnt discuss about the other aspects.. because everyone was not present.


�� 9th june ???? missing 16th june ???? missing

23rd june

Ilaria and Kaj had some useful tips from the workshop, and the most important message was..USE THE PARTS FROM REGISTRY.

In the last meeting it was decided, we have to either come up with a new project using the biobricks or modify the current one to incorporate the biobricks.

S, the first task would be to read up on previous projects and look how they have used the parts from the registry. let us each read at least 3 previous projects and discuss them next week.. i have made a list(attached) of the prize winning ones and assigned 3 of them to each member from our team, emphasis should be on how the biobricks were used.. (If the advisors want to do it as well.. choose any projects u wish.. except the ones in the list)

Also please send your photos to priyanka for updating on the wiki. We should also have a group photo sometime next week (when Prof Schwille has time) for wiki

We got a reply from Eppendorf for sponsorship :). their representative is on a tour.. and will be in dresden in the 1st week of june.. and he wants to meet us.. he will inform us about the date and time later.

QIAGEN is willing to give us some kits.. so once we have designed our experiments.. we can contact them in this regard.

Priyanka/Tomek were supposed to contact someone regarding the silver binding sequence..

30th June Ttoday we discussed about the possibilities of altering our project.

Prof Schwille suggested that we use lipid droplets instead of GUVs, also Ilaria spoke to senthil and got some info from him about microdroplets, we could discuss this futher.

Prof Stewart was at the meeting for a while, and he discussed possibilities of using site specific recombinases, so he suggested 2 options which are interesting but can’t be done in vitro, so can’t be combined with the droplets. so we have to change our project completely.. But he also said that we could do them in 4-6 weeks, taking into account our inexpertise �� we could still say.. 8-10 weeks.. Which is reasonable..

we can talk about these projects and also about improvising these projects in our next meeting..

the 3 important points to focus on are    1. making a new part    2. making it compatible with the biobribks.    3. characterize it well.


7th july

   today we spoke with Senthil Arumugam, a PhD student of the Schwille lab who is working on microfluidics. We talked about the feasibility to use microdroplets for the iGEM project and he was really confident that we could easily achieve our goal using microdroplets. In other words, if we are able to make our genetic circuit work in a cell-free transcription-translation system, then there would be no problem at all in putting everything in a microdroplet.    Moreover he offered us his support in teaching to interested students how to produce and handle microdroplets. He told me that the training will take a couple of days and you will be quite confident in using this system in no more than a week.

other technical informations:

- Definition: microdroplets are small water droplets, separated from each other by a continuous oil phase, within a microfluidic channel. Surfactants can be used to stabilize the microdroplets and avoid their fusion. - The microdroplets' stability depends on the use of surfacts or lipis, anyways they last some hours. - The dimension range of the droplets vary according to the mix speed; usually 10-50 um. - in the Schwille lab there are two different mask to create microfluidics' circuits. they have both 50 nm channels, thus we should use this type of droplet dimension. one of the circuits have two separate acqueous reservoirs, this is interesting because we can keep separate two different solutions up to the droplet formation. i.e. separate the cell-free system from the genetic circuits?!?

14th july

1) the iGEM HQs want just an informal email reply for the July check-in telling them how our team is doing. how things are progressing with your team and project and what you're currently working on: brainstorming, lab work, wiki stuff, fundraising, etc. �� Ilaria took responsibility of this.

2) Bioethics. As everyone knows we receive a request from the TU-Delft team, and more generally we need to start to think about this issue.

Again, do you want me to write him back or any of you wants to take care of it?

3) the Schwille lab has only the LacZ-alpha fragment with a MCS right in the middle. Anyway in the Registry there is the whole LacZ [BBa_I732005] as well as the alpha-fragment [BBa_E0033], both are in Spring 2009 Distribution.


21nd july

since the turn out for the meeting on tue was very low (only 3) we kept it short.. and couldnt discuss much..

well.. Divya talked to the system administrator about the home page.. he said it can be done.. we have to send him the contents also for the home page.. we will need a igem team group photo.. this has to be done by next week.. so could everyone plz attend the next meetin.. at least for the photo.. if someone can’t make it.. please propose another day/time..

ilaria is goin to order the peptide..

we have to discuss about the changes to the project and write a summary.. this can be done in the next meetin..

28th july missing ????/ 4th aug missing ???? 11th aug missing ??? 18th aug missing ???/ 25th aug missing ??? 1st sep missing ?? 8th sep missing ???

�� 14th sep Discussed about the tasks has to be done in following days

  • Track selection by E-Mail to iGEM HQ: "Foundational Advance".

  @ILARIA: one track is not enough. you need to give the TOP THREE track   selections in order of preference!!! please e-mail them again.

  • Jamboree attendance fee: 175 USD per student, 375 USD per instructor.

  To be paid by Prof. Schwille once group leaders have decided on   people/money limit.

  • Request for variance (alternative BioBrick assembly or variant plasmids).

  Here we will submit three requests: Fosmid and two pSC101 variants.   (To be done by me and those who have been involved in cloning: STANLEY,   PRIYANKA, ARNAB)

  • Project abstracts: project title (max 15 words) and project abstract (max 150

  words) to be e-mailed to iGEM HQ for inclusion in the Jamboree program.   (To be drafted by TOMEK+DEEPIKA+DIVYA, we will decide on a final version   before Friday)

  • Team rosters: make final team list, make sure to have user accounts

  (not pending), list on team information page.   DEEPIKAA must apply for an account.   Prof Schwille must approve all pending applications.   DIVYA+DANIEL need to add team member list to the team information page (wiki)

17th sep Disscussed shortly about the things are done and would be done soon. 

