Wednesday, July 6, 2011

So You Want to Be a Molecular Biologist?

Short on time tonight, but this was too cool a thing to pass up.

So You Want to Be a Molecular Biologist?
I saw this link over at Credit Bubble Stocks and you know I had to click over:
DNA is now DIY: OpenPCR ships worldwide
The eagerly awaited OpenPCR kit is now shipping! UPS picked up the first batch of kits and OpenPCRs are on their way to users in 5 continents and 13 countries around the world. For $512, every OpenPCR kit includes all the parts, tools, and beautiful printed instructions – you ONLY need a set of screwdrivers.

A PCR machine is basically a copy machine for DNA. It is essential for most work with DNA, things like exposing fraud at a sushi restaurant, diagnosing diseases including HIV and H1N1, or exploring your own genome. The guy who discovered the PCR process earned a Nobel Prize in 1993, and OpenPCR is now the first open source PCR machine.

Now first I want to congratulate the OpenPCR team. It looks like they made a true performance PCR machine using basic parts and have it at an attractive price point. $512 is amazing for a good PCR machine that is reliable. The model is a 16 well (16 samples at once) which is not too bad, I would have thought maybe a 4 sample machine at most.

Garage Labs, or Home Labs have been getting more and more popular as the price points for technology have come down and the science behind the techniques is easily gobbled up in the information age. The New York Times ran an item on this which included the OpenPCR work:
Home Labs on the Rise for the Fun of Science

So is this the time to become a mad scientist yourself? Well, maybe and no.

I have to admit I am an inch away from buying an OpenPCR machine tonight. I would love to see how it works and all the effort in the project seems like it should be rewarded. Still, garage days for new era science? A few stumbling blocks come to mind.

I can only speak for Massachusetts, but there is no way you can manage biological samples (not your own) at a residence without risking huge problems.

Some biology reagents can be had from basic household items, while others really cannot. Things like alcohol and deionized water should be easy, but PCR enzymes are going to have to be ordered. PFU and Fusion are not going to get shipped to a residential address anytime soon. Consumables like DNA-free PCR tubes and other items also are not easy to get at a non-academic or business location. Pipet tips, the list goes on and on.

A PCR reaction must be seen on an agarose gel to make sense, unless you have a cool real-time system that can read DNA bands in a tube (big bucks!). To visualize DNA you can stain with ethidium bromide (potent carcinogen) or move to newer products which are non toxic but require special equipment to visualize. SYBER Green and Gold come to mind. In any case all this stuff and all the plastic stuff needs to be disposed of and once it shows up in your garbage, you are going to get a visit from the town at a minimum, and maybe a SWAT team at worse as they track down your amateur laboratory.

Clean Start Hard to Come By
For real basic things, careful handling of samples would be acceptable, but say you wanted to type ribosomal DNA from some crazy bacteria you found in the garage? How can you be sure your work space, equipment, and tools are not covered in other bacteria? DNA is everywhere, it can be a real hassle to limit contamination. DNAase and UV crosslinking are steps taken to make sure an area is clean. You want to do that to your garage?

I don't want this to come away as a nasty "I am a scientist defending my field" sort of thing. Trust me, I would LOVE to do all my lab work at home and save the commute! Please make this happen! Maybe robots in the future can be commanded form my smart phone to do the lab work?? Now there is an idea.

I have huge respect for the work by OpenPCR, and maybe for some simplified experiments using things one can get legally and easily would be excellent fun for an at home project. This stuff is not hard to learn, but can be really fun to do when you see the results. The "A-Ha!" moment is always a winner. An OpenPCR machine along with some sets of experiments enclosed? Now we are cooking. To be fair they may already be on this.

Years ago I had this idea for a company that would take a cheek cell sample from Mom, Dad, and the kids. A RFLP analysis or other fingerprinting could be done and then a high resolution picture could me sent back as a family diagram sort of thing. Of course I never got around to it. Last check, somebody did! Just like my idea way back when for a curvy radiator for cars for more surface area cooling, too late.

Have a good night.


CT-Hilltopper said...

I want someone to develop a genetic test that, if I take a swab of DNA, will automatically tell me who I'm related to all over the entire freaking workd, so I don't have to sit for hours at and do it myself.

Actually, I love researching my family tree. It's just your posting brought that to mind. LOL

CT-Hilltopper said...

In the above post, "workd" is world.


getyourselfconnected said...

C-T, maybe you are mitochondrial Eve!?

Family Physicians said...

@CT-Hilltopper! I also love to explore my family tree, it's always better to know whom you belong to & from where it all started.

Tito said...

Hey CT-Hilltopper,
Tito here from OpenPCR. DNA-wise have you checked out They have a cheap service that tells you a lot about your ancestry, and suggests connections with any potential "cousins" you have on the site!


Tito said...

First off, thanks for taking the time to share your thoughts. We would love to have you be an OpenPCR owner :)

Every one of your stumbling blocks is right, and wanted to give you my thoughts on overcoming each.

Regulations: Depends on what you're doing. There is no regulation on extracting DNA from a sample. If you want to do genetic engineering (which also involves PCR), yes I think MA has some restrictions.

There are lots of science sites and education sites with cheap stuff. Want to identify Genetically Modified Foods? Check out this kit:

Waste is important too. Good place to discuss this is the DIYbio google group. DNA sequencing is $5 to $10 a sample which is a good, less-waste alternative to running a gel.

Clean start:
Again, depends on what you're doing. Life-or-death research might be harder to do on a garage bench. But in my experience "what does my DNA say about...", "is this food genetically modified" and such are do-able without worrying about contamination of your sample.

How's that all sound? You've got a background in all this stuff so looking forwards to hearing your thoughts.

If for some reason I forget to check back here soon, shoot me an email tito ->


Watchtower said...

"Watchtower looked on in horror as the birth of shade tree genetic engineering unfolded before his very eyes, he knew it wouldn't be long before this was implemented into the dark art of robotic science by some 'yet to be discovered' phenom."

getyourselfconnected said...

Thanks for stopping in. My points were not meant to be end-all in nature, just what jumped out at me. I really think this could be a great and fun tool. Congrats on the great work.

GawainsGhost said...

For Friday Night Entertainment, I suggest some old school folk, anything by Jim Croce. "Opertator," "Time in a Bottle," "You Don't Mess around with Jim," "Bad, Bad Leroy Brown," there are so many to choose from.

I remember the day he died. I was sitting in a barber shop, getting my hair cut, when the news came on the TV. My father got visibly upset, because he was a great fan of his music. Blue collar, real, authentic, the kind of talent you don't see anymore today.

I find the 70s odd. I mean, there was economic turmoil, war, political dissention, civil unrest, it was a difficult decade to come of age in. Yet out of it came the best music from great bands.

Maybe I'm nostalgic, but Jim Croce was one of the best.

CT-Hilltopper said...

How about some Led Zeppelin for Friday night also.

@Family Physicians...I agree totally. You can't possibly know where you are going until you know where you've been. I have found out muchabout myself just by doing this.

@ Tito...thanks so much for telling me about the site. I'm going to check it out now.

@GYSC...a mitochondrial Eve??? LOL....hmmmmmm...maybe so LOL

getyourselfconnected said...

New post up in a bit folks, I do have a request!