Friday, January 16, 2015

I'd like to add you to my professional network on LinkedIn

 
Oliver de Peyer would like to stay in touch on LinkedIn.
Oliver de Peyer
Oliver de Peyer
Lab robotics scientist
London, United Kingdom
I'd like to add you to my professional network on LinkedIn.
- Oliver
Confirm that you know Oliver
You received an invitation to connect. LinkedIn will use your email address to make suggestions to our members in features like People You May Know. Unsubscribe
Learn why we included this.
If you need assistance or have questions, please contact LinkedIn Customer Service.
© 2014, LinkedIn Corporation. 2029 Stierlin Ct. Mountain View, CA 94043, USA

Wednesday, March 16, 2011

Our contact details

Here is a reminder of our key personnel and contact details:

The High Altitude Bioprospecting Consortium

http://www.highaltitudebioprospector.blogspot.com/

http://www.nesta.org.uk/nasa

Principal Investigator (P.I):

Dr Oliver de Peyer
Email: opeyer @ nimr.mrc.ac.uk

Co-ordinating office:

5 Molasses House
Clove Hitch Quay
Plantation Wharf
London
SW11 3TN

Tel 0208 816 2688
Fax 0208 816 2580

Co-P.Is:

Dr Melissa Grant
Email: m.m.grant @ bham.ac.uk

School of Dentistry
St Chads
Queensway
University of Birmingham
B4 6NN

Website: http://melissagrantprofile.blogspot.com/


Dr Paul Shepherd
Email: P.Shepherd @ bath.ac.uk

Dept. of Architecture and Civil Engineering
University of Bath
Bath BA2 7AY
United Kingdom

Tel 01225 384406
Fax 01225 386691

Website: http://people.bath.ac.uk/ps281/

Carried out in collaboration with our colleagues in the United States:

Professor Lynn Rothschild
Email: Lynn.J.Rothschild @ nasa.gov

NASA Ames Research Center
MS 239-20
Moffett Field, CA 94035
USA

Tel U.S 650-604-6525
Fax U.S 650-604-108

Website: http://astrobiology.nasa.gov/directory/profile/845/Lynn/Rothschild/

Launch vehicles provided by:

Thomas M Atchison
Email toma @ rocketmavericks.com

Mavericks Civilian Space Foundation
NASA Research Park
P.O. Box 223
Moffett Field, CA 94035

U.S.A
Tel U.S 650 492 5978

Website: http://www.rocketmavericks.com/

Recovery & tracking services provided by:

Stratofox


Other material and coverage of H.A.B:

http://www.nesta.org.uk/library/documents/Crucible-evaluation-case-studies.pdf

Book charting our fieldtrip to Nevada 2010

Tuesday, February 22, 2011

Solar power options for a HAB II

This is for a balloon flight.
Solar flux is considerably higher at stratospheric altitude and there is much less cloud cover, so solar is a more reliable option.
Matt and the crew have launched solar powered balloon payloads before - but never mechanical stuff...

The idea of the relays would be to switch from the solar arrays to a conventional battery if the solar supply falters (so I guess I need a double-pole relay)

The next trick would be how to power the relay direct from a microcontroller, since the pins on say, a PICaxe give only 10mA. We need a relay that can handle either the 1A or so from the solar array or the massive ampeage from a battery shorting through a SMA (offscale on a 30A multimeter!). But relays often need 100mA or so to switch... So we probably need a transistor to switch on a 100mA current from a PICaxe pin.

Why do we need this?:
At Black Rock we ran our battery ragged well before landing - the last coms I got was just before the balloon burst (when we were near Frog Pond), which was only about 90 mins (about half way?) in. The intense cold probably played a part but we also had a constant power demand of a couple of amps at all times anyway.

The LiFePO4 battery I got lasts longer but Matt said they don't like balloon flight conditions at all.
So any other options would be worth trying.

It looks like the cost driver for solar arrays is voltage - say £70 for a 12V, 5W, which is a measly 400mA or so. For SMAs we only need amps, so a cheap low V, high A array might buy us something.

