Saturday, December 5, 2015

Hello Interwebs!

I have finally thwarted my own ineptitude and managed to log in to my account- Hurrah!  This is despite google rather unnervingly disagreeing about my mother's maiden name... Do they know something I don't?!

So back on the hamster wheel of science, I was about to explain how my project all kind of fits together by putting it into context with the genome- this is the DNA that makes up the chromosomes of living cells. Rather than a full description of an organism, genomic DNA contains a “how to guide” to building the organism.  This allows each cell to produce the proteins necessary for it to make the jump to the next step of it’s development.  Once it reaches this point it is able to read the DNA which instructs it on the next step yet again.

These “instructor proteins” are called transcription factors. They act as bookmarks binding to particular regions of DNA and marking it to the cell whether to “read” a (generally) neighbouring sequence or not, at a particular time or in response to a particular situation.  For instance, when we get a cut, transcription factor proteins will be made that specifically bind the genome such that the cell is instructed to make further proteins including ones involved with wound healing and immunity.  This allows a small number of transcription factors to bookmark a huge number of target sequences across the genome.

One aspect of my project is to investigate were my transcription factor “bookmarks” the genome, however what I am working on in the US of A is how this bookmarking relates to biological function- ie what do the cells actually end up doing and interacting within the embryo.

A key part of understanding how a collection of cells behave is to see how they interact with other cells that express a different pr overlapping set of transcription factors. For instance by comparing the cells that make bookmarks for brain formation how do they interact with cells that make nerves? Are they originally the same cells? If so when do they separate into different cell types, and can they change back?

Because genomic DNA is a series of instructions on how to make the next step it also instructs cells on how to diverge or differentiate into different cell types.  So as the embryo grows the amount of cells in it increases and the amount of cell TYPES increase too.  This is achieved by using a range of different bookmarks in different combinations.  By attaching fluorescent tags (like microscopic glow sticks!) we can identify which cells are using and making these transcription factors or key proteins.

Currently I’m using this cellular glow stick party to see how different cell types move and change within the embryo.  Initially I looked at how cells that make a fluorescent factor that bookmarks genes required for vessel formation (ie for blood or lymphatics) compares to my protein, which has a different colour glow stick and is thought to bookmark early blood and vessel genes.

What we can see down the microscrope is incredibly beautiful and I could stare at all day.  The majority of a PhD project generally involves working your ass off and having to wait months or years to see any result.  Seeing these embryos forming their blood vessels, heart field and blood cells, is incredibly worth it.

As I progress I hope to look at more combinations of these transcription and signaling factors and see how the cells that make them interact with my cells of interest.  The goal of this is far more than just pretty pictures- this will help us understand the contribution of each factor to the formation of the circulatory system of vertebrates.

Outside of the microscope room, I've just seen Spectre at last.  I'm pretty sure I enjoyed more than I would have done normally back in the UK- just letting the british accents wash over me was a treat!  Also I grew up about half a mile from where they filmed some of this, which gave me lovey warm fuzzy feelings seeing Daniel Craig strutting around my home turf :)  However it did make me realise that being over here may have strengthened my British mannerisms and accent even further, so please don't tease me when I get back and I'm painfully and stereotypically British.  My lab at home teased me very early on for picking up the American pronunciation of "tomato" so I blame them for my rebellious retaliation the opposite way.

Anyhoo, TTFN

Tuesday, November 10, 2015

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,

Wednesday, November 4, 2015

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!


Friday, October 30, 2015

Day Four- Inject some energy into the week.

Happy Thursday people of the web-world!

Over here I've had very busy day full of challenges and thankfully some accomplishments to keep my spirits up!  But I'll save the tales for another day- bear with me :)

However in a few hours I hopefully get to see all of the lovely ladies of the TSS lab back home in Oxford as I call in for our technical meeting.  This means a distressingly early start- but I do get to show them the work I've done so far and get their input, most likely while I wear pyjamas and try out something called "pumpkin pie".  If only all meeting could be this way...

Peace and Love,

Wednesday, October 28, 2015

Day 3- Mounting the challenge!

