Daily+Schedule+Summ15

A tentative schedule of things we will do over the first few weeks. Link to the old @Daily Schedule Summ14
 * Researcher's Names**: see Summer 15 page @Summer15
 * Lab Safety:** Have you completed 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)
 * Mentors:** Want to know when the mentors will be on? - check here Google Calendar
 * Mentor Tasks: -** see Mentors Summ 15 page using menu on the left

Research Presentations Schedule - see Journal Club Schedule
note the times that you are in lab on the paper sign in sheet at the front of lab. For Lab Safety concerns, we must have a running record of who is in the lab at which times. We will also use this to tally the total hours in lab for the summer.
 * Summer Plasmids **- for students to Transform and make more of this summer
 * Lab Safety** -- make sure you have done all the required lab safety training, print out your training record and put in the 3 ring binder
 * Hours -**

= THIS WEEK = General Items: MENTORS: Tally hours from last week and enter into spreadsheet on VDSStaff

RESEARCHERS: Print Journal Club article for you and your friends Update Lab Notebook & Wikispace page (for Tuesday night check) - update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki 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)
 * RE digest gel images, PCR gel images, Protein SDS-Page gels images
 * Nanodrop yields for your protein after purification (and after FPLC)
 * etc.
 * (TBD) Info from your Target Page (which means you need a Target page first!)


 * MaterialsSpreadsheets** - is a new folder made in GDrive for:
 * 1) Plasmid Concentrations
 * 2) Protein Spectrophotometer Calcs
 * 3) Solutions&DilutionsforGdocs

Week 8
12:30 - JC pre-meet 2:00 - Virtual Volunteers NDM-1 virtual drug screening
 * Monday, July 27, 2015**

Wikispaces check.- due Tuesday night Notebook check - Charina will check them after 6pm (put line with date and comments in each)
 * Tuesday, July 28, 2015**


 * Wednesday, July 29, 2015**

2:00 - Virtual Volunteers NDM-1 virtual drug screening


 * Thursday, July 30, 2015**

Lab Group Meeting **@ 3:15 pm**
GEA 100 Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15

lab cleanup - clean up your samples (plates, PCR and RE digest tubes in -20degc, protein gel samples and purification samples)

last day of research lab cleanup
 * Friday, July 31, 2015**


 * NEXT WEEK**

=**Dr. B NOTES:**=

Kevin H to do Pfu Polymerase and competent cells for extra Coming Up Soonest: students create folders in Mendeley for their targets - upload all relevant papers all make PFU polymerase Enzyme Inhibition Assay with YopH - all do it and then post graph of results. Start competent cells protocol in teams of 2


 * New Members:** Lab Safety Training, Pipetting Exercise, PyMol labs, Beer's Law lab, Virtual Screening 1 lab

VDS PCR ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls RE Digest

PCR pLIC Protein Expression Trials with large scale (use Andee's, Charina's, Nikki's, Pfu Polymerase - Rachel & Parker) Make Competent Cells

Lab Group Meeting @ 1 pm
GEA 100

Lab Notebook Check Update Wikispaces - or change this to a Google Drive folder /VDSclass/ResearchProgress each person make a page in GDocs called: ResearchProgress Then 'COPY' this to the main Research Progress folder

UTEID_FirstNameLastInitial_ResearchProgress"

e.g. WEB31_WilliamB_ResearchProgress


 * Special Projects**

Matthew S. DNA sequencing for Fast targets Transform NDM-1 plasmid to BL21(DE3) cells Practice purification, characterization on old protein in -20 degC (I think it is Nikki's old one) - work with Anita on this

On Fast Targets: Create target pages for these on Wikispaces Express, Purify, Characterize, FPLC, store, enzyme assay test, DSF test High Priority NDM-1

Second Priority IMP-7: (metal-dependent), pET-28b, His Tag KPC-2: (serine beta lactamase), pET-24a, His Tag

VIM-2: (metal-dependent), pET-24a - No His Tag - Rachel and Parker to re-clone this into pNIC-Bsa4 Create target pages for these on Wikispaces Express, Purify, Characterize, FPLC, store, enzyme assay test, DSF test

