Timeline+F13

=TIMELINE FOR RESEARCH= Schedule of things we will do over the semester

NOTE - see middle of page for previous weeks' schedules and things to catch up on. Definitions: 'cubby' = VDS cabinet in back of lab where all of our reagents are; 'pigeon hole' = the shelf for your lab notebook over by the window @Timeline F12

Wikispaces check on every other Sunday (Bi-weekly)

**Weeks layout**
Week 13 & 14 18-Nov - 1-Dec Week 11 & 12 4-Nov - 17-Nov Week 9 & 10 21-Oct - 3-Nov || || Week 7 & 8 7-Oct - 20-Oct Week 5 & 6 23-Sep - 6-Oct Week 3 & 4 9-Sep - 22-Sep Week 1 & 2 26-Aug - 8-Sep || PAPER COPY – Print out of **TxClass Safety Training**  - (can put in Safety section of VDS sign-in binder in lab)
 * Week 15 & 16 2-Dec - 8-Dec

Split Class Information
100113- VDSers - please close laptops and place them back on the shelves when you are done using them. - Thanks Dr. B

101513 - VDSers - we have 'orange' tape labelled some TE and Elution buffers by the Nanodrop. You want to keep those at the nanodrop and not use them to elute your sample from MidiPrep and MiniPrep and PCR CleanUp. Use the ones in the kits for elution because the ones near the nanodrop aren't that clean anymore.

101813 - Research Progress Table ResearchProgressF13

10/28/13 - For the Ligand Prep Protocol in Virtual Screening, the Maestro program is not starting. So, use the ICM Ligand Preparation Steps from the LigPrep Protocols to prepare your control ligands. **GDocs/Protocols/VirtualScreenignProtocols/Protocol_LigandPrep_VDS_v1_6.docx**

__Springers__, for Virtual Screening __only__ screen: **your Control Ligands**, **CB306** (306 ligs), **InHouseCompounds** (~40 ligs), **NIHClinicalCollection** (446 ligs), **HF9PlatesPlates5_9.sdf** (400 ligs)

10/30/13 - T4 DNA Polymerase is now from Fermentas (instead of NEB). Use the Fermentas buffer with it.

110413 - Note about Maybridge Compounds (HitFinder 9 library) __Remove the final letters__. e.g. KM10410SC needs to be changed to ---> KM10410
 * ** Maybridge ** – Login as VDSclass@gmail.com Password is painter214
 * Also __Ryan Scientific__ has info on Maybridge ligands **

11/13/13
 * There is a revised **ProtocolProteinExpression_VDS_Fall13_v5.doc** on GDocs/ProteinProtocols


 * Surrogate Enzyme:**
 * -- use YopH (the staff made a new plate in the fridge)**

11/25/13 Inhibitors to use for Phosphatases (e.g. the surrogate enzymes) Chembridge ID: - don't use the 50 mM in DMSO - USE the 5 mM in DMSO/Water (the mentors will have made some of these for you) They are in the 'Drugs' drawer in the back of the lab near our Cubby (near the yellow fire cabinet)
 * 5250098 ||
 * 5153298 ||
 * 5852635 ||


 * ===** This Week **=== || ===** This Week **=== ||
 * SPRINGERS **WEEK 15**

Finish to protein expression, purification, characterization protocols Finish virtual screening Enzyme Assay protocol Inhibition Assay protocol

See the Mentor schedule for when we will have mentors on duty:

Finish up your Peer Reviews of M&M Virtual M&M Expression, Purification, Characterization

posted to GDocs/Results&Data/ResearchReport_Materials&Methods_Guidelines VDSFall13_GuideFinalReportonTarget_VDS_v2.doc
 * Guidelines for Final Research Report:**

Lab Notebook check - Monday night (Springers only)
 * 2-Dec Monday**

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 3-Dec Tuesday**
 * 4-Dec Wednesday - last class**

Class Slides posted to Piazza resources section Lab Cleanup Day - each person do 1 hr
 * 5-Dec Thursday**

Peer Reviews DUE on canvas - cloning - expression, purification, characterization - virtual

Lab Cleanup Day - each person do 1 hr
 * 6-Dec Friday**

Final Lab Report Due @ 9pm
 * 7-Dec Saturday**

VDS Social - Dr. B's house 5pm RSVP Form
 * 8-Dec Sunday**

Wikispaces posting due - 9 pm

Lab Notebook check - Monday night || ** VETERANS ** **WEEK 15**
 * 9-Dec Monday**

Finish up your Peer Reviews of M&M Virtual M&M Expression, Purification, Characterization Enzyme Assays, Inhibition Assays

posted to GDocs/Results&Data/ResearchReport_Materials&Methods_Guidelines VDSFall13_GuideFinalReportonTarget_VDS_v2.doc
 * Guidelines for Final Research Report:**

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 2-Dec Monday**
 * 3-Dec Tuesday**
 * 4-Dec Wednesday - last class**

Class Slides posted to Piazza resources section Lab Cleanup Day - each person do 1 hr
 * 5-Dec Thursday**

Peer Reviews DUE on canvas - cloning - expression, purification, characterization - virtual

