Tag Archives: OA

Curriculum Testing – Determination of Most Useful Concentration of Sodium Carbonate Solution

After evaluating whether or not dry ice would be effective to trigger a noticeable change in pH in a solution, I determined which concentration(s) of sodium carbonate (Na2CO3) would be most useful for demonstration and usage within the curriculum. Previously, I used a 1M Na2CO3 solution a the universal pH indicator showed no change in color. What I want is a color change, but one that takes place at a noticeably slower rate than the other solutions that are demonstrated/tested; this will show how sodium carbonate acts as a buffer to CO2-acidification.

Additionally, I tested the difference in rate of pH change between Instant Ocean and sodium chloride (NaCl). The reason for testing this is to use this as a demonstration that salt water (i.e. sea water, ocean water) isn’t just made up of salt. It’s likely that many students simply think of the ocean as salt water and have not considered that the makeup of sea water is much more complex.

Finally, I performed these tests in larger volumes than I did previously to verify that the larger volumes will slow the rate of pH change, thus increasing the time it takes for the universal pH indicator to change color, making it easier to see/monitor/time.

Instant Ocean mix (per mfg’s recs): 0.036g/mL (36g/L)

For the NaCl solution, I used the equivalent weight (36g) that was used to make up the Instant Ocean solution.

 

Results:

  • Use of 0.001M Na2CO3 is passable, but due to the fact that it’s a diprotic base, the pH indicator didn’t progress lower than ~pH 6.0 in my limited tests. Adding additional dry ice (or using an even more dilute solution) are options to drive the pH lower.
  • The comparison between salt water and Instant Ocean will work well as a demonstration to introduce the concept that sea water is more complex than just being salty.
  • Using 1L volumes works well to slow the color changes of the universal pH indicator to improve the ability of the students to observe and measure the rate of color change.

The table below summarizes what I tested.

SOLUTION VOLUME (mL) DRY ICE (g) TIME OBSERVATIONS
0.1M Na2CO3 1000 3.0 No color change. Dry ice gone.
0.01M Na2CO3 1000 3.3 No color change. Dry ice gone.
0.001M Na2CO3 1000 3.3 ~20s Dry ice gone, but final color indicated a pH ~6.0.
Instant Ocean 1000 3.3 3m Initial color change noticeable within 10s; full color change after ~3m
NaCl 1000 3.0 instant Immediate, complete color change.
Tap H2O 1000 3.3 3m pH started @ ~7.5. Full color change took place.
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Curriculum Testing – Viability of Using Dry Ice to Alter pH

Ran some basic tests to get an idea of how well (or poorly) the use of dry ice and universal indicator would be for this lesson.

Instant Ocean mix (per mfg’s recs): 0.036g/mL

Universal Indicator (per mfg’s recs): 15μL/mL

Played around a bit with different solution volumes, different dry ice amounts, and different Universal Indicator amounts.

Indicator Vol (mL) Solution Solution Vol (mL) Dry Ice (g) Time to Color Change (m) Notes
3 Tap H2O 200 1.5 <0.5
3 Tap H2O 200 0.5 >5 Doesn’t trigger full color change and not much bubbling (not very exciting)
5 Tap H2O 1000 12 <1
3 Instant Ocean 200 1.5 <0.5 Begins at higher pH than just tap water. Full color change is slower than just tap water, but still too quick for timing.
2 1M Na2CO3 200 5 >5 No color change and dry ice fully sublimated.
2 1M Tris Base 200 5 >5 No color change and dry ice fully sublimated.
2 Tap H2O + 20 drops 1M NaOH 200 5 2.75 ~Same color as Na2CO3 and Tris Base solutions to begin. Dry ice gone after ~5m and final pH color is ~6.0.

 

Summary

  • Universal Indicator amount doesn’t have an effect. It’s solely needed for ease-of-viewing color changes. Use whatever volume is desired to facilitate easy observations of color changes.
  • Larger solution volumes should be used in order to slow the rate of pH change, so that it’s easier to see differences in rates of change between different solutions.
  • 1M solutions of Na2CO3 and Tris Base have too much buffering capacity and will not exhibit a decrease in pH (i.e. color change) from simply using dry ice. May want to try out different dilutions.
  • Use of water + NaOH to match starting color of Na2CO3 and/or Tris Base is a good way to illustrate differences in buffering capacity to students.
  • Overall, dry ice will work as a tool to demonstrate effect(s) of CO2 on pH of solutions!

Some pictures (to add some zest to this entry):

 

 

 

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Teaching – OA Lesson Plan Development

I’m currently collaborating on tweaking/developing a lesson plan and corresponding curriculum to teach Washington high school students about the chemistry involved in ocean acidification.

