Lab Knowledge Base

From Protists

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(→Today (13Mar09))
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*call SEJ or CC if you have any questions (if not at lab, then working from home)
*call SEJ or CC if you have any questions (if not at lab, then working from home)
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*CELL BOXES...apparently the sheets on the computer are updated now for all of the...please print them out and tape them to the top of the -80C freezer ''(SEJ posted, but call Maomao if you have questions)''
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*CELL BOXES...'''done AI 13Mar09'''
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*Make 1L [[RPS Media]]
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*Make 1L [[RPS Media]] '''done JI 13Mar09'''
*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 '''DO in progress'''
*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 '''DO in progress'''
*Make Saltwater Medium (basically AF6 with saltwater...can use filter and use 35ppt artificial seawater in carboys...not Tina's Ultramarine saltwater!)...SEJ printed Saltwater Medium instructions & put on middle table near transfer hood '''done CS&BD - in cabinet'''...where?...please put at least one bottle in the 15C incubator (Incubator #1)
*Make Saltwater Medium (basically AF6 with saltwater...can use filter and use 35ppt artificial seawater in carboys...not Tina's Ultramarine saltwater!)...SEJ printed Saltwater Medium instructions & put on middle table near transfer hood '''done CS&BD - in cabinet'''...where?...please put at least one bottle in the 15C incubator (Incubator #1)

Revision as of 22:00, 15 March 2009

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.
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Cultures & Lab Announcements

Professional Enrichment

  • The Association of Women in Sciences (AWIS)


Pressing Things TO DO!

Next Lab Meeting (20Mar09 @ 2:30pm)

  1. ?


Today (13Mar09)

Things that must be done today or tomorrow:

  • call SEJ or CC if you have any questions (if not at lab, then working from home)
  • CELL BOXES...done AI 13Mar09
  • Make 1L RPS Media done JI 13Mar09
  • 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 DO in progress
  • Make Saltwater Medium (basically AF6 with saltwater...can use filter and use 35ppt artificial seawater in carboys...not Tina's Ultramarine saltwater!)...SEJ printed Saltwater Medium instructions & put on middle table near transfer hood done CS&BD - in cabinet...where?...please put at least one bottle in the 15C incubator (Incubator #1)
  • keep an eye on PLO big flask (now has Ear in it, so should grow faster) to see if can do spin down and immediately try to do gDNA or RNA extractions from it (CC is going to try to re-streak a Kpn plate and try inoculating PLO with that)


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:

  • 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
  • Joy, please start checking the test tube racks and start making transfers ASAP done JI
  • 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
  • keep up with washing, drying and autoclaving the glass volumetric pipets so we don't run out (5, 10, 25mL) done CS - just need to be autoclaved 20Feb09
  • put cotton in the tops of pasteur pipets and fill the containers (by the dishwashing station) and autoclave them Zg & JI 6Feb09
  • Empty all tip/trash box(s)/containers on gel and molecular benches every Wed & Fri done CS 20Feb09
  • Wipe down all molecular work benches with the FIX 70% Ethanol squirt bottle every Wed & Fri done CS 20Feb09


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

    • 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
  • 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
  • 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

Phylogenetics and Systematics of Euglenozoa

Documents



See Also

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