Daily+Schedule+Summ13

A tentative schedule of things we will do over the first few weeks. -- Old 2012 Schedule Journal Club Schedule: Journal Club Summ13 Tony, Alyssa, Grace, Young, Jacky, Kevin, Katherine, Kavya, Marianna, Melissa, Nicolet, Priya, Ramiro, Vicky, Oscar, Jason, Betty, Brian, Gabe, Salil, Stephanie, Ariel
 * Researcher's Names**:

Renee, Serena, Will, Madeline, til ~July 15th, Ashlee -til July 3rd, Anita, Laraib, Karuna - til June 28th, Brendan,

NOTE - see very bottom of page for previous weeks' schedules and things to catch up on that you may have missed.


 * SEE THE ANNOUNCEMENTS PAGE FOR SUMMER SOCIAL FORM**

Research Presentations Schedule
Monday 15th: Priya & Oscar & Betty, Kavya & Vicky Monday 22nd: Tony, Katherine V., Alyssa & Stephanie, Grace & Young Monday 29th: Nicolet, Ramiro, Jacky & Kevin, Melissa & Jason

Tues, July 23rd: Research Poster Design Workshop FAC 328 3-4 PM Tues, July 30th: **Research Poster Design Workshop** FAC 328 3-4 PM Wed, July 31st: **Research Poster Presentation Workshop** FAC 328 3-4 PM Tues, Aug 6th: **Research Poster Presentation Workshop** FAC 328 3-4 PM Thurs Aug 8th: **Poster Session** WEL Grand Hall 1-3 PM
 * RESEARCH POSTER WORKSHOP SERIES:**

This Week
__People to update Target page__: __People to update Wikispaces Research Pages__:


 * MONDAY 29-Jul**

**Weekly Group Meeting** @ 1:00 PM **in** GEA 403 (Gearing Hall)
& Journal Club - see Journal Club page for paper http://vdsstream.wikispaces.com/Journal+Club+Summer+13

3:00 PM - Research Poster Design Wokshop FAC 328 -- Good preparation for the poster you will generate in the Spring for the Undergraduate Research Forum OR if you want to attend a travel conference (e.g. ABRCMS or NCUR)


 * TUESDAY 30-Jul**

Last official day in the lab
 * WEDNESDAY 31-Jul**

Check your hours on the Hours Chart Be sure you have enough towards you 160. EVERYONE:
 * Total your hours on the sign in sheet
 * Add content to YOUR research page on Wikispaces @Research Pages 2013
 * Put a line and **'Week 9'**

Finish up your Lab Notebook and leave it in your pigeon hole


 * THURSDAY & FRIDAY** - optional days. We will have mentors in the lab.


 * August 20th** - 2 page summer reports due. Essentially a progress report/research update for the summer.

**Next Week**
nothing - empty your brain.

@https://docs.google.com/spreadsheet/viewform?formkey=dGdJaEQ5cUtEQm1uaXJ5LVNNdUR4NkE6MQ
 * Naturally Obsessed Form** - when to watch this documentary- Please fill out this form....

TACC Tour at VisLab in ACES building __ON CAMPUS__ - @
(meet in lab before at to walk over) Fill out - **Medical Waiver** Fill out - **Liability form**

TACC Tour - @
(meet in lab before - then we'll catch bus up to Pickle campus)

GASF (Genome Sequencing and Analysis Facility) Tour in MBB 4.102
Paper to read before the tour:

Algae Lab Tour : Meet in PAI 2.14 - then will walk over to BIO 320
Middle Schoolers visit lab
 * Mentors: prepare RE digest products for MSers


 * Cool Stuff We May Not Get To:**

Library generation and ligand prep for virtual Homology modelling

Screening with ICM
 * pharmacophore models

DSF (Differential Scanning Fluorimetry) assays qPCR Crystallization trials

Label new reagents and supplies Dilute new 100 bp ladder in Blue Juice + TE test all tubes of __#|Taq Polymerase__ in PCR Target Discovery choices --> order primer sets
 * Staff Stuff:**

Lab Notebook Checks Protocol cost analysis (Transformation, cloning) Walk through protein expression (use current mentor's enzymes)
 * ToDo List:**
 * Joey & Christina's //Francisella// HAP enzyme
 * Sadhana's //M. tuberculosis// enzyme
 * Joshua's //M. tuberculosis// enzyme
 * J.C.'s YopH

make and run SDS-Page protein gels load and run SDS-Page protein gels

Final Summer Research Presentations (__upload to Google Docs by Sunday night__)
 * Lab Group Meeting**/Journal Club (in
 * 2-3 slides, ~ 7 minutes
 * What your disease and protein target are (since the rest of the group doesn't know exactly what you are working on)
 * Specifics about size of gene, GC% content, etc.
 * Size of protein, is there a structure in the PDB?
 * What you set out to do
 * Where you have gotten so far (show gel pics, images, graphs or relevant data)
 * Challenges, failures, side-steps
 * Future Directions (i.e. Fall semester and beyond)

Social ???

(Remember to work on your 1 page (~500) word summary of your research. No figures needed. - Motivation, What you did, What you have left to do on your project. Reflect on what you have gotten out of your summer research and if it was what you expected. - submit to Dr. B before Sept. 1st. Then I will proof and send to Dr. Simmons.

