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Basic Parts Update. Made 7 more parts since last week: cel9A, gliadin scFV, TevC, cel3A, OprF AtD, cl02365 AtD, Hia AtD Available passengers Gliadin scFv, Cub/Nub, Needle scFv, TevN/TevC, cellulases (cel3A, cel5B, cel9A, cel6A), SOD, Tir-M Available displayers

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Basic parts update
Basic Parts Update

  • Made 7 more parts since last week: cel9A, gliadin scFV, TevC, cel3A, OprF AtD, cl02365 AtD, Hia AtD

  • Available passengers

    • Gliadin scFv, Cub/Nub, Needle scFv, TevN/TevC, cellulases (cel3A, cel5B, cel9A, cel6A), SOD, Tir-M

  • Available displayers

    • VirG AtD, yuaQ AtD, AIDA-1 AtD, (ehaB, eCPX, TshA, CPG_L6, CPG_L2, upaG_short, espP(beta)?), Hia AtD, Pcryo_1225 AtD, Hag AtD, cl02365 AtD, OprF AtD, azo 1653 AtD

  • In white box labeled “correct minipreps”

  • Put minipreps on stock plates

Last two parts
Last two parts

  • Caspase(ig213) and mgfp-5(ig239)

  • mixing of forward and reverse oligos between the two

  • Purification gel looks good

  • Sequencing results:

    • Ig213 perfect! forward read, forgot to send in reverse read

    • Ig239 perfect!

Strep assay

13 constructs from class: displayer, AG4/IILK, strep tag

96-well block – hard to see if all liquid aspirated out

Multichannel pipetting – inconsistent amount of liquid (and cells)

Strep Assay

Strep assay1
Strep Assay

  • After 1 wash

  • A1= traA; A2=inv_short; A3=inv_long; A4=int-native

  • (+) control, A1, A3 had more brightness

  • Duplicates

  • C terminal displayers

  • Control is N terminal

  • Re-inoculated ~5hrs

Assay again with more cells
Assay again, with more cells

After 1 wash

Results consistent with previous experiment: A1 and A3 were brighter

Triplicates, all induced







Strep assay observations and next steps
Strep Assay - Observations and Next steps

  • Cell concentration was low after 5hours of incubation

    – overnight incubation to saturation?

  • Used 1ul strep for all experiments

  • Flat bottom plate gave lower reading than V bottom plate, but the decrease was proportional

  • Uneven growth of cells, so need to normalize to OD

    • Control cells and the 13 constructs from 140L grew faster than the 4 C-term displayers

  • Tried – optimized Z-positions: 11019um, 5720um (optimized), 5100um

    • similar results

  • After OD-normalizing, A1 and A3 had similar fluorescence

  • Image J integration for the pictures

    - the size and density of pellet seems to give a background so that smaller fluorescent pellets give similar readings as non-fluorescent larger pellets

  • Do 3 washes instead of 2 washes

  • Transfer from V to flat bottom necessary?

    • should stick to one plate type

Functional assays

Functional Assays

Assays should measure the ability of Bacteria to degrade

insoluble cellulose.

Plate based assays exist:

-dyes form a colored complex with insoluble cellulose.

-Colonies that degrade insoluble cellulose remove color

from the plates.

-These methods are not very quantifiable.


Functional assays1

Functional Assays

Assays have been preformed with purified enzyme product:

-cellulose in filter paper is degraded into reducing sugar.

-dinitrosalicylic acid is added to the solution

-absorbance at 600 nm is measured

These assays are preformed at ph 4.8 in an acidic buffer

-will the cellulases be active under non acidic conditions?

-will our cells survive under acidic conditions?


Functional assay
Functional Assay

gliadin scFv: To test whether scFv binds to gliadin


    • Coat plate with cells expressing surface scFv

    • Add 2% milk with TBS to block (to fill the bottom)

    • Add in gliadin that is tagged with fluorescent molecule (like FITC)

    • Wash 2X with TBS buffer

    • Use FACS to determine the amount of fluorescence

  • positive control

    • label cells with FITC and put through FACS

  • negative control

    • no plasmid in cell, so will not express scFv, so no binding to gliadin-FITC, therefore no fluorescence observed

    • or surface display a protein not specific for gliadin, so no fluorescence will result either

  • Can do similar binding assay with Tecan

Functional assay1
Functional assay

Mgfp-5: to test whether mgfp adheres to surfaces

- Place solution of cells (3ul) expressing mgfp-5 on glass slide

- incubate at room temperature for 10minutes

- Do successive washes with PBS to wash cells out.

- look at cells on glass slide under light microscope

- measure cell density

- positive control: glass-adherent bacteria (E. coli B117)

- negative control: solution of cells not expressing mgfp-5

- PMID: 16979252

  • Modeling possibilities

    • Signal transduction system

    • Cell surface display (?)

    • Circuit required for tranducing signal (?)

    • Glue or cellulase (?)