Bugs and DNA isolation and PCR amplification

So I have been pondering how to isolate DNA for bacterial amplification. I have found that we could use universal 16S rRNA primers to amplfy genomic DNA, which if we got all fancy later on could feed into direct sequence analysis through pyrosequencing, but lets not get ahead of ourselves. To isolate the genomic DNA we could use any number of methods, but most of them use centrifugation so I think that perhaps magnetic separation would be easier in a remote situation, so we coulf d use the Dynabeads DNA direct technology, I already have a magnet for immunoprecipitation using a similar protocol, so we're halfway there already! Time for some ordering :-) though I need to check out air capture too......what about an all-glass impinger does anyone have any quickfit glass we could play with?

first tranche of funding now here!

Just saw this...

http://www.universetoday.com/2009/08/03/launch-your-own-personal-satellite-for-8000-usd/

... and thought it might be worth considering. Why reinvent the wheel?

Magnets

I have been thinking more about the idea of capturing bacteria on petri dishes, a low tech way of getting some idea of what is out there and how it might grow. Currently I am thinking of attaching a selection of petri dishes to a baking sheet with magnets set in the agar and 'sweeping' the air - at various locations eg the Uni sports pitches and up mount Snowdon. The baking sheet was easy to find and I have been having a look on line at magnets from this company, the prices look reasonable for the volumes I need. Apparently neodymium Iron Boron (NdFeB) is the strongest material on the market and it comes nickel coated so hopefully that should do the trick.

Some interesting things to do with H.A.B after reading the most recent Nature

Here are some ideas I had after reading that issue of Nature:

Idea 1 of 3:
Planetary Protection
Nature 459 21 may 2009 308-309

Possibly an angle for the cyclo-olefin encapsulation/UVC sterilisation idea (CO/UVC) I pitched earlier for balloon canopies.
The article describes the concerns of Plan Protect people (Catharine Conley is interviewed) as to how existing spacecraft (eg Mars landers) are inadequately sterilised.
NASA is thinking of adopting hydrogen peroxide sterilisation because, for instance, autoclaving is too difficult for entire spaceprobes.
I think my CO/UVC is more practical since it allows by steady sterilisation over a period of time, so it is much less harsh than any chemical treatment.
Spacecraft could be sterilised in cruise flight by fixed UVC sources covering every nook and cranny.
A CO shroud, illuminated from within, also could be useful since it allows encapsulation of extra clean components (eg arms, scoops etc)

Could we use HAB as a near-space demonstrator of this?
Is there money to be had from people like Caroline?

Idea 2 of 3:
Public funded small scale science
Nature 459 21 may 09 p305
www.sciflies.org
Allows you to fund small projects from public donations - you pitch your project on the website.
Might be useful for some small scale funding (I.e a particular HAB flight perhaps)

Idea 3 of 3:
Nature 459 21 may 09 316-319
Mike Russell origin of life article
Not so much an idea - interested to know what you think of Mike's ideas. I heard a lecture by him some years back and was transfixed.

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Ballooning spiders

I was catching up on my viewing of the BBC's latest offering - South Pacific - last night and they talked of colonization of remote islands. One of the ways was by being caught up in typhoons, small animals and seeds, but they also mentioned the use of ballooning by small spiders. A little wander through the internet has demonstrated that this is true and that the spiders need to endure very low temperatures to do it, also that they need to be less than 1mg in weight and use enormously long silks as their lifting devices. But could they get into the stratosphere? I don't know - reports suggest 7000m and aircraft height, though the latter can be highly variable. If they did, would they survive and could they carry microbes with them?

Moving the LEDs around inside the canopy: reefing in the canopy to deflate the balloon

I had previously suggested moving the LEDs around inside the canopy on something like an automatic extending car aerial. Now we'd be talking about moving the radar reflector with LEDs.

How would we do something like this?
You could for instance have a pulley and rope made of cyclo-olefin and turned by an electric motor. But then it occurred to me that the canopy will expand during flight so it will be hard to keep the pulley tight - or not too tight. The pulley would presumably have to be attached to the roof of the canopy.

Maybe we are still looking at the extendable car aerial idea then. Heavier but simpler. A similar system could be used to deploy a sampler (perhaps surrounded by a VRS stream?) Perhaps.

(One quick thought... If the LEDs are attached to an aluminised radar reflector, then presumably this could be a common earth for the LEDs?)

Where we COULD attach something to the canopy would be for deflating it, assuming we try to reuse it and don't just burst it. Remember, this could be a custom C-O canopy.
By opening a valve and then taughtening a line attached to the inside of the canopy, which can slowly reef in the canopy like a concertina and squeeze out the Helium, triggering a controlled descent.