It's a bit the same with battery charging. For a 6V battery we need a 6V array and a decent ampeage to get a decent charge rate, which means in practice an array too expensive and too big to fly.
Besides, as far as I can tell, the only practical battery for trickle-charging from a solar array is a lead-acid one, which might burst at high altitude (since they are sealed to prevent leaking) and are bulkier. They are no good burst-wise for rocket flights either, for reasons HAB 1 well knows!

So, it might be fun to play with solar to extend the balloon flights, but have a relay to switch back to battery if needed.

In general, good DC sources for use in the field would make a lot of sense, since as it was we were constantly running AC inverters off car batteries to power power supplies to supply DC to power laptops and so on... Whereas a 19.2V battery and/or solar array could have done it directly. We spent a lot of time angsting over generator resources etc similarly. It might also be worth digging up an old low power PDA, say an Atari Portfolio, for the serial coms... Don't really need a laptop at all! Would run for hours on AA batteries...

Ol

------Original Message------
From: Paul
Subject: Re: Ideas for switching low volts, high amps?
Sent: 22 Feb 2011 20:01

I think a mechanical relay would be the only way to do what you ask. Maybe not suitable for rockets (acceleration might trigger it) but ok for balloon.
But you could maybe switch each separately (0.4A) and combine them afterwards, which might get you back into the FET range.
Solar sounds a bit unreliable though, given there's no real problem with a battery? Solar usually gets combined with a battery / large capacitor anyway to take out the peaks & troughs...

P.


On 22 Feb 2011, at 19:22, opeyer@nimr.mrc.ac.uk wrote:

> Can I ask you an electronics question?: What is the best way to switch a low voltage but at highish current? I'm looking at about 0.45V, 1.2A. I've played with the SSRs before (basically big MOSFETs) but they need at least 3V for the circuit being switched. Same for Darlingtons. Should I use a mechanical relay or is there something else?
>
> This is for a H.A.B advance project - I found some cheap 0.45V, 0.4A solar cells so, intriguingly, three of these in parallel might be enough to trigger a SMA in good light. SMAs only need current, not volts.
> Quite big, expensive solar arrays - enough to charge a battery for instance - seem to be high volt (say 12v), but not necessarily high current. So by contrast we might be able to do a solar-powered HAB quite cheaply?

------------------

Monday, November 29, 2010

Re: astrobiology sterility vs disinfections

Hi Mel,
H2O2 is stable if stored correctly - it's been used as a storable rocket fuel oxidiser for instance. However, it can be broken down by an inorganic catalyst.... Perhaps we could inject, say, a palladium slurry instead of catalase?
But it's all just more and more plumbing!
Catalase is a much more efficient catalyst for breaking down H2O2 (hence it's name) so it would be fun to see how Catalase, Bugbuster and TwistDX co-exist! Or Palladium, come to that.
Best
Ol

Hey Ol
does hydrogen peroxide have a relatively short hald life? could we take advantage of that? or will the cold prevent in breaking down by itself?
M

astrobiology sterility vs disinfections

Hi Mel,
If I can tear you away from Fluxx for a moment, what do you think of the below?:
Basically H2O2 is the gold-standard for astrobiological decontamination, but can we do this in flight?
Are we getting closer and closer to the minirobot idea?
(I.e lots of things to pipet so a pipetting robot not valves?)

Best

Ol

------------------

Many thanks, Lynn - if we tried to disinfect a system in the field or during flight (my long-term ideal) we would need to flush out or neutralise the H2O2 before adding reagents (eg TwistDX etc). The question then is whether the reagents can tolerate the presence of Catalase etc. Unless we need to flush out the Catalase etc too...

For trying to sample at altitude, something like Catalase might be problematic since the relatively high torr O2 released might nuke anything in the sample (since it would have evolved in a far less O2 -rich environment)

Perhaps this protocol is best used for in-the-lab sterilisation? I have often thought that actually we have access to a lot of plasticware that has been gamma-irradiated (the gold standard for being sterile AND is DNA-free, which is a separate criterion) and we could then try to sterilise plumbing etc (eg Tygon) with H2O2?

