Hungry

Here is an interesting quote I came across today. It is meant to help you solve problems:

"You write down the problem. You think very hard. Then you write down the answer. "
~Richard Feynman

OK, I am going to try it right now with a problem I have. I am hungry. I missed breakfast and have not had lunch yet (it's 1.15). But the isopropanol is evaporating sooooo slowly, we need to do other things once it finally goes but it's taking it's own sweet time.

Problem: I am hungry
Thinking: need food, really need food, but it's so cold outside and too far to walk and I can't be bothered and I need more money food, need food.
Answer (written after a minimum of three minutes thinking time): I will fill myself up with water and not be hungry.

...

Sort of worked. Try again:

Problem: I have a 3000 word essay to write before January 20th
Thinking: I've sort of started it, I know some stuff, I have a week at home where I can sort of work except I won't have the Internet (crap) I have the weekend except I should probably be spending that with a Certain Someone as it is my last week with them before the holidays. why is this useful anyway! Lab Rat's don't need to be able to write essays. at least I'll have 20 days when I get back, crap how am I supposed to do anything in 20 days. I can't think I'm too hungry!!
Answer: ...

Screw you Richard Feynman.

:(

And why have you used 84 plates?

The thing about scientific protocols is that they are meant to be exact and precise. Every step must be explained concisely and there should be a reason for all the methodology.

For example, for every protocol you use, you should be able to answer random questions about why you did what you did at each step. Why was the bacteria incubated for four hours? Why was the temperature kept at 50 degrees? Why was the product stored on ice?

The answers to these questions should be sensible and scientific. Temperatures, amounts and incubation's are used to optimise reactions. Every step should be planned to get the best possible result in the most efficient way.

At the moment, we're growing phages on agar plates. At one stage of the protocol, we use exactly 84 plates to grow them. Two of the plates are controls and four are for dilutions but the fact remains that every time we use exactly 84 plates, no matter what we're doing.

The answer (as can probably be guessed) is not scientific in the least. Science is not a cold and clinical organised space, no matter how much scientists want it to be. It is a wild and crazy world full of human error and things going random and even more human error. The problems are not just scientific, they are also spacial and temporal; incubators are only so big, parts of the lab are only open during certain hours.

And the big jars we use for incubating will only physically fit 42 plates. We've tried to stuff more in but the lids won't shut. And while we have three of them in total the incubator is quite small and only fits two at a time.

42 x 2 = 84

Which wouldn't seem so bad if it weren't for the dilutions and the controls, because once you've put them in there's only room for 39 plates of actual phage sample per jar. 42 is at least a nice round number, but a protocol always looks a bit odd if it starts with the phrase '39 plates were taken...' It begs the question, 'why 39?' and the answer is, scientifically, faintly embarrassing.

Science would be a lot more precise if the world stopped getting in the way.

But far less fun =D

Back to lab Rat-ing

I'M BACK IN THE LAB!

Wow, it's been a while since I've written anything here. Term finally finished (finally!) and now I am back happily being a Lab Rat and currently waiting for media to cool down so I can plate it out. Normally when making agar or other media it just gets melted in the microwave then poured instantly. However at the moment we're using media that needs antibiotics in it after it's been melted, the antibiotics don't like high temperatures so we have to let it cool down a bit first.

Other things I have to do:

• Read up papers for my project next term (More bacteria! But no phages. Antibiotics instead)
• Write a 3000 word essay about biorefinaries for the end of January
• Revise all the stuff I did this term because I am a lazy Lab Rat and didn't do enough during the term.
• Decide which options I am doing next term and organise my timetable
• Write a CV and pester the person whose Lab I will be working in over summer this time to the point where they will fill in funding forms for me (but not actually get very pissed off at me).
• Write the second chapter of a Very Geeky Story for a friend (it's about proteins...inside a cell...yeah. Currently stars Fos and Jun as the main characters, over-sentimental sacrificial cyclins and a gigantic mafia-style phosphate empire. Like a Sci-Fi/Western. But in a cell. heh)

Fun fun fun! Actually I really don't care because I'm back in a Lab and all is good :) And apart from the huge amount of work going on the rest of my life is going swimmingly.

