for the budding Bene Tleilax
December 5, 2011 11:10 AM Subscribe
The quest for the $500 home molecular biology laboratory Molecular diagnostics and molecular biology in general are becoming more pervasive every day in a range of applications. For some time there have been attempts to build an affordable diy machine to explore this fascinating science. OpenPCR (polymerase chain reaction) received quite a bit of publicity with their $599 system. Each of these have had problems and were not quite suitable for students. Here is an attempt to get the price even lower and to simply the construction process. Previously on Metafilter
Guess what was used in the very very early days instead of a machine? Three water baths at three different temperatures with the lab flunky moving tubes from a water bath to another. Failure rate was high, but it was cheap.
posted by francesca too at 11:30 AM on December 5, 2011 [3 favorites]
posted by francesca too at 11:30 AM on December 5, 2011 [3 favorites]
"Home molecular biology? Sweet- what could possibly go wrong!?"
Honestly? Not that much more than home stamp collecting. Genetic engineering of anything metazoan is still way out of the range of anything like a home anything. Whereas there really isn't much we could do to a microbe that Nature couldn't do better.
posted by Blasdelb at 11:43 AM on December 5, 2011 [3 favorites]
Honestly? Not that much more than home stamp collecting. Genetic engineering of anything metazoan is still way out of the range of anything like a home anything. Whereas there really isn't much we could do to a microbe that Nature couldn't do better.
posted by Blasdelb at 11:43 AM on December 5, 2011 [3 favorites]
I would be really excited to get one of these, but I'd have no idea what to do with it. I kind of feel like I'm failing my kids by not teaching them more bio, especially genetics.
posted by DU at 11:53 AM on December 5, 2011
posted by DU at 11:53 AM on December 5, 2011
Awesome! I shall print this out and call it my Christmas list.
posted by sc114 at 11:56 AM on December 5, 2011 [1 favorite]
posted by sc114 at 11:56 AM on December 5, 2011 [1 favorite]
All I want for Christmas is this, a breeding pair of ferrets, and one of those $1 abandoned, used missile silos.
posted by Slackermagee at 12:02 PM on December 5, 2011 [5 favorites]
posted by Slackermagee at 12:02 PM on December 5, 2011 [5 favorites]
If this will help me make better yogurt, I'm in.
("Introductory biology course not included"? Consarnit!!!)
posted by BrashTech at 12:07 PM on December 5, 2011
("Introductory biology course not included"? Consarnit!!!)
posted by BrashTech at 12:07 PM on December 5, 2011
Is there a guide online for doing DNA fingerprinting at home? It seems you'd only need the right PCR primers (are they cheap?), a PCR kit, and a gel electrophoresis setup (I know the electrophoresis machine is easy -- but are there good non-toxic dyes?). That would be a pretty amazing experiment for kids.
posted by miyabo at 12:08 PM on December 5, 2011
posted by miyabo at 12:08 PM on December 5, 2011
Oh, I see one of the links suggests using methylene blue as the dye, which is non-toxic. So are there PCR primers for the long-chain repeats used in DNA fingerprinting?
posted by miyabo at 12:11 PM on December 5, 2011
posted by miyabo at 12:11 PM on December 5, 2011
Why spend $500 when you could just get a sack of ferrets for half the price?
posted by zeoslap at 12:28 PM on December 5, 2011
posted by zeoslap at 12:28 PM on December 5, 2011
That would be a pretty amazing experiment for kids.
Though maybe awkward for their parents.
posted by phrontist at 12:29 PM on December 5, 2011 [4 favorites]
Though maybe awkward for their parents.
posted by phrontist at 12:29 PM on December 5, 2011 [4 favorites]
"The problem is, right now extracting and amplifying DNA at home still takes too many steps. The guys are worried that people won’t enjoy the process if it’s too complicated."
Living in the future is neat.
posted by poe at 12:33 PM on December 5, 2011
Living in the future is neat.
posted by poe at 12:33 PM on December 5, 2011
Getting technology like this into the hands of people outside of the pharmaceutical companies, hospitals, and universities is a very very good thing.
