Life of a Lab Rat

One of the advantages of working in a lab with a healthy gender balance is that sexist behaviour does not really get a chance. I can't vouch for the echelons of management, but at least here on the ground anyone attempting to discriminate, put down or otherwise disrespect on the basis of gender is likely to get walloped severely.

I should like to think that visiting speakers would be subject to similar scrutiny.

The problem is that this casual sexism is institutionalized. People, even 'ordinary', 'decent' people think it's normal. And it isn't. The test is to ask yourself,

"If this person was male, would I treat her the same way?"

And if the answer's "No", reconsider. Because I might be standing behind you with a cluebat.

The true molecular biologist/protein chemist will recall instantly the molecular mass of sodium chloride to two decimal places. This may easily be verified in the lab.

That one d.p. is sufficient for the sensitivity of our instruments and applications has no bearing on the matter.

The auto chip-holder.

And people get paid to (a) design (b) manufacture (c) market
these things.

We're doomed, DOOMED I tell thee.

(HT to CK.)

A common technique in a structural lab is to grow up a protein in bacteria and purify it. It's pretty much essential to all structural work (NMR of packed bacterial cell pellets is a different matter, and We Don't Do That). To make things easier for ourselves, some people like to grow 'their' protein fused to something else that makes purification easier.

For example, a protein that we'll call GST binds to a chemical known as glutathione. If you can immobilize glutathione on some sort of supporting matrix, then you can use this to pull GST out of a complex mixture of cellular protein (pretty specifically, in a lot of cases). So if you make a 'fusion protein', consisting of your protein linked to GST, you get a quick and simple way of purifying the thing you're after.

A complication arises if you then, as we often do, need to separate the GST from your protein. We do this by using specific proteases, that you can think of as a pair of molecular scissors which 'cut' the fusion protein at a certain place. In this example we have engineered (yes: "genetic engineering". It's What We Do) the fusion to contain this 'certain place' between the GST and your protein. So in theory you can bind the fusion to the supporting matrix/glutathione, treat with the relevant protease, and obtain just your protein.

There are, as ever, technical issues and nothing's ever that straightforward, but this is what goes on all the time in my lab.

Now, one of the proteases we use has the name human rhinovirus 3C protease. A certain company sells it to us under a tradename, let's call it "Scissors"™. Buying "Scissors"™ is expensive - it works out at around Aus$60 per prep. So the Black Queen finagled a plasmid from someone, worked out a method, and now makes our own "Scissors"™, for about a tenth of the price. Thing is of course that Certain Company gets really upset if we say "Scissors"™ — in a publication or whatever — and didn't actually buy it from them. BQ has been telling everyone that we can't call it "Scissors"™.

"Human rhinovirus 3C protease" is rather a mouthful, though: It's a lot easier to ask "Where's the "Scissors"™" than "Where's the human rhinovirus 3C protease?". To keep everyone happy, we've come up with a new name for it. We're now referring to human rhinovirus 3C protease as K-Zyme, which is easy to remember, say and type, and isn't a tradename. So anyone can use it.

And if you would like some K-Zyme, and instructions on how to make it, then apply to the usual place.

From The Australian:

ALL students at [Macquarie University] will have to undertake volunteer work

Well, it made me laugh.

The hot water in the Cage was turned off for what I'm guessing was the Annual Flow Test.

I must have been the first person to use the gents after the water came back on, because when I turned on the taps to wash my hands there was an airlock: the water hit the handbasin with tremendous force and splashed all over my trousers.

Two hours later I went to thaw some cells. I washed my hands with Hibiscrub. When I turned the water on there was an airlock: the water hit the handbasin with tremendous force and splashed all over my trousers.

(Never mind that I know other people had used the hood since the water came back on...)

And why was I thawing cells on a Friday? Because the bloody RNA prep from the KO experiment failed, and I need more cells:

Fortunately it's the lab advance starting this evening. And breathe two three four...

Dear Black Knight

I'm writing to invite you to Science Blogging 2008, to be held at the
Royal Institution, London on 30 August 2008. The conference, organised
by Nature Publishing Group, will unite over 100 of the world's top
scientific bloggers to discuss common issues.

