Team:SDU-Denmark/Tour41

From 2013.igem.org

(Difference between revisions)

Revision as of 22:57, 28 October 2013

Bacteriorganic Rubber

Menu

You really should use our interactive wiki tour instead. :)
Don't worry, you won't miss out on anything. Everything below is part of the tour as well.

Looking for a specific page? Below is a direct shortcut to all our wiki-pages.

Introduction

Rubber issue

Production system

Process

Results

Future

Complete Journal

Protocols & important dates

"If it is not documented, it doesn’t exist." - Louis Fried

Obviously, Louis Fried was wrong - and luckily so, we might add! But it is true that if it is not documented, we don't know whether it exist. So please, click through the tabs below and catch a quick glimpse of our most treasured moments of the summer. We kept a calender of special events since the start of the project. And if you have the yearning (particularly after reading our Results), open up our thorough protocols below.

Major events

February
28.02.2013 - Assembly of the team

March 08.03.2013 - 10.03.2013 - Teambuilding: iGEM crash course (DTU)
21.03.2013 - First meeting: get to know each other

April - Brainstorming
29.04.2013 - Social dinner and introduction to wiki design

May - Brainstorming
08.05.2013 - A consensus was reached: Bacteriorganic Rubber

July
11.07.2013 - Barbeque dinner
17.07.2013 - Tour des chambres

August
08.08.2013 - Squash tournament
22.08.2013 - Cabaret show, HCA festival 2013
31.08.2013 - 01.09.2013 - DK meetup

September
04.09.2013 - Supervisor Ann makes dinner for responsibility delegation meeting
25.09.2013 - Dinner after status meeting
26.09.2013 - Dinner with previous SDU iGEM teams

October
03.10.2013 - Late-night pizza

Lab successes

July
21.07.2013 - pSB1C3-Pcon-dxs (B. subtilis)-amilCP
25.07.2013 - B. subtilis DXS biobrick
25.07.2013 - E. coli IspG biobrick
29.07.2013 - pSB1C3-Plac-dxs (B. subtilis)-linker-GFP
31.07.2013 - pSB1C3-Plac-dxs (E. coli)-linker-GFP

August
01.08.2013 - We realized LacI should be overexpressed in order to get repression of the lac promoter
01.08.2013 - Sequencing of E. coli dxs standard part
05.08.2013 - pSB1C3-Plac-dxs (B. subtilis)
19.08.2013 - HRT2 biobrick
19.08.2013 - pSB1C3-Plac-dxs (E. coli)
19.08.2013 - pSB1C3-Pcon-lacI:LVA-term
17.09.2013 - LacI BioBrick
17.08.2013 - pSB1C3-Pcon-araC-term
21.08.2013 - pSB1C3-lacI:LVA-Plac-dxs (B. subtilis)
23.08.2013 - pSB1C3-lacI:LVA-Plac-dxs (B. subtilis)-linker-GFP
24.08.2013 - Characterization of LacI:LVA function
24.08.2013 - Confirmation that we could control the expression of Dxs with LacI:LVA using IPTG
28.08.2013 - pSB1C3-lacI:LVA-Plac-dxs (E. coli)
30.08.2013 - pSB1C3-Para-HRT2-(FLAG)
30.08.2013 - Growth experiment for MG1655/pSB1C3-lacI:LVA-Plac-dxs (B. subtilis)+/-GFP

September
13.09.2013 - pSB1C3-araC-Para-HRT2-(FLAG)
17.09.2013 - pSB1C3-lacI-Plac-dxs (B. subtilis)-linker-GFP
17.09.2013 - Characterized device with LacI and found that it functions better than LacI:LVA
20.09.2013 - Growth experiment for MG1655/pSB1C3-lacI-Plac-dxs (B. subtilis)
21.09.2013 - pSB1K3-araC-Para-HRT2-(FLAG)
21.09.2013 - Growth experiment for MG1655/pSB1C3-lacI-Plac-dxs (B. subtilis)-GFP
22.09.2013 - pSB1C3-lacI-Plac-dxs (B. subtilis)

October
01.10.2013 - Characterization of AraC function
02.10.2013 - Confirmation that we could induce and control the expression of HRT2

iGEM deadlines

August
09.08.2013 - Team project description due
30.08.2013 - Track selection
30.08.2013 - Project title

September
23.09.2013 - BioBricks Part DNA shipped to iGEM HQ
25.09.2013 - BioBricks Part DNA at the Registry (Received at iGEM)