Lab Cleanup Day - each person do 1 hr
 * 6-Dec Friday**

Final Lab Report Due @ 9pm
 * 7-Dec Saturday**

VDS Social - Dr. B's house 5pm RSVP Form
 * 8-Dec Sunday**

Wikispaces posting due - 9 pm

Lab Notebook check - Monday night ||
 * 9-Dec Monday**
 * ===** Next Week **=== || ===** Next Week **=== ||
 * SPRINGERS ||= ** VETERANS ** ||
 * **ITEMS FOR LATER WEEKS:**
 * ===** Next Week **=== || ===** Next Week **=== ||
 * SPRINGERS ||= ** VETERANS ** ||
 * **ITEMS FOR LATER WEEKS:**
 * **ITEMS FOR LATER WEEKS:**
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LICpNIC-Bsa4cloningExerciseVDS_Fall13.docx Set up target protein for Virtual Screening - Make Homology Models

ICM Protocol

Dilute tail primers - make stock in TE and working dilution in water -- store stock in VDS Primers 2013 Box -- store working dilution in YOUR own box

Midi-prep your pNIC-Bsa4 After successful Midiprep, Submit to DNA Sequencing (pNIC-Bsa4- option B) submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev) -- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall13.doc

RE Digest w/BsaI of your pNIC-Bsa4, check on agarose gel ||  ||
 * Dr. B Notes ||  ||
 * Comparison Dock (ICM, GOLD, VINA) ||  ||
 * Comparison Dock (ICM, GOLD, VINA) ||  ||


 * **ITEMS FOR THE WEEK:**

http://vdsstream.wikispaces.com/Required+Lab+Safety
 * Lab Safety training**

FIRST PRIORITY TDRTargets Exercise - enter info on spreadsheet

Choose target options - submit your preferences to Target Selection Form Fall13

Once assigned a target - enter info onto the TargetSelections Fall13 sheet on GDocs - Oligo Primer Design

SECOND PRIORITY Nanodrop plasmid DNA - ProtocolNanoDropVDS.doc -- Plasmid to work with: pGBR22 Submit to DNA Sequencing (pGBR22 - option A)

THIRD PRIORITY (can do next week too) Analyze DNA Sequence -- (only proceed to this step after TDRTargets Exercise and Target Selections Form)

Create a GDocs folder in /StudentFolders - FirstnameLastInitial (e.g. WilliamB) Visit your Wikispaces research page under Research Pages 2013 Create your own freezer box, share it half & half with someone else

@SignUps FirstWeeks Fall13 - interactive sheet as a static sheet (so you can see it better):

2 - 3pm - **Lab Group Meeting** - BUR 108
 * WEEK 1**
 * 28-Aug Wednesday**

3:30 --> ~ 5:30 pm TDR Targets Exercise & Target Selection Form in WEL 2.114


 * 29-Aug Thursday**

2:30 - 4:30 pm TDR Targets Exercise & Target Selection Form in WEL 2.114

4:30 - 6:30 pm (Wet Lab) Nanodrop pGBR22, Submit to DNA Sequencing


 * 30-Aug Friday**

2 --> ~ 5pm Overlap Primer Design in WEL 2.114
 * Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall13.doc
 * upload final primers to Google Docs/VDS/Misc/Primers/**PrimerPlateOrderFall2013**
 * post final primers to Wikispaces page

Add content to YOUR research page Research Pages 2013 Put a line and **'Week 1'** This page will run in reverse chronological order - i.e. Newest stuff on top
 * Below that** add your 'result' image for the week with brief commentary


 * 31-Aug Saturday**
 * 1-Sep Sunday** || **ITEMS FOR THE WEEK:**

continue cloning your targets

2 - 3pm - **Lab Group Meeting** - BUR 108
 * WEEK 1**
 * 28-Aug Wednesday**

cloning & expression work

4:30 - 6:30 pm Help Session: PyMol Refresher in WEL 2.114
 * 29-Aug Thursday**

cloning & expression work


 * 30-Aug Friday**

cloning & expression work

4:00 - 6:00 pm Help Session: PyMol Refresher

in WEL 2.114

Add content to YOUR research page Research Pages 2013 Put a line and **'Week 1'** This page will run in reverse chronological order - i.e. Newest stuff on top
 * Below that** add your 'result' image for the week with brief commentary

PyMol Refresher - due next Wed ||
 * 31-Aug Saturday**
 * 1-Sep Sunday**
 * **ITEMS FOR THE WEEK:**

http://vdsstream.wikispaces.com/Required+Lab+Safety
 * Lab Safety training**

See the /FirstProcotols Folder in Google Docs

PRIORITY: Oligo Primer Design ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall13.doc

Analyze DNA Sequence

ProtocolPrimerDilutionVDS_Fall13.docx - Dilute PCR primers - practice cloning -- M13for, M13Rev, SP6, T7 promoter, pLIC-for, pLIC-rev -- make working dilution in water from 100uM stock. -- Store working dilution in YOUR own box.

PCR 'VDS PCR' - practice cloning - ProtocolPCRVDS.xls

RE Digest - practice cloning

Tail Primer Design - order your own Tail Primers (as a Team)

Oligo Primer Design Nanodrop & Submit to DNA Sequencing PCR
 * WEEK 2**
 * 2-Sep Monday**
 * Labor Day**
 * -** We have mentors on duty from 10-7 pm

2 - 3pm - **Lab Group Meeting** - NOTE: changed to ** GEA 125 ** a.k.a. 'world's coolest classroom'
 * 3-Sep Tuesday**
 * 4-Sep Wednesday**

Class Slides posted to Piazza resources section


 * 5-Sep Thursday**

Tail Primer Design (**4 - 6 pm**) in Wet Lab on laptops


 * 6-Sep Friday**

Tail Primer Design (**3 - 6 pm**) in Wet Lab on laptops


 * Write in your hours into the notebook - (also add in last week's)**
 * NOTE:** hours will be totaled and graded bi-weekly