This stuff is taking ages to cool down though x|

Presenting Histones

Bravery is an interesting word. It's one of those words that has many different subtle shades of definition; ranging from altruism to stupidity. The big question is, of course, was it brave or stupid of me to volunteer to do a presentation at the first supervision of term?

To put this more in context, I haven't actually done a scientific presentation since, well, at all. We did some mini ones in our supervision group last year, but they did not go so well. I haven't had to speak in front of a large crowd of people for about three years, not since the upper sixth performance of 'Dracula' where I stumbled on stage for a few minutes to play Translyvanian Peasant With Godawful Accent.

Here is the title and the link (for those who can get it) for what I have to present:
"Rb targets histone H3 methylation and HP1 to promoters"

I'm going to go through the paper now and try to provide a quick summary of what it is about. I have no idea how I'm meant to present it (hopefully there will be a brief meeting at some point to discuss this) but I can't help but feel things will go slightly better if I actually know what the paper is talking about.

okay... a look at the abstract and one brief scribbled diagram later this is what I've got:

Pretty pictures if you follow the links!

There is lots of DNA in the cell, so in order for it to fit into the nucleus it has to be coiled. One method for coiling involves wrapping the DNA around histone proteins (beads on a string) to keep them coiled. As well as keeping the DNA wound up, histones can also signal to transcription factors (proteins that start the complex process of turning DNA into protein) which bits of the DNA they need to read by displaying chemical signals.

One such signal is the methyl group, -CH3. Sticking a methyl group onto the end of a histone signals to the cells that this DNA is in Do Not Disturb mode, and should not be turned into protein. The study the paper was doing focused on a protein that goes around putting up all the nuclear Do Not Disturb signs; SUV39H1 (which shall henceforth be known as SUVy). This methylated the histones at a certain point (lysine 9 of histone H3 for anyone interested) and keeps the DNA associated with them from being expressed. It does this by recruting HP1 which binds to the DNA and, as far as I can work out from this, just sits there and stops it being expressed.

There are two forms that DNA in the nucleus can take: heterochromatin, which is all coiled up and not doing anything, and enchromatin, which is being actively expressed. This paper was getting fairly excited because while it was known that SUVy and HP1 were good at keeping heterochromatin quiet, they found them interacting with euchromatin! What's more they were consorting with Rb, a very well known protein that is involved in all sorts of processes that supress the expression of DNA, particularly in different parts of the cell cycle.

By doing various assays involving pulling out the Rb bound to DNA and then finding what bit of DNA it was bound to, they discovered that it methylated the same H3 on the lycine that HP1 did. Furthermore, Rb can interact with SUVy, due to a 'pocket domain' which SUVy fits into quite well. The end conclusion of all this is that Rb and SUVy interact together, methylate a part of the DNA which people hadn't really known SUVy was methylating, and then HP1 comes and sits on it.

The exciting thing here (alright not that exciting, but fairly interesting at the least) is that they put forward at the end that there may be other euchromatin repressor proteins out there that bind to SUVy and mobilise the DNA repression in euchromatin. Also, as Rb is involved in cell cycle control, it helps to build a bigger picture of just what is going on in the cell cycle (which cancer reseachers tend to like).

And woohoo I get to do a presentation on it. :)

Proteomics

So, term has started. Lab Rat is out of the lab and back in the lecture theatre, which means probably less blog posts as I try to get through my rather scary reading list (thankfully it is made up mostly of papers but there's still rather a lot of it).

The first topic for this term is Proteomics; the study of the structure and function of proteins within a cell and living proof that adding the term -omics onto something gets you exciting amounts of funding. Proteomics is turning out to be fairly interesting, the paper I've just read, for example (here if you can get to it) talks about how large scale proteomics was used to compare the proteins in the malaria parasite P. falciparum in its different states of growth. The idea is to find a protein in one stage that isn't in the body naturally and then target it to kill off the parasite. Also it's really interesting finding out which proteins are expressed when, and which ones the parasite turns off at different stages for various reasons.

