Life Science Tools of the Trade

I went on a training day (”arrghh! We wants a training day!” - obligatory obscure reference for the Brits) last week. I was one of the first to arrive, and was intrigued to see the course leader placing small, stuffed toys on each of the tables. Most tables only had one but the table I sat at had two - a squeaky chick and a beanie frog.

We were all somewhat bemused and puzzled by these critters, and concluded that they must be part of an ‘ice-breaking’ session early on. But they were never used ‘from the front’, and we were told that at courses some people feel edgy and the presence of cuddly toys to play with relaxes people and gives them something to do when nervous or whatever. We ended up playing a rather vigorous game of catch (Feh. I *hate* American spell chuckers. It’s bad enough that you’ve got us spelling -ize the French way, but now you’re putting ‘u’s after every bloody ‘o’. Noah really screwed you guys up, didn’t he? Get a real dictionary) with the squeaky chick, and I wanted to demonstrate dissection on the (lavender-scented) frog but no one had brought a sharp knife.

That pointless little anecdote beings me nicely onto a flyer that, er, flew into my pigeonhole on Monday.

‘Animal of the Month’ it says. ‘Operon brings fun to your lab!’ it says. And it has a picture of a stuffed mouse peeking out of a pile of coloured eppies, presumably in a manner that’s supposed to make hard-nosed scientists go ‘aaaaaaah’.

Bleh.
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We ordered some Taq from Stratagene and the order came in the next day. What is the big deal about that? Well, Tin, the helpful sales rep stoppped by just to see if everything was okay with the order. I think he is just an honest concerned sales rep but a skeptic might say he stopped by because we spend so much money with his company. Probably both are true.

So we were decended apon by reps today. Exept they were all from the same company. Coming buy neatly in pairs to hawk their wares….oh my I’m rhyming. Sorry. But by the second set we were confused. We told them that we had spoke to two other reps from their company and they told us they wouldn’t bother us again. So here is the question. If you send a team of reps to cover a campus building etc, why not divide the work and not hit each lab extra times. Unless of course they are just trying to wear down our defenses!

Mood….better than the Caped Avengers…no bent bike.
Song: Farm Fresh Onions by REK

I’ve had a bad week.

My bike died, the frame is slightly bent, and being alloy I’m a bit leery about it being straightened. I hope the insurance assessor will agree with me. Then my external HW drive that I use for backups and iTunes at home made a *clunk* noise and won’t spin up. Nearly everything on there is backed up, except for 100 photos of the Royal Botanical Gardens at Kew and a dozen or so taken at the Loved One’s graduation. Oh, and the latest draft of a novel I’m working on. Gah. It would cost anything up to a grand to recover the data, which is worth it to me - if I could afford it. Bugger.

On the upside it’s a bright sunny day for my mum’s birthday today, but the bad news it’s already 31C (88F) in the lab and it’s not 9 o’clock yet. Aircon? What a great concept. Bah. I think I’ll move the computer to the cold room.

Anyway, beloved reader, you didn’t come here to hear me whine. We do have a products & suppliers piece of news this week. I think I’ve mentioned before that we have a rather good Stores in this building, who stock pretty much all of the day-to-day stuff we need. But in a somewhat radical move (at least for this institute) we - that is, our lab and a couple of other groups on this floor - are getting together with Invitrogen (the 500 lb gorilla, etc.) to implement a mini-stockroom in the cold room I just mentioned. The idea is that we’ll have a ready supply of gels and markers even when the rest of the building is scrabbling around because someone central hasn’t placed an order or paid an invoice (and both have happened, I assure you).
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Since we have a new member who is extremely lucid and incomprehensible at the same time, I post this is his honor:

Let me say that preformative exclusion of microbial macrobes should be studied. The subsonic-type of bacterial nucleus runs to the sound of her siren like voice where they will be degradededed into nanu-type negative charged debris by the super-trioxide activated scavengable cell type helio-matrix of the sub-type X membrane. Upon this sub-holy hyperacceleration of the immune response memory magnetic cells we shall reach a state of subconscious cleansing which clears are minds of all impure urges (not only homo, but also hetero and asexual). Skeptics claim that cleanising the asexual of their non-sexual urges will invoke the spirit of fornication. This is untrue as can be seen in my unpublished mansucript. The thoughts can literally and figuratively precipitate and be extruded on a molecular level by the routine technique of ion exchange therapy into the liver or kidney.With this state of mind-stasis equilibrium no disease can be spread. Prove it is not a non-null hyperthesis!

