Latest revision as of 03:57, 29 October 2011

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Wiki Highlights

Read our project description and summary on our Project page: more details on how team members completed work for the three sections of our project are on Design, Synthesize, and Test pages, respectively.

Results of all parts of our project (including our biobricks) are located on our Results page, along with an Attributions and Acknowledgments section.

Human practices can be found on our Human Practices page.

Please be sure to stop by our poster during the poster session with any questions.

Accomplishments

Experimental Results

✓ Researched zinc finger proteins and choose 6 novel, clinically relevant target sequences
✓ Generated 55,000 zinc finger protein sequences using bioinformatics
✓ Used three recently developed technologies together for the first time: a foundational advance
✓ Expressed those 55,000 sequences in E.coli, with a sub-library for each target
✓ Created a genomic one-hybrid selection system sensitive enough to detect one hit in a million
✓ Found at least 15 novel zinc finger proteins

Biobricks and Protocols

✓ Submitted 5 Biobricks to the registry, including our one-hybrid selection strain
✓ Created several chassis for our Biobricks, including our one-hybrid selection strain
✓ Used and shared our easy-to-follow protocols
✓ Made protocols, Biobricks, and source code freely available, so that others can adapt them for other projects

Human Practices

✓ [http://www.youtube.com/watch?feature=player_embedded&v=eBT8SaBAm80 Interviewed] zinc finger researchers Dr. Keith Joung and Dr. George Church
✓ Interviewed chip-based DNA synthesis researcher Dr. Sriram Kosuri
✓ Researched intellectual property and how it applies to zinc finger proteins
✓ Created a timeline and case study of zinc finger intellectual property
✓ Reached out to our elected representatives about the potential effects of IP on zinc finger research and synthetic biology generally
✓ Handed out IP pamphlets and chassis data sheets at our poster presentation
✓ Educated local high school students about synthetic biology to provide accurate information from sources other than the media.

Foundational Advance

Combining Computational Design, High-throughput Synthesis, and Selection

We brought together 3 new technologies to create a working pipeline that allows scientists to engineer novel protein-DNA interactions. Our methods represents a fundamentally different way of building new biological parts and devices: using selection to identify working members of a large computationally predicted library of potential designs.

Putting parts and devices directly onto the genome

The genome is the next frontier in synthetic biology. Our project has made use of genome modification in order to design a new device that allows the testing of DNA-protein interactions. We want iGEM and the broader synthetic biology community to use these techniques as an alternative to plasmids. To encourage their adoption, we have submitted new E. coli chassis that allow easy genome modification, and we have provided detailed protocols for their use.