*sigh*

Yeah, I miss phages :(

species specific mouse transcription and the start of term

Term is about to start! I still can't believe that the holiday is almost over :( On the other hand, this holiday does seem to have gone on a while, memories of exams and lectures and learning seem so far away.

I will have to step away from being a Lab Rat for a while, and go back to being a Student. Lectures, reading, more reading, desperately understanding and (a new one for this year) Seminars. Seminars are where some other lab rat stands at the front of the room and talks about their lab ratting for a bit and then everyone else has to try to think of clever things to say about it. It's all great fun and sometimes you get free wine or food.

So as it's the start of term and I'm full of Good Intentions I went over to my departmental webpage to see if any of the abstracts for the seminars were up. It turns out that the first one is up. Here it is:

"Homologous sets of transcription factors direct conserved tissue-specific gene expression, yet transcription factor binding events diverge rapidly between closely related species. We used hepatocytes from an aneuploid mouse strain carrying human chromosome 21 to determine on a chromosomal scale whether interspecies differences in transcriptional regulation are primarily directed by human genetic sequence or mouse nuclear environment. Virtually all transcription factor binding locations, landmarks of transcription initiation, and the resulting gene expression observed in human hepatocytes were recapitulated across the entire human chromosome 21 in the mouse hepatocyte nucleus. Thus, in homologous tissues, genetic sequence is largely responsible for directing transcriptional programs; interspecies differences in epigenetic machinery, cellular environment, and transcription factors themselves play secondary roles."

I actually almost fainted when I read that. A few deep breaths later and I decided to come back to it and understand it. (Why can't scientists write what they mean?)

Translation (if you want to skip my waffle and get straight to a quick translation skip to the italic bit)

I have to admit that I had a bit of a clue to help with the translation, they gave me the guys webpage. A quick look confirmed that he works for cancer research UK, which helps because there are actually a limited number of things people in cancer research tend to work with (well, at the very least it confirms that he's not working with bacteria...)

So...the first sentence. Transcription factors are proteins that bind to the DNA and control its expression. Probably a term most biochemists should really know (heh). Homologous just means 'pretty much the same'. So their problem is that they've got transcription factors in very similar species doing wildly different things.

Hepatocytes are liver cells. Aneuploidy means 'an abnormal number of chromosomes'. So they basically just stuck human chromosome 21 (the smallest one! and, incidentally, the one that leads to Down syndrome) into mouse liver cells to see what they did. The idea being to find out whether the differences were caused by the actual nuclear material or the 'epigenetic' surroundings (epigenetic = stuff that isn't DNA)

Epigenetics is a relatively new and exciting concept incidentally. It's the idea that the actual nuclear environment has a large part to play in what gets expressed rather than just the DNA as much. Also it's an idea that really pisses off James Watson and anything that pisses off James Watson is fine by me.

So what happened? Were the alien chromosome 21's expressed like mouse chromosomes (showing epigenetic control) or exactly as they would be in humans (showing DNA control). The answer is in the third sentence, the chromosome 21's were expressed exactly the same as they were in humans. No epigenetics here :(

*these aren't the epigenetic controls you're looking for*

For those who just want a simple translation here it is, to the best of my ability:

Similar sets of transcription factors are involved in controlling the expression of mouse DNA. However the way they work is very different, even in closely related species. We placed the human chromosome 21 into mouse liver cells to see if they were expressed like mouse chromosomes (showing control from factors other than the DNA) or like human chromosomes (showing that all control is from the DNA). The expression of the chromosome 21 in the mouse liver cell nucleus was almost identical to the way it is expressed in humans. Therefore, in similar tissues, it is the genetic sequence that determines how the DNA is expressed, all other factors are secondary.

Now I've got to try and think of clever questions to ask about that. I might have a try at getting hold of the paper, then at the very least I can ask poncy questions about the techniques.

