Team:Johns Hopkins/Notebook

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Contents

Groups

iGEM Groups 1.0
iGEM Groups 2.01
iGEM Groups 2.02

Important reminders and notes

 [Can make general comments here, so they don't get lost in peoples e-mail boxes]
 
 July 11: Primers for group 1 were delivered yesterday.
 July 11: Lab meeting at 7:30PM in the lab to go over miniprep protocol.
 July 15: Lab meeting at 6:30PM with Jessica. Have status reports ready. Bring labtop if you can.
 July 17: Restriction Digest/Sequencing Preparation (with James) 6:00PM.
 July 21: 6:00PM or 6:30PM Lab meeting with Jessica. Have status reports ready.

Status Reports

The status reports of each group below will continuously be updated as we work on the biobricks. The following PDFs contain progressive versions of our status reports as we continue through the sex detector project; they are added weekly. To learn more about each biobrick, please refer to the Biobrick page.

Status Report 2.1 - 07/12/08
Status Report 2.2 - 07/17/08

Please BOLD the most recent step that you have completed. Do this by placing the tag < b > in front of and </ b > at the end of what you would like to be placed in bold (with no space between letter and carrot symbol (<,>).

GROUP 1: Fluorescent Proteins

Summary for Fluorescent Proteins Group

 Date: July 22, 2008
 Status report by: Tejas
 Part no.: BBa_K110017 -> BBa_K110023
 Part Description: yESapphire , mCherry, venusYFP, and Citrine
 
  Work on yESapphire was gratiously done by James. Primers were designed. Restriction site ends
 have been added through PCR. The product was cloned into JM109. Colonies were picked and an
 inoculation was grown. Miniprep was performed and subsequent DNA was CS PCR'd and run on a gel
 to verify contents. BioBrick is currently being sequenced.
 
  Work on mCherry and venusYFP (BBa_K110018 -> BBa_K110021) is currently being done. Primers were
 designed. Restriction sites have been added through PCR. The products were cloned into JM109 and
 plated. 3 colonies per 4 BioBricks (total 12) were picked, grown out, miniprepped, and digested
 for verification on a gel.
  According to the results, ([http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.Venus%20YFP%20and%20mCherry%20Miniprep%20check%20via%20digest.Ingrid.html Venus YFP and mCherry Miniprep check via digest]), only one of the
 mCherry's (BBa_K110019) is the correct product. This product will be retransformed to yield more
 for sequencing. Colonies for the other three BioBricks were selected by Ingrid on 7.22.2008 and
 are being grown out. Process will continue as per protocol.
 
  Work on Citrine has not yet begun. Primers have been designed and ordered, but template DNA must
 be grown out. Template DNA to be grown and extracted by James should we later decide that Citrine
 will be needed.
 
 *Note that mCherry and Citrine both have restriction sites within the coding region, and are
 therefore not optimal. Advice/help on this issue would be appreciated.

GROUP 2: MATa Specific-promoters

Summary for MATa Specific Promoters Group

 Date: _________ __, 2008
 Status report by: _____
 Part no.: BBa_K1100XX -> BBa_K1100YY
 Part Description:
 
 Summary here.

GROUP 3: Short Two-Way Stops

Summary for Short Two-Way Stops Group

 Date: _________ __, 2008
 Status report by: _____
 Part no.: BBa_K1100XX -> BBa_K1100YY
 Part Description:
 
 Summary here.

GROUP 4: Long Two-Way Stops & MAT(alpha) Specific Promotors

Summary for Long Two-Way Stops & MAT(alpha) Specific Promoters Group

 Date: _________ __, 2008
 Status report by: _____
 Part no.: BBa_K1100XX -> BBa_K1100YY
 Part Description:
 
 Summary here.

GROUP 5: MATa Specific Promoters II

Summary for MATa Specific Promoters II Group

 Date: _________ __, 2008
 Status report by: _____
 Part no.: BBa_K1100XX -> BBa_K1100YY
 Part Description:
 
 Summary here.

GROUP 6: Vectors

 Status report by ____
 Vector transformed into bacteria strain DB3.1 Y/N
 Permanent culture made in the Boeke lab for future reference Y/N
 Selectable marker for this vector
 Medium made and tested Y/N  (link)
 DNA preps made Y/N
 DNA preps tested by RE digest  - (link)
 DNA preps tested by transformation into DB3.1 and DH5alpha (or JM109) – put data as 
   Table on moodle.  
 Sample format/data follows:
Amount transformed cfu/micGm in DB3.1 cfu/micGm in JM109 0.1 ng 5 * 10e7 <2 * 10e2
Preparative digests ready for use are located – where?

GROUP 7: Microscopy/Yeast

 Milestones 
 Have gfp yeast been visualized by microscopy?
 Have gfp yeast been photographed? Link to moodle – picture.  
 [If pics are nice, put on our web page]
 Can green(/other colors) colonies be photographed? 
 Has STE3-gfp sex detector been transformed into MATa, MATalpha, and MATa/alpha?  Y/N
 Have permanent cultures been banked in the Boeke lab? Y/N
 Have STE3-gfp sex detector cells/colonies been photographed Y/N  - link to Moodle