International DIY-Bio Project

[Meow-Ludo]

I propose that we set a project that everyone works on collaboratively around the globe for a few hours each week. It would be a really good way to share the resources each of us has and collectively we could do something more than each of us on our own. I would be a really good way to get to know each other more, as working in a team will provide insights about others that we might not get from just talking on the forum.

The project should be something that doesn't require us posting stuff to each other, but instead should be available where ever we are. Maybe we can pick a new organism and all work on getting it sequenced and it's genes annotated, but should be reasonably common and legal to culture in all countries. Or maybe we want to build organisms that survive on Mars and pool our information together and share design of plasmids etc.

I am really keen to get into this, as I just finished buying all my reagents. My lab is about 4 weeks away from being fully functional!

If anyone would like to be a part of a project like this, put your ideas for what you would like to do, what type of project you would like to work on, and how you would like to run it below and we'll get something started. It would be awesome if we collectively could get something published as 'hobby scientists' in a journal.

Meow

PS - I vote for the Mars project (It is good because it is very accesible to a variety of disciplines, making it easy for non-biologists). This would be really good for people joining the forum, as we can say, "help us with this project. Your job is X. Thanks for helping us!"

[Jonathan Cline]

Some projects mentioned previously: http://openwetware.org/wiki/DIYbio/FAQ/Projects


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

 

[Connor Dickie]

I like this idea!

I'm also interested in the Mars project. How do we get started?

[Meow-Ludo]

Awesome!

OK. I think the first part will be to work out how to construct a martian environment in a jar that we can all have set up so that the environments are the same.

The jars have to have:

*low pressure - about 1/3rd of 1atm I believe.

*High carbon dioxide (95%)

*They have to get cold. -20C would be the upper temperature we would be aiming for.

We should be able to achieve this with a hand-pump (to reduce the pressure) and a soda-stream type bulb to provide the carbon dioxide. The temperature should be able to be controlled by a peltier cooler. The terrain is a bit trickier, but we should be able to source a terran analogue of the regolith pretty easily.

Then we an fill it with life and see what survives. 

I will draw up some designs for the jar. Any help would be appreciated.

What is your area of speciality Connor?

[Michael Turner]

For the temperature range, consider what's expected for Martian caves.
Penny Boston's work would be the place to start.

http://www.wired.com/wired/archive/12.12/cave.html

Regards,
Michael Turner
Project Persephone
1-25-33 Takadanobaba
Shinjuku-ku Tokyo 169-0075
(+81) 90-5203-8682
tur...@projectpersephone.org
http://www.projectpersephone.org/

"Love does not consist in gazing at each other, but in looking outward
together in the same direction." -- Antoine de Saint-Exupéry

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[Mega]

I really love the idea of designing a microbe that will survive Mars conditions! But you made a mistake about the atmosphere. In Hellas planitia, we have 11 mbars.

That's 0,01mbar.

I woul sugesst liches because they were shown to survive Mars conditions. Or something that makes spores like B. Subtilis. because there definitely will be hard mars' nights.

It should produce a strong greenhouse gas too. but one that doesn't destroy an ocone layer like fcc or methane. octoflourpentan (think it's the same in english) is the gas of choice (10,000 times co2). or FS6.

[Mega]

You should definitely have a look at http://en.wikipedia.org/wiki/Sulfur_hexafluoride

It's the strongest known green house gas, and is 6 times heavier than air! That will increase atmospheric pressure dramatically too thus alowing water to be liquid in a broader temperature range.

fluorine is abundant in martian soil (even more than in earth's soil, research showed) and sulfur too.

That'd be great.

[Michael Turner]

Perhaps one potential niche to explore, for design purposes, is lava
tube "skylights":

http://news.discovery.com/space/seventh-graders-discover-martian-cave.html

Sunlight along the sides of the skylight, perhaps reaching the lava
tube floor with some frequency, admits of photosynthesis, while being
down in a shaft means a lot more shielding from radiation: GCR and
solar storms. Congealed lava itself might have some helpful properties
(e.g., higher moisture and nutrient content). The temperature
fluctuations down in lava tubes will be less dramatic. By the way,
it's not clear that radiation is a showstopper. It might even be an
enabler. They've found bacteria and fungi in very high radiation
environments (even inside the Chernobyl sarcophagus); apparently
something like photosynthesis is at work, plus high rates of damage
repair, to make such organisms possible.