October
04.10.2013 - European Wiki freeze
11.10.2013 - 13.10.2013 - Regional Jamboree Lyon
28.10.2013 - World Championship Wiki freeze

November
01.11.2013 - 05.11.2013 - World Championship Jamboree Boston

When working together in a large group, particularly on such a large project, it is simply impossible for anyone to maintain an overview over the entire project in real time. That is why it is important to keep protocols of every part of the project, to document every experiment that is performed. This allows each team member to backtrack and to resolve any issues with (or mistakes made in) previous experiments. Countless digestions and hundreds of PCR reaction were done, and the explicit protocols established which setups were effective, and which were not. Our iGEM-team has kept protocols since the dawn of the project, and they have proven to be an invaluable resource, which saved us quite a bit of time. To ensure the consistency of execution, each experiment was done by following one of our Standard Operating Procedures, which can be found under "SOPs".

Click on the project title below to expand the window and get an overview of the protocols for each project part. Each protocol name is a link to a pdf file that will open in a new window. All were written on the basis of our Protocol Template

Primer design and Site-Directed Mutagenesis

SDU2013 Protocol 0001 - USER primer design
SDU2013 Protocol 0002 - Standard primer design
SDU2013 Protocol 0050 - SDM on Plac - dxs (E. coli)
SDU2013 Protocol 0051 - SDM on dxs (E. coli) amilCP

Basic Parts

SDU2013 Protocol 0006.1 - Dxs from B. subtilis
SDU2013 Protocol 0006.2 - Dxs from B. subtilis
SDU2013 Protocol 0017 - ispG
SDU2013 Protocol 0032 - Prenyltransferase
SDU2013 Protocol 0033 - lacI
SDU2013 Protocol 0034 - araC
SDU2013 Protocol 0037 - lacI and araC
SDU2013 Protocol 0039 - lacI without LVA-tag

Devices; our Composite Production Systems

Reporter systems

AmilCP
SDU2013 Protocol 0003 - USER PCR on pSB1C3
SDU2013 Protocol 0004 - USER PCR on AmilCP-linker
SDU2013 Protocol 0005 - USER PCR on dxs (E. coli)
SDU2013 Protocol 0007 - USER cloning on pSB1C3 AmilCP-dxs
SDU2013 Protocol 0009 - PCR on dxs (B. subtilis)
SDU2013 Protocol 0027 - USER cloning pSB1C3 and AmilCP

Characterization

SDU2013 Protocol 0052 - Growth lacI-Plac-dxs (B. subtilis) vs. lacI-Plac-dxs (B. subtilis)-GFP
SDU2013 Protocol 0053 - lacI-Plac-RBS-dxs (B. subtilis) Northern
SDU2013 Protocol 0054 - lacI-Plac-RBS-dxs (B. subtilis)-linker-GFP
SDU2013 Protocol 0055 - Induction assay on pSB1C3-araC-Para-HRT2-FLAG

Sequencing
SDU2013 Protocol 0008 - Sequencing of E. coli Dxs standard part
SDU2013 Protocol 0049 - Basic sequencing

