Life of a Lab Rat

On 31st October, 1517, Martin Luther nailed his 95 theses to the door of the church in Wittenberg, accidently jump-starting what became the Protestant Reformation, scaring the bejeezus out of Roman Catholics everywhere.

W00t! Via Eva, we have the full length version of the teaser cell movie. Narrated in a very 1970s public hygiene announcement voice, but worth a look anyways.

Flash, unfortunately. . . sorry Nix.

werrington, n,
Waterproof hat.

e.g. In his Drizabone, R. M. Williams boots & werrington, Black Knight was ready for Sydney's monsoon season.

In my copious spare time (hah) I would have liked to get to grips with programming, in a real language such as C or ObjectiveC. I did have a fiddle just before leaving the UK, and indeed was able to wrestle PERL to create some useful (no, really) web-based applications such as the Protein Calculator and the Codon Usage Wrangler.

PERL has its uses but I'm really interested in learning an object-oriented language that I can easily integrate with Apple's wonderful Xcode environment to make shiny applications for my shiny Mac. It's a hobby thing. The problem I have had — aside from the lack of time — is the absence of a worthy adversary, I mean project. So the Protein Calculator and the Codon Wrangler came about because there was a need for those functions in the lab, and how I implemented them seemed the fastest and most accessible way at the time (we had some Other OS users in the lab and I was not going to beat my head about cross-platform code).

I'm not sure whether I should be pleased that the use of non-emotive language (i.e. not using the words 'clone' or 'embryo') results in such a change in public opinion or whether to be disgusted at the malleability of the Great Unwashed.

I do find the conclusion . . . people are more likely to approve of something if they don't really know what it is somewhat startling, to be honest.

The thing about the opposable thumb is that you do not notice it until it does not function correctly. You can achieve this effect by breaking a glass pasteur and shoving the jagged end into the end of the opposable thumb, and spending the rest of the day (and the next, so far) with a whopping great field dressing on it.

Have you any idea how difficult it is to wind or use a Gilson with a non-functional dominant thumb? Or how tacky red smears look on a white keyboard? The only good thing is that I had already Hibiscrubbed my hands and sprayed them with 70% ethanol and the hood was sterile, so I should not be too worried about infection.

Does anyone out there still believe that Pfu Turbo (or Ultra™) is worth it in terms of site-directed mutagenesis? Ricardipus or Hal, any ideas?

Yes, it has been a while since I've done it, but I am certain I used vanilla Pfu last time. Which, for us at least, has certain cost benefits. And I had a go at Hal a couple of months ago on this very subject, it seems.

I talked about an embryonic stem cell line (mouse, if you are wondering) last week. This particular line has a gene trap in one allele of Protein de Jour. (Aside: a piece of DNA that contains a splice acceptor site is introduced into cells. It randomly inserts into the genome, hopefully causing interruptions in useful genes that subsequently can be used to make gene knockdowns/outs, etc.)

As I mentioned, we do not think that the trap is in quite the right place, but have gone ahead and ordered the more likely-looking candidate. Which means a whole heap of paperwork.

I have a confession to make.

My name is Black Knight, and I am an RSS junkie. Ever since most of the journals started using RSS instead of email alerts (there are a couple of honorableannoying exceptions) —

the strangest thing has just happened. I was in the process of checking my facts (I was going to say, Company of Biologists, I'm looking at you) when I stumbled across an RSS aggregator with the rather unsavoury moniker BaRF. And this site aggregates new publications from what looks like most of the journals that are relevant to my research, and provides handy bite-sized RSS feeds (via PubMed, it would appear).

Yes, it is useful to have certain search terms as an RSS feed within PubMed but that is no substitute for at least skimming the titles of articles in each new journal issue. BaRF has just made this a whole lot easier.

cabramatta, n,
Debris found on and between railway lines.

e.g. Cabramatta consists of such items as newspapers, cigarette packets, paper drinking cups and bizarrely, shirt buttons and Bic pens.

This email captured my attention:

Science Faculty is requesting content for their November Issue of Science Alliance, their schools outreach newsletter (more info on Science Alliance at: http://www.science.usyd.edu.au/school/index.shtml). If you have anything suitable, please let me know.

I resisted the urge to laugh maniacally (schools? Young, malleable minds! Mwah hah hah hah!!), and instead peered over my steepled fingers at the screen,

"Ex-cellent."

I'm back!

And my cells are fine, mad props to P for looking after them, my lovely, lovely babies.

Here's a rather weird picture that I captured earlier today, of what appears to be a dividing cell in one of my transfection cloning plates:

The green is the nucleus (expressing my splicing factor) and the purply colour is the surrounding cellular stuff (the colour is just for contrast. Grey is boring).

But look at the shape of that nucleus! And the nobbly bits on the end! Just what is going on here? It's similar to the multinucleation I've been seeing (and saw lots of this morning), but stretched out rather than spread around. Maybe it is a precursor form?

Answers, please, on the back of an email to the usual place.

I saw, on the train the other day, that some wag had doctored one of the polite CityRail notices.

