Life Science Tools of the Trade

I know hbogerd has told you about the great vendor show where he came back with a banana. What he failed to mention is what became of the banana. I had seen the recipe for the banana freeze so many times on the back of the non-fat milk…I just kept forgetting to bring in the banana. So, what better use for the free one from the show.
I dissolved a little sucrose and NaCl in water and then let the mixture cool. To that I added a splash of acetic acid for a little tang and the mashed banana. The mixture went into the -80 to freeze to mushy. Meanwhile, I used Bogerds’ old monkey blender and mixed up a frothy mixture of non-fat milk and water. It took alittle while but the whipped topping finally started forming stiff peaks. I mixed the whipped topping with the banana mush mixture refroze it and voila…Banana Freeze! A delectable dessert for anytime.

P.S. I wouldn’t recommended freezing the dessert in the -140 or the -80. Have you ever seen A Christmas Story? (tongue stuck to the flag pole?)

Once again, I’ll show my age. “I have to do some sequencing today” meant that your whole day was planned. First task, scrubbing two large glass plates, pouring a gel and then repouring it because there was a large bubble in the middle of the gel.
Then you had to do actual reactions (four/DNA sample -G,A,T,C). Load and run the gel-double load if you hoped to read more than 80 bases. Take the gel system apart, hopefully without ripping the gel, transfer it to a large sheet of whatman paper and dry it down. Expose overnight and then manually read the sequence.
In all fairness, someone even older than myself, will probably remind me that they used to make their own DNA polymerase, deionize their acrylamide, etc.
With automated sequencing available ,”I have to do some sequencing today”, means I have fill out a sheet of paper and walk down the hall with my tube of DNA. Two days later I get back a printout of my DNA sequence in a string of G,A,T and Cs).
There are few true innovations in basic research. Automated sequencing is one of them. It wasn’t always this easy.

Okay, we have discussed what makes a good sales rep, now let’s rake “vendor shows” over the coals. I just returned to the lab from a vendor show sponsored by www.lifescienceexhibits.com and what a show it was! This was a small exhibit of B-list vendors hawking products you never use or maybe never even heard of. With a festive Halloween theme (meaning Tootsie Pops were handed out) it looked more like “Night of The Living Dead” as we zombies shuffled our feet waiting for another mini-tray of free food to be offered. Somehow I always missed the wave and ended up walking back to the lab sipping a room temperature coke and eating a banana. No, I wasn’t rude to anyone and politely said “Thanks for the banana” to the rep as I departed. Oh, I almost forgot the door prizes! If you could torture yourself by talking to 10 vendors and geting your tradeshow passport stamped by each of them, you could win either a miniscrewdriver kit (retail value $1), a fake Swiss army knife (retail value $1) and last but not least a manicure kit (retail value $1) which I assume was the army knife repackaged. I missed a golden opportunity to pick up some lab Christmas gifts.

SAB Ego-meter: red lined, major publications hounding G*******
Music: Dave Alvin “Out in California”

Okay, we have discussed what makes a good sales rep, now let’s rake “vendor shows” over the coals. I just returned to the lab from a vendor show sponsored by www.lifescienceexhibits.com and what a show it was! This was a small exhibit of B-list vendors hawking products you never use or maybe never even heard of. With a festive Halloween theme (meaning Tootsie Pops were handed out) it looked more like “Night of The Living Dead” as we zombies shuffled our feet waiting for another mini-tray of freal food to be offered. Somehow I always missed the wave of and ended up walking back to the lab sipping a room temperature coke and eating a banana. No, I wasn’t rude to anyone and politely said “Thanks for the banana” to the rep at the door as I came back to the lab. Oh, I almost forgot the door prizes! If you could torture yourself by talking to 10 vendors and geting your tradeshow passport stamped by each of them, you could win either a miniscrewdriver kit (retail value $1), a fake Swiss army knife (retail value $1) and last but not least a manicure kit (retail value $1) which I assume was the army knife repackaged. I missed a golden opporti=unity to pick up some lab Christmas gifts.

SAB Ego-meter: red lined, major publications hounding G*******
Music: Dave Alvin “Out in California”

We’ve spent a fair bit of blogs on products we do and don’t like and the reps we do and don’t like. So, I started wondering….what is it that makes someone a good sales rep? Are there certain qualities we all agree a rep should have or does everyone have a different idea? Does the rep have to know all about the products they’re selling or do they just have to give good pricing?

Anyway, I was wondering what others think makes a good sales rep. Or conversely, what makes a bad rep?

What reminded me of the farce I went through in my previous job was a mailing from Flowgen, who are distributing (in the UK, at least) Gentra’s VERSAGENE™ range of DNA purification kits - genomic DNA that is, from blood.

Superficially it looks like a method that was developed at the company I worked for about 7 years ago. The methodology was based on a particular filter paper from a well-known filter paper manufacturer that had special properties. The manufacturer had a line of forensic papers that it supplied to police forces around the world, and we were particularly interested in DNA profiling (we had a state of the art ABI machine and could do SNP analysis, fingerprinting, the works).

