Anyone interested in engineering cyanobacteria?
Mikel
I'd like to start a cyanobacteria engineering collective and would
like to find others who might be interested in getting involved.
Microalgae represent an interesting model, as they are photosynthetic
microorganisms that can grow easily as long as there's CO2, sunlight
and minimal nutrients available. There are several microalgae genomes
sequenced and it is possible to build home-made photobioreactors for
growing them.
Give me a shout if you happen to be interested and we can start
working on an agenda.
Cheers!!
Mikel (Australia)
Bryan Bishop
> I'd like to start a cyanobacteria engineering collective and would
> like to find others who might be interested in getting involved.
Hi there. I'd be happy to help you organize the project- CAD files,
genomes, sequences, etc. In particular there are some software tools
that might help you in your genetic engineering endeavors:
http://designfiles.org/dokuwiki/skdb
There's no photobioreactor in skdb at the moment, but maybe you'd like
to head up that project? I want to download a photobioreactor.
Dakota Hamill
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J. S. John
> working on an agenda.
>
James Field
Cathal Garvey
I'd be very eager! I have several concept projects involving cyanobacteria that I'd like to pursue at some stage for which an open forum/set of growth or transformation protocols would be exceptionally useful!
Jack Shultz
eukaryotic algae. There has been some research on hydrogen production
using Chlamydomonas reinhardtii deprived of sulphur or copper, it
triggers an alternative photosynthetic pathway. But it is very
inefficient. If however, a number of people are interested in
developing mutant hydrogenases we may actually get ourselves to a
hydrogen based economy.
--
Jack
JonathanCline
http://openwetware.org/wiki/DIYbio/FAQ/Projects#For_Algae
Please add where needed. Also there are several biofuel forums on the
net, it would be interesting to make a list of the best.
## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################
Dakota Hamill
Eric Butter
it seems that Mac and co. have built a great model for cross-country
collaboration with their bacteria project earlier this year. I have
access to pretty much any fancy equipment I would need down here in NC
(sorry, but no home-made centrifuges for me, Cathal, haha) ... who is
setting up this forum so ppl can get their ideas straight? Happy
Holidays, EB
> > diybio+un...@googlegroups.com<diybio%2Bunsu...@googlegroups.com>
Jack Shultz
http://hydrogenathome.org/forum_thread.php?id=351#2643
I've been trying to design better hydrogenases insilico but I kind of
put it on hold for a while to learn new methods.
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Mikel
It seems that I forgot to introduce myself: I'm a phd student at the
university of queensland in brisbane and my project is in a completely
different field (neuroscience). Although I got interested in
cyanobacteria too late for changing my thesis, I think I am in a good
stage in terms of my lab skills.
As some of you have pointed out, hydrogen production from algae is
promising. You might want to have a look to this site: http://www.solarbiofuels.org/
They have done all the feasibility studies and think that within the
next 10 years, we could be producing hydrogen industrially from algae
(their work is on Clamydomonas).
Personally, I am interested in engineering cyanobacteria for producing
polymers like PHB... or developing a platform technology for enzyme
production. But there's a whole number of tools and protocols of
common use that would be great if we could build/compile collectively,
independently of the individual projects that each of us is interested
in pursuing.
I liked this photobioreactor from inventgeek.com:
http://inventgeek.com/Projects/Photo-Bio-Reactor/overview.aspx
and, particularly this one that incorporates Arduino and might make
easier to try different culturing conditions:
http://inventgeek.com/2009-Projects/Arduino-Strobe-Algae-Bioreactor/OverView.aspx
A good starting point would be to perform a comprehensive literature
review / internet searching for things like:
- Cyanobacteria genomes sequences, size of their genomes, how much
biotechnology has been done on them, etc.