. Last Day of VDS Summer Research

expression, purification, characterization
 * test specific activity of your enzyme for lot to lot consistency

__**Research Presentation Schedule:**__ Date: Name


 * Instructions**: prepare 3-5 Powerpoint slides to present your work to date
 * **Intro (talk about your disease and what your protein does)**, **Objectives**, **Methods& Results**, **Future Directions**

OLD STUFF (2012 Summer)


 * Dr. B NOTES**

ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls ProtocolPCR_pLICsequencing.xls
 * PCRs to do succesfully before you can move on to Target cloning:**

Veteran VDSers:
 * 1) Pick up target tail primers (Leader and Laggers) we ordered 2 days ago (to get in MBB building)
 * ProtocolPrimerDilutionVDS_Summ12.docx
 * 1) Make your Oligo Mix for your target (first step in Overlap PCR protocol) using PLATE of overlap primers - VERY important to not cross-contaminate your primers!!
 * ProtocolPCR_PrimerOverlapVDS_Summ12.docx
 * takes A LONG time to thaw primers in box.

Transformation Efficiency:
 * pmCherry **
 * pGFP **

Veteran VDSers:
 * Make Kan/Sucrose LB Agar plates for your target cloning
 * ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
 * ProtocolPCR_pLICsequencing.xls
 * Dilute Tail primers - ProtocolPrimerDilutionVDS_Summ12.docx
 * Overlap PCRs

ProtocolMidiPrepKit_HiSpeed_VDS.doc on

(NOT YET) ProtocolBacterialGrowthCurve_VDS_Summ12.xlsx - test (needs to be modified a little)

Veteran VDSers:
 * Make Kan/Sucrose LB Agar plates for your target cloning
 * ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
 * ProtocolPCR_pLICsequencing.xls
 * Dilute Tail primers - ProtocolPrimerDilutionVDS_Summ12.docx
 * Overlap PCRs

After your Primary and Secondary Overlap PCR work, go to : ProtocolpNIC-Bsa4_cloningVDS_Summ12.doc

make SDS-Page protein gels for characterization step

Midiprep on pNIC-Bsa4 : Midiprep on pUC19 : ??

Transformation of plasmids to make stocks - pUC19

12:30, 1:00 - all day: protein expression (Max, Kaarthik , Urvashi , Janice , Rishi, Aldo (observe) ) -- we will start a little later than we normally would but we will use an abbreviated induction phase (~ 3 hrs) so that we can finish in a more reasonable time.

(NOT YET) ProtocolBacterialGrowthCurve_VDS_Summ12.xlsx - test (needs to be modified a little)

Each Person: Measure OD every few hours over ~ 8hrs time span until OD reaches 1.000 at 600nm Make LB and Autoclave with flasks that you will use. --- put 500ml into in 2x 2L flasks -- put 50 ml into 4 x 250 ml flasks
 * one flask at 30degC in water bath shaker
 * one flask at 37deg in air incubator

--ProtocolPrimerDilutionVDS_Summ12.docx --pmCherry PCR --pLIC PCR - ProtocolPCR_pLICsequencing.xls --Overlap PCR of target

Make Protein Gels (Homemade SDS-Page) with

Protein Sonication

Protein expression Monitor log phase growth in Excel spreadsheet graph make SDS-Page protein gels for characterization step

EVERYONE: determine gene inside pNIC-Bsa4 by checking your pLIC sequencing that you sent to the core the other week EVERYONE THAT HAS DONE MIDI-Prep (successfully): Have you submitted your sample to sequencing? Does it turn out to be the right plasmid? ~ 10:00 Prep Starter Culture (grow until ~ 8hrs to OD600 = 1 )

SATURDAY 29-May SUNDAY 30-May MONDAY 31-May TUESDAY 1-Jun WEDNESDAY 2-Jun THURSDAY 3-Jun FRIDAY 4-Jun SATURDAY 5-Jun SUNDAY 6-Jun MONDAY 7-Jun TUESDAY 8-Jun WEDNESDAY 9-Jun THURSDAY 10-Jun FRIDAY 11-Jun SATURDAY 12-Jun <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">SUNDAY 13-Jun <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">MONDAY 14-Jun <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">TUESDAY 15-Jun <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">WEDNESDAY 16-Jun <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">THURSDAY 17-Jun <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; 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height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">MONDAY 26-Jul <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">TUESDAY 27-Jul <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">WEDNESDAY 28-Jul <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">THURSDAY 29-Jul <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">FRIDAY 30-Jul <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">SATURDAY 31-Jul <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">SUNDAY 1-Aug <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">MONDAY 2-Aug <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">TUESDAY 3-Aug <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">WEDNESDAY 4-Aug <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">THURSDAY 5-Aug <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">FRIDAY 6-Aug <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">SATURDAY 7-Aug <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 11557.5px; width: 1px;">SUNDAY 8-Aug =PREVIOUS WEEKS' SCHEDULES (for Summer 2013)= <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 8090px; width: 1px;">|| MONDAY || 3-Jun ||

Week 1
Post your class schedule to GDOcs - Summer13 Create your own folder in Google Docs under the folder: **/StudentFolders**

2:00 - PAI 2.14 First meeting
 * MONDAY 3-Jun**

1st Journal Club (please read the journal club article prior to meeting so that we can discuss it in groups)

Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. //Bioorganic & Medicinal Chemistry Letters// 2003, 13 (15), 2493-2496.

- New guys - walk through with Dr. B
 * Lab Safety training**

http://vdsstream.wikispaces.com/Required+Lab+Safety
 * Returning VDSers
 * sign up for FF205 (firefighter training) Lab Safety classes
 * Ariel, Renee and Ramiro - verify you also have the other classes
 * New guys - have lots of online classes to take too - see the link above
 * Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab

Dilute some primers
 * ProtocolPrimerDilutionVDS_Summ13.docx
 * M13f, M13r, SP6, T7, VDS1, VDS2, VDSR1, VDSR2
 * label, place in primers box

'Learn how to submit to DNA sequencing' (starring Daniel et al.) **-** wet lab
 * ProtocolDNASequencingFacilityVDS_Summ13.doc
 * submit pGBR22, pGFP, or pmCherry using forward or reverse primer - but not both
 * post results into the RESULTS folder of GDocs


 * TUESDAY 4-Jun**

1:00 PM start time.......

