IGEM:Harvard/2007/Laboratory Notebooks/Bacterial Targeting Protocol/Week 5

MACS Assay w/o RFP cells - BL21DE3 cells vs his and strep OmpA1 cells (7/17/07)
Purpose: To test binding with OmpA1 cells with a lower concentration of cells, using BL21DE3 with his and strep antibodies + beads as negative control.


 * 1) Followed Indirect Magnetic Labeling Protocol
 * 2) Used 10 ul of Strep/His and 10 ul of RFP Bacteria with 1000 ul of buffer
 * 3) Used 10 ul his antibodies and 15 ul strep antibodies
 * 4) Used 30 ul of Beads
 * 5) Added an extra wash step after step #5
 * 6) Then follow Magnetic Separation
 * 7) Use the additional measures

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MACS Assay w/o RFP cells results (7/18/07)
Results: There was a lot of background in our negative controls - the BL21DE3 cells that expected to have very little cells had a lot of cells. Our OmpA1 contructs grew fairly well, but it's the negative control results that we are worried about, which was definetely not supposed to happen.

Conclusions: There may be protein interactions between the antibodies in other regions of the cells that we do not know of, which is causing binding in all of the other cells. In any case, we should probably look to a different region, such as the AIDA1 cells that will be transformed and the loop region of OmpA1 that will be transformed later in the month.

Electroporation of 10mer and 15mer ligation product into BL21(DE3) Cells

 * 1) First attempted electroporation without doing PCR purification of ligation products. Electroporation s resulted in either arcing or no colonies formed.
 * 2) 7/17/07 - PCR purification of remaining 10mer and 15mer ligation products
 * 3) Electroporation using 60 ng of 15mer, 60 ng of 10mer. 15mer had a time constant of 5.2/ 10mer had a time constant of 4.2

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Pick 8 colonies from random library transformation plates for sequencing (7/16/07)
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 * 1) 7/16/07 Pick 8 colonies from both the OmpA 10mer and OmpA 15mer library plates to grow in liquid LB for sequencing
 * 2) Qiagen miniprep of the 16 samples. Construct is OmpA +10mer or 15mer in Biobrick vector J04500.
 * 3) Results: Concentration of DNA
 * 4) OmpA15mer library 1 - 36ng/ul
 * 5) OmpA15mer library 2 - 42.6ng/ul
 * 6) OmpA15mer library 3 - 37.7ng/ul
 * 7) OmpA15mer library 4 - 41.4ng/ul
 * 8) OmpA15mer library 5 - 40.9ng/ul
 * 9) OmpA15mer library 6 - 34.2ng/ul
 * 10) OmpA15mer library 7 - 34.7ng/ul
 * 11) OmpA15mer library 8 - 32.3ng/ul
 * 12) OmpA10mer library 1 - 51.6ng/ul
 * 13) OmpA10mer library 2 - 45.4ng/ul
 * 14) OmpA10mer library 3 - 44ng/ul
 * 15) OmpA10mer library 4 - 31.6ng/ul
 * 16) OmpA10mer library 5 - 164.8ng/ul
 * 17) OmpA10mer library 6 - 49ng/ul
 * 18) OmpA10mer library 7 36.5ng/ul
 * 19) OmpA10mer library 8 45ng/ul

Transformation of New Surface Expression Constructs(7/17/07)
Transformed the following constructs into Nova Blue Cells (for plasmid preps) plated AIDA1 autotransporter with his tag in pET 29b+ AIDA1 autotransporter with strep2 tag in pET 29b+ AIDA1 + streptavidin in pET 29b+ OmpA1 + streptavidin in pET 29b+ OmpA2 + streptavidin in pET 29b+ pET 29b+ vector Transformed the following constructs into BL21(DE3) cells AIDA1 autotransporter with his tag in pET 29b+ AIDA1 autotransporter with strep2 tag in pET 29b+ ---

MACS Assay with AIDA1 Construct (7/19/07)
Purpose: To test binding of the AIDA1 constructs, trying the RFP selection assay again.


 * 1) Followed Indirect Magnetic Labeling Protocol
 * 2) Used 300 ul of Strep/His and 300 ul of RFP Bacteria
 * 3) Used 8 ul his antibodies and 20 ul strep antibodies
 * 4) Used 30 ul of Beads
 * 5) Added an extra wash step after step #5
 * 6) Then follow Magnetic Separation
 * 7) Use the additional measures
 * 8) Plate with 5 and 50 ul of bacteria.

MACS Assay with AIDA1 results (7/20/07)
Results: No growth at all Conclusion: Too little volume. Will leave in incubator for another day to see if there is growth.

MACS Assay Re-plate (7/20/07)
Will replate with 300 ul bacteria

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MACS Assay 2 results (7/21/07)
Results: We had very little background, with about 200 white cells to about 5 red cells in each plate. The smaller volume plates grew similarly after an extra day of incubation. Conclusion: We finally have a construct that we can use that displays surface expression!

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FACS Cell Sorting Preparation (7/20/07)

 * 1) Cell Innoculation and Induction
 * 2) Added antibodies according to the Fluorescent Labeling Protocol.
 * 3) Took the bacteria to the FACS cell sorter and sorted cells, plating them afterwards.

FACS Cell Sorting Results (7/21/07)
No growth after one night. Will come back tomorrow and check for growth.

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FACS and MACS with AIDA Construct Results (7/22/07)
See Colony Counts for exact numbers of colonies.

Observation: In general, the assay worked very well, and we were able to select for the AIDA cells against the RFP cells, with about a ratio of about 20:1 (white:red).

Conclusion: We have found a construct that works. Basically, we can now start beginning to build our library with this surface expression protein, though we're still going to look into the loop region for OmpA.

Sidenotes: There is some hinds that multiple cells/antibodies are binding to the same magnetic beads, causing a large different between colony sizes. Either this could be the reason for the difference, or just the basic fact that IPTG wasn't spread thoroughly. We will continue to check protocol and look into something that works as well as possible.

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Digestion of plasmid J04500 in preparation of OmpA loop insertion constructs (7/20/07)
BSA 100x     0.3ul J04500 plasmid  20ul 10x buffer 2       3ul SpeI                    1ul PstI                     1ul water                  4.7ul digest overnight at 37C (need to still add CIP 1ul, and incubate 45min at 37C)