This is a project that’s already been in the works and I’m being brought in to assist (or, take over?) with the development. I’m pretty interested and excited by this. The reason for my excitement is that I was in the secondary education program to become a certified secondary education teacher while I was in graduate school. So, this project lets me apply the knowledge I garnered about teaching science during that time.

The current state of the project has a lab protocol, but no real lesson plan for the teachers to utilize. The lab protocol, in my view, is a bit too dense for high schoolers to digest and is a bit too much of “do this, write down the number: that’s ocean acidification!” It currently lacks an important element of science pedagogy: discovery. My goals are to tweak the protocol in such a fashion that it is more engaging and, possibly, hypothesis-(i.e. discovery) driven. This type of teaching has been shown to greatly improve retention and help improve/develop critical thinking skills.

The lesson plan should have sufficient information for teachers to decide if the lesson is appropriate for them to teach (e.g. which Washington state standards are addressed, what learning level(s) does the lesson require, what materials/supplies are needed, etc.), if they have enough time to conduct the lesson, and if they have ample understanding of the topic to feel comfortable teaching it.

I’ve put this project on GitHub. It allows for active collaboration on projects. Although there are some hurdles for those collaborators who have not used the service before, I think there are some good organizational benefits that are worth dealing with the initial headaches that might come for beginning GitHub users.

One benefit to developing this project on GitHub is that all changes are tracked and a description of the changes are required when they are made. This makes it relatively to see what changes were made, by who, and when. Although using something like Google Docs also automatically tracks changes, it does not allow the ability to provide a comment when changes are made. Because of this, it’s not always clear why the change was made in the first place.

An additional benefit, and this is the main reason I think it’s best to develop this project on GitHub, is the Issues tracker (see screenshot):

 

The Issues section allows for targeted discussion of the project and eliminates the volleys of email that often happen on collaborative projects. It will keep all discussions about this project in a single location and won’t require exhaustive searches of emails that easily get buried during a work week. Additionally, the discussions can remain focused on specific topics without getting lost within a emails attempting to broach multiple topics at once.

 

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Oyster Sampling – Olympia Oyster OA Populations at Manchester

I helped Katherine Silliman with her oyster sampling today from her ocean acidification experiment with Olympia oysters (Ostrea lurida) at the Kenneth K. Chew Center for Shellfish Research & Restoration, which is housed at the NOAA Northwest Fisheries Science Center at Manchester in a partnership with the Puget Sound Restoration Fund (PSRF). We sampled the following tissues and stored in 1mL RNAlater:

  • adductor muscle (A)
  • ctenidia (C)
  • mantle (M)

When there was sufficient ctenidia tissue, an additional sample was stored in 75% ethanol for potential microbial analysis.

Tissue was collected from two oysters from each of the following oyster populations:

  • British Columbia (BC)
  • California (CA)
  • Oregon (OR)

Oysters were sampled from each of the following tanks:

  • 1A
  • 2A
  • 3A
  • 4A
  • 1B
  • 2B
  • 3B
  • 4B

Tubes were labeled in the following fashion:

  1. Population & Tank (e.g. OR3B)
  2. Tag#
  3. Tissue

If no tag was present on the oyster, the oyster was assigned a number (beginning at 150 and increased sequentially) and photographed with a ruler for future measurement. White colored tags were written with the number followed by the letter ‘W’ (e.g. 78W) – no tag color info was recorded for other tag colors.

Additionally, gonad developmental stage was roughly assessed: ripe, kinda ripe, or not ripe.

All info was recorded by Katherine in her notepad. All samples were retained by Katherine (not sure where she stored them).

Utensils were flame sterilized between oysters and gloves/work surfaces were washed with a 10% bleach solution between oysters.

 

Here are a few pics from the day:

 

 

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Morphometrics – Olympia Oyster OA Larvae Completed

Finished measuring Ostrea lurida larvae using NIS-Elements BR (10x objective and 10x nosepiece setting in software). That’s 2,620 larvae measured!

NOTE: Robyn previously measured 33 tubes worth of larvae, but I’m not certain where that data was saved.

All measurements by me can be found here (Google Sheet): FHL_Oly_larvae_measurements

Measured 30 larvae from each tube of the following samples:

  Box Label Color Tube Label Notes
70 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 U FB HL.L-1
71 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 V FB HL.L.2
72 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 W FB HH.L.1
73 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 X FB HH.L.2
74 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 Y SS LLH3 Many transluscent shells
75 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 Z SS LL.H.4 Many transluscent shells
76 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 AA SS LHH3 Mostly transluscent shells
77 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 BB SS LHH4
78 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 CC SS LL.L.3
79 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 DD SS LL.L.4
80 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 EE SS LH.L.3
81 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 FF SS LH.L.4
82 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LLL-1 4.3.E
83 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LLL2 4.3.F
84 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LHL-1 4.3.G
85 FHL Oly OA x DO Box 2 etOH Friedman Pink 4.4.15 FB release Low CO2 103A
86 FHL Oly OA x DO Box 2 etOH Friedman White SS Low CO2 4.4.15 release 103A All shells partially transluscent.
87 FHL Oly OA x DO Box 2 etOH Friedman Blue SS High CO2 4/5-6/15 release 103B All shells mostly transluscent.
88 FHL Oly OA x DO Box 2 etOH Friedman Pink 44/5-6/15 release FB LCO2 FB 103A

