Life of a Lab Rat

Conversation n the student office between myself and my young apprentice Beta Gal, just now (edited):

BK: I'm the only person in the world who knows what Protein-de-Jour does!
BG: Ooh! What?
BK: <Explanation>
BG: We're the only two people who know!
BK: Four. Four people.
BG: Who else? <Speculation>
BK: <Indicates other students> These two.
BG: If you tell anyone I'll kill you!

It's a cut-throat world, science.

A UK-based reader writes

I'm a UK molecular biologist with DNA oriented experience who is about to try a western blot for the first time. Are you willing to share your protocol?

To be honest, it's pretty much the standard protocol. The antibody isn't fantastic (although that might be a function of my protein, of course) and I used to get a lot of background, but here's a quick guide to getting this particular antibody against this particular epitope in these particular samples to work (standard disclaimers, caveat emptor, this advice is worth exactly what you pay for it, etc. ad nauseam). I've emphasized the points that needed to be optimized:

1. Prepare protein from cells (it was a nuclear protein, so I used this method up to and including step 6)
2. Run gel (I used Invitrogen NuPAGE pre-cast Bis-Tris gels in MOPSMES running buffer)
3. Soak gel in Towbin buffer (Tris/Glycine/20 % MeOH) for 10 - 15 minutes
4. Blot onto PVDF at 200 mA for 2h at 4°C
5. Block in 3 - 6% milk powder in PBS/0.02% Tween20 overnight at 4°C
6. Wash membrane 3 – 6 x 5 minutes in PBS/0.1% Tween20 (PBS-T)
7. Incubate in primary antibody for 3 – 4 hours at room temperature (you'll have to work out the optimal concentration yourself)
8. Wash in PBS-T
9. Incubate in secondary antibody diluted 1/20,000, no more than 30 minutes
10. Wash 6 x 5 minutes in PBS-T
11. Develop signal with Pierce Femto substrate (1.5 ml each reagent per membrane) for 1 minute. Pat dry. Leave 5 minutes for signal to burn off a bit
12. Expose and develop film, whoop loudly.

The primary and secondary antibody diluent is PBS/0.05% BSA.

My friendly reader also said

I have to develop protocols for antibody purification- possibly involving formaldehyde crosslinking- can you give me any advice?

and I do have a protocol for that, here in fact, and am happy to answer questions on it.

In lieu of a proper entry, here's a link to a very funny piece about Radovan Karadzic.

So you spend months doing knockdowns and testing antibodies and optimizing the Western protocol::

and then your (very talented, admittedly) student comes along, does her first real-life Western with your antibody and protocol and it's bloody perfect.

There is no justice, there's only me.

My young apprentice asked for help with a method this afternoon.

I put on my labcoat (it felt like meeting an old friend) and ...
couldn't find the piece of equipment we needed.

In a flash of horror I felt like I'd turned into a

supervisor.

I'm sorry. I'm sure the feeling will pass. Meantime, I need to stand right in the middle of the corridor and talk to some senior faculty.

If any of you are actually Australian, you might be interested in this.

(Not as good as Audra's place, but then very little is.)

To someone, somewhere, this means something

On the 600, the experiments with the ambient TXI confirmed a problem with the 13C slice of the ambient preamplifier. A replacement has been ordered and should be here in a couple of days. The TCI is almost cold again and a few further checks will be run tomorrow ahead of the arrival of the preamplifier slice.

With the 400, whereas the chloroform lineshape on the TXI is good, the
water lineshape is terrible and resists attempts to improve it. It is
likely that the next step is to check the probe on the 400 at Bruker but
that won't be confirmed until tomorrow.

(I still can't get used to this being described as a 'Winter Meeting')

Yours truly is talking tomorrow at the Sydney Protein Group Meeting. Be there, or don't. I don't really care.

Sniff.

As those of you who are still paying attention might remember (and I apologize for being a little uncommunicative in recent weeks) I am off to the UK at the end of August, there to attend and lead a session at Science Blogging 2008: London.