Regards,
Michael Turner
Project Persephone
1-25-33 Takadanobaba
Shinjuku-ku Tokyo 169-0075
(+81) 90-5203-8682
tur...@projectpersephone.org
http://www.projectpersephone.org/

"Love does not consist in gazing at each other, but in looking outward
together in the same direction." -- Antoine de Saint-Exupéry

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[Mega]

http://de.wikipedia.org/wiki/Deinococcus_radiodurans

This beast would totally survive. But, the atmosphere of Mars shields from some radiation. And, radiation does often not kill bacteria, but makes mutations. Mutations are what Mars needs, to quikly adapt to its environment. Also if a certain percenage of bacteria dies of radiation, that does not matter, because they multiply so quick anyway.

There are some spaces with remaining magnetized rocks. Those local magnetic fields may also shield from radiation.




What may be the most important is that the bacterium / lichen  can absorb water from  atmospheric vapour (lichens can do this, acoording to the mars experiment I read). Because on the ground, most of the time water will be frozen. In some cases that actually won't be true, when higher pressure and salt water (lowers the freezing point, was shown as low as -50°C with extremly salty and ammonia-rich water) are present.


The cell membrane of the bacteria surely will keep a pressure inside to prevent the water from boiling, but just keeping the water inside won't do the job, we want it to absorb water to be able to thrive, multiply and make photosynthesis.

Have to look up some biological pathways for making greenhouse gasses, as said, gasses harmless to ozone (and poor in hydrogen)

[Mega]

Although the sulfur hexafluoride is very georgeous, one would have to invent an (entire?) new metabolic pathway for this. (Or find a bacterium in a cave 3000 meters below the surface, which does it naturally, perhaps because there are no other substrates for living).


An 'easy' beginners step would be to let the bacterium take up nitrogen (from nitrate minerals) from the soil and release it, especailly in the form of NO2 (greenhouse gas!)

That would be very helpful because the atmosphere is so low, and quite poor in nitrogen (95% CO2, rest nitrogen, 0.01 bar  ---> 50% nitrogen 50% carbon dioxide 0.02 bar and so on would be desireable )

[Connor Dickie]

When it comes to Biology I'm just a beginner, but I'm highly motivated and learning more every day ;-)

Useful skills that I can offer to the project are research and development, particularly hardware and software engineering and logistics. I would be very interested to help with the design and build/documentation of the Mars Analogue (Terrarium?). I also have free access to a nice web-based multi-user video-conference system (through Mozilla) that we can use to host chats and share desktops/presentations etc.

I can also offer the use of some open web-based bio-design and collaboration software that I'm helping to develop with Mozilla Labs for exactly these types of projects. It's in early stages, but likely has useful features that would benefit this effort.

- Connor

[Patrik D'haeseleer]

Hm - so we're talking about a cryogenic, low-pressure chamber filled with a precise mixture of gases and minerals... that doesn't sound very DIY friendly.

To simplify things just a little, how about we drop the low pressure, and try to fit the entire experiment inside the freezer compartment of a fridge? Supply a CO2 atmosphere from evaporating dry ice, and provide light with a mixture of UV and visible LEDs.

[Mega]

> filled with a precise mixture of gases and minerals...

Hm, actually that doesn't really matter. The only reqiurement you would need is most of it is co2, and the rest nitrogen. If it can survive this, it will also survive Mars (because the partial pressure of CO2 is higher on Mars, it will absorb the co2 better for metabolic pathways)

Hm - so we're talking about a cryogenic, low-pressure chamber filled with a precise mixture of gases and minerals... that doesn't sound very DIY friendly.

To simplify things just a little, how about we drop the low pressure, and try to fit the entire experiment inside the freezer compartment of a fridge? Supply a CO2 atmosphere from evaporating dry ice, and provide light with a mixture of UV and visible LEDs.

On Earth there are already microbes that will survive this.
That may be a project for  it's own sake, but that won't produce something useful for Mars.

Prices for vacuum pumps have dropped, too. I think that isn't the problem.  How would you cool it? On the one hand, you don't need much cooling because there is barely air inside. Maybe the cöoling circle from an old fridge would do the job. 
 

[Mega]

Actually, not everyone who works on the project will need a pressure chamber.

One chamber would in fact be sufficient. When someone is finished with his part, he sends the microbe / plasmid  to the pressure chamber. 

[Meow-Ludo]

I think that the right idea is definitely to keep it simple. A low pressure environment can be created in a jar by using a vacuum hand pump (about $40AUD). This could be used to suck all the air out of a jar, and then filled again with CO2/N2 to the desired pressure. Pressure is an important variable in this experiment as at lower pressures, the water will stay liquid at lower temperatures.