- A list of repositories you can buy cyanobacteria from. I can list:
http://www.sbs.utexas.edu/utex/
https://ccmp.bigelow.org/
http://www.ccap.ac.uk/
http://www.marine.csiro.au/microalgae/supply.html
Oh!! by the way, there's a beautiful paper that just came out on
Nature Biotechnology:
http://www.nature.com/nbt/journal/v27/n12/abs/nbt.1586.html
They engineered a cyanobacteria called Synechococcus elongatus, so
that it overexpresses ribulose 1,5-bisphosphate carboxylase/oxygenase
(Rubisco), resulting in a strain that is capable of directly
transforming CO2 into isobutanol and isobutyraldehyde, with excellent
yields. Brilliant work!
Mikel
Daniel Sander Hoffmann
I wonder if (and how) one can do some bioreactor automation with PICs. I got a Microchip Explorer16 (with a PIC24fj128ga) that I would like to put to good use in a bio experiment. I also recently acquired four MRF24J40MA modules that support MiWi protocols and could be used to build a small wireless sensor network. Anyway, I admit lacking the expertise: In this area I’m a complete amateur.
Well, perhaps here’s something I could do for the group, but I would need some help.
Any ideas?
-Daniel
http://www.microchip.com/stellent/idcplg?IdcService=SS_GET_PAGE&nodeId=1406&dDocName=en024858
http://ww1.microchip.com/downloads/en/devicedoc/39747a.pdf
http://www.microchip.com/wwwproducts/Devices.aspx?dDocName=en535967
Daniel Sander Hoffmann
Bob Keyes
--- On Tue, 12/29/09, Daniel Sander Hoffmann <transp...@gmail.com> wrote:
> From: Daniel Sander Hoffmann <transp...@gmail.com>
> Subject: Re: Anyone interested in engineering cyanobacteria?
> To: diy...@googlegroups.com
> Date: Tuesday, December 29, 2009, 9:54 AM
> I wonder if
> (and how) one can do some bioreactor automation with PICs. I
> got a Microchip Explorer16 (with a PIC24fj128ga) that I
> would like to put to good use in a bio experiment. I also
> recently acquired four MRF24J40MA modules that support MiWi
> protocols and could be used to build a small wireless sensor
> network. Anyway, I admit lacking the expertise: In this area
> I’m a complete amateur.
>
> Well, perhaps here’s something I
> could do for the group, but I would need some
> help.
> Any ideas?
Daniel,
I too have some basic experience with PICs. I don't have the time to jump into a project right now, but I have thought that a PIC could be used for monitoring and control of such things as light, temperature, humidity, and carbon dioxide in a bioreactor. This would involve interfacing sensors to the PIC. Some of these are easy, but I am unaware of how to cheaply measure CO2. Controls for light and heat should be easy enough, but then you have to find some small pumps for fluids. Perhaps there are microfluidics which are available.
It seems to me that many of the requirements would be for precise and accurate measurement and control of temperature. While this doesn't sound too difficult at first, I expect that there will be difficulty in maintaining uniform temperature throughout the bioreactor.
Some people have integrated web-servers and other such software onto PICs for control and statistics reporting. I don't agree with this approach: I believe the PIC and attached machinery should perform the minimum computation possible, reporting data back to a general-purpose computer (i.e. a PC) for data processing and analysis. Of course, this requires communications, and depending on the environment and distance between the bioreactor and the general-pupose computer, bandwidth may be limited and some sort of data pre-processing and compression may be required.
In terms of communication devices, wifi is the most obvious answer but not neccessarily the best one. Bluetooth is cheaper, and other technologies have greater range (see the radio devices on http://www.sparkfun.com). Datacomm is what my 'day job' is (as a student), and I have a particular interest in mesh wifi networks. Utilizing such a radio-mesh infrastructure, some of the PIC controllers may be able to pass traffic to and from other such controllers. Again, it doesn't have to be wifi, but especially in terms of mesh networking, wifi mesh is mature and freely available (http://www.olsrd.org).
