2 17 2015 Bioanalyzer Results for BS Libraries

Today I was able to look at the bioanalyzer data that Sam sent me. It looks like most of the samples failed. A couple of the samples had very small peaks between 300-500 bp but they were basically negligible. You can also see some faint smearing in those regions in the gel view but again there was so little material that it probably not possible to retrieve any useful data from them.

Gel View of the Bioanalyzer data. 

Electropharogram View, minimal peaks seen

Electropharogram View of the 3 samples with noticeable peaks. 

8 19 2014 ImageJ Analysis

FTR 230

Hi 60s to low 70s sunny

Participants: Sam Adams and Jake Heare

Sam showed me how to do the ImageJ measurements on the trays today as well as complete several of the trays. The procedure is quite simple.

1. Open original image in ImageJ
2. Select line tool
3. Using on tray size standard (calipers or tile) draw a line
4. Click M to save after each measurement
5. repeat this 5 times on the size standard
6. On each oyster start at the edge of the umbo and draw a line to the furthest point on the bill. 
7. Click M to save each measure
8. Proceed measure all oysters in a logical manner from left to right in each quadrant. 
9. Once all have been measure click Save As in Results window
10. Save file with the tray label followed by date followed by the word Raw.
11. Open file in Excell
12. To get the size conversion you must average of the first 5 "Area" measurements.
13. Then divide the known size of the Size standard. (10 mm on calipers, 6 inches for tile) by the average you get from the firt 5 measurements.
14. Using the conversion ratio you can then multiple each ImageJ "Area" measurement by the conversion ratio. 
15. On the right side of the spreadsheet dedicate 5 columns to the measurements
16. Column 1 (C1) = Date, C2 = Tray, C3 = Oyster Number, C4 = Area measure, C5 = converted area measurement
17. Fill in columns with appropriate info
18. Save file as Excel workbook in eagle/dermochelys/ImageJake with just the tray label and date info
19. Copy and paste the 5 right side columns into the google sheets master document on Google docs
20. Repeat process for each image. This should create two files for each image, a raw data and a converted data file. 

Reproduction Survey Spring 2014 Standard Operating Procedures

SOP Anesthesia Procedure for Brood Check/Collection

1 stack consisting of 1 tray from each population is pulled out of the water where they are held for anesthesia. The stack will be different each week until all 4 stacks have been checked and then the process will repeat starting with the stack that was checked first.

Two of the trays are placed individual in roughly 10 gallons of ambient sea water in 2 twenty gallon pools.

The third tray remains outside side of the pool for approximately 45 minutes to deprive the oysters of oxygen.

Once the 45 minute mark is reached the tray is then placed in 10 gallons of a 50/50 seawater/85 g/L epsom salt freshwater mixture. These animals are then allowed 45 minutes to open up inside the treatment. Once open the animals are anesthetized by the epsom salts and remain gaping until flushed with sea water.

While the first tray is being treated the second tray is being dessicated. This repeats with the second tray treatment and the third tray dessication.

The animals are then visually inspected for signs of larvae including a grayish mass in the gills or on the lower deep cup of the shell. If anything suspect is seen, these animal is then flushed with seawater into a 52 um screen to capture any possible larvae. If larvae are present, they are washed off the screen into a 50 ml falcon with 75% Ethanol solution for preservation.

After all gaping animals are inspected, a quick count of all dead, gaping, and brooding animals is performed. Then the tray is placed in a pool of fresh ambient sea water to help the animals recover and avoid dessication until the process is completed for all trays being observed.

Once the final tray has been surveyed. The trays are then randomly organized back into a stack, secured to the hanging rope, and then returned back to their holding area.

Any brood collected will be brought back to the lab and have their solution switched out with 95% Ethanol.