If we look for organisms that are good at surviving in these types of environments, we might be able to target genes that confer survival in these environments. Some that have already been mentioned are lichens, but tardigrades (which eat lichen!) and some antarctic bacteria and archaea may be able to already survive in this environment too.

What Michael has said is important too. We should try and pick an environment that is the most friendly to our organisms and replicate that. If we combine this with picking a good selection of microbes we should be right.

My lab at home consists of a PCR thermal cycler, centrifuge, agar gel elctrophoresis equipment and basic reagents. I would be happy to any transformations, amplifications, sequencing (i have a very cheap rate at my university to do this) and should be able to get some cultures or help isolate some. I am also happy to do any transformations (non-conjugative plasmids only) and recombinant DNA techniques.

My Dad has a 3D printer so I can print any parts that we need for the gas delivery system to the jar. I am not great at the design though. I am happy to post the pieces any where in the world for free though.

Connor: would you be able to set up a wiki for us (maybe on open wet-ware) and get us an account for the mozilla labs collaboration software? I would really love it if we can make it completely open and write up everything we do, so other people can download the files and become a node of our project.

Mega: did you want to run these experiments in parallel but using different organisms? What is your set up like? Is there any equipment I might be able to help you with?

Michael: would you be keen to help out with this project on a practical level? Maybe you could help us by suggesting organisms to work with? I like your ideas about using radiotolerant fungi/microbes. If you have a lab it would be really good to run some jars there too.

Patrick: I think that your idea is by far the easiest to start with. Where are you in the world? I might be able to get you some antarctic microbes that might be suited to this environment. It would be good to see how they survive UV. This could really help set up the jars and provide some information about what we might need to do to ensure they survive in the even harsher conditions. After this it would be great to modify them with genes from some more radio-resistant organisms.

[Michael Turner]

I've only commented so far out of general interest. The connection of
Project Persephone to your project is a bit tangential. There is a
*wee* bit of astrobiology in Project Persephone's current project,
which proposes a proof-of-concept for an admittedly impractical idea:
satellite magnetorquing using "biomagnets" formed in part by
concentrated, aligned magnetotactic microbes. But that's not much
relevance, and most of it comes out of mentioning Allan Hills 84001 in
passing.

Allan Hills 84001 was a Mars-origin meteorite that contained what
looked like fossil evidence of microbes, in the form of magnetosomes.
One problem with both that theory and any connection between our
projects is that Mars has a very weak magnetic field compared to Earth
-- why would Martian microbes have evolved any such feature? On the
other hand, ALH84001 apparently predates some catastrophic impact
events that might have shut down Mars' magnetic field.

http://news.nationalgeographic.com/news/2009/05/090511-mars-asteroid_2.html

This suggests an interesting tack for (or fork or) your project: see
what kinds of extremophiles might have lived on Mars *before* those
impacts, which would have robbed Martian microbes not only of any
magnetic field to evolve with, for purposes of orientation control,
but also of their solar and GCR radiation shield. That is, you might
do it as an "areo-achaeo-bacterial reconstruction." You might then
fast-forward through any number of conjectured historical profiles for
Mars, to see what (if any) present-day microbial life might survive.

If you can make the equipment very cheap and replicable, and operable
in high school biology labs, you might consider "massive parallel
citizen science" -- do a crowdfunder campaign where you propose giving
away a lot of the equipment to schools, to try out a very wide range
of conjectured-past and present Mars environments (different
temperature ranges, CO2 concentrations, etc.) Simulating the various
radiation environments might be the trickiest part, but that's where
caves come in: there's nothing but geological background radiation
down inside caves.

Regards,
Michael Turner
Project Persephone
1-25-33 Takadanobaba
Shinjuku-ku Tokyo 169-0075
(+81) 90-5203-8682
tur...@projectpersephone.org
http://www.projectpersephone.org/

"Love does not consist in gazing at each other, but in looking outward
together in the same direction." -- Antoine de Saint-Exupéry

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[Patrik D'haeseleer]

On Monday, September 17, 2012 6:35:48 AM UTC-7, Meow-Ludo wrote:

Patrick: I think that your idea is by far the easiest to start with. Where are you in the world? I might be able to get you some antarctic microbes that might be suited to this environment. It would be good to see how they survive UV. This could really help set up the jars and provide some information about what we might need to do to ensure they survive in the even harsher conditions. After this it would be great to modify them with genes from some more radio-resistant organisms.

