Daily+Schedule+Summ14

A tentative schedule of things we will do over the first few weeks. Link to the old @Daily Schedule Summ13 **Sidestreamers**: Hailey, Zain **HSers**: Sarah, Minsu, Braxton, Roshni, Caroline W. Mentor Conflict sheet
 * Researcher's Names**: **VDSers**: Andrei, Andee, Briana, Carolyn T., Charina, Chris T., Cidia, Luis, Nikki
 * Lab Safety:** Have you complete your lab safety trainings?
 * Schedules:** please enter your summer schedule here (e.g. classes that you may be taking in the summer or other conflicts with lab work): LINK HERE
 * Mentors:** Want to know when the mentors will be on? - check here Google Calendar

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

make competent cells using Joey's protocol - HSers doing make PFU polymerase - HSers doing Set up Mendeley account for VDS. - DONE
 * Mentor Tasks:**

Research Presentations Schedule
- see Journal Club Schedule

Journal Club Presentations Schedule
@Summer Plasmids

-- Mentor to do lab safety training sheet tally - see if each researcher has their sheet pasted in the binder, then enter their name on the Summer14 page
 * Mentor**

= THIS WEEK =

Dilute new 100 bp ladder in Blue Juice + TE (only a few people) T-shirt Form for VDS shirts

ITEMS IN GENERAL TO BE MAKING PROGRESS ON: Enzyme assay on YopH or FtHap (whichever one you made) Grow up pNIC-Bsa4 and MidiPrep (if you have not already done so) Start cutting pNIC-Bsa4 with BsaI (store in freezer)

MENTOR: Tally hours from last week and enter into spreadsheet on VDSStaff

RESEARCHERS Update Wikipages - **Brianna, Andee, Luis, Martin, Braxton** Update notebooks: Update **Target** page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target.

REQUIRED ITEMS FOR NOTEBOOKS: All practice cloning work (including well labelled gels) Protein work (esp protein gel and FPLC output and nanodrop) We definitely need all of your Target work to be present in the notebook.
 * DNA Works Output file - print the text file and past in notebook
 * Tail Primer Design (protocol and what you designed)
 * Info from your Target Page (which means you need a Target page first!)

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)

Then: ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls

Print Journal Club article for you and your friends Make LB for next week (500ml per person) Agarose gel checks

Lab Notebook check - should have everything up to date.

-- sleep all day

-- watch TV all day

=**Dr. B NOTES:**=

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 DSF (Differential Scanning Fluorimetry) assays qPCR Crystallization trials
 * pharmacophore models

Label new reagents and supplies Dilute new 100 bp ladder in Blue Juice + TE
 * Staff Stuff:**

Target Discovery choices --> order primer sets

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


 * Wednesday, July 30, 2014**
 * Thursday, July 31, 2014**
 * Friday, August 1, 2014**

Mentors
Edit SignInSheetCLASS_VDSLabSummer14.xlsx and print several (and hand write date on there) Update Autoclave and Big Centrifuge Protocols and put in binder. Attach Big Centrifuge protocol to Big Centrifuge. Print 'Sign-Off' sheets for the Biq Equipment usage (See One, Do One, Teach One) -- GDocs/Misc/ --- SignOffSheet_SiteSpecific_Centrifuge_Autoclave_etc_Blue.docx - **DONE** --- SignOffSheet_SiteSpecific_Centrifuge_Autoclave_etc_Pink.docx - **DONE** make Research Pages Summer (use http://vdsstream.wikispaces.com/Research+Pages+2013 as a guide) - for each student - **DONE Melissa** make Journal Club page for Summer 2014 (see previous journal club for 2013 summer and modify) - **DONE Dr. B**

Week 1
Post your #|class schedule to GDOcs - Summer14 - ? Create your own folder in Google Docs under the folder: **/StudentFolders**


 * Thursday, June 5**

-- then we will walk over to GEA 100
 * First meeting** 3:30 PM - PAI 2.14 (the wet lab)

- 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
 * 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

Those that don't have to do Safety Training Walk Through with Dr. B

Pick up primers in MBB with mentors Dilute some primers
 * ProtocolPrimerDilutionVDS_Summ14.docx
 * M13f, M13r, SP6, T7, VDS1, VDS2, VDSR1, VDSR2
 * label very well, place in primers box

1:00 PM start time.......meet in PAI 2.14 to start Pick up primers at MBB (as a group) - if not already done. Target Discovery in computer lab **WEL 2.128**
 * Friday, June 6**


