Life Science Tools of the Trade

We have completed the network maintenance that was announced earlier this week. All our services are up and running and disruption was minimal.

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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Stealth posting:

ARTIST: Zager and Evans
TITLE: In the Year 2525

In the year 2525
If Gavilov is still alive.
If Gavilova can survive, they may find.

In the year 3535
Ain’t gonna need to tell the truth, tell no lies.
Everything you think, do and say, is in the pill you took today.

In the year 4545
Ain’t gonna need your teeth, won’t need your eyes.
You won’t find a thing to chew.
Nobody’s gonna look at you.

In the year 5555
Your arms hanging limp at your sides.
Your legs got nothing to do.
Some machine doing that for you.

In the year 6565
Ain’t gonna need no husband, won’t need no wife.
You’ll pick your son, pick your daughter too.
From the bottom of a long glass tube. Whoa-oh

In the year 7510
If Gavrilov’s a-comin, he oughta make it by then.
Maybe he’ll look around himself and say.
Guess it’s time for the judgment day.

In the year 8510
Gavrilov is gonna shake his mighty head.
He’ll either say.I’m pleased where man has been.
Or tear it down and start again. Whoa-oh

In the year 9595
I’m kinda wonderin if man is gonna be alive.
He’s taken everything this old Earth can give.
And he ain’t put back nothing.Whoa-oh

Now it’s been ten thousand years
The Gavilovs have cried a billion tears.
For what we never knew,
now man’s reign is through.

But through eternal night.
The twinkling of starlight.
So very far away.
Maybe it’s only yesterday.

In the year 2525
If Gavilov is still alive.
If Gavrilova can survive, they may find.

In the year 3535 {fade}

The author(s) recommend printing out your favorite posts from this seminal and essential blog for your offline reading during the upcoming SAB meltdown.

The Life Science Tools of the Trade Blog will experience a network maintenance outage starting on Friday May 27 at 1:00 PM EDT. Due to the nature of the maintenance some users may be able to see us back up within the hour, while others may take up to 48 hours to be able to see us back up.

Another week of failed experiments. I know bench scientists have failures, but what about computational biologists? Do they have bad weeks? How can “experiments” fail if you don’t do experiments? Drinking an old dust covered beer found in the cold room doesn’t help. Blah.

Lucky an irritating sales rep didn’t stop in this Friday PM.

What does this have to do with stamp collecting? Nothing.

Music: rare Springsteen import tracks from Japan (thanks Kenzo)
Mood ring color: black, jet black.
Weather: pissing down rain

We’ve officially heard that by December Bio-rad will no longer carry the old ready gel boxes or replacement parts. We knew it was only a matter of time but it’s taken awhile for us to transfer over to the new Criterion protein gels from Bio-rad. In general there hasn’t been any complaints with the switch. (The rep even gave us a free gel box and transfer unit to get us started) The larger gels have more wells so you can run more samples in the same amount of time as you would the smaller gels. That being said the general consensus is that these larger gels require a longer time to transfer to membrane. (All of us are really impatient and so we try to cut corners where ever possible!) That being said….I would transfer a minimum of 90 minutes with the plate electrode transfer box with these gels. I run rainbow markers and there have been a few times when they aren’t fully transferred at 60 minutes. Obviously sometimes it doesn’t matter but….when the samples are important or the protein isn’t expressed really well…take the time to let it transfer a bit longer.

P.S. There is a somber mood in the lab today…the music isn’t even playing! Not a good week for science.

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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We had an order come in yesterday that had a big sticker on it “Sat. Delivery”. Another read “refrigerate on arrival.” We opened it up and sure enough, room temp cooler packs and warm reagents. The vendor was really good about replacing the product (fresh and cold ones came in this morning) but it got me to thinking. How often does this happen, and how much is it costing vendors? I’ve actually never asked a rep this question…perhaps I could. Another issue, do any institutions have cold storage holding facilities for this type of problem? Seems like a lot of money is getting wasted b/c things get shiped on Friday afternoon.

Random iPod song: This is how it Goes by Amiee Mann

PS. I’m starting a fund for an iPod for hbogey…donations welcome…what is vinyl anyway?

Although experiments pretty much s*cked last week, I did go to a great concert on Thursday! Patty Griffin at the Cat’s Cradle in Chapel Hill, NC. What does this have to do with science? Not much but I’ll try and tie it in somehow. Can you imagine a scientist holding an audience captive for two hours and have them begging for more. Have you ever seen a standing ovation at a seminar? How about an encore…I stand up and hold my Bic lighter aloft, screaming “More, more, more”………….the crowd stamps its feet, begging for just one more slide! Perhaps the trading cards of scientists wasn’t such a good idea.
Vendor show………..Roche (Susan) last Tuesday………plenty of bagels, coffee and no b*ll$h#t. Thanks for the samples. I hope the maxipreps kits work out for us so we can give Qiagen the heave-ho. What the hell is that insoluble fuzz pellet in Qiapreps?
FYI-two sales reps (who shall remain anonymous) told me they saw their names (Susan/Roche and Rob/ISC) here. Yes, apparently someone reads these.