I'm actually at BioCurious in California. Not sure I'd want to sign up for this Mars analog project though. As DIYbio projects go, this one seems to be *very* heavy on hardware design. And the anaerobic, cryophilic, radiation tolerant bacteria you get to grow in it would likely grow extremely slowly (if at all), and be hard to study.

Personally, I'd be much more enthusiastic about, say, a project about isolating hydrocarbon degrading bacteria from gas station soils. Get some soil samples, maybe enrich them for the desired bacteria by adding some naphtalene (old style mothballs), then try to get some isolates on plates with naphtalene as the main carbon source. Do 16S sequencing to figure out what we have. Compare naphtalene degrading potential between the different strains people have isolated. Then put some money together to sequence the most promising isolate.

This is a project people across the world could start on immediately, and would be accessible to anyone with even very basic resources. Rather than having to do half a year of hardware design to come up with a setup that would probably be complicated enough that only a few groups would be willing to tackle it...

[Meow-Ludo]

Personally, I'd be much more enthusiastic about, say, a project about isolating hydrocarbon degrading bacteria from gas station soils. Get some soil samples, maybe enrich them for the desired bacteria by adding some naphtalene (old style mothballs), then try to get some isolates on plates with naphtalene as the main carbon source. Do 16S sequencing to figure out what we have. Compare naphtalene degrading potential between the different strains people have isolated. Then put some money together to sequence the most promising isolate. 

This is a project people across the world could start on immediately, and would be accessible to anyone with even very basic resources. Rather than having to do half a year of hardware design to come up with a setup that would probably be complicated enough that only a few groups would be willing to tackle it...

This is something I would love to help out with. We might be able to even make up a kit containing:

*90mm Petri Dish (polystyrene)

*Dry Media (as you suggested)

*A method to quantify their degrading potential - I am not sure how this would be done.

*A couple of microcentrifuge tubes to put colonies into for sequencing.

We could probably make a short PDF outlining the experiment and it should be pretty straightforward. We could also look at some soil fungi as they are really good at degrading poly-aromatic hydrocarbons. We can use the ITS region for ID and the only difference needed would be to lower the pH a little to encourage fungal growth.

Is this what you had in mind? I would be happy to run this project with my biohacking group if you wanted to run a sister project at biocurious and we can compare results?

[Meow-Ludo]

Hi Michael,

I have just did an assingment on ALH84001 for my astrobiology class! If I recall correctly, the proponents of the 'biological' side of the argument claim that these indeed were magnetotactic microbes and they were aligned with the (at that time) magnetic field created by the dynamo of the core of mars.

Your suggestion for "areo-achaeo-bacterial reconstruction" is great. This areo-cheological study would allow for us to create some much more pleasant environments that are a lot less technically challenging. Especially good would be wet environments that would stop most of the UV. If we could give more evidence to support the fact life could have at one time lived on mars it would really help us find microbes that could potentially live there now. Also, patrick mentioned that these current organisms would be very slow growing: this is something that I didn't think about. The experiment itself would be a long term project. This is OK, it just makes it much harder!

Is there any way that I can help on Project Persephone from Australia?

[abiologystudent]

Fun thread. For anyone interested in astrobiology I am signed up to a course on coursera (https://www.coursera.org/course/astrobio) which starts in Jan. I cannot recommend coursera enough to people. Space: The final open-source frontier...

[Cathal Garvey]

I'm not following this thread fully so forgive me if I don't know how
much "low pressure" you need. :)

A candle jar will not only remove most of the O2 and enrich for CO2, but
will reduce pressure within as it does so. Probably not much; it's
famously the principal behind sucking a hard-boiled egg into a bottle!

And, it's dirt cheap; a mason jar and a candle. :)

On 17/09/12 15:35, Meow-Ludo wrote:
> I think that the right idea is definitely to keep it simple. A low pressure

> environment can be created in a jar by using a vacuum hand pump<http://www.ebay.com.au/itm/160806830301?hlp=false#ht_645wt_1111> (about

