At 8:30 I did water quality testing. The Left tank was at 30ppt salinity, 7.8 pH, 80 Alkalinity, 0 ammonia, 0 nitrite, and 40 nitrate.
The right tank was at 30ppt salinity, 7.8 pH, 80 Alkalinity, 0 ammonia, 2 nitrite, and 40 nitrate,.
The yellow tank was at 30ppt salinity, 7.8 pH, 80 Alkalinity, 0 ammonia, 0 nitrite, and 0 nitrate.
Recent Updates
Testing cleaning methods to remove resazurin
5/21/26
At around 9:30 I set up containers to test cleaning methods for removing residual resazurin from plates.
- Container 1: 10% Clorox bleach and 90% tap water. (Plates M, E)
- Container 2: 10g Alconox in a liter of tap water. (Plates B, C)
The plates will soak for 15 minutes in the different solutions. Plates M and E are soaking in bleach, plates B and C and soaking in the Alconox. After rinsing plates, the plates will be filled with 4 ml sea water with an oyster placed in each well, and left in the incubator overnight. Plates I and K have been rinsed with just tap water, and will be filled with oysters in seawater, and left in the incubator overnight as well.
-Bleached: M,E
-Alconox: B,C
-Tapwater rinse: I,K
As the plates soaked in Alconox were soaking they let off a pink color, (it appeared only B was letting off pink color not C)
5/22/26
Around 4 pm I took the plates out of incubator. Only B (Alconox) was pink. The other Alconox soaked plate, plate C had no pink color, though C was the one that turned pink in the Alconox yesterday while B did not appear to give off color.
The bleached plates (M and E) had no pink color, as did the plates only rinsed with tap water (K and I).
I am now soaking all the plates in 10% bleach solution for 15 minutes and will rinse and leave them to dry.
Multiple plates gave off pink color in the bleach solution.
Why did plate C give off pink in the alconox and not after in the incubator, while B appeared to give off no color in the same alconox but then turn pink in the incubator?
Why did the plates only rinsed with tapwater not turn pink?
Water quality testing
5/20/26
At 12:30 I did water quality testing. The Left tank was at 30ppt salinity, 7.8 pH, 120 Alkalinity, 0 ammonia, 0 nitrite, and 20-40 nitrate.
The right tank was at 30ppt salinity, 7.8 pH, 80 Alkalinity, 0 ammonia, 1 nitrite, and 20-40 nitrate,.
The yellow tank was at 30ppt salinity, 7.8 pH, 80 Alkalinity, 0 ammonia, 0 nitrite, and 0-5 nitrate.
36C repeat exposure 7
5/20/26
Seed were held in Right blue tank (36C cup), 30ppt prior to 36C temperature exposure
Water temperature measured with a glass thermometer
Water temperature was set to 37 °C using a water bath (glass beaker with 30 ppt for clams from a 36 °C cup; the surrounding bath was DI water)—the incubator heats the water in the glass beaker ~1 degree lower than is set.
15 clams were placed in a 36 °C incubator in a water bath for 2 hrs
actual water temperature upon removal from incubator: 35.5 °C
Upon removal from the incubator (prior to transfer to recovery), 15/15 had closed shells.
-Immediately following transfer to recovery: 15/15 had closed shells
-5 min following transfer to recovery: 15/15 had closed shells
-20 min following transfer to recovery: 15/15 had closed shells
-24 hr following transfer to recovery: 11/15 had closed shells, 4/15 had slightly open shells with siphon extended. No clams initially had an extended foot. All clams were poked with a dissection probe, 3/4 open clams responded to contact with the dissection probe by closing and fully retracting their siphon; 1/4 remained open with siphon extended. 5 minutes post-dissection probe touch, 1/15 had an open shell with the foot extended
-48 hr following transfer to recovery: 14/15 had closed shells, 1/15 had open shells with only siphons extended. All clams were poked with a dissection probe. The open clam did not retract its siphon. 5 minutes post-poke, the clam with an extended siphon lost the tip of its siphon (pictured below), and afterward the same clam extended its foot.
All clams (n=15) survived the 36C repeat trial 6
Glycogen-Glo Buffer Testing pt.2
Yesterday, I ran a second test on new Glycogen-Glo buffers, to confirm results from a previous assay last week. This previous assay had much lower luminescence values than I had seen with buffers provided along with the assay kit, although the relative values (fit of the standard curve, calculated sample values) were relatively consistent with previous assays.
