genefish - Zac's Notebook

Email: zhalls@u.washington.edu
Cell: 206-355-7288
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11/3/2010
10:20am - 10:50pm (0.5)

Routine cleanup of counters, sinks, claves, ovens.

11/1/2010
10:30am - 11:30pm (1)

Routine cleanup of counters, sinks, claves, ovens.

10/25/2010
10:30am - 11:30pm (1)

Routine cleanup of counters, sinks, claves, ovens.

10/20/2010
10:30am - 11:30pm (1)

Routine cleanup of counters, sinks, claves, ovens.

10/19/2010
10:30am - 1:00pm (2.5)

I doubled the amount of growth flasks, and ignored the two feeding flasks as per Emma. We started with 2 flasks of TISO at 600ml, and 2 flasks of PLY at 300ml, I proceeded to split the flasks in half, resulting in (2) flasks of TISO at 300ml/150ml and (2) flasks of PLY at 300ml/150ml. I then proceeded to add equal parts of fresh f/2 media back up to their original levels of 600/300 mls respectively.

The current growth flasks as of 10/19 are as followed:

(2) Flasks of TISO at 600 ml
(2) Flasks of TISO at 300 ml
(2) Flasks of PLY at 600 ml

(2) Flasks of PLY at 300 ml

Preparing (4) new batches of sterilized seawater to make another 40liters of f/2 media for future use.

10/12/2010
10:30am - 1:00pm (2.5)

Began preparations for the Algae Feeding Study. Claved the necessary flasks and bottles of seawater to get us moving towards the volume of flasks needed for the study.

Placed Backup flasks into larger flasks and added 250ml of f/2 media.
Placed Growth Chambers into larger flasks and added 200 ml of f/2 media.
Later poured 300ml of both PLY and TISO into a smaller flask to provide more surface area for our growth chambers.
Began cleaning Red Rocket to give backups something to rest on rather than static non-movement.
Sizzle
Sizzle

9/21/2010
10:30am - 4:00pm

Routine cleanup, sinks, claves, ovens
- Identified sediment from autoclave, showed Sam for processing.
Finish scaling algae.
- Placing on hold, going to alloy PLY to cultivate further.
Assisted Sam in ID'ing tissue samples from -80 freezer.
Bleached tabletops and pipettes

9/20/2010
10:30am - 3:00pm

Shadow with Molly
- Go through algae culture, regular routines
Culture scaling
- Scaled TISO (Orange)
  - Did NIOT scale PLY (green)
    - Prepped seawater and flasks to scale PLY tomorrow, Tues 21st 2010.
Routine cllean-up
Checkup on adult oysters in basement
- Appeared alive and healthy
- Fed 10 ml of oyster-food.
- Emptied and refilled seawater.
Organized recon invoices for Sam.

9/17/2010
10:30am - 4:00pm

Worked with Emma at NOAA.

9/13/2010
10:30am - 4:00pm

Proof-read Steven's ref/cite.
- Discuss findings with Steven.
Begin cleaning gathered oyster shells.
Routine cleanup-- ovens, claves, sinks

9/9/2010
10:30am - 4:00pm

Routine cleanup-- ovens, claves, sinks
Helped load up seawater-tank into truck for Emma
- Tank being filled and transported to NOAA facility.
Consult with Steven about tank project, as per Emma
- Instructed to wait on plans on containers from NOAA
Continue research on metals in the puget sound and their affects on shellfish
- Added Emma and SR320 to Delicious-Network.

MEMORABLE SITES:
http://faculty.virginia.edu/metals/cases/nelson2.html

9/7/2010
10:30am - 4:00pm

Continue cleaning and rinsing oyster tank and accessories.
Routine oven/sinks/clave cleanup.
Continue processing storage space in labs, clean benches, general cleanup.

Feed oysters in basement tank room.
Trip to NOAH facility to drop off collected oyster samples.
Begin research on metals in the puget sound and their affects on shellfish

9/1/2010
10:30am - 12:30pm

Continue cleaning and rinsing oyster tank and accessories.
Routine oven/sinks/clave cleanup.
Continue processing storage space in labs.

8/31/2010
10:30am - 4:00pm

Empties and bleached oyster tanks and accessories.
Routine oven/sinks/clave cleanup.
Begin processing storage space in labs.

8/27/2010
10:30am - 3:30pm

Algae culture scaling.
Clean up tank room
- Organize shelves
- Toss un-necessary junk
- Organize supplies into containers.
Routine lab cleanup: ovens, sinks, claves

8/25/2010
10:30am - 4:00pm

Routine cleanup, ovens, sinks, claves.
Prep seawater for algae culture scaling.
Piece together the 10-bottle setup, as per Emma.
- Static Tank v1.0 is built, running air through everything to see if any of the lines give.
- Soaking in seawater, will empty and refill before day is up.
- Applied oyster larvae to static tank.