Add content to YOUR research page Research Pages 2013 Put a line and **'Week 2'** This page will run in reverse chronological order - i.e. Newest stuff on top
 * Below that** add your 'result' image for the week with brief commentary

Lab Notebook check - Friday night

Oligo Design - upload output file to GDocs, paste Oligo sequence into your Target page, in Notebook too Nanorop - 2 images for Wiki & protocol/images in Notebook Submit to DNA - protocol in Notebook, if have result - put in Notebook too Analyze DNA Sequence - upload results to GDocs (put the protocol in your Notebook - results can stay in GDocs) PCR & run on an agarose gel - images to Wiki & protocol/images in Notebook
 * What Goes Where:**

Target page updates due - 9 pm Wikispaces posting due - 9 pm || **ITEMS FOR THE WEEK:**
 * 7-Sep Saturday**
 * 8-Sep Sunday**

Primary, Secondary, PCR Squared

Setting up your Target for Virtual Screening.


 * WEEK 2**
 * 2-Sep Monday**
 * Labor Day**
 * -** We have mentors on duty from 10-7 pm

- swing by Dr. B's office (see list above for those that sill need to meet)
 * 3-Sep Tuesday**
 * Target Meeting open times 1:30 - 3:00 pm**

2 - 3pm - **Lab Group Meeting** - - NOTE: changed to ** GEA 125 **a.k.a. 'world's coolest classroom'
 * 4-Sep Wednesday**

Class Slides posted to Piazza resources section

PyMol Refresher - due


 * 5-Sep Thursday**
 * 6-Sep Friday**


 * Write in your hours into the notebook - (also add in last week's)**
 * NOTE:** hours will be totaled and graded bi-weekly

Add content to YOUR research page Research Pages 2013 Put a line and **'Week 2'** This page will run in reverse chronological order - i.e. Newest stuff on top
 * Below that** add your 'result' image for the week with brief commentary

Lab Notebook check - Friday night

Wikispaces posting due - 9 pm ||
 * 7-Sep Saturday**
 * 8-Sep Sunday**
 * **WEEK 3**

PCR 'VDS PCR' - Re Do if it failed (see Dr. B if you're not sure)

RE Digest -

Tail Primer Design - order your own Tail Primers (as a Team) - we will have appointed times for this( see Thurs & Fri Google Calendar) //ProtocolPCR_PrimerDesignTails_for_pNIC-Bsa4CloningFall13.doc//

See Google Calendar for Open Lab Times
 * Open Lab times**


 * 9-Sep Monday**

add full DNA works output file to Notebook 2 - 3pm - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 10-Sep Tuesday**
 * 11-Sep Wednesday**

Class Slides posted to Piazza resources section


 * 12-Sep Thursday**

Tail Primer Design in wet lab - Google Calendar

Optional: get a head start by growing up pNIC-Bsa4 overnight in 160ml of LB + Kan spin down on Friday


 * 13-Sep Friday**

Tail Primer Design in wet lab - Google Calendar

see safety training links on next week's section


 * 14-Sep Saturday**
 * 15-Sep Sunday** || **WEEK 3**

PCRs, Cloning, Expression work start aiming to have cloning done by late September.

Set up your Virtual Screening on your target and run control dockings

See Google Calendar for Open Lab Times 2 - 3pm - **Lab Group Meeting** - GEA 125
 * 9-Sep Monday**
 * 10-Sep Tuesday**
 * 11-Sep Wednesday**

Class Slides posted to Piazza resources section


 * 12-Sep Thursday**
 * 13-Sep Friday**

see safety training links on next week's section

See Google Calendar for wet lab times
 * 14-Sep Saturday**
 * 15-Sep Sunday** ||
 * **WEEK 4**

Show Up for **Site Specific Training (OH 102)** for Fall Semester (PAI 2.14 lab) - see times available on the Lab Safety Page

Take **CW512** online http://vdsstream.wikispaces.com/Required+Lab+Safety

Tail Primer **ordering** through IDT website (some instructions show at top of this page) https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodDJlZDlneXMtb1JuREV0MUZQYXU4YkE#gid=0 Jessica, Qasim, Kelly Aditi, Grant T. Gautam W., Anita V., Ariel C. Keely, Nicole Brandy, D'Ondria, Caroline C. Jesus, James, Jiaqi
 * Teams that still need to order their Tail Primers (should be done Mon or Tues)**

After you have ordered **tail primers** and have made your **Oligo Mix**, you can start the first step of cloning: **Primary PCR**
 * - (~1.5hrs to prepare and run PCR, then save in -20degC or run agarose gel check)**

2 - 3pm - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 16-Sep Monday**
 * 17-Sep Tuesday**
 * 18-Sep Wednesday**

Class Slides posted to Piazza resources section

4-5 PM: PAI 2.14 site-specific training (OH 102) (just show up in Lab then)

Primary PCR Make LB Make LB Agar plates (Kan only)
 * 19-Sep Thursday**

Primary PCR Make LB Make LB Agar plates (Kan only)
 * 20-Sep Friday**

Wikispaces posting due - 9 pm
 * 21-Sep Saturday**
 * 22-Sep Sunday**


 * Over the next 2 weeks:**
 * Primary PCR on your target**

Make 160ml of LB - can do in Teams, but each person makes 160ml Make 6x (LB+Kan) plates - need 6 for the whole Team ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones) || **WEEK 4**

Show Up for **Site Specific Training (OH 102)** for Fall Semester (PAI 2.14 lab) - see times available on the Lab Safety Page

Take **CW512** online http://vdsstream.wikispaces.com/Required+Lab+Safety

PCRs, Cloning, Expression work start aiming to have cloning done by late September.