Time to tighten up the membership requirements.

Another thought……………….. and yes, I’m getting old…………I don’t really want to look at the ass crack, belly or nipples of every female (or male for that matter) student who comes into the lab. I could tell stories of the sights I’ve seen as they bend over at the restriction enzyme freezer. Hell, we even have a code for it…………A.M. Use of the code lets your lab mates know that there is a serious danger of ass meat viewing.

I’m trying to work out a difficult PCR reaction so I thought I would give FastStart Taq DNA Polymerase (free sample from Roche) a try. Okay, to be honest this PCR reaction has been a pain in the butt for the past month. I can’t get specificity and I have varied reaction buffers, primers and annealing temperatures so many times the well is dry. So, yes, this particular reaction is probably doomed but isn’t that why you try a new product? If everything is hunky-dory ( or is it hunky dory?) I don’t change change things for the hell of it-if it isn’t broken, why fix it?
The nitty gritty: The specificity was greatly improved. No faint background bands, no mispriming, etc.
Unfortunately, there was NO signal anywhere with 9 primer pairs on any template. Briefly, I’m trying to PCR a spliced vs. unspliced retrotransposon with a very small intron which seems to make the primers very prone to mispriming.
PS-I never was a fan of HotStart PCR. Why would the primer misprimer at a low temperature to DNA which is already a duplex? Sorry Susan.

Because of the archaic way in which our institute does its external requisitioning (well, there’s a new system but please don’t get me started on that. Actually, it’s Part 2 of the ‘ordering’ rant , which yet bubbles in your correspondent’s cauldron) we have a level of self-authorization for orders. That is, anything less than a certain amount doesn’t need signing by the PI.

So there is a real incentive to find out the prices of reagents before writing an order. This is, I am forced to admit, not purely from the altruistic motive of not wanting to disturb the boss (or indeed from trying to save the taxpayer’s money); sometimes he’s difficult to find and at others I don’t want him to know what experiments I intend to perform. Such is the enigma that is British science in the 21st century. (more…)

I just signed up for a sample of new and improved TAQ from Roche. The claim is improved specificity. We shall see. I am always skeptical of “new and Improved” anything but when I know the sales rep I will often give it a shot. I’m having a terrible time trying to PCR a spliced vs. unspliced version of a gene (post-transcription, post splicing, post RT so yes, it is PCR not RT). I think the small intron is the problem, allowing the primer to sit down specifically on the 5′ end and then just kind of “stick” semi-specifically at the 3′ end.
Update: The world’s best dNTPs are still on the shelf. Thanks Bioline. I’ll get to those real soon. I promise. Really.

Thoughts on SAB: HOT or NOT?

NOT!

The number of posts about the “scientific” longevity field far surpass the interest of the members. The stream of longevity sewage often makes reading SAB painful. In spite of Tamara’s warning the same relentless self-promotion of mainly review articles published in low impact journals continues. Note: Letters to the editor are neither publications or research.

Enough of that. I feel I am preaching to the converted.

Music: Chuck Berry “His Best, Vol II”
Book: Midnight at the Dragon Cafe by Judy Fong Bates
Concert of the week: Ryan Adams and the Cardinals. One of the worst shows I have seen. Too much talking, too much ego, the sound wasn’t good, the crowd seemed bored, the band seemed irritated.
Science mood: hyper$h*++Y
Food of the week: carnitas. Pork marinated in milk and orange juice and then sauted until almost crunchy. Thanks Rafael.

Time to mow the lawn.

I’m not sure how the ordering is done at other institutions but here it is in your BEST interest to order just about everything from VWR. If you order from anyone other than VWR, you have to submit your order to the purchasing department who then assigns a PO number, orders it and hopefully…in two to three days you receive it.
Now if you order from VWR it is totally different. I can simply log into the VWR website and order as little or as much as I want (no spending limit) and all with free shipping. We have a VWR stockroom here on campus so you can even get items the same day. I know other institutions have VWR stockrooms but does somebody like Fisher have stockrooms on a campus.
I guess my real question is…how did VWR get all these stockrooms and why aren’t other companies fighting back.