Target Discovery Design and Order primers for target Practice Cloning Techniques Practice large scale protein expression (Andee's target, YopH, RpFabG) Make competent cells Make Pfu polymerase for our cloning work 3-D printer items:
 * Overall Flow:**
 * gel comb (1.0 mm for Bio-Rad)
 * FtHap and YopH models

Fast NDM-1 screening (750), make protein first - maybe Anita Fast target cloning - VIM-2 DSF on Fast Targets (and or YopH) - can we replicate Oscar's results (he has a protocol). - IMP-7, VIM-2 (needs tag), KPC-2 Anita - DSF on YopH (need someone to make more protein with her guidance) RpFabG
 * Special Projects:**

make competent cells using Joey's protocol - make PFU polymerase -
 * Research Tasks for Students:**

Dry Ice purchasing demo Liguid Nitrogen purchasing demo TACC tour

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)

Lab clean up - surfaces, fridges, old plates, old reagents, glassware re-hang PDB Drug Poster Organize powdered chemicals Clean Stir bars Fill & label spray bottles Write items needed on whiteboard Prep collirollers Proper freezer box label orientation

SHOPPING! --- JOHN G has already done this

go to Fisher Chemistry Storeroom in WELCH. to get dry ice (bring a styrofoam container) 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)

RESEARCHERS Update Wikipages 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.

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

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

T-shirt Form for VDS shirts ??????

Lab Notebook check - should have everything up to date.

-- sleep all day -- watch TV all day

Week 0
-- then we will walk over to GEA 100 After group meeting
 * Friday, June 5, 2015**
 * First meeting** 1:00 PM - PAI 2.14 (the wet lab)
 * Tour of Places - led by John G & Andee (BioSci, ICMB, Comp labs, Biotech lab)**

Get lab notebooks (see home page of Wikispaces for which type to get at the Coop) Update your schedule on the GDrive spreadsheet Create your own folder in Google Docs under the folder: **/StudentFolders** Complete online Lab Safety training


 * Saturday, June 6, 2015** **- watch TV**
 * Sunday, June 7, 2015** **- watch TV**

Week 1

 * Monday, June 8, 2015**
 * Start time: 12:30**

- walk through with the mentors (Andee, Charina and/or Nikki) http://vdsstream.wikispaces.com/Required+Lab+Safety
 * Lab Safety training - for those new to the lab** (HS and ACC)
 * 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

Get lab notebooks (see home page of Wikispaces for which type to get at the Coop) Update your schedule on the GDrive spreadsheet Create your own folder in Google Docs under the folder: **/StudentFolders** Complete online Lab Safety training

1. Make LB 2. Dilute primers
 * 2 tasks:**


 * 1/2 of the group does LB with Andee while other half does Dilute primers with Nikki (or Charina)**
 * Then researchers switch and do the other thing**

LB = either make 250 ml or 500 ml amounts depending on the available glassware (size of bottles) Do this in pairs - write both names and other relevant information on the labels. Andee to demonstrate autoclave usage ('See One')

Dilute some primers - with Nikki or Charina
 * ProtocolPrimerDilutionVDS_Summ15.docx
 * M13f, M13r, SP6, T7, VDS1, VDS2, VDSR1, VDSR2, pLIC-for, pLIC-rev
 * label very well, place in primers box


 * Tuesday, June 9, 2015**
 * Low Key day - Andee to lead**

Make LB and LB plates ProtocolLBAgarPlatesVDS.doc (VDS veterans) LB plates (20ml per plates) -->

Andee picks: 3 people for Green 3 people for Red 3 people for Purple 3 people for pNIC-Bsa4 3 people for YopH pNIC-Bsa4 3 people for FtHap pNIC-Bsa4

Green, Red, Purple people make: - 3 AMP plates (pair up or triple up - so that you are making 6 or 9 plates in a batch)

the rest make: each person also needs 3 KAN plates (pair up or triple up so that you are making 4-6 plates in a batch)

while autoclave go to submit to DNA sequencing.