This is somewhat what I had in mind for this summer's HAB device but in practice the syringes etc needed too much fiddling to mount them sterile. I tried a ethanol flush during the rocket launch preps but that's a moot point now :-O ;)

Ol

------------------
Fw from Lynn

Alonso

I did conduct a literature search on Hydrogen Peroxide for spacecraft cleaning.

As noted for astrobiology/planetary protection for the mars missions of the 70s Solutions of 3, 10, and 15% hydrogen peroxide were found to have pronounced bactericidal effects, as a function of time of exposure, on sporeformers and nonsporeformers isolated from spacecraft. Find the attachment, applmicro00028-0236

It appears the UMS should be cleaned with the least toxic concentration 3% as exposure time can be long 4 hours.

The disinfection Nov 2008 guide has a selection of agents for disinfection listed if H2O2 cannot be used.

I hope all is well

best
tony...

Tuesday, October 5, 2010

Computer autopsy

Much has happened since our last posts to this blog, to be documented online soon.
This is a quick announcement to say that our bruised and battered flight computer has been sent back to its manufacturer for a computer autopsy. Fingers crossed!!
------------------

Tuesday, September 7, 2010

Slide show of the field trip!



Out in the Black Rock Desert we launched the HAB device on a rocket, for an in depth account please visit our book on Blurb - link through the image on the right.

Friday, July 16, 2010

I'm about to go to the desert!

I'm about to go to the desert!
Somewhat crestfallen - could not get my experiment to work properly due to a last minute electrical problem.(On wednesday it almost caught on fire!!)

But I will fly it on balloon anyway - I'll be able to talk to its computer using a special radio link whilst it is flying; that is still pretty cool! :-)

I am hoping I can get it to work during the week and do some experiments on the ground too - that will be quite interesting in such a big desert (is there anything alive there?...)
So I will try to enjoy everything even if the actual flight isn't perfect.


------------------

Tuesday, June 29, 2010

Final preparations



The last few months have flown by and we haven't had a moment to update on our progress on the blog. Ol has been flat out, pulling all nighters to finish the device, which you can see in the picture. There have been nightmares about reagent compatibility and he has manged, with almost unbelievable cunning, to fit four syringes in to the device to pipette in the required quantities of liquids in the right order. Paul and Ol have been doing all kinds of things, remotely from Canada in Paul's case, to ensure everything will work.
We have also run a competition with NESTA and NASA for 2 students to come with us to Nevada to fly the device - welcome on board to Joe and Rainbow. We had 120 applicants and it was really hard to chose even the last 6 finalists, nevermind the 2 winners! Rachel down at NESTA has been in an organising frenzy, sorting out logistics - accommodation, flights, food (you would never normally have to put so much effort in to camping, we're just going to not have a lot of water so many things will be tinned) and much more.
With only a few days remaining before Ol heads to NASA AMES we are thinking very hard about how to get our reagents to California with out breaking any laws, but also crucially keeping them all cool. Then Rachel, Paul, Joe and Rainbow will head out, getting a brief trip to NASA too, and then I'll go out last (hampered by a conference the week before!). 12 days in the Nevada desert - to fly the device as many times as is possible - on balloons and rockets! The people we're teaming up with are the Rocket Mavericks. We're going to the Black Rock desert - home of the burning man festival. There's no phone coverage and its very remote (austere as Ol says), so we're taking GPS and satalite phones and all kinds of wizardry - hopefully there'll be some good star gazing too.
We've also been in discussion with Kira O'Reilly and Anna Dumitriu for possible art interventions and collection of materials whilst on location in the desert. Currently we're thinking of making extensive diaries and trying to communicate with bacteria.

Saturday, March 6, 2010

First ever HAB dream? New components!