Finish up yesterday's protocols...

New guys - pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)

Make LB and LB plates ProtocolLBAgarPlatesVDS.doc

Choose a Plasmid to work with on these next 2 exercises(pGBR22 or pGFP or pmCherry or pNIC-Bsa4 or pUC19)
 * 1) Nanodrop plasmid DNA - ProtocolNanoDropVDS.doc
 * 2) Transformation Efficiency Protocol -ProtocolTransformationEfficiencyVDS.docx
 * Do this exercise in pairs. (??)
 * NOTE: which antibiotic will you need

Several people: Transform a plasmid for Midi-prep (make lots of pGBR22 and pNIC-Bsa4, make a few pGFP and pmCherry and pUC19)


 * WEDNESDAY 5-Jun**

__Transformation Schedule__


 * 2:00 PM**- Jacky E., Anita, Karuna, Grace, Marianna, Tony, Kavya, Oscar, Larab, Jason, Nioclet Oscar, Jason, Laraib =Make LB and LB plates


 * 3:30 PM** - Serena, Young, Vicky, Ashley, Renee, Brenden, Madalyn, Katherine V., Kevin, Melissa H.


 * 4:00 PM** - Alyssa, Priya, Ramiro, Jackie, Will I. (only doing check of plates and overnight culture)
 * Check Transformation Efficiency
 * Start overnight culture of your plasmid in DH5alpha in 80ml of LB

WELCH computer lab open - WELCH 2.144
 * THURSDAY 6-Jun**

10 am - 1 pm Protocol Target Discovery Ashlee, Alyssa, Anita, Young, Katherine V., Manuel, Melissa, Nicolet, Priya, Ramiro, Vicky, William

2pm - 5 pm Protocol Target Discovery

Tony, Brendan, Jiaqi, Karuna, Renee, Kevin, Kavya, Madeline, Mariana, Serena, Oscar, Jason, Laraib, Serena, Grace, Jacky E,


 * Check Transformation Efficiency
 * Start overnight culture of your plasmid in DH5alpha in 80ml of LB (Maybe ???) - depends on timing
 * FRIDAY 7-Jun**

Throw your overnight LB cultures into the fridge to 'stop' them so that you can spin them down later (a few hours)

10 am - 1 pm Protocol Target Discovery - WELCH 2.144 10 am - 'My First PCR' Ashlee, Alyssa, Anita, Grace, Young, Katherine V., Manuel, Melissa, Priya, Ramiro, Vicky, William

Check Transformation Efficiency Spin down LB flasks for doing MidiPrep later (store pellet in freezer)

2pm - 5 pm Protocol Target Discovery 2 pm - 'My First PCR' Tony, Brendan, Jiaqi, Karuna, Renee, Kevin, Kavya, Madeline, Mariana, Serena, Oscar, Jason, Nicolet, Serena, Jacky E,

Input information about which culture of plasmid you have (or will) grow up. http://vdsstream.wikispaces.com/Summer+Plasmids

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

Order Overlap Primers for class

Journal article for next week is posted on Journal Club page.


 * SATURDAY 8-Jun**


 * SUNDAY 9-Jun**

Week 2

 * MONDAY 10-Jun**

Safety training check.


 * Weekly Group Meeting @ 1:00 PM in** GEA 100 (Gearing Hall)

Protocol Primer Design OverlapAssembly Order Overlap Primers for class
 * Target Discovery selections**

Transformations: Oscar, Jason, Laraib, Betty, Serena

Continue transformations Do overnight cultures of plasmids in DH5alpha - check with Dr. B to see what/if you need to grow more

Input information about which culture of plasmid you have (or will) grow up. http://vdsstream.wikispaces.com/Summer+Plasmids


 * TUESDAY 11-Jun**

11:00 am Morning session of: Midi-prep plasmids - - Tony, Ashlee, Alyssa, Anita, Grace, Young, Melissa, Priya, Vicky
 * ProtocolMidiPrepKit_HiSpeed_VDS.doc

1pm start agarose gels of last week's 1st PCR (for the people not doing MidiPrep - e.g. Katherine, Nicolet, Marianna, Kevin, Oscar, Jason, Serena, Kavya, Jacky) PCR ? - Laraib, Betty Submit to DNA sequencing - Laraib, Betty, Oscar, Jason Nanodrop a plasmid - Laraib, Betty, Oscar, Jason

2:00 pm Afternoon session of: Midi-prep -Brendan, Jiaqi, Karuna, Renee, Madeline, Manuel, Ramiro, Will

Do overnight cultures of plasmids - Oscar, Jason, Laraib, Betty

Make 500 ml of LB

New guys do Lab 1: Buffers & Solutions

**On Your Targets Page:**
Add Link to DNA Works output text file Add substrate cost, quantity, and catalog numbers (and supplier) for enzyme assay reagents Add image of BRENDA reaction mechanism (screenshot it)

11:30 am - Morning session of: Midi-prep plasmids - Katherine V, Nicolet, Marianna, Kevin, Oscar, Jason, Laraib, Betty, Serena, Kavya, Jacky
 * WEDNESDAY 12-Jun**
 * ProtocolMidiPrepKit_HiSpeed_VDS.doc

1pm start agarose gels of last week's 1st PCR

Fill out Travel Authorization Forms for field trips. -- see GoogleDocs/Misc/TravelForms -- print out and complete - put in Dr. B's box in lab (pigeon hole)

__[ACTION__REQUIRED]**: Will/Ramiro please put your DNAWorks output file into the "DNAWorks_Output" folder in vdsclass@gmail.com/Misc/Primers.**


 * Grace/Young, Priya/Vicky, Jacky/Kavya, and Serena please upload your DNA oligonucleotide sequences onto the spreadsheet titled "PrimerPlateOrderTemplate_GDocs_Summer2013".**


 * THURSDAY 13-Jun**

Repeat 1st PCR if failed (why did it fail?) Then: ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls

Analyze DNA Sequence Exercise as a group?