'Learn how to submit to DNA sequencing' (starring Andee et al.) **-** wet lab
 * ProtocolDNASequencingFacilityVDS_Summ15.doc
 * Sign up for a DNA sequenging #|account on DNA Lims.
 * 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)

Mathew S - sequence Fast targets Target Discovery in computer lab - WEL 2.128
 * Wednesday, June 10, 2015**

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)

Determine concentration of a plasmid (even if it already has it written on the tube!) (- you pick: pGBR22 or pGFP or pmCherry or a pNIC-Bsa4 vector)
 * Thursday, June 11, 2015**
 * 1) Nanodrop plasmid DNA - ProtocolNanoDropVDS.doc

Read the Journal Club article Work on lab notebooks

Charina will check these over. Things to include: What you have done each day See the LabNotebook Grading rubric for rough guidelines. We don't need hypothesis for everything nor an extensive analysis - but you need the purpose or objective, the protocol, any results, and brief analysis or comments. - Primer Dilution - Lab safety training (if applicable) - Making LB - Making plates - Submit to DNA sequencing - Target Disco - generally address what we did - do not need to print and paste info though
 * Lab Notebook check** - leave your notebook in lab (as always) when you are done around 5:00 pm

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


 * Friday, June 12, 2015**

Lab Group Meeting @ 1 pm
GEA 100 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.

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)

Matthew S. - transform NDM-1, + 2 other lactamase targets

Target Disco con't..... Analyze DNA Sequence Exercise as a group ?

in the Google Drive folder /VDSclass/ResearchProgress each person make a page in GDocs called: ResearchProgress Then 'COPY' this to the main Research Progress folder so that it can be seen in both places - your folder and in the shared ResearchProgress folder


 * Saturday, June 13, 2015 - watch TV**
 * Sunday, June 14, 2015 - watch TV**

Post data/results to your Wikispaces page - Summer15

Week 2
Target Disco con't..... Analyze DNA Sequence Exercise as a group ? Oligo Primer Design
 * Monday, June 15, 2015**

Fill out Travel Authorization Forms for field trips. -- see GoogleDocs/Misc/TravelForms There are two forms: 1. Release 2. Medical Authorization -- if you are a Minor - do the ones for minors. -- if you are an adult - do the ones for adults -- print out and complete - put in Dr. B's box in lab (pigeon hole)

Photo Release Forms too (or did we already do these?)

Matthew S - start protein expression of NDM-1 with Anita in the AM - Parker/Rachel to spin down on Tuesday evening

Ashley - Transform Pfu Polymerase (Amp or Kan - I don't know - view protocol on our ProteinProtocols to figure out.) - NOTE: this actually needs to be done into BL21(DE3) cells !!!! because it will be for protein expression.

Need 1.6 L of LB - check to see if we have enough

start o/n culture of colonies for Midi-preps - 2 x 80ml of LB for High Copy plasmids (happens to be the Amp ones for us) - (80ml is one 'culture's worth. The other 80 ml is a backup) - 1 x 160 ml of LB for Low Copy plasmids (happens to be the Kan ones for us)- (160ml is one culture's worth. The other 160ml would be a backup, but we don't have enough room in the incubator)

Do this in Pairs (Andee to assign) 2 pGBR22 1 GFP 1 pmCherry 4 - pNIC-Bsa4 1 - EhPTP 1 - Pv6PG Parker/Rachael || pmcherry ||
 * Anthony + Lisa || pNIC-Bsa4 ||
 * Diane + Matthew N || EhPTP ||
 * Ashley + Bella || pGBR22 ||
 * Kevin H + Mayur || pGBR22 ||
 * Justin + Bethany || pNIC-Bsa4 ||
 * Simone + Ana || Pv6PG ||
 * Kevin N +
 * Krupa + Arthi || pNIC-Bsa4 ||
 * Steven + (Priya) || pNIC-Bsa4 ||
 * Jeff + Hannah || pGFP ||

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


 * Tuesday, June 16, 2015**

count colonies & calculate Transformation Efficiency from last week - put in Lab Notebook with Pics. Upload pics to your Google Research Page/ Wiki.

check DNA sequencing results - put on Wiki and in notebook

-- 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 Wiki page

Make 20% sucrose - and sterile filter it - DONE Make Kan/Sucrose (5%) plates - 2 per person

Andee - buy Midi-Prep kit?