 

Example images from notes above:

 

Sample #74

 

 

Sample #75

 

 

Sample #77

 

 

Sample #85

 

 

Sample #86

 

 

Sample #87

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Morphometrics – Olympia Oyster OA Larvae Continued

Continued measuring Ostrea lurida larvae using NIS-Elements BR (10x objective and 10x nosepiece setting in software).

All measurements can be found here (Google Sheet): FHL_Oly_larvae_measurements

Measured 30 larvae from each tube of the following samples:

  Box Label Color Tube Label Notes
34 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 108B LH-L-1 D5 SS
35 2015 – DO x pH Olys FHL Friedman White 3.24.15 103A-SS Olys. Low CO2 released 3.23.15 Jagged shells; See image below
36 2015 – DO x pH Olys FHL Friedman White 3.26.15 SS LL-H1 103A
37 2015 – DO x pH Olys FHL Friedman White 103A 3.26.15SS LL-H2
38 2015 – DO x pH Olys FHL Friedman White 103B 3.26.15 SS LH-H-1
39 2015 – DO x pH Olys FHL Friedman White 3.26.15 103BSS LHH-2
40 2015 – DO x pH Olys FHL Friedman White 108A 3.26.15 SS LL-L-1
41 2015 – DO x pH Olys FHL Friedman White 108A 3.26.15 SS LL-L-2
42 2015 – DO x pH Olys FHL Friedman White 108B 3.26.15 LHL-1 SS
43 2015 – DO x pH Olys FHL Friedman Purple AR 103B FB Release 3.31.15 Many transluscent shells; See image below
44 2015 – DO x pH Olys FHL Friedman Pink LCO2 FB 103A 2d 3/25/15 release 3.27.15 All transluscent shells; See image below
45 2015 – DO x pH Olys FHL Friedman Blue LCO2 SS 3.27.15 103A from 3/23/15 release All semi-transluscent shells; See image below
46 2015 – DO x pH Olys FHL Friedman Pink 3.27.15 103A FB 3.26.15 released LCO2 – 1 day old
47 2015 – DO x pH Olys FHL Friedman Purple 3.30.15 103B FB HCO2 release
48 2015 – DO x pH Olys FHL Friedman Purple 3.30.15 FB LCO2 release 103A
49 2015 – DO x pH Olys FHL Friedman Pink AS 103A-FB released 3.31.15
50 2015 – DO x pH Olys FHL Friedman Pink FB LCO2-103A released 4.1.15 4.1.15
51 2015 – DO x pH Olys FHL Friedman White SS LCO2-103A released 3.31.15 4.1.15
52 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.GG SS HLH3
53 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.HH SS HLH4
54 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LHH2 4.3.D All semi-transluscent shells; See image below
55 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LLH1 4-3-A
56 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LLH2 4-3-B
57 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LHH1 4-3-C
58 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 I HLH-1 SS
59 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 J HLH-2 SS
60 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 K HHH-1 SS
61 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 L HHH-2 SS
62 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 M HLL-1 SS
63 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 N HLL-2 SS
64 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 O HHL-1 SS
65 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 P HHL-2 SS
66 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 S FB HHH-1
67 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 T FB HHH-2
68 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 Q FB HL.H-1
69 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 R FB HL.H-2

 

Example images from notes above:

Sample #35

 

 

Normal shell, for comparison to jagged shell image above:

 

Sample #43 – Many transluscent shells

 

Sample #44 – All transluscent shells

 

Sample #45 – Partially transluscent shells

 

Sample #54 – All transluscent shells

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Morphometrics – Olympia Oyster OA Larvae Continued

Continued measurements of larvae samples from yesterday. Measured length (hinge to growing edge) and width of 30 oysters from each tube using NIS-Elements BR (10x objective and 10x nosepiece setting in software).