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Making the radar reflector

I would envisage making this by 3D printing too and then again aluminising it or coating with mylar.

I have previously suggested mounting this inside the canopy. Perhaps this could have UVC LEDs in each of its interstices - e.g 8 LEDs - and then the entire reflector is moved around inside the canopy to achieve sterilisation.

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Your humble smartphone for balloon communications? With a parabolic dish?

If Ham radios are out, could we use a mobile phone instead?
Or are all forms of unmanned balloon radios banned? Must check!

With a smartphone that has GPS, such as a Blackberry, we could broadcast the balloon's position straight onto Googlemaps (e.g. http://www.google.co.uk/latitude ) which surely would be a publicity coup and moreover useful for Air Traffic purposes.

The only problem is, 'phones are short range transmitters - only needing to communicate with the nearest cell base station a few miles away. We will reach altitudes as high as 20 miles.

Maybe a quick way around this would be to have a parabolic dish on the balloon gondola, pointing straight down. It doesn't need to be steered.

I have already checked with Paul and we can design and 3D print parabolas OK. We could spray it with aluminised paint or line it with mylar. We could even print it as a mesh to save weight, allowing for the wavelength of the 'phone signals.

This gives our 'phone a tighter focussed beam facing straight down from altitude. This would presumably cover one or more base stations at a higher signal strength (instead of the signal going off in all directions as it would usually)
Would this be enough??
Again, something to test!

The 'phone could be mounted directly at the prime focus of the dish. Perhaps it could even be hung there by ropes. That way it will be more likely to withstand the landing, especially if we cocoon it somehow.


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Balloon safety - tethered? Where to fly!

Some more on practical considerations for flying balloons.

In the U.S at least, they need to weigh less than 6Ib, have a parachute built in, use rope of a certain strength, have a redundant means of bursting the balloon on command (say by radio and a timer), carry a radar reflector, not be flown at night, and have their position reported to Air Traffic Control by 'phone regularly (usually by the balloon radioing back its GPS coordinates to you).

If you don't know where the balloon is or can no longer control it, then it is declared "derelict", which is a very bad reputation to get!

This is all pretty stringent enough but in the U.K it would be worse.

It is fine for a 6 Ib gondola to plummet out of the sky over the Kansas prairie or whatever but I think your chances of this landing on a house or a road or suchlike in the U.K, with its much higher population density, are depressingly higher.
Also, I remember reading somewhere that you're not allowed Ham radios etc on the balloon in the U.K.

Still, it has been done - any of you remember the "Space Teddies" flown by the Cambridge Uni student space club?
(We should try and get in touch with them). I think they flew from a military range - but that must have taken some sorting!

So - we fly over water (and prepare to get wet recovering it - anybody got a boat or likes sailing?) or fly in the U.S with our friends at NASA, which was always the plan.
But it would be so nice to test some of this in the U.K...

Could we test it on a tether?
The weight of tether would quickly drag it down, but perhaps we could offset this with balloonets (multiple balloons supporting a structure, in this case the tether). How far up could we go?...


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The COCTEAU Twins? 6 Ib limit, Bluetooth

There comes an important moment in every project... when you have to give it a witty acronym.

I started off with the purely functional -
Cyclo-
Olefin
Canopy
Test,
COCT.

Well, how about adding an EAU?

Cyclo-
Olefin
Canopy
Test
Experiment for
Absorbance in
Ultraviolet

Sorted! Although I was always a more Teardrop Explodes man myself.

But then I thought... Cocteau Twins... Why not actually fly TWO balloons for the gag?

And then I realised that this was actually extremely useful from a practical point of view!

In the U.S at least, the weight limit for weather balloons is 6 Ib. Heavier than this and you need all sorts of special permission.

But... Why not launch multiple balloons at the same time??
One could do our biology experiment...
One could provide the radio communications... And so on!
"All" you'd need is some form of cross-balloon coms - Bluetooth or Wifi perhaps.
This would be imperilled if the balloons drifted too far apart, but if they weighed the same and were launched side by side simultaneously, they should stick fairly close together.
...Shouldn't they?
Again, something nice to test!

A useful away perhaps to fly more than 6Ib in one go (about 2.7kg Metric)
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Wankel engines

Robin's Facebook post reminded me to finish this post... Have been busy with other things recently, apols!

