Mentors+Summ+13

MENTORS: DANIEL, MICHAEL, ANDREW, RUIFEI

Pick up Primers at the MBB front desk - again (060313 - Monday)
Print out copies of the Nanodrop, DNA Sequencing & Primer Dilution protocols - 2 pages per sheet so that they can go in the notebooks.

Get the autoclaved water and aliquot several into 1.7 ml centrifuge tube, label and store in -20degC. We will have the students use it today (Monday) for primer dilution.

When doing Nanodrop and SUbmit to DNA ssequencing of (pGBR22, pGFP and pmCHerry) - the students should be able to track back exactly which tube they used.

Thursday May 30th @ 1-5 pm

PURCHASING at BioScience Storeroom (NHB) - for Thurs -
Gold watches, bling, etc. Porsche 911, 1962 Ferrari GTO, etc.

spray bottles - 2
 * VDS staff ||  || 1 || 25 nmoles ||   || IDT || via ICMB || VDS account || $3.57 ||   || pLIC-for ||   || TGTGAGCGGATAACAATTCC ||
 * VDS staff ||  || 1 || 25 nmoles ||   || IDT || via ICMB || VDS account || $3.39 ||   || pLIC-rev ||   || AGCAGCCAACTCAGCTTCC ||
 * VDS staff ||  || 1 ||   ||   ||   |||| Biosci Storeroom || $37.51 ||   || Tryptone ||   ||   ||
 * VDS staff ||  || 1 ||   || c0180 || ? |||| Bio Sci Storeroom || $10.21 ||   || Sodium Hydroxide Pellets ||   ||   ||
 * VDS staff ||  || 1 || kit ||   || Sigma |||| Biosci Storeroom || $61.80 ||   || PCR Clean up Kit, Genelute || EP008 ||   ||
 * VDS staff ||  || 1 || kit ||   || Sigma |||| Biosci Storeroom || $337.58 ||   || Plasmid Mini Prep 350 isolations ||   ||   ||
 * VDS staff ||  || 1 ||   ||   || Qiagen |||| Biosci Storeroom || $338.68 ||   || HiSpeed Plasmid Midi ||   ||   ||
 * VDS staff ||  || 1 || 10,000 U ||   || NEB |||| Biosci Storeroom || $49.68 ||   || EcoRI HF || E0011 ||   ||
 * VDS staff ||  || 1 || PK || N0446S || NEB |||| Biosci Storeroom || $138.00 ||   || dNTPs - individuals (Nucleotide Solution Pack) || E0065 ||   ||
 * VDS staff ||  || 1 || PK || N0447S || NEB |||| Biosci Storeroom || $49.68 ||   || dNTPs - mix for Taq PCR 8 μmol of each || E0066 ||   ||
 * VDS staff ||  || 1 || 400 U || M0267S || NEB |||| Biosci Storeroom || $54.28 ||   || standard Taq DNA polymerase with ThermoPol || E0041 ||   ||
 * VDS staff ||  || 1 || 150 U ||   || NEB |||| Biosci Storeroom || $57.04 ||   || T4 DNA polymerase ||   ||   ||
 * VDS staff ||  || 1 || 500 ug || E0060 || NEB |||| Biosci Storeroom || $184.00 ||   || 1 kb ladder ||   ||   ||
 * VDS staff ||  || 6 ||   ||   ||   |||| Biosci Storeroom || $0.54 ||   || Marker, Sharpie, Ultra Fine Point, Black ||   ||   ||
 * VDS staff || ?? Needed || 1 || kit (70) ||  || Sigma |||| Biosci Storeroom || $101.66 ||   || GenElute gel Extraction (70) ||   ||   ||
 * VDS staff ||  || 6 ||   ||   ||   |||| Biosci Storeroom || $0.54 ||   || Marker, Sharpie, Ultra Fine Point, Black ||   ||   ||
 * VDS staff || ?? Needed || 1 || kit (70) ||  || Sigma |||| Biosci Storeroom || $101.66 ||   || GenElute gel Extraction (70) ||   ||   ||
 * VDS staff || ?? Needed || 1 || kit (70) ||  || Sigma |||| Biosci Storeroom || $101.66 ||   || GenElute gel Extraction (70) ||   ||   ||