So we had this method that involved 1 ml whole blood, two solutions, a column, a heating block and 10 minutes. Whole blood was applied to the column (which was basically a holder for this filter paper), sucked through under vacuum, lysis/binding solution added, suck, wash with same, suck, add water/TE and elute with heat. This last stage I seem to remember did not require negative pressure; the eluate just dripped through. And all this happened in under ten minutes. Yeah, the DNA was shagged - single stranded and 20 kB max - but it gave beautiful PCR data. Probably because it was single stranded.

It was a world-beater, but marketing were not happy. Oh no - my brief was to scale this up to handle 10 ml whole blood, using exactly the same technology (and also apply the same technology to bacterial cultures for plasmids, yeast, faeces . . . - I kid you not. That’s the kind of mentality I had to deal with), handling twenty four (24! That’s a whole unit of blood!) samples simultaneously. I played around with it for a week and announced that it could not be done. It wasn’t possible to elute the DNA from the filter in columns that could handle 10 ml blood without cooking it completely. It could be done if the protocol could be extended to an hour (the time it took to filter the solutions was much longer than for the 1 ml prep - this is obvious if you know anything about vacuum pressures and cross-sectional area), but even then yields were pretty poor. Nope, marketing wanted 10 minutes and no black pudding.

I wasted six months of my life on the project before landing a job I saw advertised in Nature and was replaced by two people who still hadn’t got the 10 ml scale prep working two years later.

But the point is the bloody management insisted that we stuck with that particular filter paper, despite me clamouring that we needed to try something else. I swear the CEO was on the take. Had we been able to find a more suitable matrix we’d have had a decent product, without an RBC lysis step and five solutions, five years before Gentra came out with this kit which - let’s be frank - is early 1990s technology at best. And this is symptomatic of the industry - there has been no real innovation in DNA extraction technology in ten, fifteen years. Yet Qiagen, Promega, the rest of them are slapping us with 800% markup on each and every prep they sell.

You’ll forgive me if I’m somewhat disillusioned.

I started thinking about what it is that makes someone stay in research. Is it the overwhelming successes you have? Is it the sense of accomplishment one feels when they get a clone that isn’t useful? What is it that makes scientists go to work day in and day out to fail? What other job is mostly failures? I’m not sure why any of us keep doing it.
I do know why I started in research. The illusions of grandeur; finding a treatment or a cure, knowing you helped someone, or a major scientific discovery. Now I’ve been in science awhile (not nearly as long as hbogerd) and most would say that I’ve been fairly successful(again not as successful as hbogerd). I haven’t cured anything and probably won’t but I do have my own projects and a fair number of decent publications.
I guess lately I’m questioning why I’m doing this. So, my question to you is: what is your motivation to keep plugging away at things that don’t work most of them time?

If I were someone else I might recommend a certain Book to hbogerd. But I’m not, so I shan’t. And not just because he’s a prude, either.

As for cloning, I use a hand-held UV lamp (high wavelength/low energy) for cutting out from gels, and have done ever since I discovered that the low wavelength jobbies crosslink Ts. An additional benefit is that the hand-held things (and I’m with Bogey on the ‘Pure blue light? What?’ reaction) don’t give you sun burn.

I have been burned by an ‘old-school’ transilluminator. It was in my previous job, and I was demonstrating to Charlie the machine I’d just revamped and reprogrammed (Charlie = VC = Venture Capitalist. You had to be there). This was a machine that would take 12 x 1.5 ml overnight bugs and prep plasmid DNA from them. The machine itself had launched about a year before I arrived at the company and bombed spectacularly, because it didn’t work. I spent six months working on the manual DNA extraction kit range, making them work and saleable so that the company actually had an income, and because I was successful at that I was put in charge of the refurbishment of the machine, which was the company’s raison d’etre.

So in the middle of the project (I had to re-do the chemistry, and teach myself Turbo Pascal so that I could reprogram the bloody thing) we had Charlie in, and I demonstrated the New! Improved! machine. This naturally involved doing restriction digests of the plasmid DNA from different coli strains, running it all on gels and showing the results to half a dozen suits (They’re wearing black. I see you can fight in the jungle in it and at night put on some pearls and you’re ready for formal wear). We had two full face UV masks and any number of safety glasses. No worries, I thinks - let the suits have the face masks and keep the exposure down.

Wrongo. I looked like a negative racoon by the end of the day. So yeah, I’ll vote for the low energy hand-held gig
everytime.

All that is not what I came here to write about this evening. It’s something to do with that bunch of loserscompany and how if I’d been listened to we’d have been five years ahead of the market. Next time, all right?

PS I could also talk about bioinformaticians who don’t do anything useful and give talks that can be summarized in the phrase ‘proteins have domains’, but that that would be Unhelpful.