 * FRIDAY 14-Jun**


 * 11 am - 2pm Optional time to catch up on stuff.**
 * - Daniel mentoring**

Print Journal Club article for you and your friends

Make LB for next week (500ml per person)

Agarose gel checks ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls

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

Lab Notebook check - should have everything up to date.

-- sleep all day -- watch TV all day
 * SATURDAY 15-Jun**
 * SUNDAY 16-Jun**

WEEK 3
When not doing protein expression - can work on PCR's Red/Green, and then PCR pLIC sequencing, Grow up your own batch of pNIC-Bsa4 (160ml) overnight and spin down to pellets the next day, save, and midi-prep later. (if fail, redo - because you need it for cloning)
 * ProtocolPCRforREcloningRED.xls OR ProtocolPCRforREcloningGREEN.xls (if fail, redo)
 * ProtocolPCR_pLICsequencing.xls (if fail, redo)


 * MONDAY 17-Jun**

Those who need to update their Wikispaces page: **Young, Karuna, Renee, Kevin, Madeline, Manuel, Nicolet, William**

Verify your Safety training is all present.

1:00 - 4 people (Grace, Katherine, Young, Nicolet) start transformation of YopH and FtHAP into BL21(DE3) cells (instead of DH5alpha) plasmids should be in 'Plasmids' box or the 'Final Plasmids' box share your tube of competent bacterial cells BL21(DE3) with another groups - i.e. only use 1/2 of the tube for yours Grace & Kavya - YopH in pNIC-Bsa4 Katherine & Jacky - FtHAP in pNIC-Bsa4 Young - YopH in pNIC-Bsa4 Nicolet & Kevin - FtHAP in pNIC-Bsa4

OTHERS: OR AND/OR Label your flasks AND/OR -- once the plasmid is verified - move it to the regular 'plasmids' box (and but the other half in the top loading freezer in the 'plasmids' box) -- Update plasmid info on the Google 'Plasmid Concentrations' spreadsheet: -@https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
 * Start one of the PCRs listed above**
 * Make LB** for expression if you haven't already done so (500ml per person)
 * Prepare your flasks for overnight culture** for protein expression (2x 50ml OR 2 x 100 ml of LB with Antibiotic) - Alyssa, Melissa, Vicky, Priya, Tony, Renee, Ramiro, Will
 * Check DNA sequence** of your MidiPrepped samples

& Journal Club - see Journal Club page for paper
 * Weekly Group Meeting** @ 1:00 PM ** CHANGED TO @ 3:00 PM in** GEA 100 (Gearing Hall) - unless we can't get this room.

Daniel - create a 'Plasmids' box in the top loading freezer (already have one for the other freezer)

Analyze DNA sequence exercise (as a group) - in WEL computer lab 5: 00 - Overnight growth of pGBR22 2x 80 ml of LB, Midiprep tomorrow (Select 2 people) ? Betty & Laraib?

5:30 - start overnight cultures (only those people who are expressing tomorrow) ( Alyssa, Melissa, Vicky, Priya, Tony, Renee, Ramiro, Will )

ProtocolProteinExpression_VDS_Summ13_v1.doc USE THIS PROTOCOL TOO: ProtocolBacterialGrowthCurve_VDS_Summ13.xlsx
 * TUESDAY 18-Jun**
 * 10 am - Larger Scale Protein Expressions (work in pairs)**

__Alyssa__ (Not Mon or Wed) & __Melissa__ - FabV in pNIC-Bsa4 PfDXR in pNic-BSSA4 __Vicky__ & __Priya__ - PfDXR in pNic-BSSA4 __Tony__ & __Renee__ (has class til 11:30) - FabI in pNIC-Bsa4 PfDXR in pNic-BSSA4 __Ramiro__ (Tues best, Monday ok, Not Wed, Thurs?) & __Will__ - FrTUHP in pnic-BSA4 PfDXR in pNic-BSSA4

1:00 - everyone else come in to catch up on PCR's, agarose gel checks

Mentors (i.e. Michael) : During the break in expression - make Resuspension buffer (~10ml per person) - see GDocs/Misc/Solutions&Dilutions or see protocol for protein expression - make more 1 M IPTG

__Transfer your transformation plate__ to 4degC fridge (__label it correctly__, and parafilm) - only these VDSers:

Grace & Kavya - YopH in pNIC-Bsa4 Katherine & Jacky - FtHAP in pNIC-Bsa4 Young - YopH in pNIC-Bsa4 Nicolet & Kevin - FtHAP in pNIC-Bsa4

5:30 - start overnight cultures (only those people who are expressing tomorrow) - Grace, Kavya, Katherine, Jacky, Madeline, Brendan, Kevin, Marianna, Serena, Jason, Oscar