I figured up the cost of a simple DNA extraction the other day: by my quick estimates, the reagents alone could cost ~$100 dollars.
Then you need glassware/tubes, pipettes, and centrifuges, which, although possibly available through university auctions of surplus equipment, add to the cost.
That's just what you'd need to get your own DNA samples to amplify your primers on, so extraction is another economic barrier to entry.
Then you'd need primers that you think would amplify selectively, and in the case of DNA fingerprinting I think you'd be looking at microsatellite sequences (in any case, sequences with high mutation rates), so you could probably order relevant primer sequences from biotech companies.
So it's not entirely out of the hands of big pharma/big bio yet, but it's getting there, and that's exciting!
posted by edguardo at 12:33 PM on December 5, 2011
I figured up the cost of a simple DNA extraction the other day: by my quick estimates, the reagents alone could cost ~$100 dollars.
Then you need glassware/tubes, pipettes, and centrifuges, which, although possibly available through university auctions of surplus equipment, add to the cost.
That's just what you'd need to get your own DNA samples to amplify your primers on, so extraction is another economic barrier to entry.
Then you'd need primers that you think would amplify selectively, and in the case of DNA fingerprinting I think you'd be looking at microsatellite sequences (in any case, sequences with high mutation rates), so you could probably order relevant primer sequences from biotech companies.
So it's not entirely out of the hands of big pharma/big bio yet, but it's getting there, and that's exciting!
posted by edguardo at 12:33 PM on December 5, 2011
I like how he didn't calculate the cost of the consumables (polymerase, primers, gel stain, ladder, centrifuge tubes, pipet tips etc)
posted by euphorb at 12:35 PM on December 5, 2011
posted by euphorb at 12:35 PM on December 5, 2011
Fortunately for the parents, figuring out ancestry based on DNA requires a hell of a lot more equipment than anyone can fit in their basement.
posted by miyabo at 12:35 PM on December 5, 2011
posted by miyabo at 12:35 PM on December 5, 2011
Honestly? Not that much more than home stamp collecting. Genetic engineering of anything metazoan is still way out of the range of anything like a home anything. Whereas there really isn't much we could do to a microbe that Nature couldn't do better...
Not better perhaps, but...
Bird Flu Research Rattles Bioterrorism Field
I'm not saying that a $500 home molecular biology lab = bioterrorism kit, but if you make all the components for doing this sort of thing cheap and readily available, someone will eventually string them together to do not-so-nice things. This is a little more serious than setting fire to your parent's garage or blowing up the high school chemistry lab.
posted by CosmicRayCharles at 12:40 PM on December 5, 2011
Not better perhaps, but...
Bird Flu Research Rattles Bioterrorism Field
I'm not saying that a $500 home molecular biology lab = bioterrorism kit, but if you make all the components for doing this sort of thing cheap and readily available, someone will eventually string them together to do not-so-nice things. This is a little more serious than setting fire to your parent's garage or blowing up the high school chemistry lab.
posted by CosmicRayCharles at 12:40 PM on December 5, 2011
Caveat emptor w/ OPENPCR.
I like their moxie. I like DIY BIO as a concept. I've talked at a DIY bio seminar series.
I was happy to contribute to a couple of people who wanted to do so much..... I gave them money and obained a written agreement from them to supply a couple of their thermocyclers assembled by a certain date and.......... no contact ever again, despite repeated inquiries and deadlines passing.
I have left messages with both Tito Jankowski and Josh Perfetto. No reply. Money gone. Some would call this fraud or theft. At best they are simply unreliable. I hope to be able to retract this comment but as it stands: STAY AWAY.
posted by lalochezia at 2:11 PM on December 5, 2011
I like their moxie. I like DIY BIO as a concept. I've talked at a DIY bio seminar series.
I was happy to contribute to a couple of people who wanted to do so much..... I gave them money and obained a written agreement from them to supply a couple of their thermocyclers assembled by a certain date and.......... no contact ever again, despite repeated inquiries and deadlines passing.
