Lab Knowledge Base

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===Wiki===
===Wiki===
*Welcome to the Lab Wiki for Mark Farmer's Lab.  This is the place to find procedures, news, and answers to commonly asked questions.
*Welcome to the Lab Wiki for Mark Farmer's Lab.  This is the place to find procedures, news, and answers to commonly asked questions.
-
*If you are new to this wiki, you will need an account in order to edit pages.  Talk to [[Sarah]] about getting an account set up if you would like to contribute.
+
*If you are new to this wiki, you will need an account in order to edit pages.  Talk to [[Katy]] about getting an account set up if you would like to contribute.
*You can upload pictures, word, excel, and pdf documents.
*You can upload pictures, word, excel, and pdf documents.
*If you are new to wiki editing, check out the wiki help for how to edit articles in a wiki, then use the existing pages as templates and examples of how to create links, upload files, and display images.
*If you are new to wiki editing, check out the wiki help for how to edit articles in a wiki, then use the existing pages as templates and examples of how to create links, upload files, and display images.
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===Cultures & Lab Announcements===
===Cultures & Lab Announcements===
 +
Next lab assistants meeting
 +
'''TBA'''
 +
===Professional Enrichment===
===Professional Enrichment===
*'''The Association of Women in Sciences (AWIS)'''
*'''The Association of Women in Sciences (AWIS)'''
 +
== Things To Do ==
 +
=== Priority ===
-
== Pressing Things TO DO! ==  
+
=== Next Lab Meeting January 14 2pm ===
-
=== Next Lab Meeting (20Mar09 @ 2:30pm) ===
 
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#Go over Distilled Water Retrieval.
 
 +
=== January ===
-
=== Today (18Mar09) ===
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*If you have any questions call/email Katy
-
 
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*Empty all tip/trash box(s)/containers on gel and molecular benches every Wed & Fri
-
'''Things that must be done today or tomorrow:'''
+
-
 
+
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*call SEJ or CC if you have any questions (if not at lab, then working from home)
+
-
 
+
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*check flasks and '''spin down''' if ready... (don't forget the flasks in the #2 and #3 incubators)...switch over any of Sarah's in closed flasks into vented flasks or start new small ones from scratch if original big flasks dead
+
-
*CS - On Friday, start 2 large flasks of PLO w/ Kpn and 802. '''done CS'''
+
-
*Start 4 large flasks of RBS.
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-
*Make 2L of HI. '''put in cabinet CS'''
+
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*Make 2L of [[ATCC 802]].
+
-
*CS - Go to CSS to get Whatman #1 Filters (90mm diameter).
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*Wipe down all molecular work benches with the [[FIX]] 70% Ethanol squirt bottle every Wed & Fri
*Wipe down all molecular work benches with the [[FIX]] 70% Ethanol squirt bottle every Wed & Fri
-
If not finished, the last person to leave should e-mail SEJ or CC what's left to be done (depending on who it's for).
+
*Check water bath on molecular work bench if low on water please add DI H2O check every Wed & Fri
 +
*If you're not sure what to do see '''Are you a Lab Assistant with free time on your hands?'''
 +
=== List of Organisms needed by MSU ===
 +
Please find these organisms and make an additional tube of them.  If any are not alive or contaminated please indicate below next to the three letter codes, please email Katy with any questions
-
'''Priority:'''
+
*CCM '''xx, ok'''
-
 
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*EDS '''not moving'''  
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*gDNA extraction of SNB (see Sarah and CC to see if more need to be done too)...will need RBS, DIP and PLO gDNA as well
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*EPE
-
*Joy, please start checking the test tube racks and start making transfers ASAP '''done JI'''
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*ETM
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*update UGA flasks sheet as to what we have in flasks...there were a bunch of small flasks at the bottom of incubator 4 that were completely dried down and never transferred to big flasks, so SEJ tossed these and they shouldn't be on the list now unless there are big flasks for them
+
*ELU '''NOTHING IN HERE'''
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*keep up with washing, drying and autoclaving the glass volumetric pipets so we don't run out (5, 10, 25mL)
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*HYO
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*put cotton in the tops of pasteur pipets and fill the containers (by the dishwashing station) and autoclave them '''Zg & JI 6Feb09'''
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*KHQ
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*Empty all tip/trash box(s)/containers on gel and molecular benches every Wed & Fri
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*LXC '''x NOT MOVING'''
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*Wipe down all molecular work benches with the [[FIX]] 70% Ethanol squirt bottle every Wed & Fri
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*PET
-
 
