Author Archives: Casey Jessop

Group Projects

On Sunday we were all able to present to the RCN our group projects! It was a great opportunity to share with everyone our projects and to illustrate what has been keeping us busy these past few weeks.

I thoroughly enjoyed listened to the SeaStar Transcriptome Project. It was great to see how far everyone has come in developing results that are quite substantial and SO AWESOME! Go Team SeaStar! I look forward to keeping posted on their project! They have all been working so hard and appear to continue to work extremely hard to produce more great results!

I was also proud of Team Laby! We presented what results we had to far! And while some results may not be statistically significant, we are seeing trends with both our field and laboratory experiments. So hopefully in the future (once are replicated experiments are finished) we can confirm (with statistics) some of the trends we are seeing :).

Research Coordination Network (RCN)

This weekend we were lucky enough to be involved in the RCN!

Saturday we were able to listen in to some of the most brilliant scientists of today! A wide range topics were  covered and they were all very informative and interesting! Some to note include…

Kevin Lafferty: The Oceans are downstream, economic impacts

Jeff Maynard: Marine Disease Projections

Paul Hershberger: Pathogen persistence and perpetuation strategies in marine fishes: Perspectives from Pacific herring

And these are only a few! Many more speakers spoke that day and they were all AWESOME! It was very interesting to hear about all the research that is currently being conducted ..locally and internationally!

 

 

 

Team L.A.B.B.Y!

Team L.A.B.B.Y! Is working great together! Thursday we set up another Oyster filtration experiment (with a few minor edits). Since then we have been collecting water samples from each replicate from within each treatment to observe whether laby is being filtered out by the Oysters over time. We so far have tested at T0, T8, T24 and we have added another time point of T48. Hopefully we get some good results. :)

GOOOO Team L.A.B.B.Y!

Modelling

Yesterday, we were lucky enough to have Maya give us a lecture on modelling! I thoroughly enjoyed Maya’s lecture and it was interesting to learn new ways to analyse data and predict certain outcomes. After Maya’s lecture we ventured into the computer lab and were able to play around with the program Anylogic which allowed us to look at several different types of models. It also allowed us to change the parameters of the models and to see what changes over time. Overall, I thoroughly enjoyed today and look forward to using modelling in the future. :)

What makes L.A.B.B.Y so unique!

Today, team L.A.B.B.Y ventured down to the lab to prepare for another oyster filtration experiment. This involved measuring the size of oysters, preparing filtered sterile sea water, shucking some oysters and then glueing them back together with nail polish as well as several other little tasks. Additionally, Cody and I spent the afternoon conducting a lit review to gain as much information as we could on wasting disease, eelgrass and L.A.B.B.Y.

I came across a very informative paper that details what makes L.A.B.B.Y so unique. I know we had previously discussed a few characteristics of L.A.B.B.Y like their mucus net but I was curious to know more. Below are some interesting facts I found out about L.A.B.B.Y.

L.A.B.B.Y otherwise know as Labyrinthula zostera is from the Phylum Labyrinthulomycota, which contains both unicellular and colonial microorganisms. This particular phylum is classified alongside the heterotrophic stramenopiles. Other groups include the thraustochytrids and aplanochytrids. What sets these groups aside is that they produce biflagellate heterokont zoospores and their mitochondria have tubular cristae. Furthermore, as previously mentioned this phyla illustrate a mucus net otherwise referred to as an external ectoplasmic net. Their cell walls are also composed of golgi-derived overlapping scales. Labyrinthula species in particular are characterised by their uninucleate spindle-shaped cells which divide to produce colonies. and……that is not all! Read the paper attached to find out more :)

Sullivan 2013

qPCR

Yesterday Amanda, Cody, Lisa and I ventured to Seattle to conduct some qPCR at the main campus!

 

This morning we arose bright and early and started preparing for qPCR. Turns out the method is not as tedious as conventional PCR. Yay! After a first mishap we were able to get some great results second and third time around. YAY! (Pretty graphs to follow soon). Cody and I also did some more DNA extractions on our water and oyster samples. All in all it was a very productive day! We were even lucky enough to venture down to the Abalone tanks! We saw some endangered black abalone and got to get nice and close to the red abalone!

 

We we head back to Seattle tomorrow to reunite with or fellow class members!

 

 

Apples and Oranges

Today, Alison and I spent the morning conquering IPath (HELLZ YEAH)! Below is a snapshot of one of the images generated. The red colour represents Apples (aka “highly” enriched) while green represents Oranges (aka “less” enriched). This snapshot specifically shows how Apples are more common in the Folding, Sorting and Degradation specifically Ubiquitin mediated proteolysis. Screen Shot 2014-08-08 at 12.02.53 PM

After lunch, I started to look through the DEGs (Differential Expressed Genes) in search of unique proteins. The three listed below were proteins I found with a high log2FoldChange of 10 or higher. I have also given a brief description however more research would help understand these proteins more. Also something to note, a lot of proteins with a high log2FoldChange were not annotated and no information was provided……….?

Properdin (Complement factor P): This particular protein is known to participate specifically with immune responses, playing a part in tissue inflammation as well as engulfing of pathogens by phagocytes. It is also believed to help neutralise viruses.

Interleukin 6 receptor: This particular protein regulates cell growth and differentiation and is known to play a important role in immune responses.

Matrix Metallopeptidase 13 (Collagenase 3): This particular group of proteins are known to be involved in the breakdown of extracellular matrix in normal physiological processes including reproduction, tissue remodelling and disease process such as arthritis and metastasis.

Viral Pathogens

Yesterday we also had a lecture on Viruses! Just thought I would reiterate the special characteristics which make viruses so unique!!!

– Outer protein casing (Capsid)

– Some have cellular membrane made from the host

– Rely on the metabolic machinery of host cells.

– Contain either DNA OR RNA (not both)

– Can trade genes between own DNA/RNA and host DNA/RNA