I think that tinkering with some PIC bioreactors is good, even if the reactor used does not provide much new information, in order to sharpen one's skills and become aware of the issues and trade-offs in various implementations of measurement and control systems. Once you have such experience, you can branch out to work on more useful bioreactors either on your own or as member of a group.
I should mention to anyone who is interested in this area of electronics that free samples of ICs are available from many manufacturers, but these may be of limited utility to the beginner, who would be better off buying an 'evaluation kit' or similar general-purpose controller assembly.
Regards,
Bob K.
Eugen Leitl
> I would definitely be interested to help with this hydrogen idea, and
I don't think you'll have a chance beating catalyzed water electrolysis
driven by solar PV. The organisms are sure self-amplifying, but the
harvesting infrastructure unfortunately isn't.
I don't see how you can beat the ~15-20% overall efficiency with
a photosynthesizing system. I don't know what photosynthetic driven
hydrogen production efficiency would be, but at a guess it's ~0.1%
at best. You can do much better by using CO2 enrichment thus boosting
efficiency and harvesting high-lipid algae by low-energy processes
floatation or floculation. In terms of energy density, oil is equivalent
to diesel.
> it seems that Mac and co. have built a great model for cross-country
> collaboration with their bacteria project earlier this year. I have
> access to pretty much any fancy equipment I would need down here in NC
> (sorry, but no home-made centrifuges for me, Cathal, haha) ... who is
> setting up this forum so ppl can get their ideas straight? Happy
> Holidays, EB
--
Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
______________________________________________________________
ICBM: 48.07100, 11.36820 http://www.ativel.com http://postbiota.org
8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE
Jack Shultz
biochemical pathways as they exist in nature, it is clear it won't
work. The enzymes involved have a high turnover rate because they are
sensative to accumilating high energy oxygen species. Efficiency is in
the range of 0.1% - 1%. If there were a way to engineer a more
efficient chemical pathway then this would be viable option. Things to
consider
1) Increase the rate of respiration so oxygen does not accumilate
2) Modify the Hydrogenase enzymes so they are ambivalent to the
presence of oxygen
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Mikel
biofuels consortium, on biological production of hydrogen:
"I don't like to try and make it sound better than it really is. There
are efficiency issues. So at the moment we are at a conversion
efficiency of about 1% from light to hydrogen. That would be in an
outside system right now. And where we need to get to to make it
economically viable is about the 7% to 10% mark. So there are
definitely improvements that need to be made.
We've spent a lot of time working with IMBcom and with Peter Isdale's
group to do industrial feasibility studies and evaluate where those
key bottlenecks are in making those processes economically viable. One
point is to make the bio-reactors cheaper. Most bio-reactors cost in
the order of about 100 euros per square metre, and we need to bring
that down to about 10 euros."
For the full interview, click here:
http://www.abc.net.au/ra/innovations/stories/s2266152.htm
Cathal Garvey
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Daniel Sander Hoffmann
That's something to consider too, Cathal. Here’s what’s directly available to me (without importing):
http://www.multilogica-shop.com/
Do you identify something useful?
Just in case you’re wondering, 1 Brazilian Real is buying something like 0.57 US Dollars – you get the point :-)
As a curiosity, my iPhone is still waiting at the local store, because I’m not willing to pay something like 800 US Dollars for such a thing! (Besides, I’m still waiting to see what Nexus One has to offer… :-)
Cheers
Daniel
Cathal Garvey
http://www.wired.com/wiredscience/2009/12/the-lost-decade-of-algal-biofuel/
Dakota Hamill
Looks like a good article already:
http://www.wired.com/wiredscience/2009/12/the-lost-decade-of-algal-biofuel/
Cathal Garvey
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JonathanCline
wrote:
> I wonder if (and how) one can do some bioreactor automation with PICs. I got
> a Microchip Explorer16 (with a PIC24fj128ga) that I would like to put to
> good use in a bio experiment. I also recently acquired four MRF24J40MA
> modules that support MiWi protocols
Yes, PIC16, PIC18, PIC24, PIC32 are good candidates for this kind of
stuff. So is Atmel AVR (Arduino boards), and other 8-bit micros. The
limiting factor on the smaller PICs is data memory (memory blocks cost
extra pennies, and PICs are best made cheap). For performing a
function that needs to buffer data and for example run a filter
function over the data before storing it / transmitting it, data
memory can be an issue. Otherwise, for wireless comm, PICs are great
since they have multiple peripherals built in. PIC24 is the beefier
version so programming it in C is fine. For bioreactor automation in
general, I'd guess you need a couple sensors with ~10Hz sampling rate
(biology rates are very slow compared to normal stuff these chips do),
some general I/O for control, perhaps PWM for speed control or light
control, and UART for data comm (alternatively USB). All very doable
even on PIC16, in fact, PIC24 is complete overkill (which is OK), so
it should work great.
