Lab Knowledge Base

From Protists

Revision as of 21:14, 21 January 2009

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.
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Cultures & Lab Announcements

Professional Enrichment

• The Association of Women in Sciences (AWIS)

Pressing Things TO DO!

Next Lab Meeting (?)

1. See Distilled Water Retrieval.
2. Discuss change in incubators.
3. Maomao, do the "Right to Know" training online if you haven't yet or fill out the form if you have (see me for form).
4. Sarah will send out a doodle schedule maker to your email for Lab Assistant meetings, please respond to it as soon as your schedule is finalized and mark the times you are available (all times!).
5. Go through autoclaving protocol (labeling media properly with black markers, closing lids, etc.)
6. Go over policy of pipetors, pens, etc. (some should never be moved without cleaning first, whereas others can be moved if you put it back where it belongs after you are done)
7. UPDATE CELL BOXES and don't make me name names about the culprits!

Today (08Jan08)

Things that must be done today or tomorrow:

• Make tons of AF6 Media (3-4L)
• fill up spin down tube container, autoclave and set to dry in oven
• check flasks and spin down if ready... (don't forget the flasks in the #2 and #3 incubators)
• Check TET
• autoclave test tubes in walk in (put in metal racks...check with SEJ first to get correct ones and not Deniz's)
• clean/wash the test tubes after they have been autoclaved, dry them and autoclave them again with the blue caps on tightly
• autoclave any media with growth (walk-in and in media cabinet/transfer hood)
• put walk-in plates with growth (fungus, etc.; check with CC and SEJ first) into hazardous waste bags on the bacterial bench and autoclave them. put them in the dumpster after autoclaving and rinse out the autoclave trays with tap water (don't put solidified agarose down the drain, throw it in the trash!)
• dilute more 5x TBE (under gel bench sink) into 0.5x TBE
• make new 5x TBE
• put away dry items in the gel drying dish rack
• wash any glassware/dishes in the gel bench sink with soap and rinse with tap and then RO water and set aside to dry
• dump out the buffer in any of the gel rigs that are out on the bench and rinse them out well with RO water (be sure no gel particles left to dry on the rig) and then invert them to dry on the drying area

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).

Priority:

• DNA extraction of SNB (see Sarah and CC to see if more need to be done too)
• Stephen and Joy, please start checking the test tube racks and start making transfers ASAP JI started looking at Racks 1-2...Stephen, feel free to pick up wherever and update in the book so between the two of us we can eventually get it all done---I'll even do the sticky tags this time! Thanks
• 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
• put cotton in the tops of pasteur pipets and fill the containers (by the dishwashing station) and autoclave them
• 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

Cultures:

• When checking cultures, please put aside any cultures with fungus for BP fungal treatments. Let him know where they've been put.
• Brandon will be doing fungal treatment experiments using Sharan's notes in Lab Binder
  • 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:
    • LUV (4C-backup)test tube contaminated with rodifers; used older test tube to make small flask; need to watch for contamination
    • TCI (4g)done CS
    • LXF (1g)done CS
    • LXI (4c-backup)done BP
    • LXJ (9h)test tubes contaminated with ciliates
    • LXH (1f)done CS
    • TUB test tubes contaminated
    • 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
    • SNB done CS
    • THB done CS
    • LUT (13d) done CS
    • TUN (?) can't find
    • TUK done CS
    • LUF (8f) done CS
    • LXR (6c) done CS
    • TUX done CS
    • LXT done CS
    • LYI (2d) done CS
    • LUK (9a) done CS
    • LYE (7f) done CS
  • Need to make 1 small flask for DNA (indicated test tube location):
    • LYA (7C)Contaminated with cilliates + rodifers; made a small flask - need to watch for contamination
    • SXD (4i) Dead in notebook 30Jan08
    • LXL (1d) done CS
    • SXE (5f)done BP
    • TSP (10b)done BP
    • TUY (3b)done BP
    • TXB (4d) done CS
    • 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
    • LXW (6f) done CS
    • LXX (1i) done CS
    • LYB (?) Can't find
    • LUW (9b) done CS
    • LUO (4c-backup) can't find CS;This was thrown out 30Jan08, but we still have a good big flask for it- JI
    • LYS (13j done CS
    • LYT (13i) done CS
    • LUA (13h) done CS
    • LUC (13g) done CS
    • LUD (13f) done CS
    • LUG (13e) done CS
    • LYP (?) Can't find
    • LYD (7e) done CS
    • LYG (7h) done CS
    • LXN (?) Can't Find
    • SUM (?) Can't Find
    • TVL test tubes contaminated
    • LYU test tubes contaminated
    • LXW done CS
    • LUW done CS
    • LXZ done CS
    • LXP done CS
    • LUU done CS
    • SUL done CS

Lab Assistants, Please Update Sarah/Christina On:

• Updates for Sarah
  • list of all cultures I need in small flasks that have been started (any moved to big flasks yet?)
  • list of all cultures I need in small flasks that are contaminated (and preferably what they are contaminated with)

• Updates for Christina

Notes for Sarah

• 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

• 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):
  • Cell Box 2: SBR, STB, TZR, THA, TPL, TUM, TVISBR done BP
  • Cell Box 3: LXS, SNB, LUO, SXA, SSA, MUC=MUR, SSC
  • Cell Box 4: ELU, SMA, SUZ, SEU, TUA
  • Cell Box 6: TBR, LUE, TVS, TRG, TUJ, SMC
  • Cell Box 7: SUN, CNT, TUX, TUK, SUY, SBA,
  • Cell Box 8: SXB, SUI
  • Cell Box 9: TOG, TUV, TEP, TSP, SCP
  • Cell Box 10: TLF=TLV (some tubes are mislabeled as TLF when they should be TLV=Trachelomonas lefevrei)
• make new GRC big flask done CS

• Start new small flasks for these organisms if we don't already have them: updated UGA flask xls.; put all new small flasks - 4A
  • ECA dead in t.t.
  • EAN...Made new small flask (4B) ST 9Jun08
  • EGY Made new small flask (4B) ST 9Jun08
  • EHS done CS
  • EGR done CS
  • MUT contamination w/ rotifers in t.t.
  • ESN done CS
  • ESL done CS
  • UEA dead in t.t.
  • ELA no mov't, all dead in t.t.
  • DAA done CS
  • CSK done CS
  • PYR done CS, maybe contaminated?
  • CCM contaminated w/ rotifers and dead in t.t.
  • CUA done CS

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

• 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

• Protocols
• Media and Molecular Recipes
• Culture Inventory
• Inventory
• Instructional Information
• Recipes not Currently Used
• Culture Ordering Information

Phylogenetics and Systematics of Euglenozoa

• Euglenozoa Phylogenies
• Euglenophyte Phylogenies
• Phylogenetic Programs
• Farmer Lab

Documents

• PCR Reactions
• DNA Dilution Quick Calculation

See Also

• http://meta.wikimedia.org/wiki/Help:Wikitext_examples