I have mentioned these contraptions a few times so some more explanation is due. A Wankel engine is an internal combustion engine which basically has a triangle-shaped rotating piston inside a cavity instead of the up-and-down cylinder pistons you might be used to. A Wankel engine has less moving parts and inherently rotational motion, so no need for a crankshaft, vs its upright cylinder cousins. Mazda is keen on them for instance but they haven't caught on that much elsewhere.
Why my interest? I think there is no way we will have enough power for everything using batteries or solar cells, although perhaps I will be pleasantly surprised.
So, I was wondering: There is still some air at the altitude we have in mind; about 0.01bar to be precise. So can we still use an internal combustion engine, Wankel or otherwise? These have a much higher power density per unit weight than a battery.
I happened to have a Wankel in mind since there is a Wankel popular model aircraft engine, putting out a horsepower or so - I.e about 750W.
Let's imagine we rig something like this to work with ambient air. Now it can only burn about 1% as much fuel as usual (since there's only 1% as much oxygen), so let's say about 7.5W. Still pretty good though.
Any holes in this reasoning?

Obviously you'd need fuel injection, not a carburettor, since you'd need to constantly match the available air and fuel (propane, say?) stoichiometrically (sic?).

At some point the mechanical friction in the moving parts would be more than the pressure the exploding gases could generate. Who knows? Would it work?

Can you in fact compress the air to get a higher power density from the engine and still come out on top? (I.e more power out than used in the compression)

Better to take your own oxygen?

Better to use something exotic like a fuel cell?

Comments welcome!!!
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Things that would go inside the canopy:

UVC LEDs and any necessary supports
Back up parachute in case canopy bursts
Radar reflector
Pressure sensor (in case of leaks)

But all the above sterilised by UVC from outside before flight! (That way, leaks don't jeopardise sterility - only flight time)

Ahhh - here's something interesting, a bit like the Travelling Salesman Problem:
You have one LED in the middle of a big spherical balloon
You have one LED travelling up and down a cylinder balloon
At what given combination of radius and power does one sterilise quicker than the other?

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Things to measure at altitude

Air pressure
Partial pressure Oxygen
Temperature
Wind speed and direction
Solar irradiance - might be too expensive to fly a suitable spectrophotometer early, they cost $1000 - so just UVC?
GPS coordinates
Camera

Any other suggestions?

I've exhausted my Blackberry for the night, it's giving me "low battery"! Until tomorrow!
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Fly at night for sterility

UVC exposure at night is a wise move for sterilisation since it denies microorganisms the diurnal respite that they'd normally receive from solar UV damage. That's if we can fly at night however...
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Buckminster-Fuller?

You could have a spherical balloon instead of a cylindrical one, but only if you had some framework inside it, like a Buckminster-Fuller geodetic sphere, to hold the UVC LEDs. This would likely be too bulky and fragile for the weight limit. So we're back to the cylinder?

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Test one UVC LED on its own if need be

If we don't have enough money/power/weight to fly all the UVC LEDs we need, maybe just fly one illuminating a test spot on the canopy, and if that comes back significantly cleaner in microbial terms than the rest.
Ol

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I'll never hear another bad word against Gmail

Just one more:

Look what my Googlemail gave me as a directed advert!:

http://www.parcsw.co.uk/Altitude-Testing/

Not bad eh?

I'll give them a ring too (but not optimistic about price!)

The mystical beast, cyclo-olefin, finally sited! Well, Googled.

After a bit of googling, here is a likely looking cyclo-olefin with good transmission at UVC germicidal wavelengths (260nm):

http://www.zeonex.com/applications_zeonorfilm.asp

And the graph above is for a 3mm thickness! How much thinner can we go I wonder for our balloon?

It's actually pretty hard to find out what weather balloons are actually made of. Anybody know? You just buy one - for $45! This is an amazing and fun hobby I think, as long as you are not near a major air traffic corridor.

I am aware I seem to becoming obsessed with UVC illuminated balloons. But maybe this is no bad thing! This is where the biology has led us. There is no point, IMHO, building a high altitude bioprospector unless you are stone cold certain it is itself sterile.

Come the new week I think I will ring Zeonex's European office and see how game they are!

Questions I will ask:

How much does this stuff cost?

What is the sheet size?

How does one stick it together? (A thermal crimp etc?)

Can they make the entire structure for us - at a cost?

If it is cheap to make then we can burst our balloon at altitude like most normal balloon flights. If it is expensive then we find some way of reusing the balloon, for instance by letting the helium out gradually through a valve. Presumably the valve would sit in an invagination in the cyclo-olefin to allow it to be UVC-illuminated.

Bed now I think! :-)

 

Beware the dead zone! Also how to make a sterile wind vane

Let us assume we can create a really sterile canopy, most likely through UVC. What we are really saying is that we have sterilised the balloon canopy  as well as a volume of air around outside it, which has likewise been exposed to the UVC. So, streaming off downwind of the balloon is a plume of sterile air. We must make sure we DON'T sample this by accident!