 * 16-Sep Monday**
 * 17-Sep Tuesday**

Target meeting times available with Dr. B

2 - 3pm - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 18-Sep Wednesday**

Class Slides posted to Piazza resources section

4-5 PM: PAI 2.14 site-specific training (OH 102)


 * 19-Sep Thursday**

Target meeting times available with Dr. B


 * 20-Sep Friday**

Wikispaces posting due - 9 pm || See Google Calendar for wet lab times
 * 21-Sep Saturday**
 * 22-Sep Sunday**
 * **WEEK 5**

See Targets Grading Spreadsheet page for missing items on Target page

Show Up for **Site Specific Training (OH 102)** for Fall Semester (PAI 2.14 lab) - see times available on the Lab Safety Page
 * Due This Week:**

Take **CW512** online http://vdsstream.wikispaces.com/Required+Lab+Safety

Primary & Secondary PCR's - should work PCR squared - if Primary & Secondary PCR worked PyMol Refresher - can count as 2 hours of lab time

Make 160ml of LB - can do in Teams, but each person makes 160ml Make 6x (LB+Kan) plates - need 6 for the whole Team ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)

3-4 PM: PAI 2.14 site-specific training (OH 102)
 * 23-Sep Monday**

1-2 PM: PAI 2.14 site-specific training (OH 102)
 * 24-Sep Tuesday**
 * 25-Sep Wednesday**

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'

Class Slides posted to Piazza resources section Journal Club article posted for next week


 * 26-Sep Thursday**
 * 27-Sep Friday**
 * 28-Sep Saturday**


 * NOTE:** we have **Saturday** lab times this week 11:30 - 5:00 pm


 * 29-Sep Sunday**


 * NEXT STEPS** if other things completed:

Transformation of pNIC-Bsa4 (as a Team - should end up with 2 plates/person)

start growing up pNIC-Bsa4 overnight in 160ml of LB + Kan spin down next morning (save in -20degC or proceed to Midi-Prep - 2-3hrs) -- if you dont' have time to spin down in morning (~30-45 min), you can temporarily store your overnight growth flask in 4degC for a few hours

Midi-prep (to make lots of plasmid that we will need for cloning) ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v3.doc
 * Do this protocol in Teams.
 * NOTE: which antibiotic will you need

Cut pNIC-Bsa4 with BsaI (part of pNIC-Bsa4 Cloning protocol)

If you have PCR Squared product and cut pNIC-Bsa4 accepting vector, proceed to Cloning


 * || **WEEK 5**

Show Up for **Site Specific Training (OH 102)** for Fall Semester (PAI 2.14 lab) - see times available on the Lab Safety Page

Take **CW512** online http://vdsstream.wikispaces.com/Required+Lab+Safety


 * Cloning should be completed by end or September**


 * Virtual Work**
 * Control Ligands selection and LigPrep is due at end of week
 * Virtual Set up is due at end of week
 * - e.g homology model (if needed) and setting up protein in GOLD
 * Submit docking job of control ligands is due at end of week

3-4 PM: PAI 2.14 site-specific training (OH 102)
 * 23-Sep Monday**

See Google Calendar for wet lab times
 * 24-Sep Tuesday**
 * Virtual Set up Times with Dr. B**

New Protein __Expression Protocol__ posted to GDocs (v. 4) New Protein __Purification Protocol__ posted to GDocs

<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">1-2 PM: PAI 2.14 site-specific training (OH 102)
 * 25-Sep Wednesday**

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'

Class Slides posted to Piazza resources section

See <span class="wiki_link_ext">Google Calendar for wet lab times
 * 26-Sep Thursday**
 * Virtual Set up Times with Dr. B**

See <span class="wiki_link_ext">Google Calendar for wet lab times
 * 27-Sep Friday**
 * 28-Sep Saturday**
 * 29-Sep Sunday** ||
 * **WEEK 6**

PCR squared

Transformation of pNIC-Bsa4 (as a Team - should end up with 2 plates/person) - ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v3.doc
 * Do this protocol in Teams.
 * NOTE: which antibiotic will you need

Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan --spin down next morning (save in -20degC or proceed to Midi-Prep - 2-3hrs) -- if you don't' have time to spin down in morning (~30-45 min), you can temporarily store your overnight growth flask in 4degC for a few hours til you can spin it in the afternoon. Pellets can be frozen and stored til next day or so.

Midi-prep (to make lots of plasmid that we will need for cloning)

Cut pNIC-Bsa4 with BsaI (part of pNIC-Bsa4 Cloning protocol), gel check

If you have PCR Squared product and cut pNIC-Bsa4 accepting vector, proceed to Cloning


 * 30-Sep Monday**
 * 1-Oct Tuesday**

<span style="background-color: #ffffff; color: #1155cc; font-family: arial,sans-serif;">@http://bit.ly/14nfYau
 * Cool talk tonight at 6:30 - see Announcement page for details**

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 2-Oct Wednesday**

Class Slides posted to Piazza resources section

Research Report Guidelines posted: GDocs/Results&Data/ResearchReport/ GuidelinesResearchReportonTarget_VDS_Fall13.doc

Wikispaces posting due - 9 pm
 * 3-Oct Thursday**
 * 4-Oct Friday**
 * 5-Oct Saturday -** should have Sat hours (no game)
 * 6-Oct Sunday**

proceed to cloning (if you have PCR product and your vector is prepared) || **WEEK 6**
 * NEXT STEPS**