> $40AUD). This could be used to suck all the air out of a jar, and then
> filled again with CO2/N2 to the desired pressure. Pressure is an important
> variable in this experiment as at lower pressures, the water will stay
> liquid at lower temperatures.
>
> If we look for organisms that are good at surviving in these types of
> environments, we might be able to target genes that confer survival in
> these environments. Some that have already been mentioned are lichens, but
> tardigrades (which eat lichen!) and some antarctic bacteria and archaea may
> be able to already survive in this environment too.
>
> What Michael has said is important too. We should try and pick an
> environment that is the most friendly to our organisms and replicate that.
> If we combine this with picking a good selection of microbes we should be
> right.
>
> My lab at home consists of a PCR thermal cycler, centrifuge, agar gel
> elctrophoresis equipment and basic reagents. I would be happy to any
> transformations, amplifications, sequencing (i have a very cheap rate at my
> university to do this) and should be able to get some cultures or help
> isolate some. I am also happy to do any transformations (non-conjugative
> plasmids only) and recombinant DNA techniques.
>
> My Dad has a 3D printer so I can print any parts that we need for the gas
> delivery system to the jar. I am not great at the design though. I am happy
> to post the pieces any where in the world for free though.
>

> *Connor*: would you be able to set up a wiki for us (maybe on open

> wet-ware) and get us an account for the mozilla labs collaboration
> software? I would really love it if we can make it completely open and
> write up everything we do, so other people can download the files and
> become a node of our project.
>

> *Mega*: did you want to run these experiments in parallel but using

> different organisms? What is your set up like? Is there any equipment I
> might be able to help you with?
>

> *Michael: *would you be keen to help out with this project on a practical

> level? Maybe you could help us by suggesting organisms to work with? I like
> your ideas about using radiotolerant fungi/microbes. If you have a lab it
> would be really good to run some jars there too.
>

> *Patrick:* I think that your idea is by far the easiest to start with.

--
www.indiebiotech.com
twitter.com/onetruecathal
joindiaspora.com/u/cathalgarvey
PGP Public Key: http://bit.ly/CathalGKey

[Connor Dickie]

On Monday, September 17, 2012 9:35:48 AM UTC-4, Meow-Ludo wrote:

Connor: would you be able to set up a wiki for us (maybe on open wet-ware) and get us an account for the mozilla labs collaboration software? I would really love it if we can make it completely open and write up everything we do, so other people can download the files and become a node of our project.

This can be done ;-)

I'm currently in the last 48 hours of a big deadline, but will have a chance to set these up on Thursday. I'll report back with links and details when it's ready.

Connor

[Connor Dickie]

Thanks Cathal,

The Candle Jar seems like a very interesting solution to the vacuum and oxygen problem. As a novice I had to look up the specifics of the device and came across this great resource that outlines some of the math behind how the jar works:

http://www.math.harvard.edu/~knill/pedagogy/waterexperiment/index.html

According to this page we can expect to reduce the volume of gas contained in the jar by about 8% using the candle, which is decent, but a far cry from where we need to be. Meow-Ludo suggested on the 16th that we need an atmosphere of about 1/3 Earth's, but after looking up the actual numbers I was blown away by the extreme low pressures found on Mars:

Olympus Mons summit	0.03 kilopascals (0.0044 psi)
Mars average	0.6 kilopascals (0.087 psi)
Hellas Planitia bottom	1.16 kilopascals (0.168 psi)
Armstrong limit	6.25 kilopascals (0.906 psi)
Mount Everest summit[11]	33.7 kilopascals (4.89 psi)
Earth sea level	101.3 kilopascals (14.69 psi)

from - http://en.wikipedia.org/wiki/Atmosphere_of_Mars

1/3 atmosphere would recreate the environment at the Summit of Mount Everest which is survivable by humans without a pressure-suit (some can even do it without external oxygen supply).

Looking at these extreme low pressures... Is this something that we can achieve cheaply and reliably?

-- Regardless, the candle jar is very cool. Simple enough to do the egg test during breakfast next weekend ;-)

[Andreas Sturm]

The atmosphere of Mas is very thin, this is true. If it were to be 1/3 of the Earth's or even just 1/10, we could run on the surface without an pressurized suite, just oxygen mask!!

But, at Hellas Planitia and some other low-lands, it's high enough too keep (distilled) water liquid for some degrees. Salty water will be liquid even longer, boiling later and freezing later. Bacterial cell walls produce force against the water inside, so there can be bacteria who survive.


In fact, the German Wikipedia says that during an erection, 1.6 bar (1.6 times the Earth's atmospheric pressure) occur in the male ''body-part''. (http://de.wikipedia.org/wiki/Erektion) . That tells me, the eukaryotic cell membranes can also withstand Mars pressure  and keep the water molecules inside together, hindering them from boiling. 

[Meow-Ludo]

Maybe we could start with higher pressures using the candle trick, and then select organisms that do the best. After this we can lower the pressure further with a smaller group of extremophiles and will still have time to plan better machines. Anyone could use the candle jar to identify new targets, making it easier for nodes to appear.