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*SXD '''xx, ok, some dead'''
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*SXE '''xx, ok, but some dead'''
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*SUL '''xx, good'''
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'''Cultures:'''
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*TRT
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*When checking cultures, please put aside any cultures with fungus for BP fungal treatments. Let him know where they've been put.
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*TUB '''xx, good, but may be CONTAMINATED'''  
-
*Brandon will be doing fungal treatment experiments using Sharan's notes in Lab Binder
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*TUV '''xxx, very good'''
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**Need to make 2 small flasks (one labeled microscopy) of the following (indicates test tube location); grow up small flask to be put in a large flask:
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*TUY '''xxx, very good'''
-
***LUV (4C-backup)'''test tube contaminated with rodifers; used older test tube to make small flask; need to watch for contamination'''
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*TUX '''xx, good'''
-
***TCI (4g)'''done CS'''
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*TUM '''xx, good'''
-
***LXF (1g)'''done CS'''
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*TUP '''xxx, very good'''
-
***LXI (4c-backup)'''done BP'''
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*TUO '''xxxx, very good'''
-
***LXJ (9h)'''test tubes contaminated with ciliates'''
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*LXB '''xxx, good'''
-
***LXH (1f)'''done CS'''
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*LXF '''x CONTAMINATED'''
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***TUB '''test tubes contaminated'''
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*LXH '''xx, ok'''
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***TUO JI did small flask (currently in 4), but seems like two different sizes of Trachs, redo small flask from uncontaminated tube or single cell isolate to get both types of cells isolated and grown up in small flasks '''done CS'''
+
*LXJ '''xx, ok'''
-
***SNB '''done CS'''
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*LXR '''xxx, very good contam?'''
-
***THB '''done CS'''
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*LXT '''xx, good'''
-
***LUT (13d) '''done CS'''
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*LYE '''xxx, good'''
-
***TUN (?) '''can't find'''
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*LYF
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***TUK '''done CS'''
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*LYI '''xx good but contaminated'''
-
***LUF (8f) '''done CS'''
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*LUF '''xxx, very good'''
-
***LXR (6c) '''done CS'''
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*LUK '''xx, good'''  
-
***TUX '''done CS'''
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*LUT '''xxx, very good'''
-
***LXT '''done CS'''
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*LUY '''xxx, very good'''
-
***LYI (2d) '''done CS'''
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*TSP '''xxxx, very good'''
-
***LUK (9a) '''done CS'''
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-
***LYE (7f) '''done CS'''
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**Need to make 1 small flask for DNA (indicated test tube location):
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-
***LYA (7C)'''Contaminated with cilliates + rodifers; made a small flask - need to watch for contamination'''
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***SXD (4i) '''Dead in notebook 30Jan08'''
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***LXL (1d) '''done CS'''
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***SXE (5f)'''done BP'''
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***TSP (10b)'''done BP'''
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***TUY (3b)'''done BP'''
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***TXB (4d) '''done CS'''
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***TXG (1c) done CS...please do again b/c no trach cells on 26Feb08, only ciliates in small flask '''test tubes contain no living cells or ciliates; may have 1 cell in test tube 4 Oct 07 - did not make small flask'''
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***LXW (6f) '''done CS'''
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***LXX (1i) '''done CS'''
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***LYB (?) '''Can't find'''
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***LUW (9b) '''done CS'''
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***LUO (4c-backup) '''can't find CS''';'''This was thrown out 30Jan08, but we still have a good big flask for it- JI'''
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***LYS (13j '''done CS'''
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-
***LYT (13i) '''done CS'''
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***LUA (13h) '''done CS'''
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***LUC (13g) '''done CS'''
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***LUD (13f) '''done CS'''
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***LUG (13e) '''done CS'''
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***LYP (?) '''Can't find'''
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***LYD (7e) '''done CS'''
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***LYG (7h) '''done CS'''
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***LXN (?) '''Can't Find'''
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***SUM (?) '''Can't Find'''
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***TVL '''test tubes contaminated'''
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***LYU '''test tubes contaminated'''
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***LXW '''done CS'''
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***LUW '''done CS'''
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***LXZ '''done CS'''
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***LXP '''done CS'''
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***LUU '''done CS'''
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***SUL '''done CS'''
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-
 
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'''Lab Assistants, Please Update Sarah/Christina On:'''
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*'''Updates for Sarah'''
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**list of all cultures I need in small flasks that have been started (any moved to big flasks yet?)
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**list of all cultures I need in small flasks that are contaminated (and preferably what they are contaminated with)
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-
 