ProtocolProteinExpression_VDS_Summ13_v1.doc USE THIS PROTOCOL TOO: ProtocolBacterialGrowthCurve_VDS_Summ13.xlsx __Grace__ (Not Tuesday) & __Kavya__ - (Kavya has every day til 11:30 am (could skip on any day but Monday) - prefers Wed) - YopH in pNIC-Bsa4 __Katherine__ (but Tues afternoon class) & __Jacky__ (not Mon - Tuesday is ok, Wednesday better) - FtHAP in pNIC-Bsa4 __Madeline__ & __Brendan__ - any day if advance notice..... - YopH in pNIC-Bsa4 __Kevin__ (Kevin has class till 11:15) & __ Marianna __ - has class 8:30 - 11:30 (Tues is class all day) - FtHAP in pNIC-Bsa4 __Serena__ FF @ 11 on Th - YopH in pNIC-Bsa4 __Jason__ (10am free) & __Oscar__ FtHap in pNIC-Bsa4
 * WEDNESDAY 19-Jun**
 * 10 am - Larger Scale Protein Expressions (work in pairs)**

1:00 - people from yesterday - resuspend cell pellets in 10ml of buffer and store in conical tubes in -80degC

5:30 - start overnight cultures (only those people who are expressing tomorrow)

Thurs @ 9:00 - 10: Karuna, Ashlee, Alyssa, Renee, Priya Thurs @ 11- 12: Melissa, Tony, Oscar, Serena, Kavya, Anita, Marianna, Katherine
 * THURSDAY 20-Jun (Dr. B out of town) - Daniel and Co. are in charge**
 * Firefighter Training ? - who is doing this....**

ProtocolProteinExpression_VDS_Summ13_v1.doc USE THIS PROTOCOL TOO: ProtocolBacterialGrowthCurve_VDS_Summ13.xlsx Young - FtHAP in pNIC-Bsa4 Ashlee & Karuna (karuna has class til 11:30) - FabI in pNIC-Bsa4 Nicolet & Anita - YopH in pNIC-Bsa4 Betty & Laraib - (Laraib class 10-11:50 each day) - P fDXR in pNic-BSSA4
 * 10 am - Larger Scale Protein Expressions (work in pairs)**

1:00 - people from yesterday - resuspend cell pellets in 10ml of buffer and store in conical tubes in -80degC

EVERYONE: complete and place your Release form and Medical Waiver in Dr. B's 'pigeon hole' (the one that says RESERVED over by the lab notebooks)

OFF
 * FRIDAY 21-Jun**
 * (Dr. B out of town)**

-- engage in mental gymnastics -- invent something
 * SATURDAY 22-Jun**
 * SUNDAY 23-Jun**

__Alyssa__ & __Melissa__ PfDXR in pNic-BSSA4 __Vicky__ & __Priya__ - PfDXR in pNic-BSSA4 __Tony__ & __Renee__ PfDXR in pNic-BSSA4 __Ramiro__ & __Will__ PfDXR in pNic-BSSA4
 * PROTEIN GROUPS (from last week)**
 * Group A**

__Grace__ & __Kavya__ - YopH in pNIC-Bsa4
 * Group B**

__Madeline__ & __Brendan__ YopH in pNIC-Bsa4 __Kevin__ & Jacky- FtHAP in pNIC-Bsa4 __Serena__ YopH in pNIC-Bsa4 __Jason__ & __Oscar__ FtHap in pNIC-Bsa4

__Young__ - FtHAP in pNIC-Bsa4 __Ashlee__ & __Karuna__ FabI in pNIC-Bsa4 __Nicolet__ & __Anita__ YopH in pNIC-Bsa4 __Betty__ & __Laraib__ P fDXR in pNic-BSSA4
 * Group C**

__Katherine__ & Marianna FtHAP in pNIC-Bsa4

& Journal Club - see Journal Club page for paper
 * MONDAY 24-Jun**
 * Weekly Group Meeting** @ 1:00 PM **in** GEA 100 (Gearing Hall)


 * Analyze DNA sequence exercise (as a group)** - in WEL computer lab

-- once the plasmid is verified - move it to the regular 'plasmids' box (and but the other half in the top loading freezer in the 'plasmids' box) -- Update plasmid info on the Google 'Plasmid Concentrations' spreadsheet: -@https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
 * Check DNA sequence** of your MidiPrepped samples

EVERYONE: complete and place your Release form and Medical Waiver in Dr. B's 'pigeon hole' (the one that says RESERVED over by the lab notebooks)

TUESDAY 25-Jun
1:00 Make Homemade Protein (SDS-PAGE) Gels Sonication & spin down
 * Group A:** __Alyssa__ & __Melissa__ PfDXR in pNic-BSSA4, __Vicky__ & __Priya__ - PfDXR in pNic-BSSA4, __Tony__ & __Renee__ PfDXR in pNic-BSSA4, __Ramiro__ & __Will__ PfDXR in pNic-BSSA4

Sonication & spin down (maybe on to purification?)
 * Group B:** Grace & __Kavya__ - YopH in pNIC-Bsa4,, __Madeline__ & __Brendan__ YopH in pNIC-Bsa4, __Kevin__ & Jacky - FtHAP in pNIC-Bsa4, __Serena__ YopH in pNIC-Bsa4, __Jason__ & __Oscar__ FtHap in pNIC-Bsa4

Katherine & Marianna FtHAP in pNIC-Bsa4 RE digest (during incubation period - make gels)
 * Group C**: __Young__ - FtHAP in pNIC-Bsa4, __Ashlee__ & __Karuna__ FabI in pNIC-Bsa4, Nicolet & __Anita__ YopH in pNIC-Bsa4, __Betty__ & __Laraib__ P fDXR in pNic-BSSA4