I went on a HAB bender last night and ordered lots more components. Then he actually dreamt about them all night :-)
The first ever HAB dream? Unless one of you can better :-)

I have now ordered a batch of non-sterile syringes and tubing, and established a wiring colour scheme for the main circuits (it was getting confusing with 5V, 12V and 3.6V high Ampage components)

I spent some time agonising about incubation temperatures for the TwistDX reagents and in fact if we can't get it to work, we could always test at ambient room temp to start with. Having said that, I have bought:

A professional combined probe and infrared foodgrade thermometer - will try both approaches. I wanted a probe or as small as possible otherwise the thermal mass of the probe ends up setting up the sample temperature and not the other way round!
As it is, the chamber looks like being at least 12mm long to accomodate the probe during testing. The probe hole will be sealed up later.

An IR spot might work - we need an optical window in the incubation chamber anyway for the PicoGreen measurement - but even the smallest spots on various instruments were over a cm, which seems unfeasibly big?

As a curveball, I will also try thermocolour plastic (like those forehead FeverStrips)

For the actual incubation, I will try resistive wire, maybe wound around the incubation. I have also found a small hotplate to sit the chamber on, and also a miniature water heater, and to go with that a miniature immersive water pump! (with water tubing wound around the chamber)
So it could be barheateresque, hotplatesque or central heatingesque!

Will keep you posted!

------------------
Oliver de Peyer PhD
Lab 209
Division of Molecular Structure
National Institute for Medical Research
The Ridgeway
Mill Hill
London
NW71AA
United Kingdom
Tel 0208 816 2688
Fax 0208 816 2580
Mobile phone +44 7908 783367
opeyer@nimr.mrc.ac.uk

Monday, February 1, 2010

HAB on a rocket?

HAB has now been invited to become part of the Clothos project,
flying similar payloads on rockets instead of balloons!
Is this our shortcut to a rapid flight??

http://www.rocketpedia.org/index.php/Clothos_Project#Science_.26_Instrumentation

Tuesday, December 8, 2009

Flight computer has arrived!

Our lovely low-power PC104 Titan flight computer has arrived from Eurotech, complete with interface boards.
But what will we interface with now? A PIWB MAID? :-)
It is exhilirating to be involved in a project that evolves so rapidly and fluidly! A unique selling point of Crucible (R.I.P)

------------------

Pump that balleen!

Hi Gareth,

Apologies for the delay, was on my Blackberry until now so couldn't
see your answers highlighted against my original text. Also my
thoughts on the peristaltic pump idea you suggest!

(Incidentally outstanding Googlemail targetted ads appearing alongside
this email, including the reseller for the MB2, a altitude/pressure
testing company and Fluigent!)

The U2 reference:
Griffin et al Aerobiologia (2008) 24:19-25 - Google it, it's free
For my severe doubts about this, please see my earliest posts on our blog:
www.highaltitudebioprospector.blogspot.com
Like you, I was suspicious about culturing conditions.
In fact - we'd like to do THREE things:
1 Attempt to collect for culturing - but trying to keep the samples
hypobaric all the way down
2 Carry out a bioassay IN FLIGHT so that nobody could say the result
was caused by lab contamination. Of course, it could still be
contamination from the balloon in flight - see the blog for agonising
about this (self-sterilising balloon anyone?). A suitable bioassay
would be amplification of 16S ribosomal genes with a fluorescent tag.
3 Try to match the two! (i.e see if you could culture something with
the same 16S sequence)
Love to add (4) which would be to try the same microfluidically!

Your later email: A peristaltic pump is indeed a very cool alternative
to a axial fan or a syringe/bellows type arrangement. Normal lab
peristaltic pumps are usually pretty massive affairs though (they have
to be to squish the roller against the tubing really tight). Hmmm....
how about a linear ripple peristaltic pump? Like an inkjet?
I.e a flat piece of tubing being squished in waves along its length to
accomplish the pumping. Might be easier to rig (the SMA actuators I
love pack a lot of muscle for their size and are very simple, but are
linear movement only really)
How fast could we run either type of peristaltic pump though? They are
intrinsically limited to the size of the tubing perhaps? It can't be a
really wide tube or it would be unsquishable (if the walls are thin
then it would quickly tear). If it is small then it takes a lot of
pumping for a given volume. But... I love the linear wave idea, can I
play with it? :-) OOOH that might work for a reel of tubing as well!
(just like you suggested parallelising a normal rotary one)

