Life Science Tools of the Trade

So, a local sales rep for a certain Qompany that sells mainly kits, but also robots, came by my office recently with a promotional flyer. An invitation, if you will, to a V.I.P. event - a showcase of their new robotic, liquid-handling, sample-preparing, all-singing, all-dancing box. A box with a lovely name, evocative of orchestras.

Now, I’ve made no bones in the past about not this not being my favourite of companies, their sales tactics ranging from dubious to downright annoying. And this fits right in… a V.I.P. event, you say? Then why, I ask, is it from 9:00 AM to 4:00 PM in a conference room? With refreshments all day? “Oh, don’t post this notice, I don’t want this open to everyone… just a select few.” They sure know how to make a fella feel special, I tells ya.

Oh, and the robot in question? Well, the sales rep described it to me as being a box that you can put any kind of sample into, and get any kind of prep out. Cells in, RNA out. Brain in, DNA out. Fossilized pterodactyl bones in, highly purified Jak Kinase out, that kind of thing.

I think I may give this one a miss.

In this post-90’s biotech era which we all inhabit, I’m finding that brand recognition is becoming a confusing game indeed. Old favourite boutique vendors like Molecular Probes have been swallowed up by enormous, multi-tentacled distributors like Invitrogen, and keeping track of who’s distributing your favourite brand of pipettor, or water filter, or tissue culture media, can make for hours of fun and games. Even the big players keep getting bought and sold – just try to sort out the whole Merck/EMD fine chemical business, or the ownership structure of VWR, if you have some time to kill. And I’m still trying to get my head around Thermo Fisher. What does Thermo Electron have to do with distributing pipette tips and latex gloves? How, if at all, is this related to Thermo Finnigan? It makes my head hurt just thinking about it.

And then there’s my personal favourite suite of technologies du jour, loosely grouped into “next-generation” DNA sequencing, or NGS. Illumina buys Solexa, Applied Biosystems buys Agencourt Personal Genomics (but not Agenourt Bioscience, which is owned by Beckman Coulter – are you following this?), Roche gobbles up 454 Life Sciences. Pacific Biosciences is next, mark my words, with rumours of intense interest from Applied Biosystems, and probably many others. Helicos too, perhaps, so look for a merger or acquisition there, although with a market cap of $147 million and $50 million in the bank at the end of 2007, they could probably stay on their own for a while.

In the case of Illumina’s almost-works-most-of-the-time Genome Analyzer, most people still call it a “Solexa”. At the recent AGBT conference, which I’ve rattled on about in more detail elsewhere, practically the only people using the term “Illumina Genome Analyzer” were members of the large posse of Illumina employees in attendance. And most people don’t call the ex-454 machine a “Roche” GS-FLX; to most, it’s still a “454”, although this seems to me to be waning a bit under the crushing weight of Roche’s marketing machinery. Remarkably, the 454 Life Sciences website still exists, and is still a much, much better source of information on this NGS system than the Roche website, which is large, messy, and rather full of the 150,000 other things that Roche sells.

On the other hand, Applied Biosystems seems to have triumphed in branding their SOLiD system, and virtually nobody seems to remember that this was developed by Agencourt Personal Genomics and that the chemistry used was, for a time, referred to as the “APG process”, even by AB itself. Now it’s just SOLiD, small “i” and all, and the scientific community in general seems to have accepted that brand. Timing, I suppose, is everything.

Now, if someone could just explain to me why all these darn NGS boxes are blue…

The latest email from them says this is my third and final notice. If I do not respond to this email they will terminate my subscription. Thank goodness.

This is one of those mailing lists I got on from a vendor show and don’t know how to get off of. I have my doubts whether not responding to the email will actually terminate the subscription but I’m keeping my fingers crossed.

These types of magazines might interest some but I don’t have any interest in thumbing through a magazine of advertisements.

Well, as Kat mentioned over at the SAB, I am now activated, Word-Press-enabled, and ready to jump into this whole Life Science Tools of the Trade thing, joining my virtual colleagues hbogerd and hwiegand.

As some of you know, I’m a Blogger kind of person so far, so this post is as much about introducing myself as it is about seeing whether I can work out how WordPress works. So far, so good, nothing’s caught fire yet. I will doubtless be posting many erudite comments on the technologies we all use (or more likely, those that fail us miserably), but in the meantime I’l leave you with a teaser: yes, we have a next-generation DNA sequencer; no, it doesn’t work as well as advertised; and we just finished our first client project, a ChIP-sequencing experiment, after seven months of trouble-shooting since delivery. That’s about average, folks.

At a vendor fair I picked up a free sample of Agarose Tablets from BIOLINE! The little white pills of agarose eliminate the  messy task of weighing out agarose! Okay, unlike LB powder or SDS, weighing out agarose isn’t really that messy. The little pills do save you the time you’d spend weighing out the agarose. Unfortunately, the pills have to dissolve for for 6 minutes in your buffer before you can microwave/melt them. Okay, no time saved. Safer to use?? I have no idea what that even means. The agarose tablets are probably MORE dangerous. Swallow one of those suckers by accident and I bet you’d be plugged up for days. Oh yeah, and they’re more expensive.

Thanks but no thanks.

A co-worker asked if I’d help her with some cloning. She had the strategy all figured out. The oligos were here and the pcr was done for the insert. All I had to do was digest the insert fragment and the vector backbone, purify them and ligate them together. Seemed like it should be easy enough.