The Faculties* of Science and my own department have agreed to stump up what amounts to most of the airfare, thereby allowing me to actually go. Naturally of course they want their pound of flesh, and I've been talking to a couple of people about what that entails. At the end of last week I met with one of the Cage's admin officers (Policy Development, Academic Support and Marketing) and we talked about how to publicize the Cage's involvement. I'm going to write a short piece and fly it by her, hopefully to make the University News as well as the Department's website.

This afternoon I nipped over to the Faculty Office to talk with Jas Chambers waves, who is the director of the Marketing, Community & International Relations unit. We had a very pleasant conversation (that's not a euphemism; we got along famously) about what the Faculty expects, and I was agreeably surprised to learn that the Dean and the entire science communications team are very excited about the conference and my participation in it.

I came away with a list of expected 'outputs':

• a 1-2 page report for the Dean of Science regarding the conference and
  thoughts on use of new media and technology from both a ‘science
  communication’ and ‘scientists who are good communicators’ perspectives
  
• a presentation to early and mid career researchers (later in the year)
  
• a presentation to our science communicators at our October meeting
  
• an article to be written for Science Alliance and the UniNews (interview)
  

So I'm going to be a busy little bunny.

It fits in really well, actually, with the proposed panel discussion: our working title is
Embracing Change - Taking science blogging into the future
and our draft agenda looks like

1. Summary. The panellists summarize the major themes of the day
   
2. Question time. Submitted questions from delegates will be
   considered by the team. If time permits then we'll take questions
   from the floor.
   
3. Looking forward. A synthesis? Suggestions for what we can do
   individually and collectively after the conference. Closing comments.
   

What's really interesting is the homework concept — how we might take lessons learned 'home' and apply them. Obviously I'm pretty set up for that with Jas's list, but I'm also going to have to come up with concrete ideas of how blogging can actually assist science communication. Fortunately there's a number of sessions that look to be just what the doctor ordered.

I also have a whole heap of stuff from Jas about the Faculty and communication and 'outreach' activities that I need to swot up on so I can talk knowledgeably about what USyd is already doing (two-way see: I take stuff from London back to Sydney, and advertise Sydney to London as the kind of go-getting upcoming communicating place they should be taking note of). Seriously, that the Faculty is keen on this shows some sort of commitment, and today I learned quite a bit about the vision these guys have (although it's interesting to note that the Cage is one of the few departments that do not have a "Science Communication Officer": whether this is because we're doing quite well with respect to students etc. or we just can't be arsed is probably a matter for debate).

And personally, all this ties in with thoughts about my own career and what I want to do when I grow up. Interesting times.

Oh, and I'm also tying it in with a trip to Southampton for an "Open Science Workshop" organized by Cameron Neylon.

Never mind flying cars or feeding all the starving children in Africa, this is what science in the 21st Century is all about.

The PDB on your iPhone. Is that so totally frelling cool or what?

A certain supplier of laboratory equipment produced a marketing video a while ago. Most of the scientific networking sites picked up on it (no, not the BioRad one, the other one) and it finally persuaded me to edit /etc/hosts — so annoying I found it each time I visited Nature Network.

I guess it was inevitable, but knowledge of it has escaped into the wild. Georg found it, sending me a 'WTF?' email. I sent a one-word explanation:

"Marketing"

Georg writes back,

I thought as much. Still, it's mildly amusing for five minutes, even if I still don't know what they're advertising.

Now, Georg may not be the target audience, and you can wibble all you like about 'brand awareness' and what-have-you, but when people don't know what it is that you're actually selling — maybe it's time to shoot fire shoot your marketing division.*

I've said it before, I'll say it again: Whatever they pay them, it's too much.

One of my favourite places on the 'Net now has a Facebook (spit) group. Feel free to invite yourselves.

Fantastic scrap going on all over the interbloggotubes at the moment. Briefly, Declan Butler at Nature wrote a piece attacking PLoS's business model. The starry-eyed revolutionaries ("Open Access is good! Data should be free! All criticism is bad! Especially by big, nasty corporations like Nature!") got all hot and bothered, and it's quite difficult to find a rational discussion anywhere (although Timo does a fair job. But he would, see, because he's one of the bad guys at Nature).

Anyway, I'm not going to add anything. I'd just like to see this settled the old-fashioned way. That would do wonders for the perception of science.

"I don't know what I've got in my bank account, but I do know how much free disk space there is on my Mac."