GROUP 2 - comes in to make plates -make Buffers for competent cells protocol - then proceeed to MidiPrep

If time, Make IPTG - sterile filter, aliquot into 1.6 ml centrifuge tubes with 500 ul in each.  1 M IPTG in nanopure

Andee Spin downs (do in waves, not all at once) Midi-preps (group 1)
 * Group 1 ||
 * Anthony + Lisa || pNIC-Bsa4 ||
 * Diane + Matthew N || EhPTP ||
 * Steven + (Priya) || pNIC-Bsa4 ||
 * Kevin H + Mayur || pGBR22 ||
 * Justin + Bethany || pNIC-Bsa4 ||

Transformations into BL21(DE3) cells for Protein Expression:
w/ Kan plates Andee's Target Charina's Target Nikki's Target

Charina's at 4:30 pm Midi-preps (group 2) Parker/Rachael || pmcherry ||
 * Group 2 ||
 * Simone + Ana || Pv6PG ||
 * Kevin N +
 * Krupa + Arthi || pNIC-Bsa4 ||
 * Ashley + Bella || pGBR22 ||
 * Jeff + Hannah || pGFP ||

Charina's group won't do transformations

-


 * Wednesday, June 17, 2015**

Midiprep - Group 1 After - Nanodrop, then submit sample to DNA sequencing

Transformation of plasmids for protein prep - Group 2 Charinas Nikkis Andee Oscar's

Midiprep - Group 2 After - Nanodrop, then submit sample to DNA sequencing

HSers - Buffers & Solutions lab

2pm - Middle Schoolers visit lab (2 of them) Nikki to work with them (pre-make a gel), do calculations of plasmid amounts beforehand - brief intro, make gel, practice pipetting, pipette samples into tubes, pipette samples into gel and run, image gel and analyze - samples: both DNA ladders, several plasmids of different sizes. I would run 300 ng of each.

Dry Ice Tour - with Tonita Liquid Nitrogen Tour - with Tonita

Target Disco con't.....

Oligo Primer Design

Parker/Rachel - spin down Matthew's samples (at 18-20 hrs after induction with IPTG) Parker/Rachel - Grow up colonies of PFU polymerase for test - DOES IT GROW OVERNIGHT? - start 2x 5ml LB overnight culture of Pfu colonies in Amp (use existing plate)

(get mentor help - or from Anita/Tony a.k.a. 'Tonita')


 * Thursday, June 18, 2015**

Pre-meeting for Journal Club presenters with Dr. B - 12:00 in his office. Read journal article Remove plates from incubator and move to fridge (for those that did transformation yesterday) RE Digest Analyze DNA Sequence Exercise as a group ?

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 19, 2015**

Lab Group Meeting @ 1 pm
GEA 100 2nd Journal Club

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**

Biohazard Waste Boxing Demonstration - by John G.

Make and run gel for RE Digest (use Agarose Gel protocol)

???? My first PCR - Group 1 My first PCR - Group 2 (if time)

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 20, 2015**
 * Sunday, June 21, 2015**


 * Thursday, June 25, 2015**

VisLab Tour @ 2 pm POB 2.404

Lab Group Meeting @ 1 pm
GEA 100 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.

Post data/results to your Wikispaces page - Summer15 update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki

REQUIRED ITEMS FOR NOTEBOOKS: All practice cloning work (including well labelled gels)
 * Info from your Target Page (which means you need a Target page first!)

Protein Expression Schedule for this week (Mon June 22nd & Tues June 23rd) @https://docs.google.com/spreadsheets/d/1XedpP7OwNGjScpWtrpGTCX3dmFoTV0UA3v4-BL4jsaI/edit?usp=sharing media type="custom" key="27669494"

Week 3
protein expressions in Groups
 * Monday, June 22, 2015**

protein expressions in Groups, con't.....
 * Tuesday, June 23, 2015**

- HOSA - Nikki, Charina
 * Wednesday, June 24, 2015**

Middle Schoolers visit lab (2-4 pm)

Make Homemade SDS-Page gels (stagger) - how many plates do we have? Target selection & Ordering Primers Make buffers for purification - stagger

My First PCR - stagger (maybe)

- HOSA - Nikki, Charina
 * Thursday, June 25, 2015**

Make Homemade SDS-Page gels (stagger) - how many plates do we have? Make buffers for purification - stagger Purifications My First PCR - stagger

TACC VisLab Tour @ 2 pm POB 2.404

- HOSA - Nikki, Charina
 * Friday, June 26, 2015**

Lab Group Meeting @ 1 pm
GEA 100 Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15

Post data/results to your Wikispaces page - Summer15 update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki

Purifications

Target Disco con't..... Oligo Primer Design Purifications

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!)