That was until I looked at the enzymes. Urgh! They were two of those enzymes you only use under dire conditions. One cuts at 37 degrees, the other at 50. AscI only cuts 100% in NEB buffer 4, the other one only in buffer 3. I gave her a hard time about passing the more *difficult* cloning on to me. She said she knew about the temperature difference but that both enzymes cut in buffer 4. Huh? I had just checked the NEB catalog and knew that wasn’t right. BsaI only says it has 50% activity in buffer 4.

What was going on? We both felt like were going crazy. She brings her 2005-2006 NEB catalog over and shows me. BsaI and AscI both cut in buffer 4 - 100%. I look in my 2007-2008 NEB catalog and BsaI only cuts 50% in buffer 4. Turns out were both right. Sorta.

I’m not sure what changed. Is NEB purifying the enzyme differently? Did they just realize it didn’t cut as well as they had thought? Whatever the reason, the recommend buffer has changed. I’m not sure how many other buffers have changed but if you have an old NEB catalog hanging around you might what to get a newer one!

PS - Turns out neither one of us has had a whole lot of success with the cloning so far. I’m still not sure which is the best buffer to use!

The full text article is available for purchase

$59.66 plus tax

for a  1991 Virology  article? 

No thanks. I wonder what is the highest price a journal charges for access to an article? Does anyone actually buy single articles? More importantly, why am I trying to get access to that crappy (probably)  old (definitely) article on Sunday night?

Bill Clinton’s memorable attempt at legalese evasion (what the definition of “is” is) during the Monica Blewinksy hearings made me wonder what the dfinition of “it” is. Today I wore my Promega promo t-shirt. The slogan? “Research makes me do it”. It? It depends on what your definition of “It” is. What does research make you do? It certainly doesn’t make me do “it”.

It just arrived! DHL just delivered the free t-shirt that I signed up for a couple of weeks ago. It came shrink wrapped in the shape of a t-shirt. Do you know what I mean? Those shirts you can buy that are packaged to look like different shapes. I’ve seen shirts and towels being sold like that but never got one. Holy Cow! You open up the package and the shirt is so wrinkled. It really is amazing.

Promega gets credit for following through on the shirt promotion. I have to admit, though. I’m not sure I’ll wear a shirt that says “Research makes me do it.”

Has the High School musical craze reached the science world? If you haven’t seen Bio-Rads PCR song, you need to check it out!

Scientists for better PCR

I’m still undecided. Is this suppose to be taken seriously?

I received a flyer for Clontech’s In-Fusion PCR Cloning System in the mail. I do try and scan the junk mail I receive, looking for the jewel in the junk. In-Fusion is a method of cloning that uses regions of engineered homology on your PCR generated insert and vector of choice to ligate without cutting your PCR fragment. Interesting. Maybe. Looking at the “time saved” flow chart. 30 minute ligation insead of 16 hours! That saves an entire day….if you still ligate overnight. In fairness, a footnote (in small print) reads “newer 5 min T4 DNA ligase reactions could be used”.   The real laugher is provided by the jokers in advertising when they comapare In-Fusion’s cloning efficiency with T4 DNA ligase’s. In-Fusion, obviously, is rated “High” (surprise) for both  .1 to 4 kb and 4 kb to 10 kb inserts. T4 DNA ligase PCR Cloning? No data available! Really? No data available? In-Fusion is better, much better when we compare it to “No data available”.

Clontech looks like a contender for the BioTech Bullshitter award for 2008!

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The Magic Eight Ball says “Doubtful”.

I complained about the ridiculous and useless plastic boxes Operon started sending out if you ordered a single oligo in this blog a month ago. I received two shipments of oligos on Friday (1/11/08) in the paper sleeves of old. Did Operon listen or did they just run out of the Operozone destroying boxes?  I’d like to think they listened to a wave of consumer complaints. The next couple oligo shipments will tell.

Having ragged on Operon for their environmental blunder, I’ll add that Operon oligos are great quality at a great price. I  wonder if the bozo (with the MBA) that came up with the petroleum product oligo carrier was fired?

sure makes it hard to get much stuff accomplished on the Monday.  Set a few things up.  In general, though, I didn’t want to set things up that I’d have to worry about tomorrow.  Thanks to my cells looking weird this morning I’ll be in briefly to do a transfection.   Other than that it’ll be a quiet, relaxing 1st of the year.

Have a great start to the New Year!

For many months I’ve been getting science equipment fliers/magazines sent to my home address.  Somehow my name got sold and I’ve been getting all kinds of crap - AT HOME!!  The worst part is trying to gett them to stop sending stuff.

One *subscription* was finally expiring.  At least that’s what the telemarketer kept saying when he called the lab daily.  I think, finally, they got the point.  Sorry to Hal and the others who kept fielding these annoying calls.

To all you companies:  Please don’t call anymore, take me off your list, I don’t want your magazine(s)!!

Please.  Save a few trees instead.

Are you listening?

Plastics.

I guess someone at Operon saw “The Graduate” and took that advice to heart. I used to receive oligos from Operon in a paper corrugated sleeve. It could hold up to eight oligos. You could reuse it, recycle it or just throw it out and not feel too guilty.

Today I received an (meaning literally ONE) oligo I had ordered. It came in a plastic box, clearly marked OPERON, with a difficult to remove recessed lid as an added bonus. It must use about 20 times the plastic that was used in the screw top oligo tube.  I guess you could use it as a semi-waterproof bullet box on weekend deer hunting trips.

As most manufacturers (and consumers) make an effort to use less plastic in their packaging I’d like to nominate Operon for the “We support global warming award of 2007″!