To more rigorously test the new buffers, I ran parallel assays with these new buffers and the Promega-provided buffers on one previously-analyzed sample (0.0A*) and one new sample (0.0B**).
Surprisingly, both buffers returned similar results in the higher luminescence range that I have seen consistently with the Promega-provided buffers (see standard curves below). As shown in the table below, the calculated levels of glycogen and glucose in the samples were also relatively consistent between buffers. I’m not sure what to make of the dramatic change from my previous assay, but this seems to suggest that the new buffers are working well. I may run a third test to confirm that these new results are in fact accurate.
Table:
Standard curves – old buffers:
Standard curves – new buffers:
Data Reorganization
Recently I’ve been looking more at reorganizing and reprocessing my data. The reason for this is because while some of the sections of the BLAST Format-6 output are not currently of use to me, I have learned that they may contain information which will become of use to me later in data processing or in data validation (i.e. showing how well a transcript has mapped to the database). For this reason, I have been transferring some of this data from the output storage folders on my computer into Excel tables, as I happen to find Excel to be a very efficient way to look at my data.
Introduction and First WordPress Post – Samuel Slutz’s Lab Notebook
Hello, my name is Samuel Slutz, I am an undergraduate lab member studying sea star wasting disease. I’m specifically looking at the differences in the transcriptomes of three starfish species Dermasterias imbricata “leather star”, Pisaster ochraceus “ochre star”, and Pycnopodia helianthodes “sunflower star”, when exposed Vibrio pectenicida FHCF-3, the bacteria which causes sea star wasting disease. Since these different species have varying susceptibility to sea star wasting disease, with the leather star being highly resilient to it and the sunflower star being particularly sensitive to the illness, studying how their transcriptomes vary can allow us to pinpoint certain genes that may improve resilience, thus informing how we can potentially help starfish like the sunflower star to better resist sea star wasting disease as part of our efforts to recover their populations.
34C repeat exposure 7
5/18/26
Seed were held in Right blue tank (34C cup), 30ppt prior to 34C temperature exposure
Water temperature measured with a glass thermometer
Water temperature was set to 34 °C (36 °C setting on incubator) using a water bath (glass beaker with 30ppt for clams from 34 °C cup; the surrounding bath was DI water)
15 clams were placed in a 34 °C incubator for 2 hrs
actual water temperature upon removal from incubator: 33.5 °C
Upon removal from the incubator (prior to transfer to recovery), 15/15 had closed shells.
-Immediately following transfer to recovery: 15/15 had closed shells
-5 min following transfer to recovery: 15/15 had closed shells
-20 min following transfer to recovery: 15/15 had closed shells
24-hr following transfer to recovery 8/15 had closed shells, 7/15 had open shells with siphon extended, . 9/15 open clams responded to contact with the dissection probe by closing and fully retracting their siphon. 5 minutes 6/15 had closed shells, 8/15 had slightly open shells with siphon extended, 1/15 had open shell with siphon and foot extended
-48 hr following transfer to recovery: 2/15 had closed shells, 8/15 had open shells with only siphons extended. 5/15 had slightly open shells with mantle exposed. All clams were poked with a dissection probe. 14/14 open clams responded to contact with the dissection probe by closing and retracting their siphons. 5 minutes post-poke, 8/15 of the clams were open again with only mantle exposed, 7/15 had closed shells.
All clams (n=15) survived the 34C repeat trial 6
Water quality testing
5/18/26
At 12:30 I did water quality testing. The Left tank was at 30ppt salinity, 7.8 pH, 80 Alkalinity, 0 ammonia, 0 nitrite, and 20-30 nitrate.
The right tank was at 30ppt salinity, 7.8 pH, 80-120 Alkalinity, 0 ammonia, 0 nitrite, and 0-10 nitrate,. The yellow tank was at 30ppt salinity, 7.8 pH, 80-120 Alkalinity, 0 ammonia, 0 nitrite, and 0-10 nitrate.
Water quality testing
5/14/26
At 12:30 I did water quality testing. The Left tank was at 30ppt salinity, 7.8 pH, 0 ammonia, 0.25 nitrite, and 30nitrate.
The right tank was at 30ppt salinity, 7.8 pH, 0 ammonia, 0.25 nitrite, and 20 nitrate. The yellow tank was at 30ppt salinity, 7.8 pH, 0 ammonia, 0 nitrite, and 0 nitrate.
Roberts Lab 