- note: update Expression & Purification protocols were posted last week
 * Cloning should be completed by end or September**


 * Virtual Work**
 * Virtual Set up is due at end of week
 * - e.g homology model (if needed) and setting up protein in GOLD
 * new protocol (Part 2) should be posted **ProtocolVirtualScreenYOURTarget_VDS_Fall13.doc**
 * Submit docking job of control ligands is due at end of week


 * 30-Sep Monday**
 * 1-Oct Tuesday**

3-6pm Virtual Screening help with Dr. B and mentors (PAI 2.14)

<span style="background-color: #ffffff; color: #1155cc; font-family: arial,sans-serif;">@http://bit.ly/14nfYau
 * Cool talk tonight at 6:30 - see Announcement page for details**

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 2-Oct Wednesday**

Class Slides posted to Piazza resources section

4-7 pm Virtual Screening help with Dr. B and mentors (PAI 2.14) @https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodGNnQy1fTWZybTFMZ2YyV29xNXlRMkE&usp=sharing

Research Report Guidelines posted:

GDocs/Results&Data/ResearchReport/ GuidelinesResearchReportonTarget_VDS_Fall13.doc


 * 3-Oct Thursday**

1-3 pm Virtual Screening help with Dr. B

5-8 pm Virtual Screening help with Daniel, Urvashi, Max, Brandon (PAI 2.14)


 * 4-Oct Friday**


 * 1-3 pm** Virtual Screening help with Dr. B and mentors (PAI 2.14)

ACL
 * 5-Oct Saturday -** should have Sat hours (no game)

Wikispaces posting due - 9 pm || See <span class="wiki_link_ext">Google Calendar for wet lab times
 * 6-Oct Sunday**
 * **WEEK 7**

Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan --spin down next morning (save in -20degC or proceed to Midi-Prep - 2-3hrs) -- if you don't' have time to spin down in morning (~30-45 min), you can temporarily store your overnight growth flask in 4degC for a few hours til you can spin it in the afternoon. Pellets can be frozen and stored til next day or so.

Midi-prep (to make lots of plasmid that we will need for cloning)

Cut pNIC-Bsa4 with BsaI (part of pNIC-Bsa4 Cloning protocol), gel check

If you have PCR Squared product and cut pNIC-Bsa4 accepting vector, proceed to Cloning

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 7-Oct Monday**
 * 8-Oct Tuesday**
 * 9-Oct Wednesday**

Class Slides posted to Piazza resources section
 * 10-Oct Thursday**
 * 11-Oct Friday**
 * 12-Oct Saturday**
 * -** should have Sat hours (no game)

No lab notebook for Springers this week

Mid Semester Research Report due (a.k.a. Report on your Target) || **WEEK 7**
 * 13-Oct Sunday**

Cloning should be complete

Grow up positive clone overnight in DH5alpha in 160 ml of LB

Midi-prep (verify by DNA Sequencing, then store in 2 separate places, give a sample of it to Dr. B for Archival storage)

Transform positive clone into BL21(DE3) cells for expression

Virtual See Spreadsheet above or <span class="wiki_link_ext">Google Calendar for virtual help times
 * Control Docking should be complete
 * Virtual Screening of 1st libraries should be started

LICpNIC-Bsa4cloningExerciseVDS_Fall13.docx
 * Due on Saturday (for Veterans) - LIC cloning exercise**

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 7-Oct Monday**
 * 8-Oct Tuesday**
 * 9-Oct Wednesday**

Class Slides posted to Piazza resources section
 * 10-Oct Thursday**
 * 11-Oct Friday**
 * 12-Oct Saturday**
 * -** should have Sat hours (no game)

Lab Notebook check - Saturday night (__Veterans__ Only)

DUE: LICpNIC-Bsa4cloningExerciseVDS_Fall13.docx

Mid Semester Research Report due (a.k.a. Report on your Target) || See <span class="wiki_link_ext">Google Calendar for wet lab times
 * 13-Oct Sunday**
 * **WEEK 8**

Continue cloning your target, once clones proceed to protein expression

Virtual

>> Protocol_LigandPrep_VDS_v1_6.docx >> ProtocolVirtualScreenYOURTarget_VDS_Fall13.doc You don't have to do all of these protocols right away - but you should aim to have your Homology model created this week and have started on Control Ligands selection (the first part of the Virtual Screening Protocol). -- see the sign up spreadsheet above for times
 * Begin Virtual Screening setup (see meeting times with Dr. B)
 * create homology model if needed for your target
 * ProtocolHomologyModelVDS_v4.doc

Target meeting with your mentor - email or contact you mentor on Piazza to set up a time for meeting.