@@ Line 16: / Line 16: @@
 *Human practices can be found on our [https://2011.igem.org/Team:Harvard/Human_Practices Human Practices] page.
-*Please be sure to stop by our poster during the poster session with any questions.
+Please be sure to stop by our poster during the poster session with any questions.
 =Accomplishments=
-==Experimental Results:==
+==Experimental Results==
-'''✓''' Researched zinc finger proteins and choose 6 novel, <html><x>clinically relevant target sequences </x></html><br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Project/Design#Selection_of_Target_Sequences Researched] zinc finger proteins and choose 6 novel, <html><x>clinically relevant target sequences </x></html><br>
-'''✓''' Generated <html><x>55,000</x></html> zinc finger protein sequences using <html><x>bioinformatics</x></html> <br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Project/Design#Results:_55.2C000_Possible_Zinc_Fingers Generated] <html><x>55,000</x></html> zinc finger protein sequences using <html><x>bioinformatics</x></html> <br>
-'''✓''' Used three recently developed technologies together for the first time: a <html><x>foundational advance</x></html><br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Technology Used] three recently developed technologies together for the first time: a <html><x>foundational advance</x></html><br>
-'''✓''' <html><x>Expressed</x></html> those 55,000 sequences <html><x>in E.coli</x></html>, with a sub-library for each target <br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Project/Synthesize Expressed] those 55,000 sequences <html><x>in E.coli</x></html>, with a sub-library for each target <br>
-'''✓''' Created a <html><x>genomic one-hybrid selection system</x></html> sensitive enough to detect <html><x>one hit in a million </x></html> <br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Project/Test#Fine-tuning_the_one-hybrid_selection_system Created] a <html><x>genomic one-hybrid selection system</x></html> sensitive enough to detect <html><x>one hit in a million </x></html> <br>
-'''✓''' Found up to <html><x>15 novel zinc finger proteins</x></html> <br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Results#Novel_Zinc_Fingers Found] at least <html><x>15 novel zinc finger proteins</x></html> <br>
-==Biobricks and Protocols:==
+==Biobricks and Protocols==
-'''✓''' Submitted <html><x>5 Biobricks</x></html> to the registry, including our one-hybrid selection strain<br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Results/Biobricks Submitted] <html><x>5 Biobricks</x></html> to the registry, including our one-hybrid selection strain<br>
-'''✓''' Created several <html><x>chassis</x></html> for our Biobricks, including our one-hybrid selection strain<br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Results/Biobricks Created] several <html><x>chassis</x></html> for our Biobricks, including our one-hybrid selection strain<br>
-'''✓''' Used and shared our <html><x>easy-to-follow protocols</x></html><br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Protocols Used] and shared our <html><x>easy-to-follow protocols</x></html><br>
-'''✓''' Made protocols, Biobricks, and source code <html><x>freely available</x></html>, so that others can adapt them for other projects <br>
+'''✓''' Made [https://2011.igem.org/Team:Harvard/Protocols protocols], [https://2011.igem.org/Team:Harvard/Results/Biobricks Biobricks], and [https://2011.igem.org/Team:Harvard/Results/Tools source code] <html><x>freely available</x></html>, so that others can adapt them for other projects <br>
 ==Human Practices==
-'''✓''' <html><x>Interviewed</x></html> zinc finger researchers Dr. Keith Joung and Dr. George Church<br>
+'''✓''' [http://www.youtube.com/watch?feature=player_embedded&v=eBT8SaBAm80 Interviewed] <html><x>zinc finger researchers</x></html> Dr. Keith Joung and Dr. George Church<br>
-'''✓''' Researched <html><x>intellectual property</x></html> and how it applies to zinc finger proteins<br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Technology/Chip_Synthesis#The_Man_Behind_the_Research:_Sriram_Kosuri_on_Chip-Based_DNA_Synthesis Interviewed] chip-based DNA synthesis researcher Dr. Sriram Kosuri  <br>
-'''✓''' Created a <html><x>timeline and case study</x></html> of zinc finger intellectual property<br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Human_Practices Researched] <html><x>intellectual property</x></html> and how it applies to zinc finger proteins<br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Human_Practices Created] a <html><x>timeline and case study</x></html> of zinc finger intellectual property<br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Human_Practices/Letter Reached out] to our elected representatives about the potential effects of IP on zinc finger research and synthetic biology generally<br>
 '''✓''' Handed out <html><x>IP pamphlets and chassis data sheets</x></html> at our poster presentation <br>
 '''✓''' <html><x>Educated</x></html> local high school students about synthetic biology to provide accurate information from sources other than the media.
+=Foundational Advance=
+==Combining Computational Design, High-throughput Synthesis, and Selection==
+We <html><x>brought together 3 new technologies</x></html> to create a working pipeline that allows scientists to <html><x>engineer novel protein-DNA interactions</x></html>. Our methods represents a <html><x>fundamentally different way of building new biological parts and devices</x></html>: using selection to identify working members of a large computationally predicted library of potential designs.
-Our <html><x>foundational advance</x></html> is how we <html><x>brought together novel technologies</x></html> to create a pipeline that allows scientists <html><x>to engineer novel interactions with DNA</x></html>. This is a new way of making new parts: using selection on a computationally designed library. The <html><x>genome is the next frontier</x></html> in synthetic biology, and we want the iGEM and synthetic biology communities to use these techniques: we have provided detailed protocols on using lambda red and MAGE.
+==Putting parts and devices directly onto the genome==
+<html><x>The genome is the next frontier in synthetic biology</x></html>. Our project has made use of genome modification in order to design a new device that allows the testing of DNA-protein interactions. We want iGEM and the broader synthetic biology community to use these techniques as an alternative to plasmids. To encourage their adoption, <html><x>we have submitted new E. coli chassis that allow easy genome modification</x></html>, and <html><x>we have provided detailed protocols</x></html> for their use.
+</div>

Team:Harvard/Judging

From 2011.igem.org