I know that open source is the modus operandi at DIY bio, and I have
no wish to take that away. I wonder, though as synbio "grows up" what
are some small business ideas that a university student could create
with synbio? (on a university student's budget).
Not "giant" firms like Venter's Synthetic Genomics .. . but legitimate
small biz that allows a combination of
making-money-to-put-food-on-the-table and an interest in synbio?
What are the markets available to small biz synbio?
a) How does one protect intellectual property on a zero budget? Can
defensive publishing do the job?
b) I am assuming that some form of the minimal cell concept would be
involved here . . .
sorry if I sound like a novice here; I am.
Synthetic bio strikes me as exactly the same scenario. Some people are
hardcore enough (and have a good enough lab) to synthesize an
interesting sequence, PCR themselves a bunch of copies, insert it into
a vector, and transform some bacteria or tissue. Some people will buy
pre-made plasmids. Some people just want a particular strain to work
with and are willing to pay for it.
Open source certainly doesn't imply "unfriendly to business", and
indeed, I think the opportunities for open-source biology are broader
than those in open-source software.
Yeah I agree entirely, for example the homebrew stirplates that the
brewing community likes to make. The options are basicly: built it
yourself with $35 worth of parts and some electronics knowledge, or but
a commercial one for hundreds of dollars.
There is definitely a market for somebody to provide these people with a
stirplate for under $100 made from jameco parts.
Obviously this could be expanded to other types of devices and services.
Hey, do you have plans for one of those, and do they provide heat?
I've been looking for a stirring hotplate and you're exactly right, I
don't want to pay hundreds of dollars for one.
In terms of biologicals themselves, I think tools for the biotech industry
to make an existing process better/enable a new process would be very
doable. I was also thinking about non-medical diagnostic tests (e.g.,
detecting an environmental contaminant in water). For example, there was an
iGEM project on a biological arsenic detector. A lot more work would need
to be done to commercialize something like that, but the point being that
there is a need to drive testing costs lower than existing methods (for
performing frequent tests in developing world drinking wells). There are a
number of chemicals you might want to detect, including some that may have
first-world applications. It might be possible for a group of people here
to work together on commercializing some sort of test.
Actually, a question I have when it comes to these sort of tests is whether
there are existing distribution methods. I.e., if you have a test which
depends on a live microorganism, all other problems aside, is there a way to
package and distribute this cheaply (for example, without requiring
Depends on the microorganism. In any pharmacy or health food store,
you can buy Lactobacillus acidophilus tablets; the ones I have
advertise over a billion live organisms per tablet. I have
successfully cultured from these before. The tablets also contain
cellulose, calcium and magnesium stearate.
I'm not sure, though I bet you could email or call them and ask --
they no doubt have to field questions like that all the time. Still,
making E. coli competent is not particularly difficult; all you really
need is some calcium chloride, which can be purchased easily. Hardware
stores in climates that get snow will have it as a de-icer, or if you
live someplace warm and don't want to order it from a supplier, you
can make it in a pinch from calcium carbonate -- available at any pet
store that sells reptile food, you sprinkle it onto crickets so that
your reptiles get the calcium they need for bone health -- and
(If you decide to make your own calcium chloride, DO IT SOMEPLACE WELL
VENTILATED. I cannot stress this enough. A kitchen vent is not
sufficient. I learned this the hard way and had to be carried out of
my kitchen. The reaction outgasses CO2 quite rapidly.)
So far, I've been working with L. acidophilus, which is kind of a
difficult bug to work with -- it doesn't respond well to heat shock.
It's supposed to be possible to use heat shock on lactic acid bacteria
by treating them with magnesium chloride and calcium chloride to make
them competent, then performing the heat shock in polyethylene glycol
solution, but so far I haven't gotten that to work. (I've only done it
once, mind.) Everyone I've talked to has told me that electroporation
is really the way to go for Gram-positive bacteria, so I'm building an
electroporator. I've built out the control logic (prototyped on an
Arduino, though I intend to design a PCB that uses an Atmel
microcontroller once I get this working), and I've designed the HV
side of the apparatus (using a 3kV neon sign transformer as the
voltage source). The transformer puts out AC, so I need to get some
more HV diodes to build a rectifier, then wind a choke and get some HV
resistors to get the voltage down to 2.5kV. I also need to pick up
some HV probes for my oscilloscope to make sure that the pulse being
put out is a nice clean square wave.
