I’m allowed to have an opinion, and I think that people just sound ridiculous when actually saying “hashtag.” Call me old fashioned, but I prefer to save it for the post.

Up until now, I was under the impression that the DIG-labeled probes were the colored component used to stain the slides where pathogen DNA was present, but I was mistaken. The DIG probes are actually synthesized […]

We needed to make up some probes for the RLO-infecting phage, so it made sense to hold off on running ISH on our sea star probes until we could run the RLO batches with them. The control tube for the probe boiled […]

Listening to the talks at the RCN meeting, I was both surprised and pleased by the many different perspectives they had invited to speak. The topics ranged from diagnosis to forecasting to policy and more. I’m […]

We reran our probe synthesis PCR to replace the control probes that had evaporated in the thermocycler during the last round. This time we were successful in getting both the DIG- labeled probe and the unlabeled […]

We reran our probe synthesis reactions this morning. Comparing reaction conditions of the different kits, we concluded they were essentially the same, and we should continue using our original probe synthesis kit. […]

Our probe synthesis for the sea star ISH doesn’t seem to be working. We tried to synthesize probes two different times, and neither the probe nor the plain dNTP control showed up in the gel. However, a band of DNA […]

To run ISH, we need to synthesize probes that will tell us when our DNA sequence of interest has bound to the DNA on slides of our samples, indicating that the pathogen gene (can we say pathogene for short?) is […]

Dissecting the Sea Star Transcriptome

Here’s my video for week 3. Enjoy!

It’s nice when you have a lot of people power to accomplish a lot of pippetting at once, but there is a point at which there are too many people in the small lab space to be effective. We found out that number is […]

We’ve divided up into groups to make the most of the sea star genome. Our group is trying to characterize which biological processes are present in the genome regardless of health, so we are not looking with […]

My notebook for 8-7-14

We mainly focused on exploring graphics this session. The overload of SQL Share and Galaxy made it hard to do much else, but there is still a lot of manipulation that can be done with the […]

I’m putting this first, since this is where the class is most likely to see it. For the graph nerds out there: HIMYM Venn Diagram and Charts and Graphs (both ~15 seconds). We should all make our pie charts with […]

After using SQL share to join the results of our BLAST file to Steven’s GOSlim terms, we were able to get an idea of what the different sequences did and what organisms they were associated with. The sequences can […]

Today was my first attempt at working with ipython. We ran a blastx search on the sea star transcriptome sequence, which took up a lot of server power, so only one person really should have done it. We learned how […]

We collected a series of different tissues from the sea stars found at Ruby Point: tube feet, digestive caecum, armpit dermis, nerve tissues from the top and bottom of the arms, and even coelomic fluid. We also […]

Today we saw slides of sick and healthy sea star tissues. The most interesting slide had karyorrhectic tissue, which looked like the nucleus of a cell had been turned in to buckshot. The only other abnormalities […]

We removed the oysters from our seawater beakers, taking water samples before and after shaking off fecal material to count the laby concentrations later. We are also looking inside the oyster tissue itself for […]

Our oyster filtration experiments need to start with equal concentrations of laby in the treatments that require it. The only problem is that laby tends to clump on the walls of containers, making their […]

While the global prediction of ocean acidification in open water predicts CO2 increasing the acidity to an already shocking number, coastal waters can have even lower pH due to a number of local […]