We need to sample upwind, or make sure the UVC LEDs are turned off for a good period before sampling so that the plume dissipates. And how long would that be? Again, we really need some way to simulate plumes, eddies etc.  We need to monitor air currents and direction at altitude, perhaps using a tell-tale. But how to sterilise it? Oh dear... perhaps something cool like a segmented area of canopy and you mention the pressure in each segment, so you can see which segment is being distorted by the wind blowing against it?

Another thing we could do is to fire a probe out of the gondola, for instance on a small rocket, trailing a sample line well clear of the gondola and any possible plume. Since this would have been stored inside the gondola it could have been pretty easily sterilised on the ground. Does a model rocket engine withstand autoclaving? Gamma irradiation? Ethylene dioxide? An interesting experiment to find out :-)

As a simple experiment, we could imagine drawing the sample line (made of what? Coated with what?) back into the gondola and then over the different culture mediums that my colleague was discussing, so inoculating them.

UVC LEDs modulated for coms?

Here's an idea: We could modulate the UVC LEDs with rapid pulses and see if this could be detected from the ground (UVC is blocked by the atmosphere but there must presumably be residual radiation at other wavelengths from the LEDs). This could be used as a high rate, non-radio data downlink.

The inverse square law and long thin sausage balloons with internal skeletons

Our balloon could end up quite an interesting shape. If we are going to sterilise it with UVC LEDs then we want to make it as long and thin as possible. Why? Well, the intensity of UVC light at the balloon's surface from an LED in the centre of the balloon falls off with the square of the radius of the balloon - so if we can half the diameter of the balloon we boost our intensity fourfold. A normal balloon is essentially spherical at altitude, presumably to minimise the surface area, and hence the weight, of the canopy. But sterility is our overwhelming priority. Can we make a long thin balloon that can still lift its own weight to high altitude? Either way it will start looking rather like a Zeppelin - or a Skylon. The Skylon would be a better analogy, pointing straight up as our balloon will.

How do we work out the buoyancy of our balloon at a given altitude anyway? Any buoyancy experts out there?

One difference from a zeppelin though is that our balloon can have internal structures but no hoops, plates etc on the skin. We need all the parts of the skin to be illuminated, without any dead zones, by the UVC.

Something else to save weight perhaps - don't have lots of LEDs, have a few, and move them around. Imagine a central pole within the canopy which is extendable (maybe an adapted telescoping car aerial? Do they still do those??), or has a pulley mounted on it perhaps. This allows a UVC LED to be moved back and forth along the entire inside length of the balloon, illuminating its entire surface with a germicidal dose of UVC - eventually...

Nice things to make balloons out of

A chemist friend of mine thought of some very interesting things to make balloons out of. I'm still waiting to hear from him for some more details, but here are the highlights:
1) A superhydrophobic material, so that microbes can't stick to it
2) A superhydrophilic material, so that they are stuck fast and broken up
3) A photocatalytic material, which would catalyse anything on it to break down, ultimately into CO2 and water

I think (2) is out because the canopy would pick up too much moisture in the troposphere and would presumably be weighed down, reducing the height reached.

1 and 3 might well work, and 3 seems most elegant since it is an active process of sterilisation. Having said that, the same colleague still thought UVC might be best.

Our ultimate task is to kill spores - if we can kill spores then we can kill anything! Hence a massive UVC dose from LEDs etc might be necessary - if we can carry that many LEDs and enough power...

As always in "balloon material fantasies", it comes down to if we can find a suitable compound, if it is gastight for helium, robust enough for flight (without tearing etc), if someone will make balloons out of it for us, and for how much!
Cyclo-olefins is at least a name we can bandy around for the chosen property of UVC transparency... Any ideas who to order that from and any ideas about the other sorts of compounds?

If we can't fly a full size balloon made of our dream compound, then perhaps we can fall back on a small scale model, and then fly other hardware on a "dirty" normal balloon for a high altitude proof of concept?
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RTPCR as well as cultures?

We could also look for 16S RNAs by RT-PCR, which would tell us if something biological was present even if we couldn't culture it.
I saw an intriguingly small qPCR unit today in "Biotechniques", but still expensive ($10,000). I'll look into it further. With something like this we could at least detect a 16S signature in flight - and then sequence the amplicon back on the ground? (Sequencing in flight I think if for the deluxe version!)
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Culture mediums and flight durations

I would suggest we go for all the different culture mediums described! The only question then is: Are trying to culture in flight? If so, then we should be aiming for a flight of many days or weeks. We could assume that metabolic turnover will be very low at such low temperatures and Oxygen concentrations. Balloon flights are typically less than a day - longer than a day and you need radio and light beacons and so on.
But we don't need to do everything on the NESTA grant in one go - it could be enough for instance to say we have tested the unit for one day but would ideally fly for many more.
We could also, for instance, fly on a "dirty" balloon if we can't find a way to make a clean one. This would at least show that everything works at altitude.
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People with hypobaric chambers