I have left messages with both Tito Jankowski and Josh Perfetto. No reply. Money gone. Some would call this fraud or theft. At best they are simply unreliable. I hope to be able to retract this comment but as it stands: STAY AWAY.
posted by lalochezia at 2:11 PM on December 5, 2011
That's troubling, lalochezia. It's a long shot, but you could try MeFi mailing Tito.
posted by exogenous at 2:15 PM on December 5, 2011
posted by exogenous at 2:15 PM on December 5, 2011
"Not better perhaps, but...
Bird Flu Research Rattles Bioterrorism Field"
The whole business was overblown scaremongering, that incidentally will likely get in the way of useful science. There is nothing that those guys were doing with ferrets that doesn't happen daily in poultry farms on a colossal scale with avian infections in the millions on three continents. In Delaware where your chicken breasts are manufactured there are outbreaks of flu that are at least as virulent and contagious as anything they came up with but on a scale of deaths in the millions not hundreds. They were simply paying attention to what factors allow it to happen. The flu evolves fast and doesn't need someone in a laboratory to mix and match its pieces.
For the strains developed in that ferret model to present a genuine danger of being used as bioweapons on people and not just ferrets, a parallel experiment exposing people to massive doses of it over time and then serially transferring infectious fluids through more people. You'd need a hell of a lot of people under significant amounts of control and they wouldn't be enthusiastic. Even then all you would be doing is mimicking nature. Not something that isn't necessarily un-doable, also but not a lone wolf or home kind of thing and no matter how many resources the malefactors might have there would be no guarantee of success.
Of course some dude snorting ferret snot in his basement would present an incredibly serious public health risk, any non-zero chance of what could become the greatest calamity mankind has ever known is beyond serious, but that dude is vanishingly unlikely to succeed. In order of descending likelihood,
A dude in his basement would be vanishingly unlikely to make anything that would ever infect humans.
Even if they did they would most likely successfully infect themselves accidentally but be incapacitated before they could even try to spread it.
If they did infect themselves they would most likely die without ever generating human human contagious particles. As unlikely as they would be to find a particle capable of adsorbing to their cells, they would be even more unlikely to find one that can both adsorb and productively infect their cells before finding the first.
Then even if our idiot lone wolf managed to start productive infections in himself, those particles would be unlikely to be capable of both adsorbing and productively infecting the cells of those he managed to come in contact with, even if he could get out of bed.
Even if our lone wolf rolled fantastically well and passed all of these barriers to infect a someone or two, they would then only be so much more likely to pass it on
The knowledge that we can do this with diseases has existed since before we even knew what viruses were, its how we eliminated one of the great plagues of the bible.
That said if we ever got wind of someone trying to pull this kind of shit, I would be totally cool with the CDC borrowing a predator drone to address it.
posted by Blasdelb at 6:58 PM on December 5, 2011 [1 favorite]
Bird Flu Research Rattles Bioterrorism Field"
The whole business was overblown scaremongering, that incidentally will likely get in the way of useful science. There is nothing that those guys were doing with ferrets that doesn't happen daily in poultry farms on a colossal scale with avian infections in the millions on three continents. In Delaware where your chicken breasts are manufactured there are outbreaks of flu that are at least as virulent and contagious as anything they came up with but on a scale of deaths in the millions not hundreds. They were simply paying attention to what factors allow it to happen. The flu evolves fast and doesn't need someone in a laboratory to mix and match its pieces.
For the strains developed in that ferret model to present a genuine danger of being used as bioweapons on people and not just ferrets, a parallel experiment exposing people to massive doses of it over time and then serially transferring infectious fluids through more people. You'd need a hell of a lot of people under significant amounts of control and they wouldn't be enthusiastic. Even then all you would be doing is mimicking nature. Not something that isn't necessarily un-doable, also but not a lone wolf or home kind of thing and no matter how many resources the malefactors might have there would be no guarantee of success.
Of course some dude snorting ferret snot in his basement would present an incredibly serious public health risk, any non-zero chance of what could become the greatest calamity mankind has ever known is beyond serious, but that dude is vanishingly unlikely to succeed. In order of descending likelihood,
The knowledge that we can do this with diseases has existed since before we even knew what viruses were, its how we eliminated one of the great plagues of the bible.