You might want to check the processing.org examples I have on my site:
http://88proof.com/synthetic_biology/blog/archives/tag/processing-org
The PC side runs java processing.org and the microcontroller side runs
open source firmware (UBW board in case of the PIC, I forget the name
of the Arduino version). The PIC firmware might easily be burned into
your existing PIC24 board, or maybe it has it's own serial/USB/network
command set. Anyway, using processing.org is a very simple & fast way
to get "control" and "user interface" working on the PC side with
whatever electronics are needed --- plus since it runs as a Java
applet, it can be run on any machine or embedded in a web page, can
open sockets, display pretty graphics (or debug) output from the
hardware data, etc. If you have multiple wireless endpoints, you
could create a very neat graphical output dashboard with whatever
framerate you want, to update the display of endpoint data in real
time to the user.
Daniel Sander Hoffmann
Great links, Jonathan. Thank you! I’m inviting a friend of mine, who has a lot of experience with PICs and chemical sensors, to join me in the project. I’ll keep in touch.
Daniel
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Eugen Leitl
> If there is only a 1% efficient from light -> hydrogen, screw it. Isn't the
I agree. No way to compete with (catalyzed) water electrolysis
efficiency, using electricity from photovoltaics or other renewables
(especially hypervariable ones like wind).
> whole point to ultimately make electricity anyway? photons -> electrons is
Not necessarily. Hydrogen is also useful for caloric (combustion heat) value,
in ICEs, or as reduction equivalent. But the main advantage is that it
can be made from water which is cheap and ubiquitous, and hydrogen is easily
storable (gas holders, pressurized storage, hydrides, etc.), and can
be also used in electrochemical redox pairs in fuel cells, using air
as the other electrode you don't need to carry around with you.
> what we need. I've always wondered, why does nature turn light into
> chemical energy rather than electrical energy? More stable? Easier to
Density and stability. Both lipids and glycogen typically. You can't
really store electrons as is, even supercaps have a lousy energy density
and leak.
> store for longer periods of time? How come we can't make photon
> computers...or something like..photonics, where photons replace electrons.
Photons can't interact with each other (bosons vs. fermions), so they
need interaction mediation through matter, typically at high fluxes,
though nonlinear optics has been getting better and better. In general
photonics is more suitable for signalling, and electronics (or spintronics)
for computation.
> I'm drunk, don't mind me.
--
Jack Shultz
> On Tue, Dec 29, 2009 at 10:16:12PM -0500, Dakota Hamill wrote:
>
>> If there is only a 1% efficient from light -> hydrogen, screw it. Isn't the
>
> I agree. No way to compete with (catalyzed) water electrolysis
> efficiency, using electricity from photovoltaics or other renewables
> (especially hypervariable ones like wind).
>
In PSII reaction center you have electrolysis of water in a biological
system. A challenge is to engineer a system that competes with
standard photovoltaics. Just because evolution has not produced a more
efficient method in biology, does not mean its not possible. A good
question is this research path too great a challenge with too little
potential reward.
