Wednesday, April 22, 2015

4 22 2015 Heat/Mechanical Shock Experiment

Today I ran the Heat and Mechanical Shock experiment on my oysters. While most groups got liquid nitrogen treatment, the mechanical H and S groups did not due to lack of Liquid N2. For those samples I placed them on ice and moved them to the -80 as soon as possible.  The procedure went as follows.

Pre-Experiment
Oysters
  • 8°C
  • fed daily with 5-10 ml per tank commercial shellfish diet (Isochrysis 1800 mix Marine Algae)
  • Partial water changes once per week (remove 5 gallons, replace with fresh 5 gallons)
    • Seawater from Seattle Aquarium
  • Aeration with aquarium aerator/stone
  • circulation with underwater pump
  • Tanks 10 gallon plastic storage tubs (costco storage tubs)
Homogenization tubes for ctenidia prelabelled with date (42215,42315), pop (N,H,S), treatment (T,M) and time point (1, 24) or Control, and oyster # (1,2,3...)
Collection 1.5 ml tubes (screw cap) for ctenidia prelabelled with date (42215,42315), pop (N,H,S), treatment (T,M) and time point (1, 24) or Control, oyster # (1,2,3...), and tissue type (C, M)
Collection 1.5 ml tubes (screw cap) for mantle prelabelled with date (42215,42315), pop (N,H,S), treatment (T,M) and time point (1, 24) or Control, oyster # (1,2,3...), and tissue type (C, M)
15 ml conical tubes for whole oyster prelabelled with date (42215,42315), pop (N,H,S), treatment (T,M) and time point (1, 24) or Control, and oyster # (1,2,3...)
Warm fresh seawater in 500 ml beaker to 38°C by immersing it in a water bath at 38°C.

Experiment

Heat Stress

  • 22 oysters each pop in a mesh bag were lowered (stagger each pop by 1 hour) into 500 ml of prewarmed 38°C sea water (1 hr timer started)
    • N pop first, H pop next, S pop last
  • after 1 hour exposure heat stress ends, animals returned to 8°C water.
  • 1 hour post exposure 8 animals sampled from each group staggered by 1 hour
    • N pop first, H pop next, S pop last
    • collected with ethanol flame sterilized forceps and scissors
      • tools kept in 100% EtOH
      • ran through EtOH flame
      • allow EtOH to burn off
      • Collect tissue
      • replace in 100% EtOH
      • wipe occasionally with paper towel and resterilize
    • ctenidia sample (50-100 mg) homogenized in 1 ml Trizol stored at -80°C
    • 2nd ctenidia sample (any remaining) in 1.5 ml screw cap tube dropped into liquid nitrogen then to -80°C
    • mantle sample (decent size) in 1.5 ml screw cap tube dropped into liquid nitrogen then to -80°C
    • remaining tissue placed in 15 ml conical with 75% EtOH at -20°C
    • shells in individual labeled ziploc bags so correspond to sample including oyster id

Mechanical Stress

  • 22 oysters from 1 pop placed in bucket in centrifuge and spun for 5 minutes at 1000 rpm.  Samples staggered by 1 hour. Completed after all heat shock treatments and samples were taken.
    • N pop first, H pop next, S pop last
  • after 5 minutes of mechanical stress, animals returned to 8°C water
  • 1 hour post exposure 8 animals sampled from each group staggered by 1 hour
    • N pop first, H pop next, S pop last
    • collected with ethanol flame sterilized forceps and scissors
      • tools kept in 100% EtOH
      • ran through EtOH flame
      • allow EtOH to burn off
      • Collect tissue
      • replace in 100% EtOH
      • wipe occasionally with paper towel and resterilize
    • ctenidia sample (50-100 mg) homogenized in 1 ml Trizol stored at -80°C
    • 2nd ctenidia sample (any remaining) in 1.5 ml screw cap tube dropped into liquid nitrogen then to -80°C
    • mantle sample (decent size) in 1.5 ml screw cap tube dropped into liquid nitrogen then to -80°C
    • remaining tissue placed in 15 ml conical with 75% EtOH at -20°C
    • shells in individual labeled ziploc bags so correspond to sample including oyster id

Thursday, April 2, 2015

4 2 2015 EZNA Seed Isolation with Fidalgo pt 2.

Today I completed the 96 seed isolation with the EZNA kit. I isolated the last 12 samples for Fidalgo. The samples are in the freezer in 209 and are ready for GBS processing. You can read about the last Fidalgo isolation in this blogpost.