That said if we ever got wind of someone trying to pull this kind of shit, I would be totally cool with the CDC borrowing a predator drone to address it.
posted by Blasdelb at 6:58 PM on December 5, 2011 [1 favorite]
iirc, we get primers for about $0.22 per base pair (bp). This is enough for between several hundred to several thousand reactions. Basic primers generally run about 15-30 bps. Longer primers are required for site directed mutagenesis or for more sophisticated cut and paste methods and run between 30-70 bp, sometimes hundreds of bp. Longer lengths are more expensive and you get a lower yield (less reactions). Pfu Ultra II is a good polymerase for cloning and runs $100 for 40 reactions.
We got a sweet deal from a clueless business manager and we get 1kb sequencing reads for $2.5. No matter how many primers we use. We shamelessly take advantage of them; one template sample and five or six primers. $2.5 for 4 or 5kb of reads, enough for most mRNA derived genes.
There are some blue-light DNA contrast dyes that doesn't require UV and isn't particularly toxic (not that ethidium is that bad, but requires specialty disposal). They work "ok" but ethidium is still the best.
You'll need a stock of various restriction enzymes. The more the merrier. A score to a hundred. If you could figure out a way to have a communial collection, that will save a lot of money. A common dirt-cheap restriction enzyme, EcoRI runs $50 for 10,000 units so depending on how you use it, you might get something like 100-200 actual reactions.
Old-fashioned Alkaline lysis minipreps for getting plasmid out of bacteria is pretty cheap. You'll need disposable tubes and a tabletop (at least) centrifuge.
Basic agar dishes with antibiotics are pretty cheap, and doesn't necessarily require autoclaving. You'll need a heated shaker, too. I'm wary about just throwing out antibiotic bacteria so you probably really want to have at least a small autoclave or high quality pressure cooker.
Pipettes will run you a couple thousand. A basic thermocycler will run you $6k.
But as long as you avoid relying too much on kits, if at all, old-school mol biol isn't all that expensive. If you're really that hardcore, you could even start purifying your own enzymes.
posted by porpoise at 7:16 PM on December 5, 2011
We got a sweet deal from a clueless business manager and we get 1kb sequencing reads for $2.5. No matter how many primers we use. We shamelessly take advantage of them; one template sample and five or six primers. $2.5 for 4 or 5kb of reads, enough for most mRNA derived genes.
There are some blue-light DNA contrast dyes that doesn't require UV and isn't particularly toxic (not that ethidium is that bad, but requires specialty disposal). They work "ok" but ethidium is still the best.
You'll need a stock of various restriction enzymes. The more the merrier. A score to a hundred. If you could figure out a way to have a communial collection, that will save a lot of money. A common dirt-cheap restriction enzyme, EcoRI runs $50 for 10,000 units so depending on how you use it, you might get something like 100-200 actual reactions.
Old-fashioned Alkaline lysis minipreps for getting plasmid out of bacteria is pretty cheap. You'll need disposable tubes and a tabletop (at least) centrifuge.
Basic agar dishes with antibiotics are pretty cheap, and doesn't necessarily require autoclaving. You'll need a heated shaker, too. I'm wary about just throwing out antibiotic bacteria so you probably really want to have at least a small autoclave or high quality pressure cooker.
Pipettes will run you a couple thousand. A basic thermocycler will run you $6k.
But as long as you avoid relying too much on kits, if at all, old-school mol biol isn't all that expensive. If you're really that hardcore, you could even start purifying your own enzymes.
posted by porpoise at 7:16 PM on December 5, 2011
Flu? At 13.5kb, I'd want an oligosynthesizer and a flu-compatible viral vector (I'm sure they're available, but I wonder what reaction I would get requesting a sample?), which can package co-transfected genetic material. And a level 3+/4 biosafety contained room with equipment. Also, similar safety levels for sealed, isolated, individual animal habitats. We're running a tight ship.
And ferrets. Because they're cute.
posted by porpoise at 7:26 PM on December 5, 2011
And ferrets. Because they're cute.
posted by porpoise at 7:26 PM on December 5, 2011
Pfu Ultra II is a good polymerase for cloning and runs $100 for 40 reactions.
