Freiburg University 2006

From 2006.igem.org

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Revision as of 21:07, 28 August 2006

Welcome! We are Alife Mutants.

This term was invented by Martin Schneider on the Rule 110 Winter Workshop in 2004 [http://www.rule110.org/amhso/index.html]. We play without rules. We discover the rules that govern life, the universe and everything to exploit these rules and to create Artificial Life. Our short-time aim is the trip to Boston in November 2006 to take a prize in the iGEM.

The Freiburg Team (well, at least half of it...) from left to right: Irina Petrova, Andrei Kouznetsov, Daniel Hautzinger.

The Team

Students

iGEM instructor

Andrei Kouznetsov

Faculty/staff

Svetlana Santer

The project: DNA Folding

Basic Idea

Abstract

The idea is to design a strand of DNA such that it wraps into some meaningful shape. There are three different stages for this project: First, the DNA should fold into a two-dimensional rectangular sheet. Secondly, this sheet should wrap itself up into the shape of a short pipe. And last, these little pipes should hook themselves up to each other such that they form one single long pipe.

Scetches - Pipes

Pipes - Stage 1

Pipes - Stage 2

Pipes - Stage 3

The DNA sequence for the Pipes design can be found [http://omnibus.uni-freiburg.de/~kouznet/Tube-M13mp18-NEB-d.txt here].

Application: Barbie Nanoatelier

Once the process of DNA folding into 3D-structures is understood, shapes can be chosen arbitrarily. The idea of the Barbie Nanoatelier is that the DNA should wrap into a 3D-TShirt, 3D-Pants, etc.

Scetches - TShirt

TShirt - Stage 1

TShirt - Stage 2

TShirt - Stage 3

TShirt - Stage 4

Scetches - Bluse

Bluse - Stage 1

Bluse - Stage 2

The DNA sequence for the Bluse design can be found [http://omnibus.uni-freiburg.de/~kouznet/nike-oligos.txt here].

GEM Freiburg

Club

[http://omnibus.uni-freiburg.de/~kouznet/iGEM.htm Manifesto, Self-education program]
[http://omnibus.uni-freiburg.de/~kouznet/Fellow06.htm GEM Freiburg Fellow 2006]
[http://omnibus.uni-freiburg.de/~kouznet/GEMnews.htm News]

SB Preliminary

DNA plug-and-play platform [http://omnibus.uni-freiburg.de/~kouznet/DNAplatform6.pdf 24.05.06] [http://omnibus.uni-freiburg.de/~kouznet/DNAplatform6-1.pdf 27.06.06]
[http://omnibus.uni-freiburg.de/~kouznet/BioVLSI.pdf Very Large-Scale Integration design in Biology]
[http://omnibus.uni-freiburg.de/~kouznet/GS-design.pdf Genetic systems design from the DNA modules]

Old project ideas

Life_6000 Life with a price of 6000 €

Hey Mutant, have a look!

The easy and serious way

[http://www.edge.org/documents/archive/edge187.html#church George Church CONSTRUCTIVE BIOLOGY] - a nice paper about the challenges of modern biology
[http://webcast.berkeley.edu/events/details.php?webcastid=15766 The webcast from SB2.0]

These people do great things

Albert Libchaber [http://www.rockefeller.edu/research/abstract.php?id=93] Carlos Bustamante's lab [http://alice.berkeley.edu/] David Deamer [http://www.chemistry.ucsc.edu/deamer_d.html] Eric Kool’s group [http://www.stanford.edu/group/kool/] Erik Winfree [http://www.dna.caltech.edu/~winfree/] Fred Menger’s group [http://www.chemistry.emory.edu/faculty/menger/index.html] Jack Szostak’s lab [http://genetics.mgh.harvard.edu/szostakweb/] Norman Packard’s Protolife [http://www.protolife.net/] Pier Luigi Luisi’s group [http://www.plluisi.org/index.html] Radhika Nagpal [http://www.eecs.harvard.edu/~rad/] Steven Benner’s group [http://www.chem.ufl.edu/groups/benner/]

Local

An Analysis of Synthetic Biology Research in Europe and North America [http://www2.spi.pt/synbiology/] DNA synthesis: ATG-Biosynthetics [http://www.atg-biosynthetics.com/]

Bold text

@@ Line 13: / Line 13: @@
 == The Team ==
-Students:
+====Students====
 *[[User:Daniel_Hautzinger|Daniel Hautzinger]]
 *[[User:Marc_Wilnauer|Marc Wilnauer]]
@@ Line 21: / Line 21: @@
 *[[User:Mona_Klein|Mona Klein]]
-iGEM instructor:
+====iGEM instructor====
 *[[User:Andrei_Kouznetsov|Andrei Kouznetsov]]
-Faculty/staff:
+====Faculty/staff====
 *[[User:Svetlana_Santer|Svetlana Santer]]
 == The project: DNA Folding==
-===Basic Idea:===
+===Basic Idea===
 ====Abstract====
@@ Line 78: / Line 78: @@
 * [http://omnibus.uni-freiburg.de/~kouznet/GS-design.pdf Genetic systems design from the DNA modules]
-== Old project idea==
+== Old project ideas==
-* [http://omnibus.uni-freiburg.de/~kouznet/life6000.pdf Life with a price of 6000 €]
-Now we see it could be cheaper, but it will need a great intellectual impact. So, we’re opened for '''sponsors and relationships'''.
-=== Comments ===
-As I understand it, the idea is to create a "life
-automaton" consisting of 6 proteins? That is what I took
-out of your proposal. That seems quite ambitioned, but I
-can't really judge it, and even if it is quite
-ambitioned, that does not mean that it is bad, of
-course.
-My understanding says that you are using 6000 € for
-denovo synthesis of 6 genes required for making minimal
-life. Right?
-So, what if after all the simulations and tests on the
-computer, you order the DNA for minimal life and it
-turns out that it doesn't work... What will you do then?
-This is because biology is unpredictable and you must
-not assume that the DNA which you order will work in the
-first time itself... You must keep some backup money or
-plans...
-You have to separate specifically the general and specific
-objectives to long and short time; implications, obstacles
-and limitations.
-OK, fine.. So you want to go in a completely different
-direction by creating alternative life.. Good.. All the
-best for this project.
-Well, if you want to go to the extremes then are you
-limiting yourself to already established phenomena such
-as DNA, membranes, etc. You may want to adopt a
-completely new and novel ideas which might be simpler
-than DNA and other stuff of the normal cell.
-So, keep all the options open. Research the literature
-well and create Artificial Life...
-=== Questions ===
-* - Dilettante: "Where is a place of synthetic biology here - good old gene engineering > bio-nanotechnology > orthogonal life > artificial life > artificial intelligence?" <br> - Expert: "Hmmm..."
-* - Professor: "What is new in Synthetic Biology?" <br> - Student: "Wiki!!!"
-* People on a street: <br> - "What is a synthetic biology - science or technology?" <br> - "Expedition."
-* - Shrödinger: “What is life?” <br> - Alice: “It’s a play where rules are constantly changed.”
+* [[Life_6000 Life with a price of 6000 €]]
 == Hey Mutant, have a look! ==