 * Saturday, June 27, 2015**
 * Sunday, June 28, 2015**

Week 4
Lab Hours totaling (Charina or Nikki) Wikispaces check - Nikki (put commments on each one) Notebook check - Charina
 * Monday, June 29, 2015**

FPLC - Matthew S. (and other VDSers will watch to learn the process - and get a 'See One' checkoff)

Transform, grow up in 160ml of LB+Kan, Midi-prep: Diane - IMP-7 in pET28b Anthony - KPC2 in pet24a Simone - VIM2 in pet24a

Make SDS-PAGE gels - everyone that needs to Run SDS-PAGE gels

My First PCR
 * Tuesday, June 30, 2015**

Spin samples to prep for FPLC on Wed or Thurs - store in 4degC

Target picking ?
 * Wednesday, July 1, 2015**

TACC Tour We will all meet at **1:00 pm** to walk to the BUS together as a group. We will be back on campus around 4 or 5pm @https://www.tacc.utexas.edu/about/contact FPLC
 * Thursday, July 2, 2015**

Lab Group Meeting @ 1 pm
GEA 100 Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15

Update your notebook for the week Post data/results to your Wikispaces page - update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki

Optional day - no new stuff, time to catch up on things you haven't gotten done.
 * Friday, July 3, 2015**


 * Saturday, July 4, 2015 - Happy 4th of July!**
 * Sunday, July 5, 2015**

**Week 5** **OVERVIEW:**
 * ** Protein expression work (FPLC), **
 * ** starting 2nd protein ** **expression**
 * ** 2nd Practice PCR **
 * ** Design Tail Primers, Make Oligo Mix **
 * ** Make Competent Cells (in pairs) **

Lab Hours totaling (Nikki) Target Selections - fill out form to select your target Verify HIS tags on beta-metallo lactamases - Diane & Anthony & Simone - use the Translation Map functinality of the Sequence Manipulation Suite to help @http://www.bioinformatics.org/sms2/index.html - need a WORD document with highlighted regions
 * Monday, July 6, 2015**

If your protein 'worked' from last week, then concentrate protein samples for FPLC. The protein groups should work together. E.g. the two RpFabG groups would both concentrate their samples separately, but then combine them for FPLC. FPLC - see FPLC ToDo groups above

Second Practice PCR (after you have done My First PCR successfully) - PCR pLICsequencing15.xls

2:00 PM - Virtual Volunteers (NDM-1) in computer lab - gather control compounds - start some screening

- send pNIC-Bsa4 to sequencing using pLIC for and pLIC rev.
 * What are the Magical Mystery Genes inside of pNIC-Bsa4?**

Start overnight cultures of 2nd Protein Expression - (alternatively, start them in the morning depending on which Option you choose to do (A or B))

Start protein expression Round 2 - if you chose morning Option. Continue PCRs Wikispaces check.- due Tuesday night (Dr. B to check) Notebook check - Charina will check them after 6pm (put line with date and comments in each)
 * Tuesday, July 7, 2015**
 * At end of day -**

Stop Waste flow on FPLC Machine (Andee) -check on pressure Concentrate protein samples FPLC - see FPLC ToDo groups abov 2-4 PM - Middle Schoolers visit lab - Lisa & Simone host
 * Wednesday, July 8, 2015**

12:00 **-** Fellowship photo shoot on front steps of PAI Concentrate protein samples FPLC - see FPLC ToDo groups above
 * Thursday, July 9, 2015**

4:00 pm - Tail Primer Design Session (in computer lab with Dr. B)


 * Friday, July 10, 2015**

Lab Group Meeting @ 1 pm
GEA 100 Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15

Update your notebook for the week Post data/results to your Wikispaces page - update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki

2:15 - Lab Tour by Nikki for prospective students

3:30 PM - Virtual Volunteers (NDM-1) in computer lab - gather control compounds - set up proteins in GOLD - start some screening

Oligo Primer dilution (each person makes their own Oligo Mix to use)