Also, basic Taq polymerase is off patent; if you have the appropriate plasmid and some competent cells, purifying a bucket of it is supposed to be really easy and very cheap. (Sadly, the Pfu patent doesn't expire until 2013.)
posted by en forme de poire at 11:19 PM on December 5, 2011
Also, basic Taq polymerase is off patent; if you have the appropriate plasmid and some competent cells, purifying a bucket of it is supposed to be really easy and very cheap. (Sadly, the Pfu patent doesn't expire until 2013.)
posted by en forme de poire at 11:19 PM on December 5, 2011
In the bad old days when cloning with Taq - you'd expect at least a couple of errors per kilobase cloned/PCRed; you'd just sequence several/a-bunch-of clones and hope one of them ends up having the mutations being silent at the amino acid level.
I've personally run across a few entries in GeneBank that aren't correct - and don't represent SNPs - because the original clone from mRNA had Taq-induced errors.
It's cheaper and saves more time to spend more money on Pfu than to have to sequence extra clones. Also, since modern polymerases are "hot start" you'd have to figure out how much of a particular antibody against a binding site you need... so making Pfu is a *little* bit more involved than purifying a bucket of Taq.
Funny - GFP/green-fluorescent-protein has been off patent for a long time now, lots of variants of it are available for licensing... but the sequences of the modified fluorescent proteins are public domain. If you make your own mutations to GFP, identical to a mutant still under patent, are you allowed to use the new construct that you made yourself?
posted by porpoise at 7:34 AM on December 6, 2011
I've personally run across a few entries in GeneBank that aren't correct - and don't represent SNPs - because the original clone from mRNA had Taq-induced errors.
It's cheaper and saves more time to spend more money on Pfu than to have to sequence extra clones. Also, since modern polymerases are "hot start" you'd have to figure out how much of a particular antibody against a binding site you need... so making Pfu is a *little* bit more involved than purifying a bucket of Taq.
Funny - GFP/green-fluorescent-protein has been off patent for a long time now, lots of variants of it are available for licensing... but the sequences of the modified fluorescent proteins are public domain. If you make your own mutations to GFP, identical to a mutant still under patent, are you allowed to use the new construct that you made yourself?
posted by porpoise at 7:34 AM on December 6, 2011
It would be unfortunate if this is a bad idea because I WANT ONE SO BAD!!!!! OMG! And one of those super microscopes like in biology class so I can watch little ameobas squirm around and tell them how cute they are. Here little amoeba! You're such a cutie, look you have little friends! Aw, and look at those cute little bacteria wiggling around!
Happy land.
posted by xarnop at 8:43 AM on December 6, 2011
Happy land.
posted by xarnop at 8:43 AM on December 6, 2011
xarnop, I have a confession to make, the cute stuff in pond scum is exactly why I own my own microscope.
posted by Blasdelb at 5:43 PM on December 7, 2011 [1 favorite]
posted by Blasdelb at 5:43 PM on December 7, 2011 [1 favorite]
It's cheaper and saves more time to spend more money on Pfu than to have to sequence extra clones.
That's a good point, but sequencing is also getting so cheap these days that I think figuring out which is better sort of depends on the application. For making synthetic constructs like chemical-inducible fluorophores or whatever, you may not care quite so much about the occasional wrong base as you might when sequencing a disease variant or whatever.
posted by en forme de poire at 12:07 PM on December 10, 2011
That's a good point, but sequencing is also getting so cheap these days that I think figuring out which is better sort of depends on the application. For making synthetic constructs like chemical-inducible fluorophores or whatever, you may not care quite so much about the occasional wrong base as you might when sequencing a disease variant or whatever.
posted by en forme de poire at 12:07 PM on December 10, 2011
BTW, the inimitable Rosie Redfield has a great article about ethidium bromide that really changed my perception of how dangerous it is. Basically, her argument is that EtBr is used therapeutically in animals at doses way higher than what you would get in the lab, apparently without consequences, and some of the "safer" alternatives may actually be way more toxic.
posted by en forme de poire at 12:17 PM on December 10, 2011
posted by en forme de poire at 12:17 PM on December 10, 2011
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posted by hincandenza at 11:15 AM on December 5, 2011