 * Saturday, June 7 - watch TV**
 * Sunday, June 8- watch TV**

Week 2

 * Monday, June 9**
 * @ 1pm - Computer lab - Target Disco con't.....**
 * later in afternoon:**

Create your own folder in Google Docs under the folder: **/StudentFolders** Make LB (definitely Zain + partner and Hailey + partner) and LB plates ProtocolLBAgarPlatesVDS.doc (VDS veterans) LB = 4 x 500 ml amounts LB plates (20ml per plates) --> make 10 AMP plates (divide into 2 groups) + 36 KAN plates (divide into 3 groups)
 * Tuesday, June 10**

to Autoclave while autoclave go to Nanodrop & submit to DNA sequencing.

Determine concentration of a plasmid (even if it already has it written on the tube!) (- you pick: pGBR22 or pGFP or pmCherry)
 * 1) Nanodrop plasmid DNA - ProtocolNanoDropVDS.doc

'Learn how to submit to DNA sequencing' (starring Grace et al.) **-** wet lab
 * ProtocolDNASequencingFacilityVDS_Summ14.doc
 * submit pGBR22, pGFP, or pmCherry using forward or reverse primer - but not both
 * post results into the RESULTS folder of GDocs

After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
 * New people (don't worry about FF205 showing up on TxClass yet - go ahead and print out your training history verification for all the other safety classes)

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

Lab Group Meeting @ 5:30 - 6:30 pm
GEA 403

1st Journal Club (please read the journal club article prior to the next 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.


 * Wednesday, June 11**

Those that don't have to do Safety Training Walk Through with Dr. B

SIgn up for a DNA sequenging #|account on DNA Lims.


 * ProtocolDNASequencingFacilityVDS_Summ14.doc
 * post results into the RESULTS folder of GDocs

After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
 * New people (don't worry about FF205 showing up on TxClass yet - go ahead and print out your training history verification for all the other safety classes)

Lab clean up - surfaces, fridges, old plates, old reagents, glassware re-hang PDB Drug Poster hang 2014 VDS Stream poster Organize powdered chemicals Clean Stir bars Fill & label spray bottles Write items needed on whiteboard Prep collirollers clean glassware (from Kaarthik)

SHOPPING! --- go to Fisher Chemistry Storeroom in WELCH. to get dry ice (bring several styrofoam containters) Get stuff from -80degC in Biotech and Robertus Labs (competent cells, protein, etc) -- store in our -80degC in racks Proper freezer box label orientation

visit storerooms (walking by ICMB storeroom, then to biotech lab), purchase the following items (see purchasing spreadsheet in GDocs /Misc/Purchasing) - PRINT IT OUT for 3 teams - sharpies, spray bottles - Taq DNA polymerase, 100bp and 1kb ladders - Mini prep kit, midi prep kit, PCR cleanup kit, IPTG, DTT, TCEP Enter purchase information in spreadsheet Place receipt in Dr. B's 'receipt' cubby

prep new kits (midi, mini, PCR cleanup kits)

Analyze DNA Sequence Exercise as a group - ?

Analyze DNA Sequence Exercise as a group -NO Those that don't have to do Safety Training Walk Through with Dr. B
 * Thursday, June 12**

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
 * NOTE: which antibiotic will you need

Several people: Transform a plasmid for Midi-prep Some transform expression plasmids (BL21(DE3)) - IF DOING ONE OF THESE _ ALTER THE PROTOCOL TO **not** USE DH5alphas

In DH5alpha cells for Plasmid Preps:
w/ Amp plates: pGBR22 - Andrei pGFP - Andee pmCherry - Briana

w/ Kan plates: pNIC-Bsa4 - Carolyn, Hailey pNIC-Bsa4 - Charina, Zain

In BL21(DE3) cells for Protein Expression:
w/ Kan plates FtHap - Chris T., Nikki YopH - Cidia, Luis

**VDSers**: Andrei, Andee, Briana, Carolyn T., Charina, Chris T., Cidia, Luis, Nikki **Sidestreamers**: Hailey, Zain

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

Grow up colonies of PFU polymerase for eventual midi-prepping. - Melissa - start 2x 5ml LB overnight culture of Pfu colonies in Kanamycin (use exiisting plate) - start 2x 5ml of glycerol stocks overnight culture in Kan - spread 2 x glycerol stocks onto Kan plates. -- let me know if they grow. --- then later date proceed to large scale culture

check plates - image and upload results to Wikispaces Resarch page and to your Google Docs folder, paste into your lab notebook - store plates by wrapping in parafilm (just the perimeter) and storing upside down in 4degC in blue racks
 * Friday, June 13**