Taxonomists vs. Phages

Taxonomy is one of those wonderful subjects that at first seems very simple (and very boring). The word comes from Greek - taxis meaning 'order' and nomos meaning 'law', or 'science' and is at it's most basic the science of classification. Most people do varying amounts of taxonomy at school; dividing living things into plants, animals and fungi, dividing the vertebrates into birds, mammals, amphibians, fish and reptiles etc.

Putting the dubious accuracy value of these classification labels aside (particularly the bit about reptiles) taxonomy is, at it's most basic level, a simple system for ordering things and putting them in little boxes. Glorified stamp collecting, as it were. But there are still plenty of arguments and various feuds about the exact relationships of things, most often at the species level, and even whether the whole 'five kingdom' model is any use (the five kingdoms are animals, plants, fungi, prokaryotes - roughly bacteria, and protoctista - which are basically the equivalent of the filing draw marked misc.). In fact, the more you delve into the science of taxonomy, the more complications and problems you start to encounter. Even something that would seem fairly simple, such as what defines a 'species' is a matter of hot debate.

And when you get down to the level of single-celled organisms the whole system goes a bit haywire. The distinction between 'animals', 'plants' and 'fungi' completely breaks down, there are single-celled things that are motile and animal-like but photosynthesise, things that only photosynthesise at the right time of day, or are perfectly sessile and plant-like except they don't photosynthesise. Most protozoa (single celled thingys, more information under the link) are now broken up into a whole new set of labels, very few of which seem to relate to the larger multi-cellular organisms.

When it gets to things like bacteria and bacteriophages, of course, taxonomists just break down and cry. Because bacteria, unlike most other things, don't even maintain their genetic integrity. Bacteria can share bits of their genome quite happily, even with bacteria that are seemingly very unrelated, making the whole 'species' concept break down a bit anyway. Phages merrily incorporate various bits of bacteria into themselves, splice bits out, even splice themselves in to bacterial genomes and sit there for a while. It's a complete headache to try and organise the things.

Various attempts have been made, of course, since the first discovery of phages in 1915 by the wonderfully python-esquely named Frederick Twort. (to give all and full credit they were also discovered completely independently in 1917 by Felix d'Herelle). The first system was based on morphology, what the phage looked like, and was greatly helped by the electron microscope. Although most phages adopt the 'lunar landing module' look, there is plenty of variation within that. Length of tail fibres, size of capsid, symmetry of the capsule, alright, not very much variation, but still something for taxonomists to hang onto.

Size and shape are never good indications of relatedness, a dolphin is more related to a hyena than to a shark, however similar the two might look. Nucleic acid research during the 1960's shook up the whole discipline of taxonomy by providing lots of new exciting DNA information. Phages could now be classified by the amount and type of DNA, which, added to the morphological data, provided a system (albeit a slightly wobbly one).

One of the most currently most widely popular methods to classify things is to examine the genetic DNA that codes for the ribosomes. Ribosomes are complexes of RNA and protein that are used to turn the genetic code into proteins. They are very highly conserved and are therefore very useful in determining evolutionary relatedness and taxonomy.

The problem is, of course, that bacteriophages don't have any ribosomes. They use the bacterial ones; they harness the bacterial internal machinery for replicating DNA and making proteins and therefore don't need to carry any of their own. In view of this, one of the most recent attempts to organise phage taxonomy has focused on looking at their proteins. The relatedness of the proteins has been used to create clever sounding things like distance matrices and the highly impressively named 'phage proteome tree'. Of course there are several problems, possibly the main one being that phages, especially the ones that sit inside bacteria, have a distressing tendency to pick up bits of DNA that aren't theirs. Which translates into proteins that aren't theirs and makes the whole procedure just that little bit more awkward.

There's been some work comparing the genomes of just the structural components, in the hope that there won't be too much genetic exchange going on with the genes that are actually needed to build the phage. The people doing it seem fairly confident, and have managed to isolate about five separate genera. There's a paper from them here, hopefully should be accessible (in form if not in content).