The measurement data can be found here (Google Sheet): FHL_Oly_larvae_measurements

Here’s the list of tubes that were measured today and their labels:

  Box Label Color Tube Label Notes
14 2015 – DO x pH Olys FHL Friedman White AM 103B-SS LH-H-2 3.31.15
15 2015 – DO x pH Olys FHL Friedman White AL 103B-SSLH-H-1 3.31.15
16 2015 – DO x pH Olys FHL Friedman White AK 3.31.15 103A-SS LL-H-2
17 2015 – DO x pH Olys FHL Friedman White AJ 3.31.15 108A-SS LL-H-1
18 2015 – DO x pH Olys FHL Friedman Blue AG 108A-SS HL-L-2 4.1.15
19 2015 – DO x pH Olys FHL Friedman White 3.30.15 SS-103A LL-H-3 Day 3 3.30.15
20 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS-103A LLH-4 3.30.15
21 2015 – DO x pH Olys FHL Friedman White 3.30.15 SS-103B Day 3 LH-H-3 3.30.15
22 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS 103B LHH-4 Day 3
23 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS-108A LL-L-3 3.30.15
24 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS 108A LLL-4 Day 3
25 2015 – DO x pH Olys FHL Friedman White 3.30.15 SS 108B Day 3 LHL-3 3.30.15
26 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS 108B LH-L-4 3.30.15 Day 3
27 2015 – DO x pH Olys FHL Friedman Blue AH 108B-SS HH-L-1 4.1.15
28 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5-103A LL-H1 SS-D5
29 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 103A LL-H-2 D5 SS
30 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 103B LH-H-1 SS D5
31 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5103B LH-H-2 D5 SS
32 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 108A LL-L-1 D5-SS
33 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 108A LL-L-2 -SS D5

 

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Morphometrics – Olympia Oyster OA Larvae

Olympia oyster larvae were measured using NIS Elements-BR (Nikon) imaging software to measure larvae length (hinge to growing edge) and width (10x objective and 10x nosepiece setting on software). Below is a screenshot of what the software, larvae, and measurement controls look like:

Measured 30 individuals from each tube.

The following samples were measured (these are the tube labels; currently not certain what shorthand labelling scheme should be used):

  Box Label Color Tube Label Notes
1 2015 – DO x pH Olys FHL Friedman White/Blue Released: 3.25.15 103B-SS Olys High CO2 3-25-15
2 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 103A HLH-1 3.28.15 3/25/release
3 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 103A HL-H-2 3.28.15 3.25 release
4 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 103B HH-H-1 3.28.15 3/25 release
5 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 103B HH-H-2 3.27.15 release
6 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 108A HL-L-1 3.27.15 3/25 release
7 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 108A HL-L2 3.27.15 3.25 release
8 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 108B HH-L-1 3.27.15 3/25 release
9 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 HH-L-2 3.27.15 3.25 release
10 2015 – DO x pH Olys FHL Friedman Blue AI 108B-SS HH-L-2 4.1.15
11 2015 – DO x pH Olys FHL Friedman White Ap 108B-SS LH-L-1 3.31.15
12 2015 – DO x pH Olys FHL Friedman White AN 108A-SS LL-L-1 3.31.15
13 2015 – DO x pH Olys FHL Friedman White AO 103A-SS LL-L-2 3.31.15

Measurement data is here (Google Sheet): FHL_Oly_larvae_measurements

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Computer Setup – Dell Optiplex 960 for OA System

Dan had been using the Dell Studio XPS 7100 for running LabView to record data from the Honeywell Dual Input Controller for controlling the OA system at Manchester. The computer occasionally failed; it would shutdown, wouldn’t boot and would just produce six steady beeps. Although this behaviour was inconsistent, Dan needs a computer that will always remain on for data logging.

Our departmental computer support person couldn’t diagnose the problem and offered to provide a replacement computer, but only if we purchased a SSD drive for the replacement computer (at a cost of ~$250 for a 480GB SSD drive and adapter).

So, instead of wasting the money (and the continued headache of dealing with our computer support person), I grabbed the Dell Optiplex 980 from FSH 240, backed up the data on that computer (backed up to Nate’s folder on our server: backupordie). I obtained the appropriate license/serial numbers for LabView from the College of Engineering, downloaded and installed LabView 2014 and service pack 1 (SP1).

The old computer was able to boot, so I copied all the LabView files that Dan had previously been using to the Friedman Lab Dropbox and then downloaded them to the Dell Optiplex 980. Additionally, I re-seated the RAM sticks in hopes of making the computer usable again. I have moved this computer to FSH 240 to take the place of the Dell Optiplex 980.

Dan will take the newly configured Dell Optiplex 960 to Manchester to use as a data logger for the Honeywell Dual Input Analyzer and its pH and temp data.

 

 

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Quality Trimming – C.gigas Larvae OA BS-Seq Data

Jupyter (IPython) Notebook: 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb

NBviewer: 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb

 

Trimmed FASTQC

400ppm Index – GCCAAT

20150414_trimmed_2212_lane2_GCCAAT_L002_R1_001_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_002_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_003_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_004_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_005_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_006_fastqc.html

1000ppm Index – CTTGTA

20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc.html
20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc.html
20150414_trimmed_2212_lane2_CTTGTA_L002_R1_003_fastqc.html
20150414_trimmed_2212_lane2_CTTGTA_L002_R1_004_fastqc.html

 

 

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