Daniel Sander Hoffmann
But there's a whole number of tools and protocols of
common use that would be great if we could build/compile collectively,
independently of the individual projects that each of us is interested
in pursuing.
Eugen Leitl
> In PSII reaction center you have electrolysis of water in a biological
The problem is that a photosynthetic center is just a tiny component
of a practical photobioreactor plant producing hydrogen. Your only
advantage is self-replication/self-regeneration of the medium, but the
context is expensive enough to make that nice part negligible.
> system. A challenge is to engineer a system that competes with
> standard photovoltaics. Just because evolution has not produced a more
There's no longer such a thing as standard photovoltaics. Whether
nanoscale molecular complexes, quantum dots or VIS-range rectenna
anything is game. This is a potentially much richer design space
than accessible to biology, so long-term bionics and explicit
biology or hybrid systems are less and less likely to be competitive.
> efficient method in biology, does not mean its not possible. A good
> question is this research path too great a challenge with too little
> potential reward.
It's a multi-TUSD market, so the only reason it's not worth pursuing
is because it's futile.
Algal biomass is probably worthwhile, photohydrogen from algae is
most likely a dud.
Jack Shultz
Utilization Efficiency and Hydrogen Production in Microalgal Cultures"
where Dr Melis reported an increased efficiency in light utilization
when they truncated chlorophyll (Chl) antenna.
"strain exhibited a 10% utilization efficiency of incident
solar light energy, i.e., substantially greater than the 3%
utilization efficiency of the wild type."
http://www.hydrogen.energy.gov/pdfs/progress08/ii_f_2_melis.pdf
All these efficiency gains have no impact downstream where it reduces protons.
>
> There's no longer such a thing as standard photovoltaics. Whether
> nanoscale molecular complexes, quantum dots or VIS-range rectenna
> anything is game. This is a potentially much richer design space
> than accessible to biology, so long-term bionics and explicit
> biology or hybrid systems are less and less likely to be competitive.
>
You're probably right about the increased design space outside of
biology. I like the idea of machines that fix themselves as you see in
living systems :-)
Eugen Leitl
> You're probably right about the increased design space outside of
> biology. I like the idea of machines that fix themselves as you see in
> living systems :-)
You nailed the core deficit of human-designed systems. They cannot
self-reproduce (whether via macro or nanoscale self-replication), nor
do they diagnose/self-repair or even degrade gracefully.
Macroscale self-rep is largely an issue of scaling rapid-prototyping
methods along with robotics, while nanoscale either implies wet (solvated)
self-assembly or dry (UHV/inert gas) machine-phase.
Dakota Hamill
Lee Nelson
I'll grab some samples from the ocean (which is still unfrozen) on the Eastern seaboard, and try and dig up some samples from under the ice at ponds around my local.
Sure, collect your own samples, you never know what you will find. Much effort has already gone into identifying useful strains (using public money). Perhaps 'we' could get samples of the 23 strains at the University of Hawaii.
http://www.wired.com/wiredscience/2009/12/the-lost-decade-of-algal-biofuel/
Cathal Garvey
I agree, we should go down the oil route, particularly with a focus on EPA/DHA/ALA production, as a consumer need for these nutrients is one of many pressures driving fish to extinction!
If you had the choice of either burning or selling your oil for consumption, your opportunities for success and impact are doubled!
Further, it would interesting to see what amino acid synthesis pathways our model species lacked, and which we could then hack in, toward a totally minimum-input system!
