IGEM:Help/Team experience tutorial: Difference between revisions

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===Research previous year's projects===
===Research previous year's projects===
#Go to http://igem2006.com
#Go to http://igem2006.com
#Click on '''Results''' (http://www.igem2006.com/jamboree.htm)
#Click on [http://www.igem2006.com/jamboree.htm '''Results''']
#Click on '''Watch the presentations and get the powerpoints''' (http://www.igem2006.com/presentations.htm)
#Click on [http://www.igem2006.com/presentations.htm '''Watch the presentations and get the powerpoints''']
#Watch team presentations (http://parts.mit.edu/movies/iGEM2006_MIT.mov) and view the slides (http://parts.mit.edu/wiki/images/c/c0/IGEM2006-MIT-Powerpoint.pdf)
#Watch team presentations (http://parts.mit.edu/movies/iGEM2006_MIT.mov) and view the slides (http://parts.mit.edu/wiki/images/c/c0/IGEM2006-MIT-Powerpoint.pdf)
#Go to the team's wiki page by clicking '''Wiki live''' (http://parts.mit.edu/wiki/index.php/Main_Page)
#Go to the team's wiki page by clicking [http://parts.mit.edu/wiki/index.php/Main_Page '''Wiki live''']
#Click on '''Meet the 37 teams''' (http://parts.mit.edu/wiki/index.php/Schools_Participating_in_iGEM_2006)
#Click on [http://parts.mit.edu/wiki/index.php/Schools_Participating_in_iGEM_2006 '''Meet the 37 teams''']
#Click on the MIT link and read about the project (http://parts.mit.edu/wiki/index.php/MIT_2006)
#Click on [http://parts.mit.edu/wiki/index.php/MIT_2006 '''MIT''] and read about the project


Let's make a new scent! Vanilla.
Let's make a new scent! Vanilla.
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===Search the literature===
===Search the literature===
#Visit PubMed (http://pubmed.org)
#Visit [http://pubmed.org PubMed]
#Search for vanilla  
#Search for vanilla  
#Find a relevant paper ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17437627&query_hl=1&itool=pubmed_docsum])
#Find a [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17437627&query_hl=1&itool=pubmed_docsum relevant paper]
#Go read the paper (http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17437627)
#Go read the [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17437627 paper]
#Identify the useful components described in the paper
#Identify the useful components described in the paper
#You seem to need two gene ''ech'' and ''fcs'' ... let's grab some sequence
#You seem to need two gene ''ech'' and ''fcs'' ... let's grab some sequence
#Search for GenBank accession numbers
#Search for Genbank accession numbers
#Follow the link ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&dopt=GenBank&list_uids=40788116])
#Follow the [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&dopt=GenBank&list_uids=40788116 Genbank link]


==Make a part==
==Make a part==


===Enter a basic part===
===Enter a basic part===
#Go back to the Registry (http://parts.mit.edu)
#Go back to the [http://parts.mit.edu Registry]
#Login to the Registry  
#Login to the Registry  
#Click on the '''Add a part''' link (http://parts.mit.edu/registry/index.php/Add_a_Part_to_the_Registry)
#Click on the [http://parts.mit.edu/registry/index.php/Add_a_Part_to_the_Registry '''Add a part''']
#Click on the '''Add a basic part now''' (http://parts.mit.edu/r/parts/partsdb/add_part_b.cgi)
#Click on the [http://parts.mit.edu/r/parts/partsdb/add_part_b.cgi '''Add a basic part now''']
#*A basic part is a linear sequence of DNA with a fundamental function like a promoter, terminator, ribosome binding site, CDS etc.
#*A basic part is a linear sequence of DNA with a fundamental function like a promoter, terminator, ribosome binding site, CDS etc.
#Choose Allow edits by your iGEM team
#Choose Allow edits by your iGEM team
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#Enter that number into the '''Selected Part Name''' field
#Enter that number into the '''Selected Part Name''' field
#Choose a part type from the drop down menu.  
#Choose a part type from the drop down menu.  
#*Find out what the different part types are by clicking the '''Browse Part Types''' link to the left.  (http://parts.mit.edu/registry/index.php/Part_Types) The question marks next to each part type give a description of that part type.
#*Find out what the different part types are by clicking the [http://parts.mit.edu/registry/index.php/Part_Types '''Browse Part Types'''] link to the left.  The question marks next to each part type give a description of that part type.
#Enter a short description ... e.g. ''feruloyl-CoA hydratase for vanillin biosynthesis''
#Enter a short description ... e.g. ''feruloyl-CoA hydratase for vanillin biosynthesis''
#Enter a long description of the part (you can update this more later)
#Enter a long description of the part (you can update this more later)
#*Where species is the enzyme from?
#*Where species is the enzyme from? ''Pseudomonas fluorescens''
#*What reaction does it catalyze?
#*What reaction does it catalyze? ''One of two steps in the bioconversion of ferulic acid to vanillin.''
#*Does it work in ''E. coli''?
#*Does it work in ''E. coli''? ''Yes.  The authors of the paper have shown that it works already.''
#*Does it require any other parts?
#*Does it require any other parts? ''Yes.  Both ech and fcs are needed for vanillin biosynthesis''
#Enter the source of this part
#Enter the source of this part
#*Include the species, the GenBank accession number and the paper reference
#*Include the species, the GenBank accession number and the paper reference
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#*The stop codon is TGA so we changed it to TAATAA to conform with BioBrick standards
#*The stop codon is TGA so we changed it to TAATAA to conform with BioBrick standards
#Click go on to enter the sequence and add feature annotations
#Click go on to enter the sequence and add feature annotations
#Return to the Genbank entry ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&dopt=GenBank&list_uids=40788116])
#Return to the [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&dopt=GenBank&list_uids=40788116 Genbank entry]
#Click on the CDS link to get the sequence of the coding region ([http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=40788116&from=1994&to=2824&view=gbwithparts])
#Click on the [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=40788116&from=1994&to=2824&view=gbwithparts '''cds'''] link to get the sequence of the coding region
#Display it in FASTA format
#Display it in FASTA format
#Copy the sequence
#Copy the sequence
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#*We will have to remove these in fabricating this part
#*We will have to remove these in fabricating this part
#*Once the sites have been removed we can edit this information in the Registry
#*Once the sites have been removed we can edit this information in the Registry
#*See protocols on site directed mutagenesis http://www.openwetware.org/wiki/Site-directed_mutagenesis
#*See [http://www.openwetware.org/wiki/Site-directed_mutagenesis OpenWetWare protocols on site directed mutagenesis]
#Click the '''Add a feature''' link
#Click the '''Add a feature''' link
#Enter the start codon, stop codons and coding region as features.  Click '''Submit''' to save.  And anything else you think is important!
#Enter the start codon, stop codons and coding region as features.  Click '''Submit''' to save.  And anything else you think is important!
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#You should see the part in your sandbox
#You should see the part in your sandbox