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*'''Updates for Christina'''
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 +
*Organisms with no info were not found/ are not in MSU test tube rack.
 +
*'''Updates for Katy'''
 +
**katy, i have posted the info on how to prep and ship the cultures to MSU on this page [[Shipping Cultures Tubes to MSU]]...let me know if you have any questions '''SEJ 08Oct09'''
[[Notes for Sarah]]
[[Notes for Sarah]]
*Euglenozoa AToL
*Euglenozoa AToL
-
**start big flask (plug seal) of PLO & let SEJ know where it is placed '''done CS - 6C'''
 
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**CS or CC, can you please update the chloramphenicol/HI-HS specifics and the big and small culture flask details on [[Organisms for AToL Collaboration]] '''done CS'''
 
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**CS, can you please update [[Colorless Organisms]] with the already updated info from [[Organisms for AToL Collaboration]] '''done CS'''
 
-
 
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**Can '''Joy''' or someone find out where the EGN and LVO tubes are and make small flasks from them, the small flasks are already labeled and are located near the saltwater carboys, change the initials to fit yourself please (note from DO!) '''done JI 5Mar09'''
 
-
 
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*check blue rack on shelf D of incubator 3 with ELG/ELU/etc. in it...why haven't these been transferred since 2007? '''JI checked and none survived except ELU. I autoclaved/threw out dead tubes and made small flask of ELU. 6Feb09'''
 
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*CS, please spin down TET for me on '''18Apr08''', if not done already, and put it in the walk-in fridge, but let me know when it is ready (SEJ - posted 17Apr08)'''done CS in -80 freezer; cell box 4-H1'''
 
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*postponed until we have tried the RNA-cDNA process...SEJ's - Please do DNA extractions on the following organisms (be sure to check if they original spin down was done on Log phase cells before you combine/extract them):
 
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**Cell Box 2: SBR, STB, TZR, THA, TPL, TUM, TVI'''SBR done BP'''
 
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**Cell Box 3: LXS, SNB, LUO, SXA, SSA, MUC=MUR, SSC
 
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**Cell Box 4: ELU, SMA, SUZ, SEU, TUA
 
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**Cell Box 6: TBR, LUE, TVS, TRG, TUJ, SMC
 
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**Cell Box 7: SUN, CNT, TUX, TUK, SUY, SBA,
 
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**Cell Box 8: SXB, SUI
 
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**Cell Box 9: TOG, TUV, TEP, TSP, SCP
 
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**Cell Box 10: TLF=TLV (some tubes are mislabeled as TLF when they should be TLV=''Trachelomonas lefevrei'')
 
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*make new GRC big flask '''done CS'''
 
-
 
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*Start new small flasks for these organisms if we don't already have them: '''updated UGA flask xls.; put all new small flasks - 4A'''
 
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**ECA '''dead in t.t.'''
 
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**EAN...'''Made new small flask (4B) ST 9Jun08'''
 
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**EGY '''Made new small flask (4B) ST 9Jun08'''
 
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**EHS '''done CS'''
 
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**EGR '''done CS'''
 
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**MUT '''contamination w/ rotifers in t.t.'''
 
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**ESN '''done CS'''
 
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**ESL '''done CS'''
 
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**UEA '''dead in t.t.'''
 
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**ELA '''no mov't, all dead in t.t.'''
 
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**DAA '''done CS'''
 
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**CSK '''done CS'''
 
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**PYR '''done CS, maybe contaminated?'''
 
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**CCM '''contaminated w/ rotifers and dead in t.t.'''
 
-
**CUA '''done CS'''
 
== Are you a Lab Assistant with free time on your hands? ==
== Are you a Lab Assistant with free time on your hands? ==
 +
*keep up with washing, drying and autoclaving the glass volumetric pipets so we don't run out (5, 10, 25mL)
 +
*put cotton in the tops of pasteur pipets and fill the containers (by the dishwashing station) and autoclave them
*Make any media that needs to be made (generally [[AF-6 Medium]], [[ESNW]] or [[Hay Infusion]])
*Make any media that needs to be made (generally [[AF-6 Medium]], [[ESNW]] or [[Hay Infusion]])
*[[Autoclave]] media using the liquid cycle (be sure you label with autoclave tape)
*[[Autoclave]] media using the liquid cycle (be sure you label with autoclave tape)
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== Lab Binder & Notebook ==
== Lab Binder & Notebook ==
-
*[[Protocols]]
 
-
*Media and Molecular [[Recipes]]
 
*[[Culture Inventory]]
*[[Culture Inventory]]
-
*[[Inventory]]
+
*[[Culture Ordering Information]]
*[[Instructional Information]]
*[[Instructional Information]]
 +
*[[Lab Supplies]]
 +
*Media and Molecular [[Recipes]]
 +
*[[Protocols]]
*[[Recipes not Currently Used]]
*[[Recipes not Currently Used]]
-
*[[Culture Ordering Information]]
 
