Life Science Tools of the Trade

Pretty content-free, a quickie if you like, but I thought the following article might be of interest to our reader: The opposite of eureka I: nurture — Mole 118 (16): 3567 — Journal of Cell Science.

The Mole makes an important point about testing reagents, and I must admit, this is something I’m very bad at. Maybe it’s something I should get good at, but often when you buy a kit there’s only enough reagent to do the experiments you want to do . . . it’s a courageous scientist who says

“I will ‘waste’ some of this kit to test that it’s OK.”

Surely that’s what (supplier-side) QA is all about? Yes, I know if we were working to ISO 9000 we’d probably have to do this anyway, but most of us aren’t. Most of us are ‘just in time’ scientists, and maybe we do need a sea change in our behaviour.

I need to go away and think about this.

Random science tip of the day: maxiprepped plasmid DNA is cleaner than a PCR prep. This is why the PCR prep ethanol pellet appears bigger than the plasmid ethanol pellet. Just saying.

Remember I wibbled about the IVGN stock fridge? Got a flyer in the post today from Promega. They’re introducing stock fridges with RFID scanning. The stock is tagged, so as you remove an item an order is automatically raised to restock.

This is a brilliant notion (not a new idea, I was planning a similar thing to keep my tonic stocked and cold at home ten years ago) but has potential pitfalls. Are multiple copies of the same stock item differently labelled (I can see someone in this lab deliberately waving the same item past the scanner so we end up with thirty thousand tubes of ligase)? How do we know who is taking the stuff? It’ll be a free for all, which is a killer if there are different budgets with access to the same fridge. Do we have it locked and hand keys out to appropriate people? Swipe cards? RFID-tagged post-docs? Now there’s an idea.

Non-random iTunes selection: ‘Summertime’ by Janis Joplin. A truly stunning arrangement.
Mood: Nectarine.

Below is our featured Perspective for this week, which I decided to cross-post in this blog because of its relevence. I thought that it would especially resonate with our Resident Bloggers. The Perspective is by Shirin Kalyan, Ph.D.

As a researcher in the burgeoning life sciences arena, I certainly appreciate the plug and play automation of the lab environment. However, I have not lost perspective on the goal of my work. A growing number of life science researchers have come to realize that our work for the improvement of health and our drive to understand the biological processes in health and disease is incompatible with the amount of waste we produce in the process. The desire to be a part of the solution and not the cause of the problem of biological “disorders” is a stark contradiction to the immense amount of unnecessary waste generated from daily lab operations.

It would be hoped that researchers with foresight strive to ensure that product stewardship and environmental conscientiousness is part of the business mindset of companies dealt with (although such a perspective would be considered optimistically-delusional, if not simply naive). However, there are some companies serving the life science community that have been fairly attentive in this matter and have even offered small token grants to academic institutions for the implementation of ideas to improve upon the sustainable research activities of users of their products, as well as making efforts not to use excessive material when shipping items. I am sure many researchers can identify with the ridiculous amount of packaging often sent with shipments of reagents and lab accessories. I have often been the recipient of boxes that could house mini-stereo systems only to find myself digging through an endless sea of Styrofoam packing chips to finally come upon a 1 ml vial of some research reagent. Such thoughtlessness in a field requiring some thinking and innovation does little to reflect the efficiency or competency of the company indulging in such garbage.

Communicating this interest to service providers would be a good start for ensuing change. I’ve discussed some of these concerns with local reagent suppliers and many have been more than willing to initiate programs (that would likely garner consumer loyalty) involving picking up packaging material from previous shipments and reusing them. Other companies are moving away from non-biodegradable materials as packing material. The environmentally sustainable researcher also is likely to be one who will reap financial benefits from saving money as well as trees – and there are resources available to help you be both conscientious and thrifty – such as online lab equipment exchange sites that have saved us a nice sum on shakers, evaporators and such necessities on the “eBay” for scientists. The turn over rate for technology is high in this field and the cost is often astronomical for our various gadgets – so it would only be fair, if not obvious, to have some kind of product stewardship program in place to ensure that the old centrifuge you discarded doesn’t end up at your local dump – where a scavenger may report it as a tool for the production of nuclear warfare that is traced back to you. One never knows, stranger things have been known to happen… and karmas have a tendency to run over dogmas.

The regulatory red-tape is also unburdened from the shoulders of investigators who take the initiative to use methods that bypass the usage of radioactive, carcinogenic, or otherwise noxious stuff for their assays. There are a number of more sensitive, cost effective, and less hazardous developments and tools of the trade (such as new fluorescence based proliferation assays that have replaced the incorporation of radioactive thymidine) that have replaced old standards (it is difficult to accept, but, indeed, everything old is not gold) – all it takes is a little innovativeness, a touch of awareness, and douse of initiative to plan laboratory activities in sync with the regenerative states of the ecosystem.

