Timeline


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Week 13 (11/29 – 12/23)

Inhibition Assays

TUESDAY: Materials & Methods for Enzyme & Inhibition Assays – upload this to the Google Docs as a PDF.  See ‘Final Report‘ category on blog

Final Report Due Sat. Dec 4th

 

Class Party @ Kathryn’s on Sunday Dec. 5th  (7pm)

 

 

 

 

Future

MILESTONES:

gene cloned into pNIC-Bsa4, protein expressed in BL21(DE3), protein purified, characterized on gel and concentrated,  complete virtual screen jobs on libraries in DatabasesVDS, order compounds, test if enzyme is functional (Enzyme Assay), test compounds in Inhibition assay, determine IC50 of good compounds

 

1st Week
TUES afternoon or WED morning: Prepare 3 LB Amp plates
WEDNESDAY: Submit pGBR22 DNA to DNA Sequencing Facility -post to GDocs
WED or THURS: Transformation Efficiency – post image to Blog
FRIDAY: Analyze DNA Sequence Exercise – post to GDocs
Weekly update to WordPress blog

2nd Week
TUES or WED: Analyze DNA Sequence Exercise – post to GDocs
WED or THURS: Restriction Enzyme Digestion Due – post image to Blog
FRI: PyMol Refresher – post to GDocs

THURS or FRI: PCR – repeat if it fails – post image to Blog

Virtual Screen Refresher – post to GDocs

Print out of TxClass Safety Training
Weekly update to WordPress blog due on Sunday

3rd Week  (9/13 – 9/19)

PAPER COPY to Dr. B – Print out of TxClass Safety Training (can put in Dr. B’s mailbox)

PyMol Refresher – post to GDocs
Virtual Screen Refresher – post to GDocs and post table of top 10 results to Blog

Mon/Tues:

  1. ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall10.doc
  2. ProtocolDNASequencingFacilityTarget_VDS_Fall10.docx

Thurs/Fri: ProtocolPCR_PrimerDesign_for_pNIC-Bsa4Cloning.doc

Friday: Lab Notebook check
Weekly update to WordPress blog due on Sunday

Week 4 (9/20 – 9/26)

Tues: First journal club

Do a Midiprep on plasmid clone to  make extra DNA

ProtocolPCR_PrimerDesign_for_pNIC-Bsa4Cloning.doc

Start ProtocolPCR_pNIC-Bsa4cloningVDS_Fall10.xls
& ProtocolpNIC-Bsa4_cloningVDS_Fall10.doc

Sunday: ROUGH DRAFT of Research Report on Target Enzyme

Weekly update to WordPress blog due on Sunday

Week 5 (9/27 – 10/3)

Continue:

  • ProtocolPCR_PrimerDesign_for_pNIC-Bsa4Cloning.doc
  • ProtocolPCR_pNIC-Bsa4cloningVDS_Fall10.xls
  • ProtocolpNIC-Bsa4_cloningVDS_Fall10.doc

Start Virtual Screening of Your Target

Weekly update to WordPress blog due on Sunday – should include an image of results

Week 6 (10/4 – 10/10)

Continue:

  • ProtocolPCR_pNIC-Bsa4cloningVDS_Fall10.xls
  • ProtocolpNIC-Bsa4_cloningVDS_Fall10.doc
  • Virtual Screening of Your Target

Sunday 10/10 : FINAL DRAFT of Research Report on Target Enzyme

Weekly update to WordPress blog due on Sunday – should include an image of results

Week 7 (10/11 – 10/17)

Proceed with Cloning of your target gene into pNIC-Bsa4

Examine first Virtual Screening Run of Your Target

Continue screening the other libraries in the DatabasesVDS directory

Friday 10/15 – Lab Notebook Check

Weekly update to WordPress blog due on Sunday – should include an image of results

PyMol Image Contest – upload pic – Due: Tues Oct. 19th

Week 8 (10/18 – 10/24)

PyMol Image Contest – upload pic – Due: Tues Oct. 19th

Proceed with Cloning of your target gene into pNIC-Bsa4

verify positive clones with RE digest and DNA Sequencing (must virtually reconstruct your DNA first – tricky to do. Seek help from Dr. B or mentor) – must show how you did this in your lab notebook

Transform into BL21(DE3) cells

Continue screening the other libraries in the DatabasesVDS directory – complete all by Halloween

Weekly update to WordPress blog due on Sunday – should include an image of results

Week 9 (10/25-10/31)

PyMol Image Contest voting

FRI External Open House  – Oct 28th 1-4 pm

Proceed with Cloning of your target gene into pNIC-Bsa4

verify positive clones with RE digest and DNA Sequencing (must virtually reconstruct your DNA first – tricky to do. Seek help from Dr. B or mentor) – must show how you did this in your lab notebook

Transform into BL21(DE3) cells

Continue screening the other libraries in the DatabasesVDS directory – complete all by Halloween

Weekly update to WordPress blog due on Sunday – should include an image of results

Week 10 (11/1-11/7)

FINISH virtual Screening – Do the Top Ligands protocol – This is due by Tuedsday NIGHT.

We will be ordering Ligands on Wednesday so that you can have them to do Enzyme Assays soon.

Express protein into BL21(DE3) cells, purify, characterize on protein gel, concentrate protein, dialysis (?)

Weekly update to WordPress blog due on Sunday – should include an image of results

TUESDAY: Materials & Methods for Cloning is due (this will be used for your Final Report) – upload this to the Google Docs as a PDF.

see post: https://vdsclass.wordpress.com/2010/11/03/mm-for-cloning/

Week 11 (11/8-11/14)

TUESDAY: Materials & Methods for Cloning is due (this will be used for your Final Report) – upload this to the Google Docs as a PDF.

Express protein into BL21(DE3) cells, purify, characterize on protein gel, concentrate protein

Weekly update to WordPress blog due on Sunday – should include an image of results

NEXT TUESDAY: Materials & Methods for Virtual Screening is due  – upload this to the Google Docs as a PDF.

see post: https://vdsclass.wordpress.com/2010/11/08/mm-for-cloning/

Week 12 (11/15-11/21)

purify, characterize on protein gel, concentrate protein

Start Enzyme Assays (variables: enzyme amount, substrate amount, DMSO tolerance)

TUESDAY: Materials & Methods for Virtual Screening is due  – upload this to the Google Docs as a PDF.  See ‘Final Report‘ category on blog

Weekly update to WordPress blog due on Sunday – should include an image of results

NEXT TUESDAY: Materials & Methods for Expression, Purification, Characterization is due  – upload this to the Google Docs as a PDF.  See ‘Final Report‘ category on blog

Week 13 (11/22 – 11/28)

Continue Enzyme Assays (variables: enzyme amount, substrate amount, DMSO tolerance)

Inhibition Assays

TUESDAY: Materials & Methods for Expression, Purification, Characterization is due  – upload this to the Google Docs as a PDF.  See ‘Final Report‘ category on blog

Weekly update to WordPress blog due on Sunday – should include an image of results

NEXT TUESDAY: Materials & Methods for Enzyme & Inhibition Assays – upload this to the Google Docs as a PDF.  See ‘Final Report‘ category on blog

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