As one of the most popular bloggers on Nature Network, and a prominent
blogger at the University of Sydney, your participation at the
conference would be greatly valued.
...

Full details of the conference, such as they are at the moment, can be
found on Nature Network.

I look forward to your reply and, hopefully, welcoming you to London in
late August.

It ties in rather nicely with my father's birthday back in the UK, so all I need to do is raise some cash for a ticket. Anyone feeling generous?

It might not look much to you, but that rather messy blot up there helped to tell me three things this afternoon:

1. The original antibody is crap and does not reliably and uniquely detect my protein. I suspected this already
2. The detection reagents give a better signal to noise ratio when you leave them for over an hour before exposing to film (data not shown. Hopefully I'll get a nicer picture of that tomorrow)
3. The knockouts are working again.

It worked. It bloody well worked!

My young apprentice (who, according to the Black Queen, is spending too much time in my presence and picking up "bad habits". Pah, I say, it's all part of the training), Beta Gal, sent me a file of primer sequences yesterday. Obviously she needs more training, because the file was created in Microsoft Word. Oh well, she's still young.

Now the thing is, I've been using iWork for the last year or so. One of the many gorgeous things about the word processing and page layout component is how it handles Word documents. With the latest version (to which I treated myself last month) Pages will track changes and handle comments seamlessly between itself and Word. It consistently handles Word documents better than Microsoft Word (a pattern develops: $BOSS sent me a PowerPoint file that Microsoft PowerPoint screwed up - lost the images, formatting, completely buggered. Keynote, with the exception of ls possibly the most beautiful program I've ever used, didn't even blink).

So Beta Gal sends me a .docx file. The version of Office (2004) I'm running on this machine doesn't recognize it.

It's a sodding Word document for pity's sake. What kind of crack-brained pot-smoking monkeys are doing this to a simple text-processing file format? Even my trusty code-wrench BBEdit throws up its character sets in dispair. The only text it shows me that isn't binary gobbledegook says

[Content_Types].xml

Pages, of course, smiles sweetly and shows me what my young Padawan has been up to.

Breathe, BK; think sunny thoughts, find your happy place.

Told you it was in a box of old papers and memorabilia:

And November, not summer. But I remember it well.

So I know that Fu Manchu has designs on my rather spiffy 'Howie Report' labcoat, but as I strode along the corridor this morning Nurse Donovan stepped out of the offices, stopped, and said

"Wow!"

I mean, OK, so I look good for my age, but "Wow!"?

Wow.

One lab's very like another/ When your head's down over your data, brother

Gosh. Cobwebs.

This weblog is primarily about life as a scientist, and not very much about the science itself (except if I think it might be useful or interesting). For the last couple of weeks I have been getting seriously to grips with an incomplete microarray data set, to see if it can inform some paper revisions.

And the thing, the crucial thing about analysing data, is that you don't much get to interact with outher people. So that whole 'life as a scientist' thing? It's not really been happening. Well, it has, obviously, but not in a way that's immediately bloggable (and you've all had enough of Perl code, yes?).

Which might explain, but doesn't excuse the relative silence here. Sorry chaps.

Tomorrow I will emerge blinking into the light and prep some RNA, thaw some cells, set up an RT-PCR and start a Western. Then it'll be back into the Pit with me to co-write a book chapter. But I shall be on the prowl for japes and jollities — so look out.

As someone else once said, better than I could: "I'll be back".

Me navy mate, in climes foreign, received an email:

Good Morning Postdocs:

This is to inform you of a mandatory meeting with Dr. Ange E. O'Tensin (Off-Campus Guest on Site today) in Room 78 Phys Building from 1:45 p.m. - 2:30 p.m.

Mouth-Breather,
Senior Administrative Services Assistant

Now, that sounds a little odd, especially when you realize that the email was sent at 9:35 that morning. What's that? Drop everything, post-doc, and meet this guy. Never mind your experiments or your lunch date: One of our oh-so-important professors has decided not to meet our visiting speaker, and we have 45 embarrassing minutes to fill.

I wonder what thundering moron came up with this idea, and whether they've found all the body parts yet.

Steve Matheson links to an extraordinary video.

Go see it.

Laugh.

Because sometimes, that's all you can do.