==Make a composite part==
Protein coding regions by themselves aren't very useful.  We need to make composite parts.


==Make a composite part
Let's make a protein generator to express our vanilla-scent making enzyme.
 
===Finding existing parts===
#Click [http://parts.mit.edu/registry/index.php/Part_Types '''Browse parts types'''] on the navigation bar to the left.

Revision as of 11:47, 25 May 2007

Coming up with a project

Research previous year's projects

  1. Go to http://igem2006.com
  2. Click on Results
  3. Click on Watch the presentations and get the powerpoints
  4. Watch team presentations (http://parts.mit.edu/movies/iGEM2006_MIT.mov) and view the slides (http://parts.mit.edu/wiki/images/c/c0/IGEM2006-MIT-Powerpoint.pdf)
  5. Go to the team's wiki page by clicking Wiki live
  6. Click on Meet the 37 teams
  7. Click on 'MIT and read about the project

Let's make a new scent! Vanilla.

Design the system

  1. We want a device that takes an input chemical and makes vanilla scent.
  2. Need enzymes that synthesize vanilla.

Search the registry

  1. Go to the Registry (http://parts.mit.edu)
  2. Use the search box to look for existing parts
  3. Search for vanilla ... you get no real hits ([1])
  4. Search for vanillin ... ([2])
  5. No one has made a vanilla synthesizing enzyme ... phew!

Search the literature

  1. Visit PubMed
  2. Search for vanilla
  3. Find a relevant paper
  4. Go read the paper
  5. Identify the useful components described in the paper
  6. You seem to need two gene ech and fcs ... let's grab some sequence
  7. Search for Genbank accession numbers
  8. Follow the Genbank link

Make a part

Enter a basic part

  1. Go back to the Registry
  2. Login to the Registry
  3. Click on the Add a part
  4. Click on the Add a basic part now
    • A basic part is a linear sequence of DNA with a fundamental function like a promoter, terminator, ribosome binding site, CDS etc.
  5. Choose Allow edits by your iGEM team
  6. Choose the next available part number, or some number within your team's allowed naming range.
  7. Enter that number into the Selected Part Name field
  8. Choose a part type from the drop down menu.
    • Find out what the different part types are by clicking the Browse Part Types link to the left. The question marks next to each part type give a description of that part type.
  9. Enter a short description ... e.g. feruloyl-CoA hydratase for vanillin biosynthesis
  10. Enter a long description of the part (you can update this more later)
    • Where species is the enzyme from? Pseudomonas fluorescens
    • What reaction does it catalyze? One of two steps in the bioconversion of ferulic acid to vanillin.
    • Does it work in E. coli? Yes. The authors of the paper have shown that it works already.
    • Does it require any other parts? Yes. Both ech and fcs are needed for vanillin biosynthesis
  11. Enter the source of this part
    • Include the species, the GenBank accession number and the paper reference
  12. Enter design considerations
    • The stop codon is TGA so we changed it to TAATAA to conform with BioBrick standards
  13. Click go on to enter the sequence and add feature annotations
  14. Return to the Genbank entry
  15. Click on the cds link to get the sequence of the coding region
  16. Display it in FASTA format
  17. Copy the sequence
  18. Paste it into the sequence field and click Save in the upper right
  19. Change the TGA stop codon to TAATAA
  20. The Registry will automatically check your sequence for BioBricks restriction sites.
  21. Click the Add a feature link
  22. Enter the start codon, stop codons and coding region as features. Click Submit to save. And anything else you think is important!

Reviewing your part

Now you can view the part you've created.

  1. Go to the Registry main page (http://parts.mit.edu)
  2. Click Browse Parts by School (http://parts.mit.edu/registry/index.php/Type:iGEM_2007)
  3. Click on your school
  4. You should see the part in your sandbox

Make a composite part

Protein coding regions by themselves aren't very useful. We need to make composite parts.

Let's make a protein generator to express our vanilla-scent making enzyme.

Finding existing parts

  1. Click Browse parts types on the navigation bar to the left.
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