Our consumer driven shift to “disposables” is, frankly, a concept worthy of disposal itself. Unless there is a plan to recycle or reuse all these glorious “disposables” – it is neither an innovative nor a sustainable paradigm to adopt for the future of life science research. Considering the rapid growth of this field, those serving the research community would be wise to consider the consequence of the massive consumption and proportionally massive waste that is likely to ensue with such short-sighted development; and, if the ethical root of the argument of environmental sustainability is not enough to result in a change of heart, perhaps taking note of the history of companies that have fallen under the distrustful eye of public scrutiny and bad publicity would make industry providers take note. Biotechnology is an area that the public has yet to embrace whole-heartedly without suspicion of ulterior motives or being a field driven for profit and not for public good – especially after a few wrong turns with GM crops and the environmental impact of research and development. In addition to the general inert waste generated by disposable lab equipment in the form of various non-biodegradable plastics, the fact that the reagents used in research activity can be toxic when accumulated in the environment should not be ignored.

Some involved with the new exciting frontiers of nanotechnology have wisely taken notice from the get-go. Many embarking on being successful contributors in this young field have taken note of criticisms regarding the potential impact of their research and have paid due heed to public opinion and concerns about the unknown hazards of nanotechnology waste. As was eloquently expressed in a recent article published in The Scientist written by Vicki L. Colvin(1) , who is a professor of chemistry and chemical engineering at Rice University and director of the NSF-funded Center for Biological and Environmental Nanotechnology, stated “…ignoring reasonable fears and concerns about emerging technologies can halt or even derail technology’s progress. Industry now appreciates the costs of neglecting risks posed by new chemicals, materials, or devices…Safety and sustainability are no longer problems that concern only end-users well after the field is commercialized. Instead, they are flexible parameters in a new, and I think wiser, technology-design process.” Those lagging behind in this conceptualization, best take note lest they be left behind in the compost bin.

Reference Cited:
1) V.L. Colvin, “Research Vision: Sustainability for Nanotechnology”, The Scientist 18(16):26 Aug. 30, 2004.

Just to add to the glowing operon review, we typically get very high yields from even their smallest scale preps, so we almost never need to order anything larger. We have only had a couple problems with oligos ordered (one failed quality control and took a couple extra days), the vast majority show up on time without hassle early in the day. I think the Fedex shipping helps with this.

over all, two thumbs up!

Remember the bad protein marker story?

I ordered some SuperScript II (not III) on the advice of a post on the Scienceboard. It arrived in timely fashion, but the tube of 0.1M DTT was empty. Not a major problem, but I’ve paid for it so I damn’ well want it. An email to the tame rep resulted in a vacation message, so I called the support line and got them to sort it out. I had to email the order number, etc., and then I got an email from someone else at Invitrogen asking for the same information, and duly replied.

On consecutive days later in the week I received a new SSII kit and a M-MLV RT buffer pack (which contains DTT). So I’ve ended up with two SSII kits for the price of complaining. I guess the rep must have chased the problem up when he got back, setting a second set of wheels in motion. I’m not complaining, mind.

Oh, and apropos nothing in particular – if you’re a publisher or a journal marketroid, it takes more than one bottle of wine and three small baskets of nibbles in the foyer to get 400 scientists interested in your flagging journal. What a surprise no one stayed to talk to you.

FYI…you can get NEB to sell more concentrated enzymes than what’s in the catalogue. A co-worker is cloning microRNAs and needed RNA ligase at a higher concentration than what NEB sells. After calling tech support, it turns out that you can customize some of their enzymes. NEB sent the same overall units of enzyme but the enzyme was twice as concentrated. (Important for microRNA cloning because it doesn’t work so well!)
I’m not really sure how helpful this is but just wanted to pass on the info.

By the way, just heard the song…You can eat dog food by the Austin Lounge Lizards. Not something you hear everyday!

I hate spam. The electronic form screws up a brilliant form of communication for everybody, and the paper version destroys forests and bungs up the postal system.

Anachem are one of the worst offenders of the second kind of spamming. It’s probably because they’re too successful; they are the primary distributor of Gilson Pipetman®s (Pipetmen?) over here, and come on, when was the last time you bought a Gilson? If you’re really lucky and are setting up a lab, you might get to buy one or two sets (four or five in a set). But you join a new lab and you use the previous incumbent’s set, or rifle through a few drawers until you find some, get them serviced and calibrated, and you’re away. We have an excess of Gilsons in this lab. We’re saturated (what is the Km of a Gilson anyway? No, that way madness lay).

Essentially, Gilsons are too good. They don’t break. Get them serviced occasionally and they last for ever. They can be dropped, autoclaved, washed in ethanol, flamed . . . Brilliant. But there’s no built-in obsolescence so people, obviously, aren’t buying them because every month I get junk mail from Anachem with news of their latest deals on the bloody things. If there was an accident in our lab, such as – Oh, I don’t know, a nuclear meltdown and all the plastic tragically melted – and I wanted to replace my set of Pipetmen then obviously I’d know who to contact, but that doesn’t happen very often, believe it or not.