If I had some E. coli, I'd definitely try heat shocking them, but I
don't have an appropriate freezer. Working on solving that problem,
Does anyone know if ATCC will ship to individuals? It would be nice if
we could develop our own cell lines, but doing so from an established
line might be tricky from a legal POV. Last time I checked into Steve
Kurtz's situation, the only thing the government was still hassling
him about was the fact that he got his cultures from someone else who
had ordered them from ATCC and violated the material transfer
agreement by giving them to him.
And sure, I'd be happy to do a video about the electroporator, just
let me get it working first. :)
The historically important way of storing strains for long periods was
with "stabs", which are small tubes filled with agar medium. Stabs are
made and sterilized, then inoculated with a needle to infect the
culture. The stab is then cultured for a day or so uncapped until
replication starts, then sealed tightly and held at refrigerator
temperature for long periods (1 year +). There can be genetic drift in
these, and some may die, but this was the common strain maintenance
technique for decades. Reculturing every year or so is essential.
Some strains don't respond well to this treatment, and it has almost
been abandoned in favor of -80 storage. Find an old microbiology
Please don't kill yourself with the high voltage power supply. The
electroporators use a (mechanical) relay to charge a capacitor on an
internal high voltage supply, then transfer the capacitor to the output
wires. There is a high value bleeder resistor across the capacitor to
remove charge when the unit is powered down. It's easy to make
something that is quite dangerous with 2-3 KV power supplies if you
don't know what you are doing, and they can stay dangerous even if
Thanks, but you're telling me stuff I already know. :) I'm actually
using HV power transistors rather than a capacitor because HV
capacitors are expensive and hard to find. The HV side of the circuit
is optoisolated from the 5V side, and I'm using high-voltage lead wire
and insulating all my joins. I've also run my design by a couple of
guys who have been doing electronics design far longer than I have,
and they've all given it a safety thumbs-up.
Now, that said -- one concern I have about using a transistor design
rather than a relay/capacitor design is that it's not clear to me how
much current is supposed to pass through the cuvette. Other designs
I've seen involve a 5uF or 10uF capacitor rated at 5kV, which
translates to a hell of a lot of charge. The instantaneous current
through a capacitor is given by the equation
i = C(dv/dT)
where i = current, C = capacitance, and dv/dT = instantaneous rate of
The papers I've read have talked about a duty cycle of 150ms on /
350ms off. So, assuming that the voltage across the capacitor rises to
2500V during that 350ms, and assuming a 10uF capacitor, that
translates to about 71 mA available to the cuvette. (Definitely not
something to mess with lightly!) What I'm not clear on is whether this
level of current is actually *necessary*. The neon-sign transformer I
have will provide 3kV at 10mA. I'm not certain whether the available
current is actually enough to do anything to the bacteria.
All that said, though, I suspect that the high capacitance is intended
to provide a relatively long time constant, since the ideal waveform
for this sort of thing is a square wave (which I'm addressing by doing
it in digital logic). I'll go back through the papers I've read and
work out the math on that.
That said -- if anyone happens to know what sort of current is needed,
I'd appreciate your input!
I should have emphasized "about" more strongly here -- the rate of
change in voltage in a charging or discharging capacitor is not linear
at all. Particularly during the early part of the charge/discharge,
the rate of change will be quite high and thus the current will be
higher as well. It largely depends on what the time constant of the
circuit is. Over a single charging time constant, the rate of change
in voltage is steep, but the second derivative is shallow; over
several time constants, the rate of change drops off a bit.
http://www.tpub.com/neets/book2/3d.htm for pretty graphs.
Anyone here got an IEEE Explore account?
be useful. I can get it at Berkeley, but my VPN is lame and doesn't
get me offsite access most of the time.
On Sun, Nov 2, 2008 at 1:31 PM, Meredith L. Patterson