   * Jamboree attendance fee          Prof Schwille will do it tomorrow

    * Request for variance              done     * Track selection                   done     * Project abstracts                 to be discussed, when?     * Team rosters                      done

21st sep Kaj distributed tasks in Stanley , Priyanka, and divya for further days:

All 7 constructs arrived from Geneart: P-F3-zeoR-F3-RFP: pMA-RQ vector �� TT-FRT-GFP-BsdR: pMA vector P-FRT-dhfr_00500bp: in pMA vector P-FRT-dhfr_01000bp: in pMA vector P-FRT-dhfr_02000bp: in pMA vector P-FRT-dhfr_05000bp: in pMA vector P-FRT-dhfr_10000bp: in pMA-RQ vector

Kaj attached GCK plasmid maps of them all, together with the original data sent by Geneart, which includes sequencing reads (Geneart_files.zip).

If not completed yet: dissolve the 5 ug that were sent by Geneart, in 50 ul ddH2O (37 degC, gentle rotation for 15 min). electroporate GB2005 (electrocompetent cells from -80 freezer) with 0.5 ul of DNA from all 7 constructs. Prepare midi preps & check by diagnostic digest (see cloning scheme for enzyme name). Check that pMA-RQ-P-F3-zeoR-F3-RFP is resistant to Zeo15, whereas GB2005/GB205-red/GB2005-red are not and pTetFlp-KanR/pRhaFlp-CmR-KanR are not either. Check that pMA-TT-FRT-GFP-BsdR is resistant to Low-salt Bsd40, whereas GB2005/GB205-red/GB2005-red are not and pCCFos2-SpecR is not either. Check that all five pMA-P-FRT-dhfr plasmids are resistant to Trimethoprim50 (Tmp50), whereas GB2005/GB205-red/GB2005-red are not and pCCFos2-SpecR/pCC2Fos-GFP are not either.

in the meantime cut out the construct from the plasmid using 40 ul of remaining DNA & digest in 100 ul with the same enzyme.


pTetFlp construction: Sequences of three pTetFlp-KanR clones arrived. There are a few minor differences between the electronic map and the actual sequence (i've included them in the updated file 02_pTetFlp-KanR.gcc). However, all clones are all the same, so it does not matter, which one to use for the next step.


pRhaFlp construction: pRhaFlp-CmR needs to be sequenced still (check 3 different clones that came from independent re-electroporations, using the BmR 5'out and 3' out primers that I gave you. the melting temperature (Tm) is 59 degC for both). Diagnostic digest needs to be done for the minipreps from pRhaFlp-CmR-KanR. Find out enzyme first.

pCC2Fos construction: Diagnostic digest of pCC2Fos-SpecR minipreps (pCC2Fos-BsdR as control) with HincII. Double streak clones on LS-Bsd40 plates -> only consider clones that are sensitive and �� don't grow.

sarah will give you some LB-Zeo15 plates, which you need, when working with the F3-zeoR-F3-RFP construct, which is for both pTetFlp and pRhaFlp. This is also the plates to use, when checking Zeo15 resistance/sensitivity.


29th sep

we had 3 logos.. and we voted for them.. but there was a tie.. and some suggestions for change.. ilaria has made those changes.. and sent the logos around.. plz vote for the ones u like.. and we have to make the decisions soon.. cos the team T shirt is on a hold.

Ilaria will take care of the T shirts.. but the design is yet to be decided..plz come up wid suggestions.. also we thought of asking the uni store to give us TUD sweatshirts.. which we could wear with our team T shirts..and mayb try to get it for free for the team.. we will b representing TU also.. and thats the least they can give us.. so regarding this tomek said he’ll speak to someone he knows at the university.. and we will also have to speak to Prof Schwille about this.

we have 3 collaborations.. TU Delft.. Paris and Valencia.. the TU Delft survey time is over.. I hope all of u responded to the suvey... v have another survey from team valencia.. please respond to it.. also v have to make  a movie for the paris team..

the vesicle part is goin very good..the transcription-translation kit will b tried this week.. The cloning stuff is working fine.. we are working on cloning the parts that we had ordered into the fosmids.. Stanley is doing the part with the fosmids. and Divya will work on the Flp plasmids.. silver stuff is not workin out.. so tomek n deepika are lookin for other protocols.. tomek also spoke to eugene on Friday .. he offered some advice n help.. so they are going to try out some new stuff this week..

no news from the visa..

some students have been registered for the jamboree.. travel and  stay have to be looked for.. we are considering youth hostels.. and also couch surfing as a last resort..

daniel made a new and nice wiki template.. we will have a wiki meeting today.. so if anyone is around and wants to contribute to the wiki.. please come to the pc pool.. if u �� dont find me/ daniel der.. jus call me.. cos the venue for the wiki meeting is not fixed..

other imp deadlines.. 2nd oct - late registration. 21st oct - submission of parts to the regsitry.

hope to c u guys at the wiki meetin today.. if not we meet as usual tomo.. at 5pm.. 2nd floor kitchen.. 

6th oct

although anja did not vote, the results would not change. summing up the final result: the people who will go to Boston are Divya, Tomek, Priyanka, Deepika and Arnab. Stanley was ranked third overall, but was VISA-rejected twice as you all know - he is replaced by Arnab.

Since Daniel has already booked his flight to Boston, we will try to add him to the list of registered students so he can attend the jamboree at MIT. We will also make an accommodation reservation for him together with the other 5 but he will not be refunded by igem.

Ilaria and I will circulate more news as they appear.

Keep up the momentum, there's only 12 days left before the final set of deadlines for wiki, project description, and parts submission.

Retrieved from "http://2009.igem.org/Team:BIOTEC_Dresden/Scratch"