The whole thing is really all a bit up in the air, with some fairly amusing piss-ups between the different schools of thought. Horizontal gene transfer can be a bitch sometimes :)

What to do with DNA

Now we've actually managed to extract our DNA (like this) we get to cut it all up into tiny pieces. It might seem a bit pointless, but this is how to determine that we actually have the right bits of DNA in our extracts. Cutting DNA with little enzymes called restriction enzymes produces different restriction patters depending on what DNA you have.

Restriction enzymes are naturally produced by most bacteria, and what they do is cut pieces of DNA at very specific points. EcoRI, for example, cuts DNA after the G in the DNA sequence GAATTC. As each viral genome has a different DNA sequence, each one will produce a different restriction map, producing a characteristic number of bands on a gel:

(this picture is not from my research, it is from here)

Each band is a blob of a certain size of DNA lit up with ethidium bromide (which is a dye, nothing very exotic). Different restriction enzymes, and different genomes, will produce different band patterns on the gel.

So, what do the bacteria need to produce DNA cutting enzymes for? The answer (naturally) is bacteriophages! One way the bacteria can protect themselves against viral invasion is to have lots of these enzymes around. As soon as the viruses inject their DNA into the bacteria cell, the restriction enzymes chop it all up.

But bacteria also contain DNA, and unlike people (and other eukaryotes), they don't keep it all tucked up in a nuclear membrane. So how do they stop the restriction enzymes from cutting up their DNA? One of the most common ways is to methylate the DNA, essentially sticking a methyl group (a carbon atom attached to three hydrogen atoms) onto some of the bases. in the example shown above, therefore, the restriction enzyme is looking for the sequence GAATTC. It sees this in invading DNA and slices it up, but in the bacterias own DNA it sees GA(methylated)A(methylated)TTC, which it doesn't recognise. And therefore, does not cut.

Restriction enzymes were first discovered my Daniel Nathans, Werner Arber, and Hamilton Smith. They won the Nobel Prize for it in 1978. (see here)

Writing in officialese

One of the things about science nowadays is that it tends to generate impressive amounts of paperwork, which you have to wade through to get to the actual science. For example, I want to keep working as a Lab Rat to help out my supervisor. The money is available to fund me, but I can't actually get at it without filling out a little form explaining why.

It isn't too bad, two sides of A4 with mostly just information about who I am and what my details are. There's only one part where I have to do any actual writing, so I'm currently trying to figure out how to say "I want to work in a lab! It is fun! It will give me CV points!" in officialese. I have a feeling that writing "I want something on my CV. Duh, why do you think I want to work in September?" would probably be frowned upon. As would seeming excessively keen. I don't know though, is it acceptable to write that you actually enjoy lab work on a form? Or will they just think I'm making it up.

It's all good practise though. Sticking with lab work means that my future will be full of funding forms and various other bits of paperwork in whch I try to find convincing and acceptible reasons for doing what I do. And then trying to couch them in slightly better terms than "I want money. I like lab work. Give me money, I will give you work."

heh. It's like applying to university all over again. ("As well as achieving impressive exam results I have had lots of experience doing all sorts of intelligent things-FOR THE LOVE OF ALL THINGS HOLY JUST SOMEONE LET ME IN")

sometimes life gets you like that

This was going to be quite a long soul-searching post about the general usefulness of science, based on a conversation held the other evening about whether the Large Hadron Collider was actually worth it. Huge amounts of time, money and energy (and a slight amount of danger) all for ... what? The Higgs partical? Why? Seriously, is there any point to finding this thing except just ... because?

But I am tired, and vaguely upset, and really not in the mood to spend a goodly amount of time talking about how the subject I ended up doing (and will keep on doing) is a mighty large pile of intellectual w*nk. It is starting to look very definitely like science is going to constitute a large part of my life, and I need to be a lot more awake and cheerful before pulling my life apart like that.

So I'm going to read firefly fanfiction instead.

Literature degree? Should'a could'a would'a.