On Dec 31, 2009 2:26 AM, "Dakota Hamill" <dko...@gmail.com> wrote:
I think we should work on engineering algae/cyanobacteria that have increased lipid/oil production. Hydrogen through algae/cyanobacteria doesn't seem to be the wave of the future. I'd leave that to fuel cells. I have heard of companies in Cambridge who base their entire business model on cells that can produce 90% weight oil, but I haven't searched for much in terms of literature down that road. I imagine they have kept it secret and are trying to patent it. I for one would like to try and come up with it ourselves. I'll grab some samples from the ocean (which is still unfrozen) on the Eastern seaboard, and try and dig up some samples from under the ice at ponds around my local. I don't know shit about identifying them, but I have a professor at school who deals exclusively in marine algae etc so I'm sure he can help me. I'm going to build some of the cheap photobioreactors I saw from one of the links above, which require nothing but an aquarium pump, some sunlight, and a plastic bottle to grow algae. After I have a steady supply (which I imagine I can have within 2 weeks) I can start some testing. I just saw the microbiology professor at my school at the grocery store, and she said the lab is always open to me after I told her about the DIYBio project...which is cool. I say we all start looking for literature that deals with the genes in cyanobacteria/algae that regulates phospholipid/oil like molecule production. My university opens back up on January 3rd, so I have free access to most of the big journals around the world, and can save and email them as .pdfs. Keep me up to date if you guys want to do this. I think it would be a kick ass project to take simple cells we find growing in ponds, and engineer them to produce more per cell weight of oil.-Dakota
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Lee Nelson
I agree, we should go down the oil route, particularly with a focus on EPA/DHA/ALA production, as a consumer need for these nutrients is one of many pressures driving fish to extinction!
If you had the choice of either burning or selling your oil for consumption, your opportunities for success and impact are doubled!
Further, it would interesting to see what amino acid synthesis pathways our model species lacked, and which we could then hack in, toward a totally minimum-input system!
This article is about zinc fingers - it briefly mentions using them to alter algae.
http://www.nytimes.com/2009/12/29/health/research/29zinc.html?_r=1&pagewanted=1
Dakota Hamill
Ok, tomorrow I'm going to collect samples with pictures from Marblehead, MA. I agree going down the oil route is best....as that is what actual companies are trying to do. We have to identify what genes control lipid production, what oils are actually produced, and how we can manipulate the environment to be conducive to growth.
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Jack Shultz
experiment but met with some difficulty using open source solutions. I
discussed this study with one of the authors (Dr. Fontecilla-Camps)
with great length. Even he thinks hydrogen from algae is a dead end.
Still none of the reasons against it have sufficiently resonated with
me. Maybe re-engineering this enzyme will help or maybe not. This
paper describes computational predictions of proton transport pathways
from the active site. From that data they have attempted for the past
2 years to mutate regions of the enzyme to filter out highly reactive
oxygen species from the active site. There have been no breakthroughs
that I am aware of. Since this reaction is reversible H2 <--> 2H+ +
2e- it is plausible that the model applies to proton migration to the
active site when hydrogen production is up regulated.
What I am proposing, is setup a system where I computationally model
mutant enzyme structures to determine which structures are better at
filtering the oxygen species from entering the active site. We would
only make single amino acid modifications and hope that the minimized
structure makes an accurate prediction of native state. We would use
parameters similar to the ones decribed in the article to model both
proton transport and oxygen diffusion. Then at some point when I have
improved designs, there could be a collaborative effort to purify
those proteins and test their catalytic activity.
Here is the abstract and reference material if you are interested in
further reading.
A QM/MM study of proton transport pathways in a [NiFe] hydrogenase
Ignacio Fdez. Galván 1 *, Anne Volbeda 2, Juan C. Fontecilla-Camps 2,
Martin J. Field 1
Published Online: 15 Apr 2008
ABSTRACT
A theoretical QM/MM study of the [NiFe] hydrogenase from Desulfovibrio
fructosovorans has been performed to
investigate possible routes of proton transfer between the active site
and the protein surface. We obtained the minimum
energy paths, with a modified version of the nudged elastic band
method, for a set of proposed pathways. The
calculations were carried out for the crystallographic structure and
for several structures of the protein obtained from a
molecular dynamics simulation. The results show one of the studied
pathways to be preferred for transport from the active
site to the surface, but the preference is not so strong when
transport occurs in the opposite direction. Proteins 2008. ©
2008 Wiley-Liss, Inc.
--