Before using the EZNA Kit I dissected out whole body tissue from 12 seed oysters into the homogenization tube. The oysters are labeled NF 21-32. I used flame sterilized equipment to dissect the animals. 

The protocol is as follows:

  1. Added 350 ul ML1 Buffer
  2. Added 25 ul Proteinase K solution
  3. Used pestle in homogenization tube to grind tissue in solution
  4. Vortexed
  5. Incubated at 60 C for 30 minutes
  6. Added 350 ul Phenol:Chloroform:Isoamyl Alcohol (25:24:1)
  7. Vortexed
  8. Centrifuged 10,000 g for 2 minutes
  9. Transferred the upper aqueous phase to new tube (~300 ul)
  10. Added 300 ul MBL Buffer
  11. Added 10 ul RNase A
  12. Vortexed for 15 seconds
  13. Incubated at 70C (started at 67.5 C) for 10 minutes
  14. Cooled to room temperature sitting for 5 minutes
  15. Added 300 ul 100% EtOH
  16. Vortexed for 15 seconds
  17. Put spin column in collection tube
  18. Added 750 ul sample solution to column
  19. Centrifuged at 10,000 g for 1 minute at 4C
  20. Discarded flowthrough
  21. Repeated 18-20 with remaining sample
  22. Discarded collection tube and replaced with a new one. 
  23. Added 500 ul HBC solution. 
  24. Centrifuged at 10,000 g for 30 seconds at 4C
  25. Discarded flowthrough
  26. Added 700 ul DNA Wash Buffer
  27. Centrifuged at 10,000 g for 1 minute at 4C
  28. Discarded flowthrough
  29. Repeated 26-28
  30. Centrifuged Empty column for 2 minutes at 10,000 g at 4C
  31. Discarded collection tube and put column into microcentrifuge tube for sample collection
  32. Added 100 ul preheated 70C Elution Buffer
  33. Incubated for 2 minutes
  34. Centrifuged at 10,000 g for 1 minute at 4C
  35. Repeated 32-34. 
  36. Stored DNA at -20 C

DNA is in a box labelled:
Seed Oly DNA HL NF
3/23/15 Jake Heare 1 of 2

Seed Oly DNA SN 
3/31/15 JH 2 of 2

Wednesday, April 1, 2015

4 1 2015 EZNA Dabob pt 2 and Oyster pt 3

Today I continued the seed DNA isolation. I completed the 32 Dabob Seeds and the 32 Oyster Bay Seeds as appropriate. You can read about the previous Dabob isolation here. You can read about the other Oyster bay Isolations here and here.

Before using the EZNA Kit I dissected out whole body tissue from 14 seed oysters into the homogenization tube. The oysters are labeled SN 31-32 and HL 21-32. I used flame sterilized equipment to dissect the animals. 

The protocol is as follows:

  1. Added 350 ul ML1 Buffer
  2. Added 25 ul Proteinase K solution
  3. Used pestle in homogenization tube to grind tissue in solution
  4. Vortexed
  5. Incubated at 60 C for 30 minutes
  6. Added 350 ul Phenol:Chloroform:Isoamyl Alcohol (25:24:1)
  7. Vortexed
  8. Centrifuged 10,000 g for 2 minutes
  9. Transferred the upper aqueous phase to new tube (~300 ul)
  10. Added 300 ul MBL Buffer
  11. Added 10 ul RNase A
  12. Vortexed for 15 seconds
  13. Incubated at 70C (started at 67.5 C) for 10 minutes
  14. Cooled to room temperature sitting for 5 minutes
  15. Added 300 ul 100% EtOH
  16. Vortexed for 15 seconds
  17. Put spin column in collection tube
  18. Added 750 ul sample solution to column
  19. Centrifuged at 10,000 g for 1 minute at 4C
  20. Discarded flowthrough
  21. Repeated 18-20 with remaining sample
  22. Discarded collection tube and replaced with a new one. 
  23. Added 500 ul HBC solution. 
  24. Centrifuged at 10,000 g for 30 seconds at 4C
  25. Discarded flowthrough
  26. Added 700 ul DNA Wash Buffer
  27. Centrifuged at 10,000 g for 1 minute at 4C
  28. Discarded flowthrough
  29. Repeated 26-28
  30. Centrifuged Empty column for 2 minutes at 10,000 g at 4C
  31. Discarded collection tube and put column into microcentrifuge tube for sample collection
  32. Added 100 ul preheated 70C Elution Buffer
  33. Incubated for 2 minutes
  34. Centrifuged at 10,000 g for 1 minute at 4C
  35. Repeated 32-34. 
  36. Stored DNA at -20 C

DNA is in a box labelled:
Seed Oly DNA HL 
3/23/15 Jake Heare

Seed Oly DNA SN 
3/31/15 JH 2 of 2

Tuesday, March 31, 2015

3 31 2015 EZNA with Oyster Bay oysters Pt. 2

Today started using the new EZNA 200 reaction kit we received yesterday. Before beginning I added Isopropanol to the HBC buffer and 100% EtOH to one bottle of DNA Wash buffer. Then I continued the procedure as normal. These samples are related to the samples I extracted yesterday.