On the IPOD-what iPOD?
On the turntable: Steve Jordan (the Jimi Hendrix of the accordian). Yes, real vinyl.
Books on tape with the family: “Joey Pigza swallowed the key?” by Jack Gantos A first-person fictional story about a 10 year old with ADHD (ages 8-11). Both funny and sad, well worth reading for kids and adults.
Book: “The Bones” by Seth Greenland

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.

AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCKKKKKKKKKKKKKKKKKK!
I tried to enter a blog and it never uploaded from my computer (or so it seems)………….I look at the SAB site and my stuff is published a dozen times…………as I delete it, it replicates like a virus……………which edit do I click on?
Ah, it probably wasn’t worth reading or writing anyways.
Blah.

Nothing much to report, since I have never seen a sales rep on Saturday. Last week was the kind that makes you think of alternative careers, but here I am Sat. AM, back on the horse, repeating the stuff I screwed up last week. While ligating, I’ll stream a random thought. As I kid I collected trading cards and bdoehle’s glob about postage stamps got me thinking………………are there trading cards honoring scientists. Forget those steroid munching baseball players…………….. what about the real heroes? Would fanatical scientist trading card collectors trade 4 bdoehles for one Aubrey de Grey? Linus Pauling for Gavilov? What would a rwintle or hwiegand card be worth? Would a hbogerd card be worth anything? A google search led me to this site:
http://www.sagecrossroads.net/Default.aspx?tabid=147
I wonder if they include a stick of gum with every pack?

When I read the article entitled “New Postage Stamps Honor Four Scientists” online today I couldn’t believe that our blog had become so prostigious so quickly. How could it be that we had been so honored without even a hit of this getting to us before it hit the newswire? Why is the cerimony being held at Yale without us in attendance? Then I realized that we were not being honored, instead Josiah Willard Gibbs, Barbara McClintock, John von Neumann, and Richard P. Feynman will be adorning the US postage stamps. Oh well, I guess I need to win a Nobel Prize before I get a stamp with my picture on it.

For anyone who is interested here is a link to the story on Yahoo!:
http://news.yahoo.com/s/ap/20050504/ap_on_sc/science_stamps;_ylt=AlIicTdreZjxItKVLxer0ses0NUE;_ylu=X3oDMTA2aWxpajE2BHNlYwNzYw–

I liked the Caped Avenger’s Random iPod Selection so I will add my own: Blue Bayou by Roy Orbison
Caloric Intake: 10X Hbogerd’s

A sales rep stopped by the lab a few weeks ago. Noticing the blue wall of Qiagens he hawked their spin columns for mini-preps. The catch-you need to have Qiagen solutions leftover to use them (they only supply the columns). I took the two spin columns, tossed them on a shelf and forgot about them. Like an elephant, a sales reps never forgets (except the time she forget to get me a quote-no names, but you know who you are). “Have you tried those samples yet?” I had completely forgotten and just couldn’t get excited about saving a few pennies per sample, and those pennies were dependent upon having leftover solutions from another kit. I wonder how many times he’ll come back before he gives up on me and considers those two spin columns a write off? Oh, the company is Genesse Biosomething, thus the reference to a really really bad beer of my youth.

NEB #1-did you know that NEB enzymes will only cut in NEB buffers? Obviously, that is not true but I was told that once by a post-doc.
NEB #2-the NEB supplied BSA is great to use as a protein standard. I have never added it to a restriction digest.
NEB #3 their enzymes and catalog are top quality.

Caloric intake: ~1800 calories
Book: “Mongo -adventures in trash” by Ted Botha (a non-fiction book which examines the culture of dumpster diving/recycling).
Music: The Pleasure Barons “Live in Las Vegas”
Obscure hbogerd reference that is not worth mentioning: the seminal, yet nearly forgotten: “Human retrovirus-related synthetic peptides inhibit T lymphocyte proliferation”, Immunology Letters, 19 (1988) 7-14

Bonus question : Does publishing in journals with extremely low impact factors actually hurt your career?

I’m sitting here, trying to work out how I can mutate leucine into aspartate and simultaneously introduce a restriction site so that I can check if the mutagenesis worked with a simple digest rather than having to wait for sequencing. Let’s see . . . TTA to GAT, and there’s ATC before that - TCGA is palindromic, plus A and T . . . ClaI!

Page 214 of the NEB catalogue, I salute you.

I’ve known labs that don’t even use New England Biolabs (NEB) enzymes keep a copy of their catalogue. On the off chance that you’ve been living on Mars for the last decade or more and don’t know what I’m talking about (say ‘Hi’ to the rovers for me, and what did you do with Beagle 2?), the NEB catalogue is an indispensable reference. It is little exaggeration to claim that I use it every day when I’m doing molecular biology.

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