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 14-Oct Monday**
 * 15-Oct Tuesday**
 * 16-Oct Wednesday**

Class Slides posted to Piazza resources section Lab Notebook check - Saturday night (__Springers__ only)
 * 17-Oct Thursday**
 * 18-Oct Friday**
 * 19-Oct Saturday**

DUE: LICpNIC-Bsa4cloningExerciseVDS_Fall13.docx

Wikispaces posting due - 9 pm PyMol Image Contest || **WEEK 8**
 * 20-Oct Sunday**

expression trials

Virtual
 * Virtual Screening of 1st libraries should be started (Chembridge Diversity, HF9 maybridge)

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 14-Oct Monday**
 * 15-Oct Tuesday**
 * 16-Oct Wednesday**

Class Slides posted to Piazza resources section No lab notebook for Veterans this week
 * 17-Oct Thursday**
 * 18-Oct Friday**
 * 19-Oct Saturday**

Wikispaces posting due - 9 pm PyMol Image Contest || See <span class="wiki_link_ext">Google Calendar for wet lab times
 * 20-Oct Sunday**
 * **WEEK 9**
 * **WEEK 9**

Finish cloning, transform into BL21 cells

Meet with your Mentor for your Target Team Start your virtual screening control docking

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 21-Oct Monday**
 * 22-Oct Tuesday**
 * 23-Oct Wednesday**

Class Slides posted to Piazza resources section http://vdsstream.wikispaces.com/PyMolImageContest_F13
 * 24-Oct Thursday**
 * 25-Oct Friday**
 * PyMol Image Voting Form:**

No lab notebook check
 * 26-Oct Saturday**

Homology Model due and Control Ligands
 * 27-Oct Sunday**

Cloning Materials & Methods due **POSTPONED UNTIL Wed 10/30 at 3 am** || **WEEK 9** Expression and enzyme assays test Continue virtual screening on CB Diversity library

21-Oct Monday 22-Oct Tuesday 23-Oct Wednesday 1:30 pm (early) 2:30 pm (late) - Lab Group Meeting - GEA 125 - a.k.a. the 'wcc'

Class Slides posted to Piazza resources section 24-Oct Thursday 25-Oct Friday

http://vdsstream.wikispaces.com/PyMolImageContest_F13
 * PyMol Image Voting Form:**

26-Oct Saturday No lab notebook check

27-Oct Sunday Control Ligands Docking due Start CB306 and Chembridge Diversity Cloning Materials & Methods due **POSTPONED UNTIL Wed 10/30 at 3 am** || use this link to edit and enter your name: @https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodGNnQy1fTWZybTFMZ2YyV29xNXlRMkE&usp=sharing media type="custom" key="24019602" ||  ||
 * **Virtual Screening Set Up Times with Dr. B**
 * **WEEK 10**

After your 3rd cloning attempt, move to surrogate enzyme target Print protocol and talk to Mentor or Dr. B about scheduling Plates for **YopH** and **FtHap** are in the 4degC fridge Proceed to protein expression protocol Day 2 -- ProtocolProteinExpression_VDS_Fall13_v4.doc


 * Control Ligands Docking**

http://vdsstream.wikispaces.com/PyMolImageContest_F13
 * 28-Oct Monday**
 * 29-Oct Tuesday**
 * PyMol Image Voting Form:**

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc' Journal Club Class Slides posted to Piazza resources section
 * 30-Oct Wednesday**

Cloning Materials & Methods due at 3 am - i.e. Wed night -- see Piazza resources to post questions and get help

Control Ligands Docking Due
 * 31-Oct Thursday**
 * 1-Nov Friday**

No lab notebook check
 * 2-Nov Saturday**

Wikispaces posting due - 9 pm || **WEEK 10**
 * 3-Nov Sunday**

Protein PurificationEnzyme Assay Trials

**Virtual Screening**CB Diversity (50K ligs) screening Due: - will order compounds at end of week-- Oscar, Priya, Serena, Madeline, Brendan, Vicky, Kavya, CB306 Library Screening Due:- Grace, Melissa, Jason, Aliquoting Substrates for Assays: Oscar - yes Vicky - yes Kavya (?) Melissa - yes Priya Serena - yes Brendan - yes Madeline - yes Grace - Jason -

**WEEK 10** **28-Oct Monday** **29-Oct Tuesday****PyMol Image Voting Form:** http://vdsstream.wikispaces.com/PyMolImageContest_F13

**30-Oct Wednesday** 1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc' Journal Club Class Slides posted to Piazza resources section Cloning Materials & Methods due at 3 am - (i.e Wed night) -- see Piazza resources to post questions and get help

Lab Notebook check - Saturday night (Veterans Only)
 * 31-Oct Thursday**
 * 1-Nov Friday**
 * 2-Nov Saturday**

Wikispaces posting due - 9 pm ||
 * 3-Nov Sunday**
 * **WEEK 11**
 * **WEEK 11**

After your 3rd cloning attempt, move to surrogate enzyme target Print protocol and talk to Mentor or Dr. B about scheduling Plates for **YopH** and **FtHap** are in the 4degC fridge Proceed to protein expression protocol (Start on Day 2) -- ProtocolProteinExpression_VDS_Fall13_v4.doc

-Finish Control Ligands Docking

- start on 1st Libraries
 * ---InHouseCompounds** (~40 ligs)
 * ---CB306** (306 ligs)


 * 4-Nov Monday**
 * 5-Nov Tuesday**

Journal Club Q's from last meeting are due tomorrow in Class

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 6-Nov Wednesday**

Class Slides posted to Piazza resources section

Lab Notebook check - Saturday night (Springers only)
 * 7-Nov Thursday**
 * 8-Nov Friday**
 * 9-Nov Saturday**

Peer Review of M&M Cloning is due @ 11:59 PM - you will have 2 to review - make 5 constructive criticisms - make 2 compliments || **WEEK 11**
 * 10-NovSunday**

**Enzyme Assay First Attempts**- Grace, Melissa, Jason, Alyssa, **Aliquoting Substrates for Assays:** Jason - **Virtual Screening - ALL****---InHouseCompounds** (~40 ligs) **---CB306** (306 ligs) **---NIHClinicalCollection** (446 ligs), **---HF9PlatesPlates5_9.sdf** (400 ligs)


 * 4-Nov Monday**
 * 5-Nov Tuesday**

Journal Club Q's from last meeting are due tomorrow in Class

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 6-Nov Wednesday**

Class Slides posted to Piazza resources section

No lab notebook check
 * 7-Nov Thursday**
 * 8-Nov Friday**
 * 9-Nov Saturday**

Peer Review of M&M Cloning is due @ 11:59 PM - you will have 2 to review - make 5 constructive criticisms - make 2 compliments ||
 * 10-NovSunday**
 * **WEEK 12**

We will have more widely spread mentor coverage to help you with protein expression, etc.

