Team:Johns Hopkins/Notebook

From 2008.igem.org

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(GROUP 3: Short Two-Way Stops)
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Part Descriptin: Short one-way stop (BBa_K110012 was found to be a 1-way stop), YFP, a-promoter
Part Descriptin: Short one-way stop (BBa_K110012 was found to be a 1-way stop), YFP, a-promoter
Summary: We cut the Chlor vector containing one-way stop 12.3 and YFP (Left to right) with XbaI and PstI. We then ligated the MFa1 (Left to right) with 12.3 and YFP in a Kan vector, transformed it in DH5alpha competent cells. We performed a miniprep on successful white colonies (low concentrations ~100 ng/ul) and perfomed a restriction digest on the Kan vector with EcoRI and PstI. Unfortunately, we did not see any bands on the gel. We are currently repeating the miniprep and digest.
Summary: We cut the Chlor vector containing one-way stop 12.3 and YFP (Left to right) with XbaI and PstI. We then ligated the MFa1 (Left to right) with 12.3 and YFP in a Kan vector, transformed it in DH5alpha competent cells. We performed a miniprep on successful white colonies (low concentrations ~100 ng/ul) and perfomed a restriction digest on the Kan vector with EcoRI and PstI. Unfortunately, we did not see any bands on the gel. We are currently repeating the miniprep and digest.
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  Date: August 25, 2008
 
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  Status report by: James
 
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  Part no.: BBa_K110011 -> BBa_K110013
 
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  Part Description: Short Two way Stops
 
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  Summary: Sequence files from parts sent for sequencing showed incorrect sequences for 3/4 biobricks sent in. However 1 clone
 
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  of '''BBa_K110012''' was correct. That clone was cut and '''ligated into iGEM vector'''. A '''PCR will be tried again for 11-->13, however direct
 
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  ligation into iGEM vector will be attempted''' to evade problems with incomplete products ligating into PGEM-T.
 
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  The '''Two way stop biobrick was then attached to the end of the Fluorescent Protien Venus YFP''', using iGEM standard assembly.
 
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  This Venus YFP had come from iGEM headquarters, as we as still waiting for sequence verification of our biobricks.
 
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  We have yet to run the product on the gel, but the expected band length should be around 900bp.
 
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  (700bp Fluorescent Protein + 200bp Two way stop)
 
=== [[Team:Johns Hopkins/Notebook/GROUP 4: Long Two-way Stops & Mat(alpha) specific promotors | GROUP 4: Long Two-Way Stops & MAT(alpha) Specific Promotors]] ===
=== [[Team:Johns Hopkins/Notebook/GROUP 4: Long Two-way Stops & Mat(alpha) specific promotors | GROUP 4: Long Two-Way Stops & MAT(alpha) Specific Promotors]] ===

Revision as of 23:25, 2 September 2008

Contents

Groups

iGEM Groups 1.0
iGEM Groups 2.01
iGEM Groups 2.02

Important reminders and notes

 [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.
 July 29: 7:00PM Lab Meeting. Meet in Conference Room across from lab. Have Status Reports ready
 Aug. 05: 7:00PM Lab Meeting. Meet in Conference Room across from lab. Have Status Reports ready.
 Aug. 12: 7:00PM Lab Meeting. Have Status Reports Ready. 
               Journal Club Topic: Fluorescent Proteins; James and Ingrid.
 Aug. 19: 7:00PM Lab Meeting. Have Status Reports Ready. 
               Journal Club Topic: Yeast Mating Pathway/MAP Kinase Pathway ; Jasper and Tejas
 Aug. 26: 7:00PM Lab Meeting. Have Status Reports Ready!
               Journal Club Topic: S. cerevisiae Promoters; Allison and Nate

Journal Club

8/12/08
Fluorescent Proteins
Ingrid and James
Fluorescent Protein Powerpoint
Paper: Green Fluorescent Protein as a Marker for Gene Expression

8/19/08
Yeast Mating Pathway/MAP Kinase Pathway
Jasper and Tejas
[[Media:]]
Paper: [[Media:]]


8/19/08
Yeast Promoters
Allison and Nate
Gene structure powerpoint
Paper: Genomic Footprinting of the Promoter Regions of STE2 and STE3 genes in the Yeast Saccharomyces cerevisiae
Additional Reading: Interspecies variation reveals a conserved repressor of alpha-specific genes in Saccharomyces yeast
A genomic code for nucleosome positioning

Data

To upload data, go [http://www.jhu.edu/iGEM/X_files/Read2.html here], click on [http://www.jhu.edu/iGEM/X_files/Read2.html upload data], and provide the necessary information and results.

How to submit data:

1. log-in as you once had to from the www.jhu.edu/iGEM website "login"

  • User: ****** etc...
  • Pass: ***** etc...

2. click on UPLOAD DATA from the 'x-files page'
3. add data etc.... and click submit: This generates a webpage and the URL to it is linked in the page you are directed to after you press submit. Copy that URL and past it into the wiki or into the web-browser url box to see what it looks like.
\* If you find that the picture you are uploading is not showing up e-mail Tejas.

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
Status Report 2.3 - 08/07/08

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 (<,>). Click on your group name for the detailed changes occurring to each biobrick.