8/24/2010
9:00am - 1:00pm

Prepare new tank setups for the rest of the day.
- Equipment is rinsed and ready for construction.

8/23/2010
10:30am - 3:00pm

Prepare f/2 media for culture
- Observed black flakey particles in the seawater containers
  - Later confirmed from Dave that the seawater tank was in fact, contaminated with identical substance.
    - Dave stated that he would empty/refill seawater tanks in basement "after lunch"
    - Stored sample of black substance under a slide for further examination.
  - Filtered 1000 ml of f/2 media to remove black substance
    - Did not use filtered media for culture. Stored for further examination.
  - Used remaining 400 ml of f/2 media from last culture to give culture more temporary food.
    - Poured 50 ml into each of the 4 culture samples.
    - Poured 100 ml into each of the 2 backup culture samples.
- Preparing supplies for culture scaling tomorrow, 8/24/2010, after Dave refills seawater tanks in basement.
Usual cleanup routines: ovens, claves, sinks
Walk-thru with Emma and Steven in the basement
- Begin reconstruction of tanks. 8/24/10
Walk-thru with Steven in labs
- Begin clean-up overhaul of cupboards, drawers, tables, sinks.
Finished Identifying algae samples, and placed into the freezer.

8/20/2010
10:30am - 12:00pm

Conduct Routine cleanup, ovens, sinks, claves, washer
Check Algae, write up adjusted process for culture.
- 300 ml f/2 media
- 100 ml algae sample
- Replace backup samples
  - Add more media to new leftover culture to produce more food for backup

8/9/2010
1:30am - 3:30pm

Clave/Oven/Dish Clean-up
Algae cultures renewed

8/6/2010
10:30am - 12:00pm

Clave/Oven/Dish Clean-up
Sanitizing seawater for F/2 media
Cataloging Algae ID Pictures, preparing for samples for ID

8/4/2010
1:00pm - 1:00pm

Emergency came up, had to leave.
Will be available via cell phone and email if something important comes up.

8/3/2010
11:00am - 1:00pm

Clave/Oven/Dish Clean-up
Assisted Sam in clearing out fridge, made room for more algae
Preparing more sanitized seawater for F/2 media.
- Preparing for next Monday's algae

8/2/2010
9:00am - 11:30am

Empty/Fill autoclave/oven
Unloaded algae bags into fridge
identified more Algae samples

7/28/2010
11:00am - 12:00pm

Picked up new specs from Brent
Went over protocol in basement regarding access, etc

7/27/2010
12:00pm - 3:00pm

Glassware upkeep
- Dishwasher, Autoclave, Sink, Oven
  - Accidentally broke small flask
    - Placed broken flask in "broken glass box"
Gathered intel for tank-build designs.

7/26/2010
1:00pm - 4:00pm

Forgot algae identification books at home
- Must wait until tomorrow in order to finish ID's
Clean-up all glassware and autoclave items left over from last week.
- All dishes picked up, unloaded/loaded dishwasher
- Oven emptied and put away
- Dishwasher loads packaged and placed into autoclaves.
Transport supplies to basement
- Bleach, etc, that Emma ordered.
Main Alage
- Build new flasks
- Set aside backups
- Get rid of old un-needed backups.
Sizzle

7/23/2010
10:00am - 4:00pm

1) Researching documents on algae in order to properly identify given samples.

Check out books from library.
Created Google-Spreadsheet
- Began identifying algae

7/22/2010
11:00am - 12:00pm

1) Gathering materials needed to identify algae samples for Emma.
2) Emptied the oven, autoclaves, and dishwashers.

7/21/2010
2:00pm - 4:00pm

1) Thought there was a meeting scheduled at 2:30pm as per the SR calendar so I wandered around looking for anyone; found nobody, gave up on the meeting and later ran into Sam who informed me that the scheduled meeting block on the calendar was an erroneous revolving entry made a while ago that is no longer in affect.

2) Discussed the logistics with Brent, regarding building the new tank according to the specs as per Emma. Going to compromise with a build similar to the original but utilizing the new data received from the plans. Began preparing a list of materials needed in order to build to nerw tank setups.

3) Spent some time loading and unloading the dishwasher and autoclave, labeling some new glassware with the initials "SR".

4) Went back to work on finishing my A-Term Final for the rest of the day.

7/20/2010
12:00pm - 12:30pm

1) Minor pickup, removed items from autoclave, placed more in. Relatively uneventful day. Spent a few hours in the break room studying for midterms and working on completely A-Term final.