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

check DNA sequenging results - put on Wiki and in notebook

Clean out fridge by the front of the lab (has a bunch of old LB) Biohazard Waste Boxing Demonstration Make more LB+Kan plates, make more LB media for next weeks expressions

- make notes about Pfu polymerase in the MentorLabLog - in GDrive - check Pfu polymerase colony growth from yesterday (from melissa and Grace) -- if it grew - spread a little bit out on a new Kan plate.
 * Mentor**

-- Mentor to do lab safety training sheet tally - see if each researcher has their sheet pasted in the binder, then enter their name on the Summer14 page

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

**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)

Update your lab notebook for this Week - ALL Update your weekly Wikispaces Research page - ALL


 * Saturday, June 14**
 * Sunday, June 15**

Wikispaces: Update Wikispaces Page: Andee, Andrei, Carolyn, Zain Just add DNA sequencing result to Wikispaces: Brianna, Charina, Chris, Cidia,Hailey Completed Wikispaces: Luis, Nicole
 * WEEK3**
 * Monday, June 16, 2014**

Mentor - print new VDS SIgn IN sheets, write dates on them and put in binder (it is in the Google Docs for VDSclass/Scheduling)

Dr. B out 1-3pm, 4-5 pm

Make more LB+Kan plates (10), LB+Kan+Sucrose (20), LB+Amp (10), make more LB media for expressions (2 liters worth, best if they are in separate Erlenmeyer flasks that they will be doing the expessions in) --e.g. for a 80 ml expression - put it ina 500ml flask --.e.g for a160 ml expression - put it in a 1000 ml Erlenmeyer flask -- rule of thumb is that volume of container is 4-5 times bigger than volume of media.

While the autoclave is running, Make some 20% sucrose.

Fill water bath shakers with water and get to temp #|Install flask clamps.

Someone do a single transformation of FtHap into BL21(DE3) - just one plate - not the 3 plate thing.

Clean out fridge by the front of the lab (has a bunch of old LB), wash all this glassware Biohazard Waste Boxing Demonstration (as in putting waste in a box....not hitting each other. That's not nice)

Transformation Efficiency calculations.

Mentor - grow up a colony of PFU Polymerase from DR. McDonald overnight. Mentor - make Research Pages Summer for the new High School students (use http://vdsstream.wikispaces.com/Research+Pages+2013 as a guide) - for each student -

Grow up DH5alpha cells for Plasmid Preps:
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later. -- for each plasmid in DH5alpha, see the MidiPrep protocol

HIGH COPY PLASMIDS: w/ Amp in 2x80 ml of LB: (80ml is one 'culture's worth. The other 80 ml is a backup) pGBR22 - Andrei pGFP - Andee pmCherry - Briana

LOW COPY PLASMIDS: w/ Kan in 1x160ml of LB: (160ml is one culture's worth. The other 160ml would be a backup, but we don't have enough room in the incubator) pNIC-Bsa4 - Carolyn, Hailey, Chris T and Nikki pNIC-Bsa4 - Charina, Zain, Cidia, Luis

NOTE: the Kan or Amp is not what makes them high or low copy. It is a function of the plasmid. You get more copies of DNA made from a high copy plasmid.

Follow this protocol for the following plasmids: pGBR22, pGFP, pmCherry ProtocolTransformationforPlasmidPrepVDS.doc

Follow this protocol for the following plasmids: pNic-Bsa4 ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v4

ToDo: next day (Tuesday) spin down your samples. We need to do this in the mid-morning. So, I would like one person to come in around 10:30 and move everyone's Erlenmeyer flasks to the 4degC fridge to 'stop' their growth until the rest of us can get there at 1:00 pm.

5:00-5:30 - Chris T and Carolyn T and Dr. B meet to discuss paper and slides.


 * Tuesday, June 17, 2014**

10:30 - one unlucky person gets to come in and move the flasks to the 4degC fridge. - Nicole W. (mentor)

1:00 PM - spin down your cultures from yesterday. #|Store pellets in -20degC.

Charina - check FtHap plates

Make some more LB (3 liters) Make some 20% sucrose.

