Day 16- Data data data!

So I'm back to the blog- the supervisor is away so the mice will play... with RNA-Seq data!  To set the scene for this and pretty much the whole approach to my project I'm going on a descriptive analogy ramble as we zoom in on what is going on in all of us at a molecular level.
So all of us as animals are made up of
Systems- these are important features that lead us not only functioning but out-competing other species. Going back to the car analogy, this is like the entire brake system, or the lights & wiring or the engine, and just like each of these, a system is made up of smaller key parts. In a living creature these are
Organs and tissues- an organ is a collection of tissues that act together to make a functional unit all in one place, such as the heart, lungs and brain.  A brake caliper would represent an organ, made up of lots of smaller bits of mechanics, while brake fluid vessels would be the supportive tissues, that link it up and form the system.  All of these tissues are made up of collections of specialised cells.
Cells- sadly this is as far as I can stretch the straight up car analogy, but bear with me I hope this doesn't get too trippy! A cell is actually a little bag of awesomeness. Every living thing is made up of cells (Don't mention viruses...) from bacteria living in the bottom of the ocean to mushrooms, to tangerines to hedgehogs and humans too. Bacteria are cells basic and lack a lot of the complexity that plant and animal cells have evolved, but they still use the same basic principles, which I will shortly introduce to you. So lets imagine each cell is a tiny factory that makes the component that is needed for a specific part of the brake caliper.  It takes lots of tiny factories working together to produce enough to be useful, these factories working together are like the specialised cells that act together forming a tissue.  
The factories (cells) actually produce lots of little parts that are assembled to make the component- so every factory produces the correct balance of springy bits, curvy bits, hinges and bolts, so that the component can be formed efficiently by these factories. Each of these bits are analogous to PROTEINS- now these are the things you hear about in ridiculous shampoo adverts. 
Proteins are little widgets, we think we have over 20,000 different proteins in humans, with each cell (factory) making a subset of these widgets.  The particular combination of widgets a factory makes, determines what component it will produce- just as the levels of each protein a cell makes determines its identity and what tissue it should contribute to.

I'm going to take a pause here because I think that's plenty enough mechanics for one night, but bear out my explanations and you may get to understand both car and molecular mechanics!

On a side note I have come to realise that I have an addiction to a soda they have over here called HiC- it's basically vitamin C enriched Um Bongo! Yum but so addictive. So if I'm a bit hyper upon my return to jolly Britain it's probably the combination of a small sugar farm flowing through my veins and a super boosted immune system- hoorah!

Peace, Out,

Day 9- Time for some Movement

Hi y'all,

After a bit of a busy few days I'm back to the blog.  Today I was able to use our 780 microscope to image the cells in the head end of my fish as they move to form immature blood, immature blood vessels and the central layer of cells in the developing heart called the endocardium. This is totally awesome in its own right, but I got to do a significant part of this process myself under the supportive guidance of my supervisor.  Those of you who know me and my strengths- sophisticated microscopy really is far far from a strength or even a capability for me.  This made today even more special for me as I was learning and practicing a fantastic technique while collecting impressive and beautiful data.  Working in science may not be the most financially rewarding but it really has the potential to be one of the most rewarding vocations.  Obviously I'm saying this at the end of a day spent capturing the most beautiful movie of my career to date, not at the end of a fruitless day adding colourless liquid to another colourless liquid, of which there are many to bear in a PhD.  

This wasn't even the time course (movie made from a series of images) we had intended to capture, or the backup, this was plan C!  Yesterday I prepared embryos that would have my cells of interest (the ones that contain the Scl factor) labelled in green, the outer edge (membrane) in bright blue and the nucleus (the bag of DNA in the centre of a cell) in red.  Sadly we couldn't separate the signal from our green cells from the blue signal made by every cell- the head of the fish looked amazing but had no scientific relevence- poop.  Cliche- but beauty really isn't everything!

Toodle-pip,