@@ Line 72: / Line 72: @@
 <b>July</b><br>
-.07.2013 - pSB1C3-Pcon-dxs(B. subtilis)-amilCP <br>
+.07.2013 - pSB1C3-Pcon-<span class="specialWord">dxs (B. subtilis)</span>-amilCP <br>
-.07.2013 - B.sub DXS biobrick  <br>
+.07.2013 - <span class="specialWord">B. subtilis</span> DXS biobrick  <br>
-.07.2013 - E.coli IspG biobrick   <br>
+.07.2013 - <span class="specialWord">E. coli</span> IspG biobrick   <br>
-.07.2013 - pSB1C3-Plac-dxs(B. sub)-linker-GFP <br>
+.07.2013 - pSB1C3-Plac-<span class="specialWord">dxs (B. subtilis)</span>-linker-GFP <br>
-.07.2013 - pSB1C3-Plac-dxs(E. coli)-linker-GFP <br>
+.07.2013 - pSB1C3-Plac-<span class="specialWord">dxs (E. coli)</span>-linker-GFP <br>
 </p><p>
 <b>August</b><br>
 .08.2013 - We realized LacI should be overexpressed in order to get repression of the lac promoter<br>
-.08.2013 - Sequencing of E. coli dxs standard part <br>
+.08.2013 - Sequencing of <span class="specialWord">E. coli dxs</span> standard part <br>
-.08.2013 - pSB1C3-Plac-dxs(B. sub) <br>
+.08.2013 - pSB1C3-Plac-<span class="specialWord">dxs (B. subtilis)</span> <br>
 .08.2013 - HRT2 biobrick <br>
-.08.2013 - pSB1C3-Plac-dxs(E. coli) <br>
+.08.2013 - pSB1C3-Plac-<span class="specialWord">dxs (E. coli)</span> <br>
-.08.2013 - pSB1C3-Pcon-lacI:LVA-term<br>
+.08.2013 - pSB1C3-Pcon-<span class="specialWord">lacI:LVA</span>-term<br>
 .09.2013 - LacI BioBrick<br>
-.08.2013 - pSB1C3-Pcon-araC-term <br>
+.08.2013 - pSB1C3-Pcon-<span class="specialWord">araC</span>-term <br>
-.08.2013 - pSB1C3-lacI:LVA-Plac-dxs(B. sub) <br>
+.08.2013 - pSB1C3-lacI:LVA-Plac-<span class="specialWord">dxs (B. subtilis)</span> <br>
-.08.2013 - pSB1C3-lacI:LVA-Plac-dxs(B. sub)-linker-GFP <br>
+.08.2013 - pSB1C3-lacI:LVA-Plac-<span class="specialWord">dxs (B. subtilis)</span>-linker-GFP <br>
-.08.2013 - Characterization of lacI:LVA function <br>
+.08.2013 - Characterization of LacI:LVA function <br>
-.08.2013 - Confirmation that we could control the expression of Dxs with lacI:LVA using IPTG <br>
+.08.2013 - Confirmation that we could control the expression of Dxs with LacI:LVA using IPTG <br>
-.08.2013 - pSB1C3-lacI:LVA-Plac-dxs(E. coli) <br>
+.08.2013 - pSB1C3-lacI:LVA-Plac-<span class="specialWord">dxs (E. coli)</span> <br>
-.08.2013 - pSB1C3-Para-HRT2-(FLAG)<br>
+.08.2013 - pSB1C3-Para-<span class="specialWord">HRT2</span>-(FLAG)<br>
-.08.2013 - Growth experiment for MG1655/pSB1C3-lacI:LVA-Plac-dxs(B.sub)+/-GFP <br>
+.08.2013 - Growth experiment for MG1655/pSB1C3-<span class="specialWord">lacI:LVA</span>-Plac-<span class="specialWord">dxs (B. subtilis)</span>+/-GFP <br>
 </p><p>
 <b>September</b><br>
-.09.2013 - pSB1C3-araC-Para-HRT2-(FLAG) <br>
+.09.2013 - pSB1C3-<span class="specialWord">araC</span>-Para-<span class="specialWord">HRT2</span>-(FLAG) <br>
-.09.2013 - pSB1C3-lacI-Plac-dxs(B. sub)-linker-GFP <br>
+.09.2013 - pSB1C3-<span class="specialWord">lacI</span>-Plac-<span class="specialWord">dxs (B. subtilis)</span>-linker-GFP <br>
-.09.2013 - Characterized device with lacI and found that it functions  better than lacI:LVA <br>
+.09.2013 - Characterized device with LacI and found that it functions  better than LacI:LVA <br>
-.09.2013 - Growth experiment for MG1655/pSB1C3-lacI-Plac-dxs(B.sub)<br>
+.09.2013 - Growth experiment for MG1655/pSB1C3-<span class="specialWord">lacI</span>-Plac-<span class="specialWord">dxs (B. subtilis)</span><br>
 .09.2013 - pSB1K3-araC-Para-HRT2-(FLAG) <br>
-.09.2013 - Growth experiment for MG1655/pSB1C3-lacI-Plac-dxs(B.sub)-GFP <br>
+.09.2013 - Growth experiment for MG1655/pSB1C3-<span class="specialWord">lacI</span>-Plac-<span class="specialWord">dxs (B. subtilis)</span>-GFP <br>
-.09.2013 - pSB1C3-lacI-Plac-dxs(B. sub) <br>
+.09.2013 - pSB1C3-<span class="specialWord">lacI</span>-Plac-<span class="specialWord">dxs (B. subtilis)</span> <br>
 </p><p>
 <b>October</b><br>
-.10.2013 - Characterization of araC function <br>
+.10.2013 - Characterization of AraC function <br>
 .10.2013 - Confirmation that we could induce and control the expression of HRT2<br>