Clean out fridge by the front of the lab (has a bunch of old LB), wash all this glassware Biohazard Waste Boxing Demonstration (as in putting waste in a box....not hitting each other. That's not nice)

High Schoolers 1st day - get setup on GDrive, Wikispaces, etc - pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS) - PyMol 1 lab Eventually, someone transform FtHap into BL21(DE3) & DH5alphas - and transform YopH into DH5alphas

Make 3L LB - Cidia, Luis, Charina Make 20% Sucrose - Zain, Nikki My First PCR - Cidia, Luis, Charina, Zain, and Nikki

MidiPrep- pGBR22 - Andrei and Carolyn pFGP - Andee, Hailey, Briana

Overnight Cultures for #|Protein Expression: YopH - Zain & Cidia, Carolyn & Andee, Hailey & Brianna & Chris FtHap - Luis & Andrei, Charina & Nikki

Dilute some primers (go in this order until we run out of new primers to dilute) - Andrei, Hailey, Zain **HSers**: Sarah, Minsu, Braxton, Roshni, Caroline W.

Andee, Briana, Carolyn T., Charina, Chris T., Cidia, Luis, Nikki
 * ProtocolPrimerDilutionVDS_Summ14.docx
 * M13f, M13r, SP6, T7, VDS1, VDS2, VDSR1, VDSR2
 * label very well, place in primers box for VDS

Lab Group Meeting @ 5:30 - 6:30 pm
GEA 403 Reminder to read the Journal Article and bring it with you to meeting


 * Wednesday, June 18, 2014**

Protein Expression - all day - this means that we have to start in the morning (10:00)

HSers - Buffers & Solutions lab

Make IPTG - sterile filter

 1 M IPTG in nanopure Make Lysis buffer (see purification protocol)
 * < LYSIS BUFFER (for sonication) ||  ||   ||
 * < Tris ||> 50 ||< mM ||
 * < NaCl ||> 300 ||< mM ||
 * < Imidazole ||> 10 ||< mM ||
 * < pH 8.0 w/ NaOH ||  ||   ||

submit Midiprep plasmids to DNA sequencing (for those that did Midiprep)

#|start agarose gels of 1st PCR ?

Luis & Cydia & Nikki -- start an overnight culture of pNIC-Bsa4 in DH5alpha for making more DNA plasmid for MidiPrep 2 x 160ml of LB + Kan -- steal from the plates of: Carolyn, Hailey, Charina, or Zain -- spin down tomorrow


 * Thursday, June 19, 2014**

HSers - Nanodrop and submit to DNA sequencing pGBR22

Luis, Cydia, Nikki - spin down overnight cultures of DH5alphas

Protein Expression Groups: YopH - Zain & Cidia, Carolyn & Andee, Hailey & Brianna & Chris FtHap - Luis & Andrei, Charina & Nikki

Sonication - and store in -20degC -- These guys start first:

MidiPrep (for those that haven't done it yet) - **Zain, Cidia, Chris, Luis, Charina, Nikki** -Use this Kit Protocol for each one. -ProtocolMidiPrepKit_HiSpeed_VDS_v3.doc

Agarose gels for those that have done PCR. My first PCR

Input information about which culture of plasmid you have (or will) grow up. @https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
 * GoogleDocs/Misc/Plasmid Concentrations**


 * Friday, June 20, 2014**

HSers - dilute a primer from lyophilized powder - transformation of pGBr22

Submit samples to DNA Sequencing (group that did Midi-prep yesterday)

Input information about which culture of plasmid you have (or will) grow up. @https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
 * GoogleDocs/Misc/Plasmid Concentrations**

Nickel purify samples from sonication. Collect samples for characterization gel. Store main elution samples in 4degC for next week

start agarose gels of 1st PCR Restriction Enzyme digest

My First PCR - for those that haven't done it yet

Mentor - grow up overnight culture of pBGR22 in DH5alpha for midi-prep

Update your lab notebook for this Week - ALL Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES Put a line and **'Week3'** 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

Print out: Journal article for next week that is posted on Journal Club page and in the GDrive folder


 * Saturday, June 21, 2014**
 * Sunday, June 22, 2014**

Wikispaces updates: Andrei, Charina, Luis, Nikki, Zain

Week 4
PCR pLIC Safety training check. distribute collirollers to tubes (sterily)


 * Mentor -** check lab notebooks to see if up to date.