 * Saturday, July 11, 2015**
 * Sunday, July 12, 2015**

FPLC COMPLETED:
 * MtDdla || Ashley C. || Lisa S. ||

FPLC ToDo:
 * EhPTP || Anthony A. - Kevin H. || Ana R. - Justin H. ||
 * MtDdla || Kevin N. || Hannah K. ||
 * Pv6PG || Diane C. - Bella D. || Arthi K. - Simone M. ||
 * RpFabG || Bethany R. - Matthew N. || Parker D. - Jeffrey X. ||
 * Pfu Polymerase || Krupa S. - Mayur P. - Priya M. || Steven T. - Rachael B. ||

**Week 6** **OVERVIEW:**
 * ** Protein expression work (FPLC), **
 * ** finish 2nd protein expression **
 * ** Make Oligo Mix **
 * ** Make pNIC-Bsa4, midiprep it, send to sequencing, cut with BsaI for cloning **
 * sequence using pLIC for and pLIC rev.
 * ** Make Pfu Polymerase **
 * ** Make Competent Cells (in pairs) **

Week 6

 * Monday, July 13, 2015**


 * 1:00 - Virtual Volunteers NDM-1 virtual drug screening**
 * - finish ligand prep for controls**
 * - prep proteins in GOLD**
 * - dock control ligands**
 * - compare results for control set**
 * - start runs of libraries**

Paste your Tail primer sequences into the Targets spreadsheet https://docs.google.com/spreadsheets/d/1dymtoVCnFwbX-kOaDWTyWh7KrQ5OZXLw5voZP9xaPb0/edit#gid=0

Oligo Primer dilution (each person makes their own Oligo Mix to use) Primary PCR


 * Tuesday, July 14, 2015**

Oligo Primer dilution (each person makes their own Oligo Mix to use) Primary PCR

Wikispaces check.- due Tuesday night (Dr. B to check) Notebook check - Charina will check them after 6pm (put line with date and comments in each)
 * At end of day -**


 * Wednesday, July 15, 2015**

grow up ovenight culture of pNIC-Bsa4 (160ml of LB). Either save in freezer in the morning, or midi-prep it.

3:20 - meet in lab and we'll walk over to PCL as a group 3:30- 4:30 PM - Roxanne Bogucka - Literature reading instruction activity (with the **Aptamer stream**! - PCL 1.124
 * Thursday, July 16, 2015**

Once you have your pNIC-Bsa4 sequencing back, **What are the Magical Mystery Genes inside of pNIC-Bsa4?** - send pNIC-Bsa4 to sequencing using pLIC for and pLIC rev.


 * Friday, July 17, 2015**

Lab Group Meeting @ 1 pm
GEA 100 Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15

Work on Target Pages in Wkispaces (Target pages vs. Research Pages)


 * Saturday, July 18, 2015**
 * Sunday, July 19, 2015**

Week 7
**OVERVIEW:**
 * ** finish 2nd protein expression **
 * ** Make pNIC-Bsa4, midiprep it, send to sequencing, cut with BsaI for cloning **
 * sequence using pLIC for and pLIC rev.
 * ** Make Pfu Polymerase **
 * Monday, July 20, 2015**
 * 1:00 - Virtual Volunteers NDM-1 virtual drug screening**
 * 1:00 - Virtual Volunteers NDM-1 virtual drug screening**

Yes, yes - the cloning protocol is finally uploaded to GDrive/Protocols
 * Tuesday, July 21, 2015**

Wikispaces check.- due Tuesday night (Dr. B to check) Notebook check - Charina will check them after 6pm (put line with date and comments in each)
 * At end of day -**


 * Wednesday, July 22, 2015**

1 PM - Virtual Screening - generate a final list of NDM-1 inhibitor candidates


 * Thursday, July 23, 2015**

UT Honors Colloquium for visiting HS students to UT - Lisa and Charina to attend and represent FRI. 1:00 - Virtual Volunteers - finalize NDM-1 list of compounds to submit to Dr. Fast

Documentary viewing at 4:00 in PAI 3.00? lecture hall


 * Friday, July 24, 2015**

Lab Group Meeting @ 1 pm
GEA 100 Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15

Work on Target Pages in Wkispaces (Target pages vs. Research Pages)
 * Saturday, July 25, 2015**
 * Sunday, July 26, 2015**