Looking at that weblink you sent us of the monster peristaltic, you
can apparently have peristaltics with 1/2" tubing!
Another maths experiment...
Let's assume 1cm tygon tubing, which we are more likely to lay our hands on
That has a cross section of about 0.5cm2
1L is 1000cm3
So, you would a 20m length of tubing to pump 1L
(1000/0/5 = 2000cm)

What I was even thinking was - the 16S or culturing reagents could be
INSIDE the tubing already - this would only weigh 1L=1kg in the
example above. But the tubing might be heavier...

(Let's check the axial fan situation further but Fred was adamant they
couldn't shift anything in low pressures)

The balleen idea is a beautiful comparison and I'm floundering how to
think it through biochemically (this is almost an unintended marine
pun! No, to be honest it's an intended one). What would be mixed with
what?
How thin can you make the film? Say it was 0.1mm thick.
Say the axle of the winding barrel for the 1km MAID ribbon I
postulated was 50cm across.
That would be a circumference of about 1.57m
So a 1km ribbon would wrap around the barrel about 637 times
637x0.1=64mm wound thickness

You could indeed either capture bugs on the film and try and grow them
on the ground, OR try to grow them in flight (paradoxically the better
bet perhaps, especially if you have a long flight, since the growth
conditions are most similar to the bugs' natural environment) - but
the problem with those two is you don't know what to grow them on. A
bioassay in the film itself might be best - i.e chamber 1 lyses the
cells, chamber 2 adds reagents, chamber 3 amplifies 16S etc. Mel has
already succeeded with this in the lab - see blog - but not
microfluidically! (Can you do all this in a 0.1mm thick film etc? 1mm?
I've always been fascinated by microfluidics from the outside but know very little of it's parameters!)

Oooh.... here's a lovely idea... I'm going to call it PIWB for Pumped by Inkjet Wave Balleen!
A thicker film with a pump layer made up of microfluidic channels that pump into the culturing or 16S channels - and the pump channels are pumped peristaltic fashion in linear waves, like an inkjet! All integrated in one.

But how do we activate the pump channels? Over to you Gareth!
(In your simpler passive sampler idea, how would you start the epoxy
sealant curing come to that?)

(Reading in the 16S fluorescent results from a PIWB MAID ribbon
(sorry!) is easier - you just reel it in again and scan the ribbon as
it comes back in, like a pianola.)

Night night and best wishes!

Olly

------------------

Monday, December 7, 2009

Pumping at altitude

Been writing this all day in spare moments :-)

I got the basic bioaerosol numbers (I.e 1cfu/L at ground level) from the person (Fred) who builds the MB2 samplier, and I knew him through a science charity, so it was an interesting coincidence!

I think we need to work out some better way of getting the air through the sampler - according to my sums you'd have to pump a 50ml syringe for 60 years!!

Hmmm let's think that through
500ml - 6 years
5L - 0.6 years (219 days)
50L - 22 days, getting interesting
500L - 2.2 days (so a 1 day flight is worth it, the chances of finding something would be 50:50)

That's 500L per return syringe stroke - in say 10s, eqv to a continuous pump pumping 50L/s

The MB2, straight out of the box, is useless b.t.w, because its fan could never pull a vacuum Fred says - it is designed for ground level use whereas we need a pump that pump essentially to vacuum (I.e from 0.01bar, 10mbar, to something less than that, which to all intents and purposes is a lab vacuum).
Fred is quite interested in building us a hotrod version if we can think of a way round it though.

