Thought I’d be switching my online notebook over to the Open Notebook Science network, but when trying to write this post I found that I could not add a new category. Will try to figure that out, but until then will keep posting here.

Took my samples and reagents from the freezer in my lab on campus to the Pritzker DNA Lab at the Field Museum, where I do the bulk of my molecular work. Spent the day alternating between writing my Doctoral Dissertation Improvement Grant (DDIG) and some lab work.

Common Garden Experiment

• Extracted DNA from 14 broodstock samples using the EZNA Mollusc kit (protocol here). Left to digest for 2.5 hours.
  1. SS2_6
  2. SS2_7
  3. SS2_8
  4. HC1_6
  5. HC1_7
  6. HC1_8
  7. HC1_9
  8. HC1_10
  9. NF1_3
  10. NF1_4
  11. NF1_5
  12. NF1_6
  13. NF1_7
  14. NF1_8
• Ran out a gel from the DNA extractions of larvae samples done on 8/11/12 at Manchester.

  • 	Population	Tank	Family	Size	Date	Storage	Est. #	Date extracted
    1	Hood Canal		LC	>100	7/13/2015	75/95 EtOH		8/11/2015
    2	Fidalgo Bay	NA	LC	100	7/13/2015	75% EtOH		8/11/2015
    3	South Sound	NA	LC	100	7/13/2015	RNALater		8/11/2015
    4	Hood Canal	NA	HC2	100	7/17/2015	RNALater		8/11/2015
    5	Hood Canal	NA	LC	100	7/17/2015	RNALater		8/11/2015
    6	South Sound	NA	LC	100	7/17/2015	RNALater		8/11/2015
    7	Hood Canal	NA	LC	100	7/20/2015	RNALater		8/11/2015
    8	Fidalgo Bay	NA	LC	100	7/20/2015	RNALater		8/11/2015
    9	South Sound	NA	LC	100	7/20/2015	RNALater		8/11/2015
    10	Hood Canal	HC_Tank1_160	NA	160	7/20/2015	RNALater		8/11/2015
    11	Fidalgo Bay	NF_Tank1_new	NA	160	7/20/2015	RNALater		8/11/2015
    12	South Sound	SS_Tank1_new	NA	160	7/15/2015	RNALater		8/11/2015
    13	Hood Canal	HC_Tank1_new	NA	160	7/24/2015	RNALater		8/11/2015
    14	Fidalgo Bay	NF_Tank1_new	NA	160	7/24/2015	RNALater		8/11/2015
    15	South Sound	SS_Tank1_new	NA	160	7/24/2015	RNALater		8/11/2015
    16	Hood Canal	HC_Tank1_new	NA	160	7/27/2015	RNALater		8/11/2015
    17	Fidalgo Bay	NF_Tank1_new	NA	160	7/27/2015	RNALater		8/11/2015
    18	South Sound	SS_Tank1_new	NA	160	7/27/2015	RNALater		8/11/2015
    19	Hood Canal	HC_Tank2_160		224	8/3/2015	RNALater		8/11/2015
    20	Fidalgo Bay	NF_Tank2_160		224	8/3/2015	RNALater		8/11/2015
    21	South Sound	SS_Tank2_160		224	8/3/2015	RNALater		8/11/2015
    22	Hood Canal	HC_Tank2_160		>224	8/7/2015	RNALater	350	8/11/2015
    23	Fidalgo Bay	NF_Tank2_160		>224	8/7/2015	RNALater	504	8/11/2015
    24	Oyster Bay	SS_Tank2_160		>224	8/7/2015	RNALater	641	8/11/2015

  • The computer hooked up to the UV camera wouldn’t recognize a USB drive, so I just have a phone picture of a printed out picture for now. 12 and 13 are cut off, but they did not show up on gel. For gels of DNA extracts, I give a ranking from 1 (did not work at all) to 5 (bright band of high molecular weight DNA). These are put of the Sample Master Sheet.
    • 
      1. 3.5
      2. 4
      3. 4
      4. 1 (rerun)
      5. 4
      6. 4.5
      7. 3.5
      8. 3 (low)
      9. 5
      10. 4
      11. 1 (rerun)
      12. 1 (rerun)
      13. 1 (rerun)
      14. 1 (rerun)
      15. 5
      16. 3 (degrad)
      17. 2.5 (degrad)
      18. 2 (degrad)
      19. 5
      20. 1 (rerun)
      21. 4.5
      22. 3 (degrad)
      23. 2.5 (low)
      24. 5
• Playing around with data!
  • Looked at larvae release from each population across time. Did this partially out of burning curiosity and because it would be nice to have some preliminary data to put in my DDIG proposal.
  • First, I had to edit the Google Sheet to include zeros for days when a population released no larvae and to have total counts across families. Then in R:

  •  > larvae = read.csv("Larval counts - Day 1 (1).csv", header = TRUE) 
    > names(larvae)

    [1] “Date” “Population” “Family” “Tank.added.to” “Volume.of.tripour..mL.” “Vol.of.drop.counts” “Ethanol.used.”
    [8] “Live.Count.1” “Live.Count.2” “Live.Count.3” “Live.Count.4” “Total.Live.Larvae” “X…” “Notes”
    [15] “Dead.count..1” “Dead..2” “Dead..3” “Dead..4” “Total.Dead” “Total.Larvae” “Total.by.date”

 > pop_Total_Date_na <- na.omit(pop_Total_Date)
> ggplot(data=pop_Total_Date_na, aes(x=Date, y=Total.by.date, \
group=Population, colour=Population)) + geom_line() + geom_point()

• Interestingly, the South Sound population produced more larvae earlier. This mirrors the reciprocal transplant experiment, where SS oysters reached their maximum percentage of brooding females sooner at two of the 4 sites.

Oly Population Structure

• In addition to making libraries for samples from the common garden, I need to start getting DNA ready for one more sequencing run for my project looking at rangewide population structure in Olympia oysters. Did 10 extractions concurrently with the common garden extractions.

1. WA1_16
2. WA1_14
3. BC1_19
4. BC1_18
5. CA6_16
6. CA6_17
7. CA6_18
8. CA7_13
9. OR3_7
10. OR3_20