5:00 - After RE digest, people from last Thursday's expression (**Group C**) - resuspend cell pellets in 10ml of buffer and store in conical tubes in -80degC (20-30 minutes)

WEDNESDAY 26-Jun

 * 11:00 AM**

Sonication & Spin Down & Purification & run SDS-Page gels
 * Group A:** __Alyssa__ & __Melissa__ PfDXR in pNic-BSSA4, __Vicky__ & __Priya__ - PfDXR in pNic-BSSA4, __Tony__ & __Renee__ PfDXR in pNic-BSSA4,

RE digest (during incubation period - make gels) __-- Change to Purification__ __RE digest (during incubation period -__
 * 1:00 PM**
 * Group B:** Grace & __Kavya__ - YopH in pNIC-Bsa4, __Madeline__ & __Brendan__ YopH in pNIC-Bsa4, __Kevin__ & Jacky- FtHAP in pNIC-Bsa4, __Serena__ YopH in pNIC-Bsa4, __Jason__ & __Oscar__ FtHap in pNIC-Bsa4

Make Homemade Protein (SDS-PAGE) Gels


 * Group C**: __Young__ - FtHAP in pNIC-Bsa4, __Ashlee__ & __Karuna__ FabI in pNIC-Bsa4, __Nicolet__ & __Anita__ YopH in pNIC-Bsa4, __Betty__ & __Laraib__ P fDXR in pNic-BSSA4, __Katherine__ & __Marianna__ FtHAP in pNIC-Bsa4,, and __ Ramiro __ & __ Will __ PfDXR in pNic-BSSA4

__Sonication& Spin Down), purification__


 * THURSDAY 27-Jun **

run gels, stain, destain
 * 10:00 AM**
 * Group A:** __Alyssa__ & __Melissa__ PfDXR in pNic-BSSA4, __Vicky__ & __Priya__ - PfDXR in pNic-BSSA4, __Tony__ & __Renee__ PfDXR in pNic-BSSA4, __Ramiro__ & __Will__ PfDXR in pNic-BSSA4

__purification__
 * Group C**: Young - FtHAP in pNIC-Bsa4, __Ashlee__ & __Karuna__ FabI in pNIC-Bsa4, __Nicolet__ & __Anita__ YopH in pNIC-Bsa4, __Betty__ & __Laraib__ P fDXR in pNic-BSSA4 , __Katherine__ & __Marianna__ FtHAP in pNIC-Bsa4,


 * For everyone else - Open time - come in to work on stuff (PCR's, gels, Wikispaces updating, Notebooks, etc.)**

12:30 PM - NOTE TIME CHANGE - we need to be early enough to catch the bus.
 * EVERYONE: Gather together to get on bus to go to Pickle Research Campus for the TACC Tour (starts at 2pm there)**

To get to PRC: take #3 Burnet/Manchaca bus.


 * Depart: || [|GUADALUPE & DEAN KEETON][[image:http://www.capmetro.org/planner/images/info.png caption="info" link="@http://www.capmetro.org/gismaps/stops/599.html"]] (Stop #599) ||> 1:14 PM ||  ||   ||   ||
 * Arrive: || [|10401 BURNET & MC HALE][[image:http://www.capmetro.org/planner/images/info.png caption="info" link="@http://www.capmetro.org/gismaps/stops/5719.html"]] (Stop #5719) ||> 1:46 P ||^  ||^   ||^   ||

4:00 - Dr. B meet with Vernier

Dr. B meet with Nicolet and Kevin about paper

__ Ramiro __ & __ Will __ PfDXR in pNic-BSSA4 - add Ni-NTA resing (only 0.5 ml) overnight

WEEK 4
FRIDAY 28-Jun -

finish purifications, nanodrop, enter data to Google Spreadsheet (Protein Spectrophotometer Calcs) Run gels (Protein gels), stain for 1 hour, destain overnight Dry gels if already de-stained Make protein gels (if we have enough combs) RE digest if not doing protein stuff
 * 11:00 AM**

EVERYONE:
 * Total your hours on the sign in sheet
 * Add content to YOUR research page on Wikispaces @Research Pages 2013
 * Put a line and **'Week 4'**
 * **Below that** add your 'result' image for the week with brief commentary
 * This page will run in reverse chronological order - i.e. Newest stuff on top
 * Lab Notebook check - should have everything up to date.

Play Golf Run a marathon
 * SATURDAY 29-Jun**
 * SUNDAY 30-Jun**

5th Week
& Journal Club - see Journal Club page for paper
 * MONDAY 1-Jul**
 * Weekly Group Meeting** @ 1:00 PM **in** GEA 100 (Gearing Hall)

Training is pretty much over see GDocs/Misc/ Targets/Target_Selections..
 * Target Assignments announced **

Design & **Order** 'Tail Primers': __ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningSumm13.doc__ GDOcs/Misc/Primers/DNAWorksOutput
 * **the original, full gene sequences are in (be sure to use the Codon Optimized sequence!)**
 * **also, don't use a file if it says 'BAD' on it.**

Re-run VS4 docking with Histidines protonated (Group 1)

TUESDAY 2-Jul

11:00 AM - mentors on duty

RE digest (if not done already)

Complete __successful__ Practice PCRs (pGBR22 and then Red OR Green)

Finish up Tail Primer Design and Ordering: Nicolet, Tony, Renee, Kevin

Start Overlap PCRs Re-run VS4 docking with Histidines protonated (Group 2)

Grow up your own pNIC-Bsa4, mdidiprep, sequence verify it, store in your own box Cut your pNIC-Bsa4 to prepare the vector for cloning, save in -20degC in your box

11:00 AM - mentors on duty
 * WEDNESDAY 3-Jul**

Dilute tail primers

submit pNIC-Bsa4 to sequencing, to verify plasmid & determine what gene is in the middle

OFF - celebrate and shoot off some fireworks
 * THURSDAY 4-Jul**

11:00 AM - mentors on duty
 * FRIDAY 5-Jul**

We'll have open lab time (with mentors)- for people to catch up on stuff but not an organized activity

?? 1:00 Re-run VS4 docking with Histidines protonated (Group 2) ?? 1:00 FPLC of PfDXR - for those that expressed it.

submit pNIC-Bsa4 to sequencing, to verify plasmid & determine what gene is in the middle


 * SATURDAY 6-Jul**

Do people need more hours? - If so we can have lab times on Saturday. Let Dr. B know via email or in person (or carrier pigeon).