One place with hypobaric chambers is the RAF. I had explosive decompression training about 13 years ago. Without going into too much detail this was also for a space-related experiment, in this case a zero gravity airplane flight. You had to have full safety training.
Unfortunately the flight never happened but the explosive decompression experience was, in my opinion, the best fun you can have with your clothes on. A tale for another time perhaps!
The RAF did this for me for free at the time since some of the older medical officers were sympathetic to spaceflight. They have since retired. I know this since a colleague in the RAF checked a few years later and was given a curt no for the same request. You have to pay for it now! :-(
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Atmosphere structure

To educate myself a little I have borrowed this image from Rashid's blog, we live down in the tiny troposphere and that the tropopause is a barrier to things getting above into the stratosphere. Ideas out there for getting things up there include volcanoes, blue lightning strikes, concurrent thunderstorms and forest fires, and lastly gravito-photopheresis (through this it would take 50years for a piece of soot to get to 20-80km up but it has to be less than 1µm). Or panspermia.

Thoughts on bacteria

I have been trying to find out a bit about what kinds of bacteria have already been found in the atmosphere, so that we can take some educated guesses in trying to culture them in situ. All of the articles I have read thus far have captured some air and tried to culture things from it - and this started back in 1878 by Mr Dowdeswell! But more contemporary accounts ranging from 2m off the ground to 41km up find remarkabley similar types of species. The vast majority are Gram positive from two main groups of G+ve bacteria - Firmiculates and Actinobacteria. There are also reports for the species Pseudomonas from the Proteobacteria but these are G-ve, though very hardy, and are very good at nucleation in clouds. The G+ve are a mix of rods and cocci in shape. And as far as I can tell they're all spore formers - which is a good way of getting through a tough spot. As for the two fungi that have been reported - Engyodontium and Penicillium - they also form spores. Lots more information can be gleaned from the Microbewiki.

So what could we grow them on - they're likely to be anaerobic, and hopefully cold adapted if we're going to grow them, if we start looking at interesting agars may be we'd need something with a low redox potential (like Schaedler's) or something with inorganic nitrogen ( eg Czapek-Dox or Simmon's) or may be try and mimic other extreme environments (Marine) or just go for bog standard stuff (nutrient) in an anaerobic environment. All suggestions welcome, and I'll go and seek advice from some of the micro people here in Brum. I'm going to do some ground level (sea level and ~1000m ie up Snowdon) experiments and comparisons.

Bathyscaphe

I'm Paul. You can find out a bit more about me here.
I also met Oliver on the NESTA Crucible 2008 (can't be bothered to hunt for the links, just use Mel's).
My role on the team is minor, as is the amount of time I will have free to fill in this blog thingy. Especially compared to Ol as you can see.

I have experience in 3D computer modelling - the use of the computer to generate and manipulate shapes. I have also played around with Rapid Prototyping / 3D Printing and the general extraction of 3D geometry back out of the computer and into the physical world. I have mainly worked in the building / architectural field, but that's just a question of scale. (And I wouldn't put it past Ol to decide he wants to launch a whole Lab building into the stratosphere one day...).

So I've agreed to help produce some of the more bespoke parts for the project by modelling them to great accuracy in the computer and then 3D printing them. I'm relying on the others to tell me what they need. But you've got to admit that printing something out one day and launching it into the sky the next is pretty cool...

Hypobaric chamber

We need to be able to test the balloon in a large chamber down to 0.01bar pressure, for instance to see if seams hold, things inflate and deflate OK, we can flush stale air from the sampler, and so on. If we tested the coronal discharge idea, we'd need to do that in chamber too. Also we'd need to see if any coatings etc on the canopy stay laminated. If we ever tested something like a Wankel engine generator we'd need to see if that could work at altitude as well since it would still be using whatever air was there.
It'd have to be a pretty big chamber but we could settle for testing scale models of things!
Probably the only people who have chambers like this are in aerospace. Often they are for testing satellites etc and have lamps to simulate the sun, which would actually be very helpful for us. But pricey?
Due to the danger of implosion it wouldn't be something to jerryrig I think!
The alternative is to just fly stuff and hope it works. Actually, this isn't a bad way to test IMHO - if you could fly the balloons really frequently and if you could find out what had gone wrong. At the moment, you need to track the balloons all the time, report this to Air Traffic, buy insurance etc.
Perhaps the answer is heavier balloons with transponder for air traffic worries? Actually not so pricey (FAA approved transponder and battery for about £2K, say 2.2kg total).