== Phylogenetics and Systematics of Euglenozoa ==
== Phylogenetics and Systematics of Euglenozoa ==

Current revision as of 18:57, 14 January 2010

Contents

News

Wiki

  • Welcome to the Lab Wiki for Mark Farmer's Lab. This is the place to find procedures, news, and answers to commonly asked questions.
  • If you are new to this wiki, you will need an account in order to edit pages. Talk to Katy about getting an account set up if you would like to contribute.
  • You can upload pictures, word, excel, and pdf documents.
  • If you are new to wiki editing, check out the wiki help for how to edit articles in a wiki, then use the existing pages as templates and examples of how to create links, upload files, and display images.


Cultures & Lab Announcements

Next lab assistants meeting TBA


Professional Enrichment

  • The Association of Women in Sciences (AWIS)

Things To Do

Priority

Next Lab Meeting January 14 2pm

January

  • If you have any questions call/email Katy
  • Empty all tip/trash box(s)/containers on gel and molecular benches every Wed & Fri
  • Wipe down all molecular work benches with the FIX 70% Ethanol squirt bottle every Wed & Fri
  • Check water bath on molecular work bench if low on water please add DI H2O check every Wed & Fri
  • If you're not sure what to do see Are you a Lab Assistant with free time on your hands?

List of Organisms needed by MSU

Please find these organisms and make an additional tube of them. If any are not alive or contaminated please indicate below next to the three letter codes, please email Katy with any questions

  • CCM xx, ok
  • EDS not moving
  • EPE
  • ETM
  • ELU NOTHING IN HERE
  • HYO
  • KHQ
  • LXC x NOT MOVING
  • PET
  • SXD xx, ok, some dead
  • SXE xx, ok, but some dead
  • SUL xx, good
  • TRT
  • TUB xx, good, but may be CONTAMINATED
  • TUV xxx, very good
  • TUY xxx, very good
  • TUX xx, good
  • TUM xx, good
  • TUP xxx, very good
  • TUO xxxx, very good
  • LXB xxx, good
  • LXF x CONTAMINATED
  • LXH xx, ok
  • LXJ xx, ok
  • LXR xxx, very good contam?
  • LXT xx, good
  • LYE xxx, good
  • LYF
  • LYI xx good but contaminated
  • LUF xxx, very good
  • LUK xx, good
  • LUT xxx, very good
  • LUY xxx, very good
  • TSP xxxx, very good
  • Organisms with no info were not found/ are not in MSU test tube rack.


  • Updates for Katy
    • katy, i have posted the info on how to prep and ship the cultures to MSU on this page Shipping Cultures Tubes to MSU...let me know if you have any questions SEJ 08Oct09

Notes for Sarah

  • Euglenozoa AToL

Are you a Lab Assistant with free time on your hands?

  • keep up with washing, drying and autoclaving the glass volumetric pipets so we don't run out (5, 10, 25mL)
  • put cotton in the tops of pasteur pipets and fill the containers (by the dishwashing station) and autoclave them
  • Make any media that needs to be made (generally AF-6 Medium, ESNW or Hay Infusion)
  • Autoclave media using the liquid cycle (be sure you label with autoclave tape)
  • Using sterile technique, add any additional ingredients to complete media post-autoclaving (eg. vitamins)
  • Wash test tubes, media containers and their respective caps (keep LIVE and FIX glassware separated)
  • Autoclave the test tubes, media containers, 9" pasteur pipets, pipet tip box(es), volumetric pipets, etc. in appropriate containers with containers underneath if available
  • Using sterile techniqe, add media to the autoclaved tubes or sterile culture flasks
  • Check and make notes of cultures without opening the tubes or culture flasks using the appropriate microscopes. Some cultures need to be checked daily, weekly, bi-weekly or monthly depending on their growth patterns.
  • Make transfers of healthy cultures (all culture information can be found on the Cumulative Culture Inventory.xls sheet on the Farmer Lab PC desktop)
    • tubes
    • big/small flasks
  • Spin down log phase cells in big culture flasks and rejuvenate with fresh media (aseptically)
  • Extract DNA from concentrated cells and update the DNA.xls sheet
  • Qualify/Quantify DNA on Nanodrop
  • Maintain molecular buffers, reagents
  • Maintain at least one carboy of DI water
  • Keep everything clean and organized
  • Ask if anyone in the lab needs anything done



Lab Binder & Notebook

Phylogenetics and Systematics of Euglenozoa

Documents



See Also

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