After your 3rd cloning attempt, move to surrogate enzyme target Print protocol and talk to Mentor or Dr. B about scheduling Plates for YopH and **FtHap** are in the 4degC fridge Proceed to protein expression protocol (Start on Day 2) -- ProtocolProteinExpression_VDS_Fall13_v5.doc

-Finish Control Ligands Docking

- start on 1st Libraries after you have finished the Control Ligands docking


 * ---InHouseCompounds** (~40 ligs) -**use 1 processor**
 * ---CB306** (306 ligs) **- use 1 processor**


 * ---NIHClinicalCollection** (446 ligs), **use 1 processor**
 * ---HF9PlatesPlates5_9.sdf** (400 ligs) - **use 1 processor**

Journal Club paper posted for next week: http://vdsstream.wikispaces.com/Journal+Club+Fall13

Dr. B in during the morning - if you need to ask questions
 * 11-NovMonday**
 * 12-NovTuesday**
 * 13-NovWednesday**

NO CLASS - DR. B to ABRCMS

Journal Paper for next week is posted to vdsstream.wikispaces.com/Journal+Club+Fall13

No lab notebook check
 * 14-NovThursday**
 * 15-NovFriday**
 * 16-NovSaturday**

Virtual M&M due -- see Piazza resources to post questions and get help Guidelines: @https://drive.google.com/file/d/0B_Gl3lMyhDsoSDFsNjJvVENXcGs/edit?usp=sharing
 * 17-NovSunday**

Wikispaces posting due - 9 pm || **WEEK 12**

For Enzyme Assays, see general Enzyme Assay protocol on GDocs.

- Melissa, Jason, Alyssa, Jason -
 * Enzyme Assay First Attempts**
 * Aliquoting Substrates for Assays:**

---CB306 (306 ligs) ---NIHClinicalCollection (446 ligs), ---HF9PlatesPlates5_9.sdf (400 ligs)
 * Virtual Screening - ALL**
 * -- finish libraries**
 * --**-InHouseCompounds (~40 ligs)

Journal Club paper posted for next week: http://vdsstream.wikispaces.com/Journal+Club+Fall13

Dr. B in during the morning - if you need to ask questions NO CLASS - DR. B to ABRCMS
 * 11-NovMonday**
 * 12-NovTuesday**
 * 13-NovWednesday**

Journal Paper for next week is posted to vdsstream.wikispaces.com/Journal+Club+Fall13

No lab notebook check
 * 14-NovThursday**
 * 15-NovFriday**
 * 16-NovSaturday**

Virtual M&M due -- see Piazza resources to post questions and get help Guidelines: @https://drive.google.com/file/d/0B_Gl3lMyhDsoSDFsNjJvVENXcGs/edit?usp=sharing
 * 17-NovSunday**

Wikispaces posting due - 9 pm ||
 * **WEEK 13**

move to surrogate enzyme target Print protocol and talk to Mentor or Dr. B about scheduling Plates for YopH and **FtHap** are in the 4degC fridge Proceed to protein expression protocol (Start on Day 2) -- ProtocolProteinExpression_VDS_Fall13_v5.doc

- Finish these Libraries after you have finished the Control Ligands docking


 * ---InHouseCompounds** (~40 ligs) -**use 1 processor**
 * ---CB306** (306 ligs) **- use 1 processor**


 * ---NIHClinicalCollection** (446 ligs), **use 1 processor**
 * ---HF9PlatesPlates5_9.sdf** (400 ligs) - **use 1 processor**

Journal Club paper posted: http://vdsstream.wikispaces.com/Journal+Club+Fall13

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 18-NovMonday**
 * 19-NovTuesday**
 * 20-NovWednesday**

Class Slides posted to Piazza resources section No lab notebook check
 * 21-NovThursday**
 * 22-NovFriday**
 * 23-NovSaturday**

Expression, Purification, Characterization M&M due -- see Piazza resources to post questions and get help Guidelines: @https://drive.google.com/file/d/0B_Gl3lMyhDsoWldaOEN5eHZNZDg/edit?usp=sharing
 * 24-NovSunday**

M&M Virtual M&M Expression || **WEEK 13**
 * Peer Reviews** for both of these have been assigned:

Move to surrogate enzyme if you have not already done so.