Well done on sticking with me- if anyone has! I can live in hope…

Today is an awesome day.  I’m sure I will look back on it and think how menial today’s accomplishments were but for now I’m going to live in the moment.  As I’ve previously discussed I work with fish, but I missed out the part where they GLOW :)  I will get back round to that- I promise, but tonight I’m going to keep it brief.  I think my fish are possibly the most beautiful things on the planet, of course I do they are my molecular biology babies, however even other people think they’re pretty too.  Today I was shown how we are going to use a very powerful microscope to look at how cells that contain my protein move and divide into more cells, in the head of a fish embryo from approximately 12 hours old.  This had many steps to get the perfect picture and although I didn’t get a cover shot, I’m starting to understand the process of how to get one.  
A key task is getting these baby fish to be in the correct position, without mushing them.  At this stage they are about the size of an uncooked piece of couscous (#OverheardInWaitrose) and about the consistency of toothpaste contained within a tiny tissue paper bag- yep pretty mushy.  In the wild these fragile embryos are contained within a protective case called the chorion, which they eventually hatch out of much like a chick out of an egg, we have to remove these chorions so we can closely look at the embryo.  Anyway I’ve been practicing how to put these embryos into a special type of jelly that gently holds them in place, is translucent so we can see the embryos and still allows the embryo to grow- this is called "Mounting".  I still need to polish my embryo-orientation skills, but they are a lot better than they were this morning!  I also practiced getting these embryos out of the jelly and cleaning them off so that they can continue to grow up happily to adult fish, this actually went surprisingly well and they are all still happily swimming in their dish now several hours later.
As with anything that involves a computer, the next task is getting it to play ball, today ours was more in the mood for being a bit stubborn, but my supervisor over here fixed it in the end- hurrah!  Yes- regardless of complexity the computer specialist will always recommend turning it off and then turning it back on again.

As our prize for bearing with it, we now have a 3-dimensional video of the Scl-containing cells moving in the head of the zebrafish as it develops (grows/matures) over a 4 hour period- IT IS FANTASTIC (to me, at least). We can resolve for the first time exactly how these cells are arranged at this early stage and can even follow individual cells as the move around the head of the fish.  Already this has thrown up some interesting questions, that I’m keen to delve into over the coming days.

However students can not live off data alone, so I am off to hunt & gather and get some sleep so I’m ready for what looks to be a good day tomorrow.

On a side note today was actually quite chilly, so some of the clothes I have brought with me might actually be suitable on this trip hurrah!  And by chilly I mean 25 degrees Celsius rather than the 32 degrees we had at the beginning of the week, which is just unnecessary really.  Also on day three of trying to get a bit fitter, let’s see how long I can resist the multitude of temptations that American bakeries have to offer…

Over and out,


Tuesday, October 27, 2015

Day 2- Finally fish!

Welcome back! I hope you've had a great day out there and are ready for another peer down the microscope into my adventure. By now you may be wondering why all the fish references- well this is because I study how the protein Scl works in zebrafish. These small freshwater fish have beared with me through the trials and tribulations of my PhD research and are definitely one of my favourite aspects of my project. 

When someone tries to work out how something works there's a lot of tinkering plus trial and error that goes on. My project is aiming to understand how the blood and circulatory system forms in the embryos of vertebrates, so in some way I need to poke around with the inner workings of this complex mechanism, to see how everything fits together. 

Fish are a fantastic choice for this type of research as they offer a balance between ease and relevance/morals. For instance if you're going to investigate how a Ferrari engine works, the most relevant model to work with is a Ferrari, however there aren't that many of them, they're super expensive and some would argue that taking a Ferrari engine to pieces is morally wrong. At the other end of the scale we have the wind-up toy car- this costs practically nothing, they are easily available and no one is going to be upset when they get taken to pieces. However a toy car really is nothing like a Ferrari, yes it has wheels, axles and cogs like the Ferrari but how these are arranged are completely different. 

In this analogy the Ferrari is like a human, if we want to understand our own biological processes and try out disease treatments the most accurate test subject is a human. However some people frown on cutting up babies for research... Ptsh!!  The toy car on the other hand is like a very simple organism such as yeast- these are single celled fungi so more complex than bacteria but still a huge way off humans. We can learn some basic principles from studying them but these may not be conserved (i.e. the same) in more complex organisms such as mammals. 