[Connor Dickie]

Hey everyone!

I recently had an opportunity to chat with a few folks at NASA who work at the Space Life Sciences Lab at Kennedy Space Centre, and of course I asked them about how they prepare their Mars Analogues. I was given 6 papers to read through - some characterize Martian conditions, and others offer insights into how to build an analogue in the lab. Great stuff!

I've only had a chance to skim them, so I'll post them here for everyone to take a look at. Sorry for being so tardy in my tasks... Tough week!

Ugh. Google says my attachments are too large to post. Why let me upload them then?

Here is a direct link to the files: http://synbiota.com/diybio/mars_analogue_papers.zip [~6MB]

Regards,

Connor

On Tuesday, August 21, 2012 6:18:40 AM UTC-4, Meow-Ludo wrote:

[Michael Turner]

> Ugh. Google says my attachments are too large to post. Why let me upload
> them then?

Think about it from Google's point of view. If you were sending them
to an individual, it might be OK. If you send them to a Google Group,
that's a lot of people, and much more potential for abuse. Quite a few
Google Groups drown in spam, much of it bulkily p0rn0graph1c.

Consider breaking the papers out, sharing them out on Google Drive,
and sending links to the list.

Regards,
Michael Turner
Project Persephone
1-25-33 Takadanobaba
Shinjuku-ku Tokyo 169-0075
(+81) 90-5203-8682
tur...@projectpersephone.org
http://www.projectpersephone.org/

"Love does not consist in gazing at each other, but in looking outward
together in the same direction." -- Antoine de Saint-Exupéry

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> You received this message because you are subscribed to the Google Groups
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[Bryan Bishop]

On Sun, Sep 23, 2012 at 11:18 PM, Michael Turner <michael.eu...@gmail.com> wrote:

Consider breaking the papers out, sharing them out on Google Drive,
and sending links to the list.

bah...

http://diyhpl.us/~bryan/papers2/diybio/mars_analogue_papers/

http://diyhpl.us/~bryan/papers2/diybio/mars_analogue_papers.zip

- Bryan
http://heybryan.org/
1 512 203 0507

[Andreas Sturm]

http://www.ncbi.nlm.nih.gov/protein/406780405

A (putative) UV  resistance protein. (Found it while looking for F' plasmid sequence :D )

When constructing a Mars bacterium, UV resistance'll be helpful ;)

[Patrik D'haeseleer]

This seems relevant:

Build a Mars base with a box of engineered bugs

"NASA has already begun research to realise this dream, says Lynn Rothschild at the Ames Research Center in Moffett Field, California. Rothschild is leader of NASA's new Synthetic Biology Initiative, which aims to build designer microbes for future crewed space mission.
[...]

Using the approach, a microbe with the potential to survive on an alien world can become one that could sustain human life there.

Take the need for energy. Many earthly microbes would die in extraterrestrial atmospheres rich in carbon dioxide and nitrogen - the two main constituents of Martian air. An ancient cyanobacterium called Anabaena thrives in those conditions, though, metabolising both gases to make sugars. "As long as it has warmth and some shielding from ultraviolet light radiation, it should do well on gases in the Mars atmosphere," says Rothschild.

Naturally enough, Anabaena uses most of the energy it produces from CO₂ and nitrogen, but synthetic biologists can encourage the cyanobacteria to share its supplies. Last year, at a synthetic biology competition - International Genetically Engineered Machines (iGEM) - a team from Brown University in Providence, Rhode Island, and Stanford University in California showed how inserting genetic machinery from E. coli makes Anabaena excrete more of its energy as sugar. The team even showed that they could support colonies of other bacteria on the sugar. In theory, such microbial colonies could make oil, plastics or fuel for the astronauts.

The team, led by recent Brown graduate André Burnier and advised by Rothschild, has also come up with a way to supply human settlers on Mars with bricks and mortar. They began with a bacterium called Sporosarcina pasteurii, which, unusually, breaks down urea - the principle waste product in urine - and excretes ammonium. This makes the local environment alkaline enough for calcium carbonate cements to form.

The idea is that the waste produced by astronauts could feed the microbes. The microbes, in turn, would help cement together fine rocky material on a planet's surface to create bricks.

As a proof of principle, Burnier's team confirmed in experiments that loose material can be cemented together in about two weeks to create a house brick with the compressive strength of concrete. They also managed to isolate the cement-building genetic component of the bacterium, creating a biobrick that they have inserted into E. coli to give this hardy bacterium the same cement-enabling properties."