re-do 1st PCR if failed - if it works, proceed to PCR pLIC Analyze DNA Sequence as group HSers - make more LB, grow up pGBR22 colonies overnight in 2x80ml of LB each Print out: Journal article for next week that is posted on Journal Club page and in the GDrive folder
 * Monday, June 23, 2014**

Input information about which culture of plasmid you have (or will) grow up. @https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing Nickel Purification, Characterization, practice PCRs Midi-prep pGBR22 (high schoolers) Reminder to read the Journal Article and bring it with you to meeting
 * Tuesday, June 24, 2014**
 * GoogleDocs/Misc/Plasmid Concentrations**
 * Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403**

HSers: make LB, make plates, submit DNA to sequencing that you made yesterday Expression and Spin down for those re-doing protein expression work on PCRs Protein Gel for - Andrei, Luis, Andee, Carolyn (maybe do FPLC too?)
 * Wednesday, June 25, 2014**

Take ownership of the Target Page for your new target on Wikispaces (update, revise or create page) http://vdsstream.wikispaces.com/Targets
 * Thursday, June 26, 2014**

Lab Tour - there is a lab tour today by visitors - so it is doubly important to wear proper clothing in lab (long pants and close toed shoes)

Purification & Protein gels for people who expressed protein yesterday FPLC, storage - Andrei, Luis, Andee, Carolyn

11:45 - meet in lab before walking over to POB for the: 12:00 1:00 - **TACC VIsLab Tour** []
 * Friday, June 27, 2014**

T-shirt Form for VDS shirts

Make Oligo mix for Targets PCR pLIC (2nd practice PCR) Design Tail Primers for targets, order tail primers

Update your lab notebook for this Week - ALL Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES Put a line and **'Week4'** 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


 * Saturday, June 28, 2014**
 * Sunday, June 29, 2014**

WEEK 5

Wikispaces to be updated: __Andee, Andrei, Carolyn, Sarah, Martin, Braxton, Caroline, Roshni__
 * Monday, June 30, 2014**

Figure out FPLC schedule - who has YopH, vs FtHap. Who can do Wed 11am.

Input information about which culture of **plasmid** you have (or will) grow up. @https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
 * PLASMID INFO**
 * GoogleDocs/Misc/Plasmid Concentrations**

Enter your **protein yields** into: Protein Spectrophotometer Calc @https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodC1mRVpNLVlDOUE4NlNxdldqNEZwRmc&usp=sharing
 * PROTEIN INFO**

Design **Tail Primers** for targets, order tail primers - in Computer Lab
 * in GDrive/Protocols/CloningProtocols
 * ProtocolPCR_PrimerDesignTails_for_pNIC-Bsa4CloningSumm14.doc

Make Oligo mix for Targets PCR pLIC (2nd practice PCR) Make FPLC buffers

print journal club article (and read) for tomorrow - it's a long one!

High schoolers do RE Digest

Week 5
Dilute new 100 bp ladder in Blue Juice + TE (only a few people) T-shirt Form for VDS shirts
 * Starting Week 5, Mentors will be in lab at 11am. **

HSers - run gels for RE digest - streak out a plate of PFU Polymerase for growing up - print PFU polymearase protocol off of Gdocs (GeneMcDonald one) - print Competent cells protocol and start making some.
 * Tuesday, July 1, 2014**

FPLC - FtHap: Nikki, Charina, Zain, Andrei, and Luis at 1:00 PM --- start concentrating down sample ASAP (on last part of either Characterization or Purification protocol?) --print FPLC protocol -- then turn on machine

retrieve and clean out old FPLC buffer bottles from Biotech lab

Make Oligo mix for Targets - for those that haven't done it yet (be sure to get the spiel from a Mentor - not from another researcher because there is too much of a 'telephone' gossip effect)

PCR pLIC (2nd practice PCR) - everyone who hasn't done it and has the time Make FPLC buffers - for those doing YopH tomorrow

Reminder to read the Journal Article and bring it with you to meeting
 * Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403**

HSers - Pfu polymerase work, figure out how to make competent cells - start growing up cultures for overnight expression. - make glycerol stocks of some of your overnight culture - see GycerolStocks protocol. Store in 80degC in a separate well labelled freezer box.
 * Wednesday, July 2, 2014**


 * FPLC - YopH : Chris, Cidia, Andee, Carolyn, Brianna, Hailey at 11:00 AM**

Reconcentrate, Snapfreeze in liquid nitrogen, and glycerol store - **Nikki, Charina, Zain, Andrei, and Luis**

PCRs RE Digest

5:00 - Naturally Obsessed documentary viewing in Painter.