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Careful with the sampling invagination

We'd have to sterilise the inside of the gondola sampler invagination but we'd need to make sure we could then flush it for fresh air to actually sample. We'd need to know how quickly the air in the invagination turns over with the outside to make sure it isn't stale, sterile air.
A fan or something could be used by might be very ineffective in the high stratosphere. But we could test this... If we had a hypobaric chamber...
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How to sterilise the gondola

The gondola, inside its cyclo-olefin canopy, could be sterilised on the ground by running the UVC LEDs inside a mirrored chamber! That sterilises the outside of the gondola; its own canopy gets recontaminated during flight and then is resterilised by the LEDs as previously described.
Since the gondola canopy has to have a sampling port - an invagination to the gondola itself insiden if you will - effectively the gondola can be prepared and attached to the port on the canopy with the canopy inside out, which can then be turned right side out and invaginate the gondola within it!
But would cyclo-olefin take this much punishment? Who makes it anyway?
Oooh! We could have a reusable balloon? Instead of bursting it we could incorporate controllable valves? After all, we need to have our custom cyclo-olefin job made anyway...
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Gondola canopy as parachute

Small high altitude balloons usually have to have a parachute for a controlled descent. In our case perhaps the gondola cyclo-olefin canopy could be the parachute, or "ballute" to be exact. It could be filled with an inert, heavier than air gas like argon perhaps.
For those of you who don't know, balloons usually have to return on command, for instance by firing a small squib to burst the main canopy.
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Two balloons not one for fewer LEDs

Instead of studding the gondola surface with UVC LEDs, you could encapsulate the gondola in its own small balloon made of cyclo-olefin again, and sterilise that with LEDs on the gondola shining through it. That way you might only need 4 or 6 LEDs, say. There could be one opening for the sampler.
The gondola within could be left "dirty" or could be extensively sterilised groundside. The trick throughout is to sterilise everything exposed to the air in flight - main balloon canopy, lines, gondola canopy - in flight! Hence the LEDs.

Any cyclo-olefin manufacturers out there?
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99 Red Balloons...

A coronal discharge toy balloon test would be easy - using a metallicised "birthday greetings" style balloon! Maybe a cyclo-olefin balloon would be a major custom fabrication task.
Even a small balloon of either type could perhaps be used as a self-sterilising sample-grabber that would rise separately of the main gondola, like the mortar idea I posted earlier. Since ground contamination concerns are still valid (see earlier post), the sampler would then be reeled in for in-situ analysis - somehow?
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Mini balloon sterilisation tests?

Could we test UVC and coronal discharge balloon sterilisation using small balloons on the benchtop? But we'd need a hypobaric chamber...
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Coronal discharge balloon sterilisation?

Or could the balloon canopy be metallised and sterilised by a high electrical field and coronal discharge, as previously described?

Must... sleep...!
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UVC balloon illumination

A UVC-illuminated balloon would be an impressive sight - after all we need to sizzle any microorganisms on the balloon with germicidally more significant amounts UVC light than the sun itself provides at altitude!
What would its safe viewing distance be? Could this double as a beacon for nighttime flights?
Would pulsing the UVC source be more effective than continuous illumination?
Blacklight type fluorescent strip lights or LEDs?
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Self-sterilising UV transparent balloon! (SSUTB)

Ohh here's a good one - what if the balloon was made of something like cyclo-olefin which is UVC transparent? Then the entire balloon could be illuminated from below by a brilliant UVC source on the gondola to sterilise it in flight! The gondola itself, being fairly small, is itself easily sterilised by UVC sources on its surface. Then we no longer need a pipe of any sort.
Is cyclo-olefin impermeable to helium? (At least long enough to last the flight?) How much does it cost? Can we have a balloon made out of it? Where would we find a really brilliant UVC source?

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Update on my vortex ring state idea

It occurred to me yesterday that a VRS "corridor" idea has an obvious flaw, which is that the VRS toroids will expire eventually and then release their presumably contaminated air from the balloon and gondola into the "corridor".
However, this can be fixed by sterilising the air in the VRS' as they are generated, for instance by UVC LEDs. Is this possible? Even with air rapidly moving past the LEDs? We'd need to try experimentally.
If this begins to sound like requiring unfeasible amounts of power then it is worth remembering that actually, the sample corridor would maybe only need to work for a few seconds - after that the air samples would have been drawn in and be ready for analysis.
VRS is just one idea. Do you have others? Perhaps a "Self Sterilising Mortar Round" (SSMR) as described in my earlier post is better?
Let us not forget the obvious approach - a long pipe to stick out from the gondola. But how to make a Self Sterilising Pipe? (SSP). You can make flat packing or inflatable pipes (that's another blog!) to deploy during flight, but could you do this with the surface studded with UVC LEDs? Wouldn't this get really heavy and full of cabling? Maybe you could illuminate the pipe from the gondola with a very bright fixed UVC source - an LED or laser, sterilising it from a distance. But this might need to be very powerful... perhaps it doesn't have to be a UVC source at all? Coronal discharge is a potent sterilising agent as well (a company called Cerionx was trying this, as I recall). Could we build up a high electrical field on the pipe, just below that that would arc at high altitude? Is this a cool experiment in its own right?