This post has been sitting in my ‘out-tray’ for ages. I’ve got a rant about Qiagen brewing that will probably spill over into two episodes, I’ve got the second part of the Ordering System madness to get off my chest, and I have to go to the dental hygienist tomorrow morning. So, I’ll throw this one to you hungry beasts.

In a previous existence I used Boehringer Mannheim (who were swallowed by Roche) restriction enzymes and made my own buffers. Five different buffers (L, M, H, 1 and 2 I think), 50 ml stock of each, 1 ml aliquots for use. Everyone I worked with agreed that BM made the best enzymes, and places like Promega and NEB were rank upstarts with no QC to speak of. Of course, no one in their right mind would even have considered using Sigma enzymes.

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Sat. night…………..haven’t blogged in about a week and I hope this doesn’t seem too much like a “contractual obligation”.

Starting out with some picks:

Film: “The Lost Skeleton of Cadavera”, an ode to the cheesy black and white sci-fi films of the fifties.
Favorite quote from above film:
Ranger Brad: “Say, you don’t believe all of those stories about the Lost Skeleton of Cadavera, do you?”
Dr. Armstrong: “Ranger Brad, I’m a scientist! I don’t believe in anything!”
In the CD player: Johnny “Guitar” Watson
Sandwich: “Torta al Pastor” from Super Taqueria on Roxboro Rd. Durham, NC
Lawn sport: badminton with the kids

Science………..
BioRad precaset gels.Love them of hate them? Love them!
I’ve been running sucrose gradients and I know I would hate to pour 8 gels in one day to run out all the fractions I’ve collected. Walk to the cold room and there you go-ready to rip. Some scientists preach “waste of money, I pour my own…blah blah blah”. Okay if you come from some poorly funded lab and the head thinks you haven’t got anything better to do with your time than to pour an $8 gel (which is really pouriing two gels-main gel and stacker) be my guest. Me, I’m buying the gels, running all eight of them on Friday and spending Sat. with my kids.
Goofy product anti-plug: Seen these “rolly-polly” (or some other goofy name that some idiot with a marketing degree came up with) glass beads? It is a great way to spread bacteria, but you can buy the glass beads from Fisher, VWR, etc. Autoclave them (no you don’t need to wash them first) in a 100 ml bottle and you are ready to plate. Several companies sell them in various incarnations,tubes and bottles. I’m not sure who developed the spreading technique but it certainly wasn’t the guy who actually wrote up a Biotechniques paper about three years ago and tried to name it the ” Copacabana method”. That was a real career booster. I heard about it over 10 years ago from a yeast lab.

Oh, and the title……..not outage completed, but outrage completed.
Mood: mellow, red wine kind of mellow.

So a vender on campus repeated one of the better sales we get, buy 2 precast gels, get one free. Considering we go through a bunch of said gels, we went down to order away (and to get pizza). We had been told that pizza was coming at 11:30 but didn’t make it down right away. When we got there we had to line up in a cramped hallway and watch those ahead of us grab as much pizza as they could get before running away. Now to be fair it was only a select few who were taking more than their fair share, but it did cause the sales reps to put a 2 slice limit on everyone. I find that there are always those people in the crowd. So this really makes me wonder, do these people not eat other than the free food randomly found around vender shows? Do they scurry back to their lab and flash freeze it for the entire week?

Perhaps the world will never know…

Random CD from our lab pile: Pete Yorn - The Day That I Forgot
Mood: Free (no boss)
Most recently bought software title : PCillin

I was sitting at lunch the other day talking to an ex-lab rat who has moved on to greener pastures, and we got to talking about ordering systems and the current stinking mess that passes for such here at the Institute for Medical Advancement.

It strikes me that there are three basic models for institutional ordering. The first, which I deem the American model, is where each group is autonomous and responsible for its own ordering and budget. At least I’m assuming this is what happens from what I’ve picked up in conversations with American colleagues and from the questions on the surveys we fill in for the SAB. I imagine that in this model Jane Labrat approaches Joe Labtech and asks for a particular reagent, or maybe writes it down. Joe picks up the Sigma catalogue, gets a product number, types on his computer, and picks up the ‘phone or sends a fax directly to Sigma, who will then despatch the reagent directly to the lab.
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