I have been trying to learn something about bioinformatics. “Bioinformatics for Dummies” doesn’t appear to be the place to start. Perhaps it should be titled “Dummies for Bioinformatics”. This primer, is too simple for someone with a minimal knowledge of bioinformatics (that would be me) but probably too complicated for a layman or laywoman. I’ve picked up a couple of bioinformatics textbooks and within the first chapter I’m lost in a gobbledegook mess of mathematics/models/statistics/jargon/etc. It all makes you feel kind of stupid until you realize the seminar you just saw was totally theoretical and didn’t contain one piece of actually data. Synteny-blah. Go do some work.

Clare Chemical Research offers a “revolutionary new optical system for transilluminators using pure blue light”. The flyer hung in the hallway warns that “UV light rapidly degrades DNA. Even during the few seconds that it takes to excise a DNA band…………..blah….blah……….blah”. This is a product that is so useless that it boggles the mind. I’ve made over a thousand clones using old school UV transilluminators. I’m not sure who would fall for this snake-oil salesmanship.

Nobody needs the “Dark Reader Transilluminator”.

But if you’re interested call………….nah, I’m not promoting this crap.

Of sexual matters: First, call me a prude but I must confess. I have never had pillow talk with the lab manager unlike some bloggers who shall not be mentioned. Of course there is nothing more erotic than a whispered “overnight ligation” or “digested to completion” but I prefer to keep my professional and personal lives separate.

RTP Gossip: Which suave, sexy (formerly) Stratagene sales rep has not only changed jobs but is apparently ready to settled down with his sweetheart?

Lab related: Roche Protease Inhibitor Cocktail Tablets.
Do these actually work? I have no idea but I add them whenever I do a protein purification out of E. Coli or do a pulldown experiment. For all I know these are sugar pills but everyone knows about the placebo effect. If it makes you feel better who cares how it works? They come in two sizes “regular” and “mini”. I use the “minis” to save a little money. The smaller tablets dissolve a little bit faster giving you a complete cocktail of protease inhibitors. I use this product and I’m not really sure why. How is that for faint praise?

Publications: A rejected manuscript! The second go around of “submitted”, okay, “resubmitted” as I climb down the ladder of success. On a positive note, I’m still one step above the ridiculous “manuscript in preparation” that shows up on CVs.

SAB: What was wrong with the site last week?
Music: Gram Parsons Anthology
Book: ” Drive Like Hell” a novel by Dallas Hudgens (is “Hell” going to activate the obscentiy filter?)

There was a question on the SAB fora a while ago regarding what to do about catalogues when you change labs. This question has taken on a new relevance for me - as I’m going to be moving in the new year. But this isn’t to a new lab in the same city or even across the other side of the country; it’s clear out to the Antipodes. So the problem has probably been answered for me - there’s no way I’m taking more than is absolutely necessary (note to self: steal the NEB catalogue).

And all my favourite suppliers are going to change. There’ll be new reps, new catalogues, new incentives . . . and new mailing lists. I’m currently torn between silently disappearing (in terms of company mailings), or returning all to sender with “HA HA SO LONG SUCKERS” in black marker on the envelopes. It’ll be interesting to see how long it takes for the new address to ‘take’.

I’ll be faced with a major problem - where do I buy the even the simplest reagents from? I’ll be probing the other lab rats of course, but as an added bonus my spouse is going to be the lab mangler. Should make for interesting pillow talk.

I got into the yeast two-hybrid business and was hoping to stun the scientific world with the great interactions I would see. It’s now been a couple of months and I feel confident when I say….I got crap! That being said the technique to transfect yeast is very simple and straight forward especially when you use the Alkali-Cation Yeast Kit from BIO 101. The kit provides everything you need to make the yeast competent and a simple protocol that you follow. Grow the yeast overnight, dilute in the AM, spin down, wash, incubate in lithium cesium-acetate, add DNA, add PEG-TE/Cation Mixx, incubate at 42 degrees and plate.
The one thing I would recommend is making the yeast competent fresh each time. They don’t seem to like being frozen like bacteria. The technique to transform yeast isn’t very complicated…..it’s getting the data you want that’s the hard part!

P.N.A.S. = REJECTED

Of course, it’s not just the science that requires reliable suppliers of quality equipment and consumables. The scientists, too, need victualization. I once read on Usenet that the four food groups are sugar, salt, fat, and chocolate. Caffeine and alcohol, however, are among the essential vitamins (Steve VanDevender).

Of these nutrients, scientists generally can not do without at least two, and usually three, of them on a weekly or more frequent basis. Free pizzas at trade shows and grad student soirees satisfy the fat and salt requirements, but this phenomenon is not widespread outwith the continental US. Caffeine, on the other paw, is consumed widely with much ceremony and gratefulness the world over on an incident timescale of minutes to hours. Alcohol is frequently used as a broad-spectrum analgesic and muscle relaxant, and when diluted with water is also very useful for cleaning and sterilizing benches. On average, we are looking at a timescale of hours to days here. Ultimately, the scientific world runs on various incarnations of the humble cocoa bean, and that my lab mangler does not like it is further proof of her continuing contribution to the oxygen deficit.
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