We could perhaps try buying an "Air Bazooka" toy and seeing if the VRS' it generates can actually be sterilised by UVC LEDs. For instance, we could rig such a "Self Sterilising Air Bazooka" (SSAB - I feel like making acronymns tonight!) And then fire it continuously onto an agar plate with the LEDs turned either on or off. If you see a circle of fewer bacterial colonies where the VRS hit the dish, you'd know the air in the VRS was indeed sterile.
Do you think this would be worthwhile spending some of the NESTA cash on?

At the root of all of this are the questions: How far away from the gondola and the balloon do we need to sample? What are the winds at altitude? How turbulent? Do we need to measure this in flight?
Is there a fluid dynamics expert reading this? What is the safe distance beyond which any eddy bearing contamination from the balloon is unlikely to travel? Just how far from our balloon mothership do we need to go to sip pristine stratospheric air?
Goodnight!
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Ionic fluids for liquid-filled uv transparent pores for balloon flights

And some more...
Comments from Ionic fluid experts welcome!!

All this balloon talk reminds me of something else I thought of last week which got lost in a hectic weekend.

I have a colleague who makes nanocrystalline porous films and I wondered if these could be used to make a truly UV-transparent material for our balloon radiobiology experiments. Even quartz for instance absorbs more and more into the UVC at any mechanically feasible thickness. It's no longer transmitting a representative solar spectrum.

I wondered if you could seal the pores with a very, very thin film of quartz, cyclo-olefin etc - something nice and UV friendly and even more so due to being extremely thin. The pore structure would provide physical support, and the pores would be wider than half the wavelengths of UVC, and so wouldn't interfere with transmission. For that matter they would be
bigger than half a wavelength of any part of the solar visible spectrum of any possible biological relevance.

I had also wondered if you could seal the pores with a liquid, which would wick into the pores, but I couldn't work out how you'd stop it boiling off at high altitude.

My colleague gently poured cold water on the thin film idea, saying it was in fact very hard to do; the thickness and coverage is very variable.

However, he hit upon the same idea as me - a wicking liquid - but as a highly capable chemist he knew which to use, at least conceptually: An ionic fluid. These can be long and complex molecular chains and as such essentially have no vapour pressure, hence no evaporation. Again, since they
are long and complex, they have short-range order and are unlikely to absorb in the UV.

Air capture + in situ analysis + VertiTech

I had an idea during the washing up,

I have strong suspicions that most micro-organisms that are claimed to be captured at high altitude are in fact the result of lab contamination back on the ground or contamination off the balloon or experiment package. Even if you could efficiently sterilise both, they are still going to ascend through the troposphere on the way up, which is laden with bugs anyway. I give an example below which i is mainly a microbiological argument.

Finally, sampling missions to date, as far as I have read so far, made no allowances for atmospheric pressure - I can't believe bacteria grow the same at 0.01 bar versus 1 bar on the ground.

So, to sample at high altitude, IMHO, you need:
A) to be able to re-sterilise in flight after passing up through the troposhock, or jettison some sort of disposable cover to reveal a sterilised sampling vessel

B) carry out your biological experiments whilst at altitude to rule out post-flight lab contamination

C) find some way of preventing air flowing from the balloon canopy or experment gondola from reaching the sampling vessel

D) capture the samples completely airtight so they stay at 0.01 bar for instance throughout the descent back to the ground and/or (B)

Here's my preliminary design ideas for each point as a molecular biologist:

A) use a germicidal UVC light source such as UVC 260nm LEDs, to both blast the sampling port and any pipework for the molecular biology within.

B) my forte - I automate labs terrestially for a living. I'd like to make a miniature pipetting robot

D) do (B) but be very careful of vapour pressure at this altitude - water and reagents will boil at 3-4'C. Stray heat from the electronics. Might be enough to boil the samples dry therefore. It might be safer to pressurise the samples just a little bit, say 10s of mBar, with something inert like Argon.

What about (C)?
Well, this is what I thought of whilst washing up! Could you generate a vortex ring state around your sampling port? As I understand it, VRS is a toroidal body of moving air that self-circulates within itself and is therefore stable over distance. This is the principle behind "air bazookas" which are fun toys for blasting friends with intense bursts of air from some distance away. I think smoke rings are VRS' for instance. Wikipedia has quite a good description!