[Nathan McCorkle]

Seems like Anabaena has more immediate use on our own planet, cleaning
up CO2 and NOx in our environment. Air->fuel conversion project
anyone? Seems the only major thing needed is water...

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[Cathal Garvey]

Hey Jerry, thanks for posting!
One question: is this part of that whole DARPA-funding grab on DIY space
I've seen so much about? Where's the funding for the grants coming from?
Thanks!
Cathal

On 09/10/12 09:16, Jerry Isdale wrote:
> Pardon my jumping in a bit late, but I just stumbled on DIYBio group and
> this International DIY-Bio Project.
> I am the US Director of the new SpaceGAMBIT.org program - an alliance of
> hackerspaces (of all variants) working to build grass roots collaboration
> by providing grants to encourage education and research projects
> promoting humanity's survivability and expansion into space.
> We are just getting started with our kickoff meeting Oct 19 (nasa ames).
> There are a lot of ideas kicking around this thread that have me fairly
> excited about the possibilities.
> We expect to have our first grant RFP out within a month with funding in
> January.
> These will be very small grants (<$10k, probably < $5k) with short time
> lines for having some results (3-6mo) and results must be shared openly
> (open source, CC, etc). Although we have a long range goal of expanding
> into space, real space science is generally orders of magnitude more $$
> than we have in our budget. But there are lots of Bio activities that are
> low hanging fruit - as have been discussed in this thread.
>
> Check out our web site <http://spaceGambit.org>, ask questions and watch
> for announcements.
> I, and our UK director, will be in SF Bay and Los Angeles area next week
> giving some talks at various venues
> (sunday at East Bay Mini-maker faire, monday at Crashspace in LA, tuesday
> at Mojave Makers, perhaps thursday at BioCurious, etc.)

[Andreas Sturm]

Incidentally, I have a student looking for genes responsible for UV sunscreen synthesis in cyanobacteria collected from extreme hypersaline and desert environments. His progress and experimental set up may be of interest.

Wow, that sounds great! 

Additionally they're Cyanobacteria, so they do photosynthesis (which will probably be THE (abundant) energy source of Mars) 

[Mega]

I just came across the key word CyanoBacillus. 2005 one researcher combined the genome of those two. 

Sounds awesome, perfact for a starting point as Mars bacterium. It can make spores, so it survives everything. And it can do photosynthesis.

Gotta go to university, but surely will dig up papers about it. A quick google resarch didn't show much though... 

[Patrik D'haeseleer]

Very cool! Here's the original article:

Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome
http://www.pnas.org/content/102/44/15971.full

It's not clear that they were actually able to get the resulting organism to grow photosynthetically though - seems like they would have made a much bigger deal of it if that was the case.

Patrik

[Andreas Sturm]

Yeah also read that *some* genes from the cyanos weren't expressed.

It was not even written explicitly, if they could form spores... 

 

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[Koeng]

I have done some research myself about Mars bacteria, since I am a big time mars advocate :). 

I was thinking about, for ease of use, Deinococcus radiodurans as a starting bacteria. If you remember one of the discussions I made on "worker cells" this was one of the reasons. Use genetically modified cyanobacteria for photosynthesis inside the Deinococcus radiodurans. Or, use plant plastids to create chloroplasts (since these have already evolved to serve the plants). The reason I think of Deinococcus radiodurans because it is resistant to many of the things already on mars and can be modified with "worker cells" to uptake different niches specifically designed by us. A possibility would be Thiobacillus ferrooxidans with iron oxidation, possibly with a modification to help soil creation.

Now I think that that adding of 2 genomes would be best. Morphing the most resistant bacteria on earth with the genetics of a autotroph would be outstanding.  I also have looked at Martian temperatures and at the equator it would be possible for bacteria to live, however there is very little water. Possibly this enzyme, LEA, could help

http://2010.igem.org/Team:Valencia/Parts

I love your idea Mega, but I do think that they did not think of Mars when creating their bacterium, and potatoes aren't going to be found on Mars, so an entire new bacteria will be needed.

I am planning once I finish my Halobacteria project I am going to start a Mars bacteria one. If anyone has started one, I would LOVE to help on it :D

-Koeng

(also here is something I just wanted to add)

(A random idea I wanted to share)_

 I have created some ideas on terraforming different planets as well, and I will attempt to retype my ideas below, since the website I have them on (moon mars) is currently down.