Before using the EZNA Kit I dissected out whole body tissue from 24 seed oysters into the homogenization tube. The oysters are labeled SN 7-30. I used flame sterilized equipment to dissect the animals. 

The protocol is as follows:

  1. Added 350 ul ML1 Buffer
  2. Added 25 ul Proteinase K solution
  3. Used pestle in homogenization tube to grind tissue in solution
  4. Vortexed
  5. Incubated at 60 C for 30 minutes
  6. Added 350 ul Phenol:Chloroform:Isoamyl Alcohol (25:24:1)
  7. Vortexed
  8. Centrifuged 10,000 g for 2 minutes
  9. Transferred the upper aqueous phase to new tube (~300 ul)
  10. Added 300 ul MBL Buffer
  11. Added 10 ul RNase A
  12. Vortexed for 15 seconds
  13. Incubated at 70C (started at 67.5 C) for 10 minutes
  14. Cooled to room temperature sitting for 5 minutes
  15. Added 300 ul 100% EtOH
  16. Vortexed for 15 seconds
  17. Put spin column in collection tube
  18. Added 750 ul sample solution to column
  19. Centrifuged at 10,000 g for 1 minute at 4C
  20. Discarded flowthrough
  21. Repeated 18-20 with remaining sample
  22. Discarded collection tube and replaced with a new one. 
  23. Added 500 ul HBC solution. 
  24. Centrifuged at 10,000 g for 30 seconds at 4C
  25. Discarded flowthrough
  26. Added 700 ul DNA Wash Buffer
  27. Centrifuged at 10,000 g for 1 minute at 4C
  28. Discarded flowthrough
  29. Repeated 26-28
  30. Centrifuged Empty column for 2 minutes at 10,000 g at 4C
  31. Discarded collection tube and put column into microcentrifuge tube for sample collection
  32. Added 100 ul preheated 70C Elution Buffer
  33. Incubated for 2 minutes
  34. Centrifuged at 10,000 g for 1 minute at 4C
  35. Repeated 32-34. 
  36. Stored DNA at -20 C

DNA is in a box labelled:

Seed Oly DNA SN 
3/31/15 JH 2 of 2

3 30 2015 EZNA with Oyster Bay

Last week I started isolating DNA from seed oyster from Dabob and Fidalgo. Yesterday the new kit didn't come in until later so I started with the remaining six reactions from the previous kit. I got busy and forgot to post about it so here it is. The samples are labelled SN 1-6.

Before using the EZNA Kit I dissected out whole body tissue from 6 seed oysters into the homogenization tube. The oysters are labeled SN 1-6. I used flame sterilized equipment to dissect the animals. 

The protocol is as follows:

  1. Added 350 ul ML1 Buffer
  2. Added 25 ul Proteinase K solution
  3. Used pestle in homogenization tube to grind tissue in solution
  4. Vortexed
  5. Incubated at 60 C for 30 minutes
  6. Added 350 ul Phenol:Chloroform:Isoamyl Alcohol (25:24:1)
  7. Vortexed
  8. Centrifuged 10,000 g for 2 minutes
  9. Transferred the upper aqueous phase to new tube (~300 ul)
  10. Added 300 ul MBL Buffer
  11. Added 10 ul RNase A
  12. Vortexed for 15 seconds
  13. Incubated at 70C (started at 67.5 C) for 10 minutes
  14. Cooled to room temperature sitting for 5 minutes
  15. Added 300 ul 100% EtOH
  16. Vortexed for 15 seconds
  17. Put spin column in collection tube
  18. Added 750 ul sample solution to column
  19. Centrifuged at 10,000 g for 1 minute 
  20. Discarded flowthrough
  21. Repeated 18-20 with remaining sample
  22. Discarded collection tube and replaced with a new one. 
  23. Added 500 ul HBC solution. 
  24. Centrifuged at 10,000 g for 30 seconds 
  25. Discarded flowthrough
  26. Added 700 ul DNA Wash Buffer
  27. Centrifuged at 10,000 g for 1 minute 
  28. Discarded flowthrough
  29. Repeated 26-28
  30. Centrifuged Empty column for 2 minutes at 10,000 g 
  31. Discarded collection tube and put column into microcentrifuge tube for sample collection
  32. Added 100 ul preheated 70C Elution Buffer
  33. Incubated for 2 minutes
  34. Centrifuged at 10,000 g for 1 minute 
    1. Internal lid in centrifuge failed which resulted in tube caps being sheared off. 
    2. Pipetted sample in collection tube to new tube
    3. Moved the spin columns to the new tubes
  35. Repeated as normal 32-34. 
    1. Under calculated amount of Elution buffer needed to be preheated. 
    2. SN 4, 5, and 6 had cold Elution buffer added instead
  36. Stored DNA at -20 C