So back to the fish. Fish are like mopeds (small petrol driven bikes). They look completely different to a Ferrari but actually share a huge number of features such as pistons, brake systems and a petrol driven motor. What we discover in zebrafish is likely to be strongly related to the same process in humans, especially the key components which are crucial for the function of the motor/ survival of the animal. 

A pair of zebrafish can lay hundreds of embryos every week and these reach maturity (i.e. can lay embryos themselves) at roughly three months of age. Another great feature of fish is how the zygote (fertilised egg) is formed: zebrafish are "scatter spawners" so embryos are formed outside the body of the adult and can easily be collected for study without any harm to the adult. In mammals however the embryo grows within the mother so to study these really crucial and early stages the embryos have to be removed from the mother- often harming all those involved.  The embryos also develop on a very pleasant time frame- by 24 hours one cell has divided and differentiated (developed into a variety of tissue types) sufficiently for a functioning heart to start circulating blood, eye and ear have formed and the tiny fish can start to beat its tiny tail (ahh cute!).  A major bonus of fish research is it's much cheaper and easier to maintain 100,000 zebrafish than 100,000 mice, thus research funding can go much further. Finally zebrafish embryos are see-through so we can see all the internal organs developing, blood circulating and the heart contracting without any need to dissect or treat the embryo. Only at 3-4 days post fertilisation so they start to loose their translucent nature. 

All round zebrafish are pretty damn awesome. 

Basically that's why today I am happy that my fish, who have been living out in L.A. for five months, have finally started laying fertile embryos of their own. This means tomorrow I will be able to look at them under the microscope and hopefully get some pictures for you guys. 

'Till then be most excellent to each other, 

ps: in no way do I condone testing on human children, even if they are screaming and disgusting germ-ridden little brats.  Their parents are probably more suitable anyway...

Monday, October 26, 2015

Hello interwebs!

Hello All,

Welcome to my blog, this is my first time blogging so bear with me as I recount my tales of scientific endeavour and exploration of the mighty city of Los Angeles!

I'm one very lucky grad student, who with five months left to complete my PhD at the University of Oxford, has come to L.A. to undertake a fantastic 2-month project working with collaborators at the University of Southern California (USC). Back home at Oxford my research has focused on elucidating the role of a crucial protein, called Scl, in the formation of blood and blood vessels as a vertebral embryo grows.  Without Scl mice embryos die of anaemia as the blood doesn't form and blood vessels fail to properly join together to make an ordered circulation system.  This shows how important this protein must be in the complex process of producing a fully functional circulatory system.  Interestingly in humans having too much of Scl in certain immune cells causes them to multiply out of control and leads to T-cell Acute Lymphoblastic Leukaemia , a devastating form of blood cancer.

I have being trying to work out how Scl functions at early stages of the growth of zebrafish embryos, this is within 1 day of the eggs being fertilised.  Scl and the other factors it has so far been shown to interact with, are very similar and seem to act in the same fashion in zebrafish as in humans.  This means that anything we can learn in zebrafish is likely to be relevant to treating human conditions.  Studying how a single fertilised egg develops into a fully formed adult creature, is not only interesting for furthering our understanding of life, but also has potentially huge medical benefits.  If we can work out the necessary steps for a whole organism to arise from a single cell, maybe we can partially reverse it.  Many diseases are linked to ageing, such as cancer, Alzheimer's, COPD and certain organ failures. If we can understand how factors such as Scl are involved in the formation and maintenance of crucial tissues, such as blood vessels, we could potentially use the correct combination of drugs to promote growth or healing of crucial blood vessels.

So over the next few weeks I will try to explain how the research I am undertaking out here in sunny L.A. will help us progress towards a better understanding of how Scl functions in vivo (in living animals).  Hopefully this will be interesting for you and will certainly help me organise my thoughts for writing up my research into a thesis!

Till tomorrow, 
TTFN (Ta-ta-for-now = goodbye)