7/19/2010
1:30pm - 4:00pm

Items Completed:
1) Made (2) 1L bottles of f/2 media.
2) Autoclaved various flasks
3) Cleaned up glassware in lab sink. (incomplete)
4) Filled out paperwork with Karen regarding pay
5) Picked up new tank-build specs from Brent
... A) Was informed to speak with Dave before starting tank construction

7/14/2010
2:00pm - 5:30pm

1) Checked on fish tanks, they seem to be doing well, no major leaks.
... A) Filled hot-side can with more salt-water.
2) Walked through algae culture process with Steven.
... A) Made 3 "greens" and 3 "yellows"
3) Cleaned (2) new 1L bottles of seawater to be used as f/2 media.
... A) Placed into autoclave.
4) Filling up the remaining 2ml screw-cap vials for Emma.

7/12/2010
1:30pm - 5:30pm

Worked on finishing up basement tank for oyster larvee. Went over a few things with Emma and Elene, and began preparations for when Emma leaves for Term-B.

Scheduled short meeting with Emma to discuss protocol on Thursday morning.

7/8/2010
11:15am - 4:00pm

1) Check on salt water left in autoclave yesterday. (complete)
... A) 1L bottle of salt water found on Emma's bench. (complete)
2) Review Emma's to-do list.
... A) Table (complete, used existing)
... B) Build 2nd System (incomplete)
....... a) Positioned table
....... b) Built bottle base
....... c)
... C) Move Oyster/Ocean acid to other building.
... D) Sterilize new glassware. (complete)
....... a) Place into autoclave(s) (complete)
... E) Prepare f/2 media with sterile seawater
... F) Sampling with Emma @ 3pm.
3) Finish filling 2ml screw-cap vials with RNA Later.

Emma's to-do list.

1. find a table
2. get the second system ready to go. i've already made the bottles for the larval chambers so all it needs is proper drainage and something to affix the bottles to. i will put all the materials you need on the metal bench in the lab. sam is bringing in a glue gun so you will need to get that from him. the white plastic is styrene and the green is pvc foam. there should be plenty of ethanol in the flammables cabinet below the hood in the lab where my bench is not.
3. move all oyster/ocean acid. stuff to the other building (steven will tell you more about this).
4. sterilize the new glassware. sam washed it today but it needs to be autoclaved.
5. go ahead and make more f/2 media with the sterile seawater (the bottle is on my bench). there's still a partial bottle in the hood you can use up. you can also scale up the algae that is already cultured. there are more algae cultures going in the friedman lab that i will show you tomorrow afternoon.
6. if you're still around 3-ish i should be back in. i'll be doing final sampling of the experiment going now and then rinsing and bleaching everything. so you can help me with that if you want!

7/8/2010
9:00am - 9:30am

To-do items:
1) Re-sanitize bottle of salt-water - (placed into autoclave)
2) Check on RNA solution (complete.)
3) Check on basement tank (complete)
4) Visit biochem storage. (complete)
... A) Picked up (2) 100ml bottles of RNA Later (complete)

7/7/2010
1:30pm - 4:00pm.

1) Setup "Shop" (complete)
2) Review Emma's "To Do" List. (complete)
...A) Empty flasks from autoclave and replace in lab. (complete)
...B) Place salt bottle in autoclave. (complete)
......a) Error Message 1: Not enough Water, retry in the morning.
...C) Prepare (120) 2ml screw-cap vials (incomplete)
......a) Partially complete, (88/120)
3) Review basement tanks for Friday-Project. (complete)

7/7/2010
9:00am - 10:00am

Trying to track down Emma to see what she's working on so that I can observe and assist accordingly.

Emma's List of things to learn:
1) Drainage for larvae tanks
2) Secondary tank maintenance
3) Saw-horse build
4) Algae culture (See [*1])
. a. make media
. b. sterilize glassware
. c. basic scaling up existing cultures
5) 120 2-mil screw-cap vials
. a) fill with RNA later.
. b)
Remind Emma to send me Algae culture document

[*1] Algal starter cultures
Sterilized 2 L of seawater in glass bottles (just sterilization cycle in autoclave).
Sterilized varied flasks & graduated cylinders for growing algae on full sterilization through exhaust cycle.

To make 1 L of pro-culture for algal starter cultures:
Procul A & B = Kent Marine Pro-cultures A and B
10 mL Procul A + 10 mL Procul B for 20 gallons of water
1 L = 0.264 gallons
0.264 gallons * (10 mL/20 gallons) = .132 mL = 132 uL of Procul A & B for 1 L seawater

Adding silicates:
1 gallon Procul A + 1 gallon Procul B makes 7,680 gallons culture water
Add silicates at 20 g per 1,000 gallons of culture water
0.132 mL of Procul A + Procul B makes 38.425 gallons of culture water
Need to add 0.7685 g of silicates

Sterilized all equipment needed to make culture media in germicidal hood for 15 minutes. Made 1 L of regular culture media (Procul A & B) and 1 L of regular media + silicates. Media are made in sterile bottles, labeled, and at 4C (behind my bench).**