If you could generate essentially continuous or pulsed VRS, you could essentially exclude air currents and contamination from elsewhere on the balloon. Since VRS' travel in a stable manner over distance, this presumably prevents any recontamination from eddies nearby the balloon. Effectively you might have a "clean" sampling corridor down the middle of the toroids?

You could achieve the same thing with a long pipe, but then - how do carry the weight and how do you sterilise the pipe? And presumably you have to stick it out sideways, not downwards, since most contamination from the balloon will drift downwards under gravity (presumably?)

I suppose another alternative could be to blast a sample container free - maybe one that would self-sterilise itself and then take the sample. Think maybe a sphere studded with UVC LEDs shot from a mortar in the gondola? You could either retrieve it on the ground, reel it back to the gondola somehow, or carry out the biology in the container.

If this begins to sound heavy or power-hungry, IMHO we should not shirk from that. We could easily fly bigger balloons for longer, for instance by adding a transponder for air traffic worries, and maybe a high-density power source - I had in mind something like a Wankel engine adapted to work at high altitude. But that's another discussion!

Anyway, those are some initial ideas!
(I should really be in bed but have batted this out over some OJ, chocolate, a cup of tea and a shower!)

Microbiological details :
For instance, Griffin et al Aerobiologia (2008) 24:19-25 claims to have
found non-sporulating bacteria in the high atmosphere. Non-sporulating?? That doesn't make any sense. I wouldn't be at all surprised to find hardy spores from sporulating bacteria. But non-sporulating?

Also, they claim they bacteria didn't show up until they'd cultivated the bacteria for several weeks. Personally, I feel any agar plate or equivalent will grow *something* after long enough, no matter how much you autoclaved the media.

Finally, they made no allowances for atmospheric pressure - I can't believe bacteria grow the same at 0.01 bar versus 1 bar on the ground. Surely an aerophile will just roast itself with massive oxidative respiration? (Unless there's negative feedback regulation for occasional excursions to lower altitude... Interesting...)

PS and finally, how did I find out about VRS?:
A wikipedia binge as follows:
Iranian satellite launch
Iranian space program
Iran
Iranian revolution
Iranian hostage crisis
Failed american rescue mission
VSTOL Hercules C130 designed for above
V22 Osprey tiltrotor (also VSTOL)
V22 Osprey crashes
Vortex rotor state! (Has caused V22 crashed due to VRS from the rotor blades).

VertiTech: a miniatured robotic system Ol has been dreaming
of (short for Vertical Technician.)

Ring Vortex States

This is a test post to the H.A.B blog. Tonight I am thinking about Ring Vortex States to provide a way to prevent the balloon canopy or outside of the H.A.B casing contaminating our sampling device.
Ol
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What are we going to do?

The stratosphere is a potential habitat for exotic life forms of relevance to industry and human health. We aim to analyse these life forms in situ, with the long term goal of bioprospecting for novel ways of coping in extreme habitats. The air and clouds contain bacteria and fungi. When these fall to earth they are suspected carriers of disease. Craig Venter for instance is undertaking a massive effort sequencing genomes of airborne life. But how far up does this go? Ultrahigh altitude clouds are still ice crystals condensed around dust, like “normal” clouds: An Astrobiologist would tell you this is an excellent hiding place for life! As long ago as 1935, the Explorer 2 Balloon found fungi and bacterial spores above 35,000ft; similar experiments have been performed since then (rev Griffin Aerobiologia (2008) 24:19–25). However, samples are snatched blindly and analysed on the ground, hours or days later. After such journeys, can researchers be sure they have not just contaminated samples terrestrially? And are they truly representative of high altitude life after enduring rapid temperature and pressure changes during descent? By contrast, we will perform active molecular biology experiments to study life in situ at high altitude. This has never been done before.

Up in Birmingham

My name is Melissa Grant and I don’t have that many professional activities outside of work - but I do like blogging (so you can keep track of my other hobbies), they keep me pretty busy at the Dental School with projects looking at making new toothpastes that fight inflammation.

Ol and I are doing this project after we met at NESTA’s Crucible Labs last year (2008) and won some funding to do this project - needless to say its an amazing opportunity! Through this blog I hope to document what I am up to - what research is going on and hopefully the outcome of the experiments.

Here we go

My name is Oliver de Peyer and these are my main professional activities outside of my place of work. Click here for a report on my British Association Media Fellowship placement at Nature in summer 2000
Click here for the Society for Chemical Industry. Since 2002 I have been the Chairman of their London Section (soon to be renamed the London Regional Group), with a responsibilty to provide lectures and events for over thirteen hundred members.Click here for the University College Union. I am an active union member and am a member of the MRC Committee.Click here for previous events in my career, such as my time at NASA and Reading University Why not email me at opeyer@nimr.mrc.ac.uk ?