Hard Clam Challenge – QPX Strain S-1

Challenged 2 FL hard clams and 1 BX hard clam with ~100uL of unwashed, 11 day old cultures. 2 FL hard clams and 1 BX hard clam received ~100uL of QPX media, as controls. Injections were done through the hinge using 20G1 needles and aimed for the pericardial cavity. After injections, clams were left out of water for 1.5hrs, then return to small containers of sea water. They will be incubated for 24hrs.

MBL Shipment – Hard Clam gill tissue in RNA Later

Received samples from Scott Lindell today. Two Ziplock bags taped together labelled “11/16/09 Clams scudders.” The bags contain 2mL screw cap tubes with small tissue samples in RNA later. One group of tubes is labelled with FL-3 # and the other group with BX-4 #. Samples will be stored at 4C to be processed later this month.

MBL Shipment – Sepia tissue samples

Received sepia tissue samples in RNA Later from Kendra Buresch. Here’s the list of tissue we received, according to the Post-It with the samples:

  1. 4th arm

  2. ventral mantle center

  3. ventral mantle side

  4. fin

  5. dorsal mantle center

  6. dorsal mantle side

  7. retina x 2

Samples were temporarily stored @ 4C. Will discuss with Steven on long term storage (if necessary).

MBL Shipment – Hard Clams

Received hard clams from Scott Lindell today. Two bags. One group (4 live clams, 1 empty shell) labelled as “FL” and another group (9 live clams) labelled as “BX.” Clams were transferred to separate plastic shoebox containers with sea water and sand. They were stored at 15C until ready for experiment.

Herring 454 Data

Data from MoGene was received today on two DVDs and one HDD. Data is two runs of two libraries, due to MoGene concerns that the data of the first run looked bad (too few reads). They performed a second run at no charge and provided us with that data as well.

 

UPDATE 20150310

Data is located here: http://owl.fish.washington.edu/nightingales/C_pallasii/

PCR – “Unknown” Dungans/Lyons

This is a repeat of yesterday’s set up with LABY primers, but with an annealing temp of 53C in hopes of improving the number of amplicons generated from additional samples. See yesterday’s PCR run for info on samples.

Results: Samples were loaded 1-29 and three negative controls from left to right, top to bottom.

The lower annealing temperature clearly resulted in more products. The ~500bp band was cut from each lane and stored @ -20C. All bands will be purified using Millipore spin columns and then sent for sequencing.

PCR – “Unkown” Dungans/Lyons

This was done on the numbered tubes using the LABY A/Y primers for eventual sequencing. Turns out many of the tubes have some info (other than just a number) on their sides which might provide more information regarding which isolate they actually are. PCR set up is here. Annealing temp 55C.

Tube-# Side Label
1 VA1423-1
2 VA1423 2CB
3 VA1423-3
4 VA-1423 4
5 VA1423-6 6
6 VA1423-10
7 VA1423-12
8 VA1423-15
9 VA1423-26
10 VA1423-28
11 VA1423-290 2003 Isolate
12 VA1423 29 2004 Isolate
13 VA-1423-33
14 VA1423-37
15 XMAC13T
16 X-MAC-19T
17 XMAC 20T
18 X-MAD 10T
19 X-MAD-14T
20 X-MAD-18T
21 XMAE 11T
22 XMAE 13T
23 BC05CA8T
24 BC05CA 15T
25 BC05CA 18T
26 BC05CA 20T
27 98 MFS 61A
28 CRT W 1HE/H11
29 CRSH 5B3

Results: Samples were loaded 1-29 and three negative controls from left to right, top to bottom.

There are four prominent bands from Tubes 23, 27, 28, 29. These four bands were excised and purified with Millipore spin columns according to protocol. They will be sent for sequencing. There are faint bands visible from Tubes 9 & 11. Due to the faintness, they were not excised as there may not be enough product for sequencing. The remainder of the samples failed to produce any amplicons.

Hard Clams – Shipment from Rutgers

Received Hard Clam gill samples on “wet ice” in RNA Later from Rutgers. Samples were collected on 11/4/09 (clams held in refrigerator) and preserved (gill tissue collected) on 11/9/09 according to the paper included with the samples. Samples will be stored @ -80C until we are ready to process.