GROUP 1: Fluorescent Proteins

Summary for Fluorescent Proteins Group

 Date: July 22, 2008
 Status report by: Tejas, Ingrid
 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. ([http://www.jhu.edu/iGEM/Group3:ShortTwo-wayStops/2008-7-22.Short%202Way%20Stop,%20Alpha%20Promoters,%20&%20Sapphire%20FP.Allison%20Suarez%20and%20Nate%20Sotuyo%20.html Short 2Way Stop, Alpha Promoters, & Sapphire FP]) 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. ([http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-23.PCR%20Products:%20mCherry%20and%20Venus%20YFP,%20both%20RtL%20and%20LtR.Ingrid,%20Tejas.html PCR Products: mCherry and Venus YFP, both RtL and LtR]) The products were cloned into JM109 and plated. 3 colonies per 4 BioBricks (total 12) were picked, grown out, mini prepped, 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. A second Digest was preformed to check this, meanwhile new colonies have been picked on 7.22.2008 and are being grown out for a higher yield of DNA so that it can be sent off for sequencing. [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-23.Re-Digest%20of%20three%20samples%20of%20mCherry%20BBa_K110018.Ingrid%20.html Re-Digest of three samples of mCherry BBa_K110018]
Work on Citrine has not yet begun. Primers have been designed and ordered, but template DNA must be grown out. Template DNA will 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.
Another Digest was done [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-8-19.mCherry%20and%20YFP%20Digest%20Gel.Ingrid%20Spielman.html mCherry and YFP Digest Gel] and weird lines exist.

GROUP 2: MATa Specific-promoters

Summary for MATa Specific Promoters Group

 Date: August 19, 2008
 Status report by: Allison and Nate
 Part no.: BBa_K110008 -> BBa_K110016
 Part Description: A promoters: MFA1 (L+R) and Ste2 (R+L), respectively. 
 Sequences were analyzed. BBa_K110016 had a perfect clone. Since there is not 
 much miniprep left, a transformation was done to generate more clones with the correct sequence. BBa_K110008 had 
 one mutation. Another transformation into a Kan BioBrick vector was attempted but was unsuccessful.
 September 2: Transformation into a Kan BioBrick was completed and assembly of MFA1 (L+R) to YFP will take place
 soon.

GROUP 3: Short Two-Way Stops

Summary for Short Two-Way Stops Group Date:September 2,2008 Status report by: Raghav and James Part no.:BBa_K110012, E2030, BBa_K110008 Part Descriptin: Short one-way stop (BBa_K110012 was found to be a 1-way stop), YFP, a-promoter Summary: We cut the Chlor vector containing one-way stop 12.3 and YFP (Left to right) with XbaI and PstI. We then ligated the MFa1 (Left to right) with 12.3 and YFP in a Kan vector, transformed it in DH5alpha competent cells. We performed a miniprep on successful white colonies (low concentrations ~100 ng/ul) and perfomed a restriction digest on the Kan vector with EcoRI and PstI. Unfortunately, we did not see any bands on the gel. We are currently repeating the miniprep and digest.

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

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

 Date: July 29, 2008
 Status report by: Jaime
 Part no.: BBa_K110001, BBa_K110003, BBa_K110005, BBa_K110006
 Part Description: Long Two-way Stops & Mat(alpha) specific promotors
 [http://www.jhu.edu/iGEM/Group4:LongTwo-wayStopsANDMATalphaSpecificPromoters/2008-7-25.Restriction%20Enzyme%20Digest%20of%20Mini-Preps.Jaime.html Restriction Enzyme Digest of Mini-Preps]
 
 Summary here:
 Need to be sequenced.

GROUP 5: MATa Specific Promoters II

Summary for MATa Specific Promoters II Group

 Date: August 12, 2008
 Status report by: Richard Group
 Part no.: BBa_K110009
 Part Description: Ste2
 Summary here: We hit a dead end when we ran out of the miniprep DNA. We are going to have to start again from
 scratch        I suppose.
 Part no.: BBa_K110015
 Part Description: Mfa1
 Summary here: Same place as on Ste2.

GROUP 6: Vectors

Summary for Vectors Group

 Date: July 31, 2008
 Status report by: Tejas
 Part no.: BBa_K1100XX -> BBa_K1100YY
 Part Description: Vectors for concatenating and executing BioBricks
 
 The vectors to be used were delivered to us in STABS from MIT. They are pSB4A5 (amp), pSB4C5 (cam), pSB3K5
 (kan), and pSB4K5 (kan). The vectors come pre-inserted with the ccdB gene, preventing growth in all E. coli
 strains except DB3.1. Total amount of DNA extracted from mini-prep is estimated between 5 to 20 ug per
 vector. Restriction digests confirmed the extracted DNA was vectors.([http://www.jhu.edu/iGEM/Group6:Vectors/2008-7-24.Vectors%20(CAM,AMP,KAN3,KAN4)%20after%20Digest.Tejas.html Digestion of all four vectors]). Vectors
 were transformed into JM109, BB#2198 (DB3.1), and BB#5777 (DB3.1). Alll gave expected results. 1 ug of each
 vector was digested for future use. Gel of digestion shows DNA is correct.([http://www.jhu.edu/iGEM/Group6:Vectors/2008-8-12.Digest%20of%20vectors,%20ready%20for%20distribution.Tejas.html Vectors ready for insertions])

GROUP 7: Microscopy/Yeast

Summary for Microscopy/Yeast Group

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