The much improved (I thought) version read

At night, rave near the guard's compartment naked with a blue light.

Parramatta, n,
In antiquity, the principal river of the netherworld, said to encircle Hades seven times.

Pausanias, Description of Greece, 8.XVIII.6:

ἔδωκε δὲ ἄρα ὁ θεὸς τοῖς μάλιστα ἀπερριμμένοις κρατεῖν τῶν ὑπερηρκότων τῇ δόξῃ. τοῦτο μὲν γὰρ τὰ μάργαρα ἀπόλλυσθαι πέφυκεν ὑπὸ τοῦ ὄξους, τοῦτο δὲ τὸν ἀδάμαντα λίθων ὄντα ἰσχυρότατον τοῦ τράγου κατατήκει τὸ αἷμα: καὶ δὴ καὶ τὸ ὕδωρ οὐ δύναται τῆς Παρραματτα ὁπλὴν ἵππου βιάσασθαι μόνην, ἀλλὰ ἐμβληθὲν κατέχεταί τε ὑπ' αὐτῆς καὶ οὐ διεργάζεται τὴν ὁπλήν. εἰ δὲ καὶ Ἀλεξάνδρου τοῦ Φιλίππου συνέβη τὴν τελευτὴν διὰ τοῦ φαρμάκου γενέσθαι τούτου, σαφῶς μὲν οὐκ οἶδα, λεγόμενον δὲ οἶδα.

I'm on leave this week.

This (time off) is a problem for scientists, because as I've intimated previously, experiments do not stop when we do. It is especially bad for cell biologists to go away for more than a couple of days, because our cell cultures need feeding and looking after. This means getting the cells to a stage where they will not be much bother for the absence period and finding someone you trust to check on them and change their media. Think getting someone in to feed the hamster or goldfish and you'll understand.

I was particularly badly burned in this respect early on in my career. As a final year grad student with young Kiwi bride I went to New Zealand for a month. I got my stable, monoclonal transfections growing up and left detailed instructions with the post-doc for their care. When I got back I discovered that he had managed to contaminate at least half of them while trying to freeze them down for long-term storage. That is a lesson I have not forgotten.

I talked about the Australian Workplace Agreement (AWA) hoo-hah a couple of months ago. The University set 28th September as the cut-off date for receiving a bribepay rise if you applied to sign an AWA.

Thing is of course, if you remain covered by an EBA you get a pay rise this week anyway. A group of us sat down at coffee and looked at the AWA terms in respect of pay increases, and it turns out that there is no advantage in signing an AWA (surprise!). The offer for signing the AWA was 5% soon and 5% in a couple of years, but the existing agreement awards the same percentage increase over the same amount of time. Although 5% is more than the 3% we get this week, we get another 3% (and I think the third) while AWAers would still be waiting. There wasn't much in it overall but for anyone staying longer than six months they'd be worse off just in terms of pay rises under the AWA.

dundas, pl n,
Grazing marsupial, similar in size and appearance to the Eurasian badger. Indigenous to the ACT, this nocturnal animal is also confined to the ACT due to its inability to cope with the faster pace of living just about anywhere else in the world.

e.g. Herds of dundas eke a peaceful living on the central reservations of Canberra's deserted roads.

Funnily enough, twice in the last couple of weeks — once in Canberra and once in Sydders — I've paid for something with my credit card, and both times the personable young, um, person has noted the 'Dr' bit in front of my name and said something like,

"Oh, you're a doctor. Is that a PhD?"

I guess I don't much look like a medic. Perhaps medics do not buy bottles of chilli wine or strimmers and spray paint (what do you think, Georg?). But of course they weren't, either of them, satisfied just to discover that I am a real doctor, but both wanted to know what I did.

Great advances in the biological sciences often depend on technological or intellectual innovation.

The microscope enabled us to see that there was a whole world just below our tangible existence, X-ray crystallography allows us to solve protein structures, nuclear magnetic resonance allows us to torment students and the internet allows us to waste our time in ways undreamed of. The major reasons, I believe, that the human genome first draft was published so quickly after the project was started was the competition between the public and private endeavours, and the advances in sequencing technology and contig assembly software.

So when my very good friend Ricardipus says that he is researching 'New DNA Sequencing Technologies', those in the know should sit up and listen.

As soon as he stops photographing hawks and doves and gets rid of his VIC-20, that is.

At dinner in Black Castle[0] the other evening - digression: It's difficult for me to get home in time to eat with the Black Horde, but occasionally I'll nick off early so we can have dinner together. Youngsters get tired very quickly and if I don't watch it I can make it through the door only to find the Pawns (ages 9 and 6 and three quarters) in their pyjamas and a scowl on the face of the Queen. And it's a shame to do that to such a pretty face.

Where was I? Oh yes.

At dinner the other evening we got to talking about veins and arteries and what were the functional and structural differences. Look, just don't ask, right? Do not ask. So I pulled a basic anatomy & physiology text from the bookshelf and found the chapter on circulation and we had a really good discussion about blood vessels. I can not believe I just wrote that.