First of all is Venus. A lot will needed to be added first for successful terraformation such as crashing asteroids into the planet to increase the water level in the atmosphere (mostly for hydrogen) and to speed up the rotation of the planet. After that is complete, the bacterium would be added in different tests lasting about a year (the rotation of Venus, so once the bacteria drop into the void of darkness they die, allowing for increased testing). The entire bacteria would have to use Bacteriorhodopsin since there is no magnesium in the venus atmosphere. They would stay floating using similar mechanisms that the bacteria here on earth use. Now here comes the tricky part. A scientist (gotta get name sorry) calculated that biological systems could not in fact remove all the atmosphere. I, however, propose we create them to as CO2 eatin' as possible, using a cell WALL as the area. Normally cells would use sugar in the wall (plants, but that is WAY not Hydrogen efficient for the planet we are talking about) or protein, but if they only had walls out of a polyanhydride using CO2, then the CO2 consumption would be much greater. Now here is an important part that could only be done in the far off future, using automatic, self replicating robots that use the bacteria as fuel and as a source of plastic for recreating themselves (along with a robotic mini factory on an orbiting metal asteroid). The robots would collect the bacteria and use all of the components for "printing" new robots that would be used to mine or ship things to and from earth. Since the bacteria could be used as (most likely inefficiently though) fuel, the robots could travel throughout the solar systems doing useful things.

Thats one idea; please spell out the things that are totally wrong and impossibru so I can change them

That relates to bio since the enzyme would need to synthetic, possibly using a distributed game, *cough* fold it *cough* for people to help contribute to the project.

[Mega]

Imo the spore forming mechanism is the most important (in addition to being autotrop).

Because in harsh night or during solar erruptions, all living bacteria may die, but the spores will grminate again... Those bugs can then undergo great evolution.

[Mega [Andreas Stuermer]]

Just had a look at this again.

Looked at D. Radiodurans, and was forwarded to http://de.wikipedia.org/wiki/Chroococcidiopsis .
Wiki article only available in German though.

But it says:

Chroococcidiopsis tolerieren hohe Strahlung, extreme Temperaturen, Austrocknung, osmotischen Stress und extreme pH-Werte. Zum Überleben sind lediglich Licht, Kohlendioxid, ein Minimum an Wasser und Spurenelemente notwendig. Ihren Stickstoffbedarf können die Bakterien durch Fixierung molekularen Stickstoffs aus der Atmosphäre decken.

they tolerate high amounts of radiation, extreme temperatures, (total?) drying, osmotic Stress and extreme pH. For surviving, it needs only light, CO2, and trace amounts of water and trace elements. They can fix atmospheric nitogen.

Die Einzeller werden daher als ideale Organismen zur initialen Besiedelung unbelebter Himmelskörper angesehen.

Those bugs are seen as the ideal organisms for initial colonization of planetary bodies.




Will dig into english papers about it :D

[Mega [Andreas Stuermer]]

There is an english article about it, without being linked.

http://en.wikipedia.org/wiki/Chroococcidiopsis

They say it were to cold for them on Mars. I don't thnik so... The only barrier for life is that water can be liquid. And in Hellas planitia, with > 10 mbars, salty water actually can be liquid. and, incidentally, this bacterium can stand extreme salinity!


Chemical reactions will go slower, that is true. But life will find its way, undergo evolution. Maybe one would have to expose a native strain to -30°C, their daughter strain (f1)  to -35, f2 to -40°C, etc. in a controlled environment to prepare them for living on Mars.

[Mega [Andreas Stuermer]]

Better organism.

http://www.dailygalaxy.com/my_weblog/2014/01/photosynthesis-possible-on-the-surface-of-mars.html

This lichen can actually do photosynthesis on the surface on Mars. At least in a simulated Mars environment.

On Mars in most regions the air pressure is too low to sustain liquid water. However, above water-ice ther can be a very small film of liquid water even at -15°C or thelike (see article).

We should get our hands on those lichens someday :D

[Patrik D'haeseleer]

Lichens also grow really slowly though. We're talking a couple cm per year, if your lucky. The extereme cold adapted ones probably grow much slower than that. Heck, there's a technique called lichenometry, to estimate the age of rocks up to ~1000 years old, based on the size of the lichens growing on it.

Not exactly a very rewarding organism to work on...

Patrik

[Mega [Andreas Stuermer]]

Sure, but if you grow them on Mars, evolution will happen. Those lichen mutatants that grow the fastest spread the most, without any competition.

[Patrik D'haeseleer]

Oh sure, they're quite attractive for terraforming - provided you give them a couple thousand years. A bit less attractive for an International DIYbio project though...

Patrik