WET LAB WORK
Prep collirollers - split into 2 bottles and rinse then autoclave

Remove ice from Top Loading freezer. Remove ice on top and on the bottom - maybe de-thaw the whole thing. Organize and re-label freezer boxes for us (ideally we want each 'type' of reagent to have its own box. We can use up to 3 metal racks. Use new plastic boxes when needed. New Boxes to Make for Top Loading freezer: Old Primers 2, Modifying Enzymes, Buffers 2 re-locate all of the buffers to the metal racks. Make a new VDS Class Plasmids box for the upright -20degC

Organize dry chemicals above weighing bench

Prep DNA ladders - 100bp and 1 kb (see protocol on GDocs). Then aliquot into 5-10 different tubes, well labeled


 * On Wikispaces page, Update the 1 month vs 2 month people - move 1 month people to separate list -**
 * Assign students to Red, Green or Purple for Plasmid work and Transformation Efficiency

Update Laptops and Desktops

 * Clean off old icons from Desktops of Desktop computers
 * Do Windows Updates
 * Start up laptops and do updates on them. Remove security credentials.
 * Install both printers on each laptop and each Desktop (see below)

- in the back of the lab (on top of fire cabinet) - use plastic sheet protectors
 * Organize and print new protocols (updated) for the white protocols binder**

Clean water baths (the big ones - probably need 2 people for this). Only use Alconox soap - no bleach or anything harsh.

Get gel extra dryer from Malcolm Brown, Jr. Lab. Test functionality.

Consolidate Kits - Miniprep, Midiprep, PCR Cleanup. Put spare solutions into 1 box and label it spare solutions for that Type of Kit. Verify that all components are present (or in sufficient number

Count protein gel spacer plates vs. short plates vs. combs.

Check on how much glassware we have. If low - purchase more.

send pGBR22 samples to DNA Sequencing so that we can figure out which ones had the contamination (maybe have the students do this)

Dispense collirollers into individual 600 ul tubes with each containing ~6 beads. Do this sterily (student to do?)

Check lab safety completion for all students
-- see the printed sheets in the lab binder and then cross check them to the Wikispaces 'Required Lab Safety' page - cross reference to UTEIDs of Class Roster (can be found in VDSstaff@gmail.com account

**Check Ice Room access list -**

= Printer Installation =


 * 1) Login as Mentor, Start Menu,
 * 2) Devices And printers
 * 3) Add New Printer
 * 4) Add "local" printer
 * 5) Create New Port --> standard TCP pathway
 * 6) Enter IP 128.82.195.186
 * 7) Printer Name Lexmark C543
 * 8) Add Printer (if can't find printer do Window Update)


 * For installation of a different Printer (such as Dell) change the IP address and Printer Name**

Printer Name: Lexmark C543 IP: 128.83.195.186

Printer Name: Dell IP: 129.116.152.49

**SOLUTION RECIPES**

 * Make LB** - 2Liters - and autoclave


 * Make 5 M NaCl** - 500 ml in water, sterile filter into a bottle, label, store at Room Temp


 * Make Kanamycin**- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. __Sterile filter with syringe filter__before aliquoting into tubes. Label. Store in -20degC


 * Make IPTG** - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC


 * Make Lysozyme** - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC


 * Make TCEP -** make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.


 * Make PMSF -** 30 x 500 ul aliquots of 10mM in **__Isop____ropanol__** 1.7 ml tubes. Label. store in -20degC


 * Make Imidazole** - 1M stock **make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp**

Lysis Buffer for Sonication (make 500 ml)

 * (see GDocs '**Solutions&Dilutions**' in /**Misc **folder for calculations)**

Tris 100 mM

NaCl 300 mM

Imidazole 30 mM

pH 8.0 w/ NaOH

label, store at 4degC


 * NEW Wash and Elution Buffers and Storage Buffer(see GDocs '**Solutions&Dilutions**' in /**Misc **folder for calculations)**