Tuesday, March 24, 2015

3 24 2015 EZNA with Fidalgo Seed Oysters

Today I completed isolation of 20 seed oysters from the Fidalgo population using the EZNA extraction kit. This is the same kit I used yesterday. I also ran a gel on those samples and found that even though there was more HMW DNA there was still a lot of degradation in the samples. You can read about it in my other blogpost today. I expect the same results from these samples. I will run a gel on them when I get back next week to check the quality of the extraction. Right now everything is stored in the -20 C Freezer in 209 in a box labeled Seed Oly Extraction 3/23/2015. 

Before using the EZNA Kit I dissected out whole body tissue from 20 seed oysters into the homogenization tube. The oysters are labeled NF 1-20. I used flame sterilized equipment to dissect the animals. 

The protocol is as follows:

  1. Added 350 ul ML1 Buffer
  2. Added 25 ul Proteinase K solution
  3. Used pestle in homogenization tube to grind tissue in solution
  4. Vortexed
  5. Incubated at 60 C for 30 minutes
  6. Added 350 ul Phenol:Chloroform:Isoamyl Alcohol (25:24:1)
  7. Vortexed
  8. Centrifuged 10,000 g for 2 minutes
  9. Transferred the upper aqueous phase to new tube (~300 ul)
  10. Added 300 ul MBL Buffer
  11. Added 10 ul RNase A
  12. Vortexed for 15 seconds
  13. Incubated at 70C (started at 67.5 C) for 10 minutes
  14. Cooled to room temperature sitting for 5 minutes
  15. Added 300 ul 100% EtOH
  16. Vortexed for 15 seconds
  17. Put spin column in collection tube
  18. Added 750 ul sample solution to column
  19. Centrifuged at 10,000 g for 1 minute at 4C
  20. Discarded flowthrough
  21. Repeated 18-20 with remaining sample
  22. Discarded collection tube and replaced with a new one. 
  23. Added 500 ul HBC solution. 
  24. Centrifuged at 10,000 g for 30 seconds at 4C
  25. Discarded flowthrough
  26. Added 700 ul DNA Wash Buffer
  27. Centrifuged at 10,000 g for 1 minute at 4C
  28. Discarded flowthrough
  29. Repeated 26-28
  30. Centrifuged Empty column for 2 minutes at 10,000 g at 4C
  31. Discarded collection tube and put column into microcentrifuge tube for sample collection
  32. Added 100 ul preheated 70C Elution Buffer
  33. Incubated for 2 minutes
  34. Centrifuged at 10,000 g for 1 minute at 4C
  35. Repeated 32-34. 
  36. Stored DNA at -20 C

3 24 2015 EZNA Seed Isolation Gel Run

I ran a subset of the samples from yesterday. The samples were HL 1-6. The DNA looks very degraded still. There were only two of the 6 that I would consider usuable, 2 were questionable, and 2 were fully degraded. Moving forward, it looks like the EZNA kit can salvage usuable samples from some of the seed but not all of them. This is pretty similar to the Qiagen 96 Well Plate kit in this instance. Since we've already ordered the 200 reaction kit for the EZNA and I've processed 20 dabob seed and am processing another 20 Fidalgo seed today it seems only reasonable to continue using this kit.

Gel Protocol:

75 ml Low TAE with 0.6 g Agarose and 7.5 ul EtBr.

Run at 120 V for 55 minutes.

10 ul Ladder, 20 ul sample mixed with 3 ul loading dye.

Gel Layout:
Well12345678
SampleLadderHL 1HL 2HL 3HL 4HL 5HL 6Ladder

Gel with Dabob Seed DNA Isolation

Close up of High Molecular Weight Material.