Invent a new language
 * SUNDAY 7-Jul**

6th Week
PROTEN GROUPS FROM OTHER WEEK: Katherine & Marianna FtHAP in pNIC-Bsa4
 * Group A:** __Alyssa__ & __Melissa__ PfDXR in pNic-BSSA4, __Vicky__ & __Priya__ - PfDXR in pNic-BSSA4, __Tony__ & __Renee__ PfDXR in pNic-BSSA4, __Ramiro__ & __Will__ PfDXR in pNic-BSSA4
 * Group B:** Grace & __Kavya__ - YopH in pNIC-Bsa4,, __Madeline__ & __Brendan__ YopH in pNIC-Bsa4, __Kevin__ & Jacky - FtHAP in pNIC-Bsa4, __Serena__ YopH in pNIC-Bsa4, __Jason__ & __Oscar__ FtHap in pNIC-Bsa4
 * Group C**: __Young__ - FtHAP in pNIC-Bsa4, __Ashlee__ FabI in pNIC-Bsa4, Nicolet & __Anita__ YopH in pNIC-Bsa4, __Betty__ & __Laraib__ P fDXR in pNic-BSSA4
 * MONDAY 8-Jul**

**Weekly Group Meeting** @ 1:00 PM **in** GEA 403 (Gearing Hall) - NOTE THE ROOM CHANGE!!!!!! Same building
& Journal Club - see Journal Club page for paper

After class - PfDXR group spins down sample (combine together) __Alyssa__ & __Melissa__, __Vicky__ & __Priya,__ __Tony__ & __Renee__ PfDXR, __Ramiro__ , Betty

4:00 - 5:15 - **Naturally Obsessed** documentary viewing in PAI 3.02 (with popcorn?)


 * TUESDAY 9-Jul**

1:00 - FtHAP group spins down sample (combine together) FtHAP group: Kevin & Jacky, Jason & Oscar, Katherine,

1 PM - FPLC for PfDXR group __Alyssa__ & __Melissa__, __Vicky__ & __Priya__ - PfDXR, __Tony__ & __Renee__ PfDXR, __Ramiro__ PfDXR

2:00 Re-run VS4 docking with Histidines protonated (Group 2): __Melissa (?), Vicky__, __Priya__, __Tony__, __Renee__, __Ramiro__,

Learn Virtual Screening: Oscar, Jason, Stephanie, Brian, Gabe, Betty, Salil

4:00 - FPLC people collect fractions of protein and spin down again, Nanodrop it, enter on Google spreadsheet (Protein Spectrophotometer Calcs) ? Store in Liquid Nitrogen (-80degC) and/or Glycerol (-20degC)


 * WEDNESDAY 10-Jul**

1:00 - YopH group spins down sample (combine together) YopH group: Grace & Kavya, Brendan, Serena, Nicolet, Young

1 PM - FPLC for FtHAP group FtHAP group: Kevin & Jacky, Jason & Oscar, Katherine

2 - 4pm: Middle Schoolers (Shadow a Scientist) - Alyssa & Tony

4:00 - FPLC people collect fractions of protein and sping down again, Nanodrop it, enter on Google spreadsheet (Protein Spectrophotometer Calcs) ? Store in Liquid Nitrogen (-80degC) and/or Glycerol (-20degC)

1:30 or 2:00 PM - FPLC for YopH group YopH group: Grace & Kavya, Serena, Young
 * THURSDAY 11-Jul**

1:00 PfDXR group - **__Alyssa__ & __Melissa__, __Vicky__ & __Priya__, __Tony__ & __Renee__ , __Ramiro__ - with ANDREW** YopH (i.e. PTP1b) group -**Kevin, Jason & Oscar, Katherine - with DANIEL** Spin down FPLC'ed sample from the other day (to about 2 ml) Nanodrop it, enter on Google spreadsheet (Protein Spectrophotometer Calcs) Go get liquid nitrogen (with a mentor!) Store in protein in Liquid Nitrogen (-80degC) and/or Glycerol (-20degC) 1:00 - FtHAP group spins down sample (combine together)

3:00 Re-run VS4 docking with Histidines protonated (Group 3): Grace, Young, Kavya, Ariel Virtual Screening 1 (Part 2) - using GOLD: Oscar, Jason, Betty, Stephanie, Salil, Gabe, Brian

~ 4:00 - FPLC people collect fractions of protein and sping down again, Nanodrop it, enter on Google spreadsheet (Protein Spectrophotometer Calcs) ?

Wikispaces Research Pages that need to be updated: **Brian C., Gabe H., Young, Jacky, Katherine, Kevin, Ramiro**, - 070913 http://vdsstream.wikispaces.com/Research+Pages+2013


 * FRIDAY 12-Jul**


 * Dr. B in a workshop all day**
 * Daniel & Michael are in charge** (scary!)