Wash Buffer

Tris 100 mM

NaCl 300 mM

Imidazole 30 mM

pH 8.0 w/ NaOH


 * Elution Buffer**

Tris 100 mM

NaCl 300 mM

Imidazole 300 mM

pH 8.0 w/ NaOH


 * FPLC column buffer - tris Also 'storage' buffer**

Tris 50 mM

NaCl 150 mM

pH 8.0 w/ NaOH

Then filter sterilize

Then degass**

6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)

(In a separate tube) - 30 ml of Nanopure water

--- 1.635 g Tris powder

--- 3 g SDS poweder

--- 0.3 g Bromophenol blue

2.3136 g DTT

Mix contents of second tube into tube with glycerol

Add some more Nanopure water to 50 ml total final volume

**Mentor Notes from Spring 13**

**Mentors**

|| 1 || 25 nmoles || || IDT || via ICMB || VDS account || $3.57 || $3.57 || pLIC-for || |||||| TGTGAGCGGATAACAATTCC || ||
 * 1 || 25 nmoles ||  || IDT || via ICMB || VDS account || $3.39 || $3.39 || pLIC-rev ||   |||||| AGCAGCCAACTCAGCTTCC ||   ||
 * 1 ||  ||   ||   |||| Biosci Storeroom || $37.51 || $37.51 || Tryptone ||   ||   ||   ||   ||   ||
 * 1 ||  || c0180 || ? |||| Bio Sci Storeroom || $10.21 || $10.21 || Sodium Hydroxide Pellets ||   ||   ||   ||   ||   ||
 * 1 || kit ||  || Sigma |||| Biosci Storeroom || $61.80 || $61.80 || PCR Clean up Kit, Genelute || EP008 ||   ||   ||   ||   ||
 * 1 || kit ||  || Sigma |||| Biosci Storeroom || $337.58 || $337.58 || Plasmid Mini Prep 350 isolations ||   ||   ||   ||   ||   ||
 * 1 ||  ||   || Qiagen |||| Biosci Storeroom || $338.68 || $338.68 || HiSpeed Plasmid Midi ||   ||   ||   ||   ||   ||
 * 1 || 10,000 U ||  || NEB |||| Biosci Storeroom || $49.68 || $49.68 || EcoRI HF || E0011 ||   ||   ||   ||   ||
 * 1 || PK || N0446S || NEB |||| Biosci Storeroom || $138.00 || $138.00 || dNTPs - individuals (Nucleotide Solution Pack) || E0065 ||  ||   ||   ||   ||
 * 1 || PK || N0447S || NEB |||| Biosci Storeroom || $49.68 || $49.68 || dNTPs - mix for Taq PCR 8 μmol of each || E0066 ||  ||   ||   ||   ||
 * 1 || 400 U || M0267S || NEB |||| Biosci Storeroom || $54.28 || $54.28 || standard Taq DNA polymerase with ThermoPol || E0041 ||  ||   ||   ||   ||
 * 1 || 150 U ||  || NEB |||| Biosci Storeroom || $57.04 || $57.04 || T4 DNA polymerase ||   ||   ||   ||   ||   ||
 * 1 || 500 ug || E0060 || NEB |||| Biosci Storeroom || $184.00 || $184.00 || 1 kb ladder ||  ||   ||   ||   ||   ||
 * 6 ||  ||   ||   |||| Biosci Storeroom || $0.54 || $3.24 || Marker, Sharpie, Ultra Fine Point, Black ||   ||   ||   ||   ||   ||
 * 1 || kit (70) ||  || Sigma |||| Biosci Storeroom || $101.66 || $101.66 || GenElute gel Extraction (70) ||   ||   ||   ||   ||   ||
 * 6 ||  ||   ||   |||| Biosci Storeroom || $0.54 || $3.24 || Marker, Sharpie, Ultra Fine Point, Black ||   ||   ||   ||   ||   ||
 * 1 || kit (70) ||  || Sigma |||| Biosci Storeroom || $101.66 || $101.66 || GenElute gel Extraction (70) ||   ||   ||   ||   ||   ||
 * 1 || kit (70) ||  || Sigma |||| Biosci Storeroom || $101.66 || $101.66 || GenElute gel Extraction (70) ||   ||   ||   ||   ||   ||