So you’re thinking about doing a PhD, eh?

It’s that time of year, the undergraduates are finished and wondering what to do WITH THE REST OF THEIR LIVES OH NOES! So a number of them have been directed to me, and told “ask her what it’s like, see if she’d recommend it”. I shall restate most of my advice below, for those of you who haven’t got to hear it from my face and because, apparently, it’s not bad advice.
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Phospholipid bilayers made easy

Some scientists are artists, I am not one of these. Sadly, that doesn’t get me out of making diagrams to explain my work.

Some glycoproteins (proteins with sugar groups attached) sitting pretty in a phospholipid bilayer (that twin layer of pink circles with tails).

My work deals primarily in cell membranes. Glossing over the details, these can be condensed down to some proteins lodged in a phospholipid bilayer. The proteins are drawn when needed, but the bilayer occupies all the other space and its many repeating units need to be drawn to make sure the illustrated cell doesnt spill its contents into the extracellular space… (ok, that won’t actually happen, but the membrane still needs to be drawn).

Phospholipids are generally drawn the same way, circle for the phosphobit (it’s a short charged group) and a pair of long tails for the lipid part (very hydrophobic). So the phopho head points into the aqueous compartments (the cell interior or the external environment), and the lipid tails of each layer point toward each other (like oil and water, these lipid tails like to stay away from water too).

So how did I draw them I hear you say, by using the awesome free, opensource image editing software that is the GIMP (runs on any platform too, so give it a try).

First thing I did was draw a phospholipid unit with a transparent background and zealous crop so the edges of the image are tight with the drawing. Then I saved it to my images folder (as a .xcf for later use) and to my brushes folder as a .gbr (on linux it’ll be in the .gimp directory). Then when you go to the brush tool, hit the “brush” box in the tool box, then down the bottom right “open brush selection dialog” and hit refresh. Your new paint brush should be ready for use.

There are two options to consider then, the spacing between the brush images and the scale of the image. The scale is pretty easy to figure out, resize until you like the size of it. The space is measured in percent (be nice if they pointed that out more clearly), as you dont want your phosopholipid units overlapping, go for 110% or greater.

You can then draw with the phopho-brush. You can stamp it one piece at a time, or if you draw a curve, the image will be spread across it and spaced by your chosen percentage. You can also use it to stroke a curved path, which is what I ended up doing, very handy (just set the paintbrush settings before you select stroke path). I made two phospho-brush units, one pointing up and the other pointing down, then later I made brushes for each sugar unit I’d have to draw on to glycoproteins.

Don’t forget to erase some of phopholipids to make room for your proteins!

Things I learned today (I)

So today I got to do some Proper Lab Work, ie, mixing chemicals to make liquidy chemicals (a buffer today) for putting delicate proteins in. Buffers are solutions that provide the optimum environment for the little cells or proteins or nucleic acids that you work with, so they dont change conformation or otherwise break.

I was given the list of ingredients, and being a happy little chemist for the morning set about making the buffer. As always, I got all the tubs of powders and worked out what weight I needed of each to get the right molarity (that’s a measure of concentration). Then I proceded to add each of the powders to my glass bottle and poured most of the water I would need into it (If you’re going to be pH’ing something, don’t put in all the liquid, you might change the volume when you’re adjusting the pH with your acid or base). And then, I was utterly confused, the nice solution I was expecting to be clear was a muddy brown… sort of like when the water is turned off for a few hours and turned back on.

Panic! None of the solutions I had used for biological purposes before were this colour! So I went into the neighbouring labs and showed my bottle to the postdocs, and lo, my problem was solved (or at least identified). It turns out that manganese (being an awkward transition element) has variable oxidation states depending on the pH of its environment. So my very basic solution had caused it to turn brown. They tell me the thing to do is to add the MnCl2 after I had corrected the pH, and after redoing the solution like this, I had a lovely clear buffer. \o/ hurrah!

So all in all, beware the oxidation states of transition metals (or add them last), your local postdoc can diagnose problems by looking at a bottle of brown liquid, and that manganese poisoning can lead to a neurological disorder resembling Parkinsons disease (looking at the wikipedia article on manganese is fascinating!).

Where is the perfect review article?

So, I’m back in a lab, doing the first rotation of this structured PhD programme. The people are lovely, and the subject seems pretty fascinating, but I’ve been stumped searching through the literature.