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We had a batch of dodgy protein marker from Invitrogen. Back in January, I think it was. I made a phone call to their support desk (“We’ve not had any complaints” “You have now”) and extracted a promise of some replacement marker. Months passed, and I nearly forgot about it, until I was introduced to the new rep (I’ve talked about him previously) and in a flash of quite uncharacteristic brilliance remembered to quiz him about the replacement marker.

Turns out (after I emailed him a reminder, grr) that they’d closed the ticket because they’d sent out a replacement that, naturally, I’d never received. Got on the blower to the tech service girl, who says they have not had any complaints about the replacement batch.

“But I never received it.”

“That batch is all gone now, but there were no complaints.”

“That’s not the point . . .” after going round in circles for a bit I persuaded her to send some more (maybe it was the bit about ripping someone’s head off and pissing down the hole that convinced her) which, much to my surprise, arrived three days later, with my name on the parcel.

Score. Of course, they had the last laugh by sending two customer satisfaction survey emails out to me. I filled in one of them – and to be honest I was quite pleased with the (eventual) outcome, but I have this mental image of two tubes of Benchmark Ladder languishing somewhere in a warehouse near Milton Keynes, with no one to love them or give them a home. Poor things.

Things I must remember to blog about this month: Invitrogen versus Qiagen, Our Crazy Ordering System Part II.
Mood: Green
RiTS: They Don’t Know by Kirsty MacColl

Note added in proof:
IVGN are doing really well for themselves, aren’t they? They’ve landed the first licence in ABI’s expanded licensing system, whatever the hell that is.

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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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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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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The Invitrogen rep (last week) sold me a maxiprep kit for half price, as an introductory offer. We had a brief discussion about discounts and how all scientists seem to ask for one. He didn’t get this at all, until I pointed out that people need to make grants go as far as possible and part of this is playing companies off against each other to get a good price. He’s right of course, if there’s a discount at all then we all get the same, and the companies just hike the list price to compensate. I guess there’s a psychological thing here – your list price might be less than Qiagen’s, but you don’t give me a discount. Never mind that your list price is less than Qiagen’s discounted price . . . Yeah, it’s odd. The boss always wants me to ask for a discount when I’m talking to reps, but what can I do?

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Some people here at the Institute for Medical Advancement have had problems with their Southern blotting. Apparently this isn’t down to the usual culprit (*cough*user error*cough*) but rather a bad batch of Amersham’s Hybond(TM) N+ membranes. This surprises me somewhat, Amersham having had a good reputation for quality (and corresponding expense, but you get what you pay for) in the past. I must admit, I was also a little surprised last year when General Electric bought Amersham, given the latter’s stranglehold on quality radiochemicals in this country and its commercial success since it was privatized in 1982 (to such an extent that it was able to swallow Pharmacia whole, without getting indigestion).
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After waxing lyrical about the NEB Catalogue I’ve found that Novagen have some really useful resources too. In my line of work we try to express proteins that have as little vector sequence as possible, so use an in-house vector that is essentially pBR322 with a T7 promoter, Shine-Dalgarno and TATA boxes and a useful multiple cloning site. NdeI and NcoI are there (CATATG, CCATGG, remember) as well, meaning we can start translating at the first methionine codon without all that tedious mucking about in hyperspacegetting the frame right, minimizing extraneous linker residues, etc., etc.
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As another clueless sales rep walks into the lab for a company that I’ve never heard of, I always end up wondering…how many of these companies make it. You know the ones I’m talking about. Two guys decide to make the garage a warehouse and now they’re giving out glove and pipette tip samples to the willing. How do you decide to compete against the likes of Fisher and VWR. I must be misunderstanding something because I do not know how you can make a successful business selling the same 6 items that are sold by larger companies. I’m convinced….the individuals that start these companies are the same ones who couldn’t make it in research.

As t

Uninvited, in strolls the dreaded Sales Rep. I am in the middle of setting up several reactions………….”Do you do PCR? We have the best dNTPs on the planet”………………………………………….I found it insulting, and told him so, to be interrupted and for him to make such an idiotic claim. “Like anyone can even know that Napoleon?”* There must be literally hundreds of companies selling quality dNTPs with purities >99%. I have NEVER had a pcr reaction fail because of “bad”dNTPs. Bad oligos, yes. Bad dNTPs, no. He persisted, telling me he would undersell (meaning undercut if he knew what I currently pay for dNTPs) any vendor and offered me a sample. I refused the sample. I won’t be doing business with Bioline anytime soon.

*Kip’s response to Napoleon’s claim that Uncle Rico’s video “was the worst video in the world”.

Rant time: Do the SAB members constantly posting in the “Humor Forum” really think that crap is funny?

Book suggestion: “Blink” by Martin Gladwell

Playing in the lab: Patty Griffin’s “Impossible Dream”