 * 1:15 PM - TACC VisLab Tour (on campus in ACES building) - meet in our lab first and walk over**

YopH group: **Grace & Kavya, Serena, Young** Spin down FPLC'ed sample from the other day (to about 2 ml) Nanodrop it, enter on Google spreadsheet (Protein Spectrophotometer Calcs) Go get liquid nitrogen (with a mentor!) Store in protein in Liquid Nitrogen (-80degC) and/or Glycerol (-20degC) 1:00 - FtHAP group spins down sample (combine together)
 * After TOUR:**

EVERYONE:
 * Total your hours on the sign in sheet
 * Add content to YOUR research page on Wikispaces @Research Pages 2013
 * Put a line and **'Week 6'**
 * **Below that** add your 'result' image for the week with brief commentary
 * This page will run in reverse chronological order - i.e. Newest stuff on top
 * Lab Notebook check - should have everything up to date.

- bake a cake - cure cancer
 * SATURDAY 13-Jul**
 * SUNDAY 14-Jul**

ON YOUR OWN: Move your Target page to top of Targets Page and add in missing information Update your Plasmid Concentrations to the Google Sheet if they have been verified by DNA sequencing: Grow up your own pNIC-Bsa4, midiprep, sequence verify it, store in your own box after submitting pNIC-Bsa4 to sequencing - determine what gene is in the middle Cut your pNIC-Bsa4 to prepare the vector for cloning (one of the 1st steps in the cloning protocol), save in -20degC in your box Continue Overlap PCR's Begin cloning after successful PCR's
 * http://vdsstream.wikispaces.com/Targets
 * @https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing

Target group meetings with Dr. B

Everyone make two (2) Kan+Sucrose LB Agar plates - we have lots (thank to Jacky, Oscar and Priya!), but I want you to know how to make them. -- make 20% (w/v) sucrose solution, sterile filter it ........ w/v = weight to volume -- make LB agar plates as usual, autoclave -- after cooled, add Kan and Sucrose (final conc of Sucrose should be 5% (w/v)) - NOTE: don't want to autoclave Kan or Sucrose

GOLD on your target - validation library ICM run VINA run, windows box only


 * MONDAY 15-Jul**

**Weekly Group Meeting** @ 1:00 PM **in** GEA 403 (Gearing Hall) - NOTE THE ROOM CHANGE!!!!!! Same building
& Journal Club - see Journal Club page for paper

2:30 - Session to update Wikispaces Target pages

Nanodrop protein, enter on Google spreadsheet (Protein Spectrophotometer Calcs) Go get liquid nitrogen (with a mentor!) Store in protein in Liquid Nitrogen (-80degC) and/or Glycerol (-20degC)
 * TUESDAY 16-Jul**


 * WEDNESDAY 17-Jul**


 * THURSDAY 18-Jul**

__People to update Target page__:Nicolet, Grace & Young, Vicky & Kavya, Jacky & Kevin

__People to update Wikispaces Research Pages__: Grace, Jacky, Jason, Katherine, Nicolet, Ramiro,

__Send your research presentation slides to Dr. B__:Tony, Katherine V., Alyssa & Stephanie, Grace & Young


 * FRIDAY 19-Jul**

Check your hours on the Hours Chart Be sure you have enough towards you 160. EVERYONE:
 * Total your hours on the sign in sheet
 * Add content to YOUR research page on Wikispaces @Research Pages 2013
 * Put a line and **'Week 7'**
 * **Below that** add your 'result' image for the week with brief commentary
 * This page will run in reverse chronological order - i.e. Newest stuff on top
 * Lab Notebook check - should have everything up to date.


 * SATURDAY 20-Jul**


 * SUNDAY 21-Jul**


 * MONDAY 22-Jul**

**Weekly Group Meeting** @ 1:00 PM **in** GEA 403 (Gearing Hall)
& Journal Club - see Journal Club page for paper


 * TUESDAY 23-Jul**

Jacky, Kevin, Kavya, Vicky grow up some pUC19 buy some Sma1 or HincII from ICMB Core Facility Store. Get NEB version. Midi prep pUC19 make Xgal/IPTG plates with Ampicillin resistance make some LB too (500ml)

Tues, July 23rd: **Research Poster Design Workshop** FAC 328 3-4 PM - optional. Good preparation for the poster you will generate in the Spring for the Undergraduate Research Forum


 * WEDNESDAY 24-Jul**

__Send your research presentation slides to Dr. B__: Nicolet, Ramiro, Jacky & Kevin, Melissa & Jason


 * THURSDAY 25-Jul**

HSers (Brian, Gabe, Betty, Salil) - work on Purchasing budget for reagents. In GoogleDrive/Misc/Purchasing - examples of past orders are on second sheet in the file. - copy and past a past order to the first sheet and then modify it to reflect what you used - Thx. - Dr. B Then do VS3

Grace & Young - meet with Dr. B about journal paper

Send slides to Dr. B - Nicolet, Ramiro, Jacky & Kevin,

Journal Paper is uploaded: http://vdsstream.wikispaces.com/Journal+Club+Summer+13

Social - 6 pm at Dr. B's

@http://goo.gl/maps/M0KWQ media type="custom" key="23519724"

media type="custom" key="23519866"


 * FRIDAY 26-Jul**

Check your hours on the Hours Chart Be sure you have enough towards you 160. EVERYONE:
 * Total your hours on the sign in sheet
 * Add content to YOUR research page on Wikispaces @Research Pages 2013
 * Put a line and **'Week 8'**


 * SATURDAY 27-Jul**


 * SUNDAY 28-Jul**