The Chembridge Inhibitors have come in for the 1st round of ordering (FabG, 6PGDH, NDM-1) - mentors will make Stocks of each to 50 mM - each person doing an inhibition assays should do Working Stock solubility test - then make a Working stock for inhibition assays. -- for directions, see GDocs/Misc/Compounds/instructionsdilutingcompounds

For Enzyme Assays, see general Enzyme Assay protocol on GDocs. - Melissa, Jason, Alyssa, ? Jason - ?
 * Enzyme Assay First Attempts**
 * Aliquoting Substrates for Assays:**

---CB306 (306 ligs) ---NIHClinicalCollection (446 ligs), ---HF9PlatesPlates5_9.sdf (400 ligs)
 * Virtual Screening - ALL**
 * -- finish libraries**
 * --**-InHouseCompounds (~40 ligs)

Journal Club paper posted: http://vdsstream.wikispaces.com/Journal+Club+Fall13

1:30 pm (early) 2:30 pm (late) - **Lab Group Meeting** - GEA 125 - a.k.a. the 'wcc'
 * 18-NovMonday**
 * 19-NovTuesday**
 * 20-NovWednesday**

Class Slides posted to Piazza resources section Lab Notebook check - Saturday night (Veterans Only)
 * 21-NovThursday**
 * 22-NovFriday**
 * 23-NovSaturday**

Expression M&M due -- see Piazza resources to post questions and get help Guidelines: @https://drive.google.com/file/d/0B_Gl3lMyhDsoWldaOEN5eHZNZDg/edit?usp=sharing
 * 24-NovSunday**


 * Peer Reviews** for both of these have been assigned:

M&M Virtual M&M Expression ||
 * **WEEK 14**

Finish to protein expression, purification, characterization protocols Finish virtual screening Enzyme Assay protocol

Inhibition Assay protocol

Finish up your Peer Reviews of M&M Virtual M&M Expression, Purification, Characterization

2:00 pm (early) 3:00 pm (late) -
 * 25-NovMonday**
 * Lab Group Meeting** - GEA 100 (Turkey Week shuffle)

Class Slides posted to Piazza resources section


 * 26-NovTuesday**
 * 27-NovWednesday**

-- mandatory time out of lab - go eat a turkey
 * 28-NovThursday**

n/a
 * 29-NovFriday**
 * 30-NovSaturday**


 * 1-Dec Sunday** || **WEEK 14**

Finish up your Peer Reviews of M&M Virtual M&M Expression, Purification, Characterization Enzyme Assays, Inhibition Assays

2:00 pm (early) 3:00 pm (late) -
 * 25-NovMonday**
 * Lab Group Meeting** - GEA 100 (Turkey Week shuffle)

Class Slides posted to Piazza resources section


 * 26-NovTuesday**
 * 27-NovWednesday**

-- mandatory time out of lab - go eat a turkey
 * 28-NovThursday**

No lab notebook check
 * 29-NovFriday**
 * 30-NovSaturday**

Turkey Week Shuffle Form
 * 1-Dec Sunday** ||

Turkey Week Shuffle
- we will do a split class on the Monday before Thanksgiving. see the Schedule below for Week 14


 * EARLY CLASS: 2-3 pm Monday - GEA 100 (unfortunately not the 'WCC' - but still very cool)**

KEELY W ||  ||   ||   ||   |||| CAROLINE C D'ONDRIA P ||   ||   ||   ||   || Jiaqi Z ||   ||
 * SERENA Z || ANITA V ||  || ANTONIO G |||| JACQUELINE E || SEO K || KEVIN E ||   || MELISSA H || OSCAR V ||   || Renee || KATHERINE V ||
 * WILLIAM E || JESSICA N ||  ||   || JULIA C ||   || PRIYA P || BRANDY C ||   || Mohammad A || Shelby F-G ||   || MANUEL Z || IMRAN Z ||
 * || NICOLE W


 * LATE CLASS: 3-4 pm Monday - GEA 100 (unfortunately not the 'WCC' - but still very cool)**
 * BRENDAN C |||| MARIANNA U || ARIEL C || GRACE T ||  || ASHLEE W |||| HYUN-YOUNG L ||   || RAMIRO R ||   || VICTORIA G || Madeline J ||
 * KAVYA K || FENG G ||  ||   || GAUTAM W ||   || DANIEL D || JENSEN G ||   || JAMES T || NICOLET F ||   ||   || Jesus De La O ||
 * GRANT T || ADITI S ||  || JASON P ||   ||   ||   ||   ||   || Alyssa K ||   ||   ||   ||   ||


 * Target meetings:**
 * 1st one completed:** Tony & Renee, Serena & Madeline & Brendan, Oscar & Priya, Alyssa & Stephanie, Kavya & Vicky, Nicolet, Katherine V., Melissa & Jason, Ashlee & Marianna**,** Young & Grace , Ariel & Anita

Everyone designs their primer - but we will only order one person's set. Be sure you use the correct DNA Works output file to get your codon optimized DNA sequence (not just the CDS). -- If you are use a Summer A,B,D,D, or E plate - you need to get your DNA Works Output file from **Misc/Primers/DNAWorks_OutputSummer13** -- If you are use a Fall A or B plate - you need to get your DNA Works Output file from **Misc/Primers/DNAWorks_OutputFall13**
 * Primer Ordering Instructions (Sept. 13th 2013)**

Save the Word doc of your primer design into your GDocs Print Word doc and paste into your Lab Notebook Crosscheck your sequence with your Teammates Put the sequences of the Tail Primers on your team's target page. -- Enter your name for the person whose primers we will order - once you have designed the primers Put the info and sequence on the Target Spreadsheet https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodDJlZDlneXMtb1JuREV0MUZQYXU4YkE#gid=0 Order your primers -- go to the ICMB core site (see our Targets Spreadsheet for the link) -- find the IDT link -- enter our username: VDS (all caps) and password: same as the password to get on to the laptops buildingname+labroomnumber --Products/DNA/RNASynthesis/CustomDNAOligos --select 2 for the Multiple Entry -- leave defaults for Scale and Purification -- enter your 2 primers and the Prefixes. -- save to Wishlist, Dr. B will order when we have several of them.