 * Thursday, July 3, 2014**
 * Friday, July 4, 2014 - off for 4th of July**
 * Saturday, July 5, 2014**
 * Sunday, July 6, 2014**

Week 6
Dilute new 100 bp ladder in Blue Juice + TE (only a few people) T-shirt Form for VDS shirts

ITEMS IN GENERAL TO BE MAKING PROGRESS ON: Protein storage (liguid nitrogen snap freeze to -80degC + 20% glycerol on -20degC) finish practice PCRs (pLIC PCR) Make Oligo Mix Enzyme assay on YopH or FtHap (whichever one you made) RE Digest Overlap PCR's (Primary and Secondary) Grow up pNIC-Bsa4 and MidiPrep (if you have not already done so) Start cutting pNIC-Bsa4 with BsaI (store in freezer)


 * Monday, July 7, 2014**

MENTOR: Tally hours from last week and enter into spreadsheet on VDSStaff Print Travel Forms and fill in date, location etc. - Give to studetns to sign and return. -- for the lab tour at TACC on Friday (See @Summer14 page), Print and have each student sign the release forms (in GDocs ) /MISC/TravelAuthorization -- enter on Summer 14 page who has gotten theirs turned in so that we know who is missing

RESEARCHERS Update Wikipages Update notebooks:

NOTEBOOKS MISSING

Update **Target** page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target.

REQUIRED ITEMS FOR NOTEBOOKS: All practice cloning work (including well labelled gels) Protein work (esp protein gel and FPLC output and nanodrop) We definitely need all of your Target work to be present in the notebook.
 * DNA Works Output file - print the text file and past in notebook
 * Tail Primer Design (protocol and what you designed)
 * Info from your Target Page (which means you need a Target page first!)

We will do a notebook check on Wednesday.

HSers: Pfu Polymerase work make competent cells and test out start overnight cultures of Pfu Polymerase colonies in 4ml of LB for Glycerol Stocks tomorrow (see protocol on GDrive)

RE Digest - must be completed before you begin LIC Cloning


 * Tuesday, July 8, 2014**

Reminder to read the Journal Article and bring it with you to meeting
 * Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403**

hand out LIC cloning Exercise (due next week)

MENTOR: check Target pages and note here which need updating (i.e. have missing info)


 * Wednesday, July 9, 2014**


 * Thursday, July 10, 2014**


 * Friday, July 11, 2014**

TACC TOUR mentors on at 11 if you need to do lab work


 * 1:30 - Meet in Lab to go to the:**
 * 2:00 - Bus for the:**
 * 2:30 - TACC Machine Room Tour at the Pickle Research Campus**


 * ~ 4:30 return back from Tour**

Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES Put a line and **'Week6'** 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


 * Saturday, July 12, 2014**
 * Sunday, July 13, 2014**

Week 7

 * Monday, July 14, 2014**


 * HSers -** test competent cells, test PFU polymerase


 * ALL -** determine what gene is inside pNIC-Bsa4 (i.e. what you get back from DNA Sequencing. You will need to BLAST it and do a little detective work)

LIC cloning Exercise due
 * Tuesday, July 15, 2014**

Reminder to read the Journal Article and bring it with you to meeting
 * Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403**


 * Wednesday, July 16, 2014**
 * Thursday, July 17, 2014**
 * Friday, July 18, 2014**


 * HSers -** enter all VDS citations for Poster and Oral presentations into Mendeley and Endnote Web Online.

Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES Put a line and **'Week7'** 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


 * Saturday, July 19, 2014**
 * Sunday, July 20, 2014**

Week 8

 * Monday, July 21, 2014**
 * HSers -** enter all VDS citations for Poster and Oral presentations into Mendeley and Endnote Web Online.


 * Tuesday, July 22, 2014**

Reminder to read the Journal Article and bring it with you to meeting
 * Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403**


 * Wednesday, July 23, 2014**


 * Thursday, July 24, 2014**

Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES Put a line and **'Week8'** This page will run in reverse chronological order - i.e. Newest stuff on top
 * Friday, July 25, 2014**
 * Below that** add your 'result' image for the week with brief commentary


 * Saturday, July 26, 2014**
 * Sunday, July 27, 2014**

Week 9
Reminder to read the Journal Article and bring it with you to meeting
 * Monday, July 28, 2014**
 * Tuesday, July 29, 2014 - Last Day of Research for Summer**
 * Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403**