I tend to underestimate the value of text books, but for the basic beginning of looking into a subject they’re fantastic. Naturally the most relevant books in the library have been checked out (and thanks to the clear website of the library, I dont realise this until I’m over there and the books not on the shelf). So I start looking for review papers, and here’s the problem, noone writes textbook level introductions to topics. There’s wonderful review pieces on small topics within the whole, but no crash course on families of molecules or the mechanism of glycosylation. The primary research is great, but in order to understand something in a slightly new field (or a field that you didnt study so well as an undergrad), you just can’t beat the simple introduction. The wikipedia is great for the super-superficial look at things (the science pages can be surprisingly detailed, though nowhere as impressive as the pages discussing comicbooks).

So if you’d like to write some nice detailed but not excessively dense articles on anything I could possibly be researching in the next few years, that’d be well appreciated, cheers :)

The PhD hunt

So further to my IRCSET application, I was turned down.  Which was pretty crushing at the time, given how much effort I had poured into it.  I’m still waiting to get feedback on my application, so that should be pretty interesting.  When that arrives, the IRCSET chapter should be closed (until I need to look for more funding in the future).

 

In the meantime I had applied for the BioAT programme.  It’s a multi-disciplinary programme that combines research with addtional relevant taught modules.  The idea is to give the student a better range of skills and exposure to more than one research lab.

Happilly I was granted an interview, just before Easter.  At the time I wasn’t sure how well it went (I waffled on quite a bit about science).  I think my enthusiasm didn’t put the panel off however, as I was offered a place on the tenth of May.  Naturally I am over the moon!  Taking up the place means I can stop hunting for funding and that I have a rough plan for my next four years.  While I don’t have an exact project, it will hopefully be in diagnostics or a closely allied field.

 

 

The wonderful world of IRCSET’s EMBARK application

So I’m currently enjoying the struggle that is getting a PhD application together.  Every year IRCSET run a programme for funding shiny fresh-faced wannabe PhD students (it’s called the EMBARK initiative, you can find it here).  Like many other funding bodies, it has reduced the number of places available, going from two calls in a year to one.  However, it’s certainly still worth having a go off, the stipend is quite reasonable (althought it only covers three years) and the grant also throws eight grand towards fees and supplies.

The toughest part is the personal statement.  You have 1200 words in which to say how awesome you are, why you have the relevant skills, and what you want to do with your life (there’s actually a bunch of questions in the guidelines, but that’s broadly it).  So at the beginning it’s hard, you throw together some lines about your skills and experiences, and you don’t oversell yourself.  Then your supervisor points out that you really do have a bunch of strenghts, so you have another stab at it, it’s easier and you spill out loads of awesome words on to the page.  Then it gets hard again, you *have* to stay under the word count, the webform just won’t accept the superfluous words.  After you’ve been reminded how great you are, cutting out the words of awesome is difficult, but eventaully you succeed.

Finding a supervisor is both hard and easy, you might get lucky or you could spend quite a time trying to find someone in your field of interest who’d be happy to take you on.  In general, they say if you can turn up to a potential supervisor with your own funding, it makes you look super (because you did all the legwork, and stuff).  I was lucky in that one of my masters lecturers was interested in taking me on, and I have a big interest in applied immunology.

So you have a statement and a supervisor, now you need a project proposal.  Again here, you could find that your supervisor already has a project they have in mind, or you might be able to approach them with ideas of your own.  Either way,  you need to condense the project into 800 words and point out all the marvellous things you will learn by undertaking the work.

So, statement – check, supervisor – check, proposal – check, next you need to grapple with the IRCSET website.  Most of it is easy enough to deal with, although the subwindows with their own scroll bar is rather frustrating.  The main issue I had with the submission process was that they didn’t seem to take ladder degrees into account (the ones where you get a cert/ordinary degree/honours degree, and not always in the same college).  There’s only one box for entering undergraduate results, and likewise only one for postgraduate results.  Maybe they don’t expect people from the IT’s to want to do further research.

After that you just have to chase up your supervisor and referees to make sure they say lovely things about you.  It’s never a bad idea to get on to a referee before you use them, to ask politely to use them (they rarely mind) and also to remind them you exist and how you were awesome.

The relieft at completing the application is massive, as it involves a fair bit of your brain time, but after that it’s still back to studying hard and getting that result you told them you’re expecting….