Life Science Tools of the Trade

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.”