The problem with an axial-based fan design for a pump - what would first spring to mind - is that you can't really pump to a vacuum this way, which is what we are asking (see above)
In fact, electron microscopes etc use plunger-piston type pumps to pull a high vacuum - so not far off a syringe pump after all. You can't spin a fan that fast or that efficiently, but if you withdraw a given volume into a syringe or piston etc then you really have caught something in the barrel, even if it is very tenuous (ie.g 50ml at 0.01bar is eqv to only 0.5ml of sea level air)
Hmm can we cannibalise an EM pump? A surplus one perhaps? But likely to be heavy and high voltage. After all, all we need to pull is 10mBar to 1mBar, not from 1000mBar to zero (which is what the EM pump has to do)

How big a plunger would you need to shift 500L?

500L is 0.5m3

Let us assume a piston with a working stroke of 17cm - 0.17m (this is because this is the useful return stroke of the SMA actuators I have in the lab)

0.5/0.17 = 2.94m2
I.e, the piston has to have a surface area of 2.94m2 for a stroke of 0.17m to have a pumping volume of 0.5m3 (500L)

2.94=4pi(r)squared
0.74=pi(r)squared
0.23=(r)squared
0.49=r
So say 0.5m radius, I.e a drum 1m across - just about doable, especially if you have a bigger stroke (multiples of 17cm perhaps or a different mechanism altogether) for a smaller radius - OR multiple pistons

Who makes really airtight, sterile pistons? Life support machines perhaps?

The other alternative is to pull a chamber to vacuum on the ground, put it on the balloon, and then suck from ambient air pressure at altitude (e.g about 0.01bar) into the chamber. I have no idea how much a such a chamber would weigh though. Remember it needs to resist 1 bar of ground level air pressure whilst holding vacuum at ground level.

Could you pump it to vacuum in early flight, once the air pressure is less but still "pumpable", say 100mBar?
But is the pump heavier than the chamber?
And so on!!

Any ideas/maths to add my friends?
Can I pump you for ideas? :-)

Ol
------------------

Sunday, December 6, 2009

Very hard to happen upon aerophiles!

I'm writing this on my Blackberry so I can't check the aerophile literature right now! But here goes anyway:
I found out recently that the biodensity of airborne microorganisms, in colony forming units (cfu), is about:
1 cfu per 10l at ground level.
If same biodensity at altitude, allowing for lower air density:
Say 0.01 bar
1 cfu per 1000l
This is the same as a clean room :-O

How much air at this density would a detector 10cm2 square have to travel through to detect one colony?

10cm3 is 1l

Since 1 cfu per 1000l expected:
So, 1000 x 10cm cube=10,000cm
Or 100m air needs to be travelled through to detect 1 cfu at altitude
So 10cfu per km

U2 aircraft have flown similar transects of the high atmosphere.
A 1000km U2 flight could therefore theoretically detect about 10000cfu.
But only a single colony was detected during such a flight in real life using a similarly sized detector, suggesting that at the culturing conditions used in the experiment is question, biodensity is about 10000 less than at ground level, even correcting for altitude (and actually U2s fly slightly lower and atmospheric pressure is somewhat higher than 0.01bar). And that's assuming the single colony seen wasn't a ground contaminant.

If it was 10,000 less biodense then on the ground, then this means (allowing for altitude) not 1 cfu per 1000l but 1cfu per 10 million l !

But balloons fly far less far. If one opened a sampling port at final altitude, this suggests you'd need to allow the balloon to drift 1000km - OR pump 10 million L through your sampler.

Say you have a 50ml syringe pipetting up and down. 20 strokes is 1L

You would therefore need approximately 200 million strokes to detect one cfu. If each return stroke took 10s, this is 2 billion seconds
This is about 60 years!!

A long duration drifting balloon, flying thousands of kilometres, therefore seems more feasible.

One must also however be aware of sample port size.
The above calculations are for a 100cm2 detector (eg 10x10cm)
If your sampler had only a 1cm2 aperture, this would obviously be a hundred times less. Then the balloon would have to drift for 100,000km to detect 1cfu!

Could a large volume pump be developed, for instance using bellows?

Alternatively, could the sampler area be massively increased?
For instance, imagine a Massive Array of Inexpensive Detectors, MAID - a ribbon 10cm by 1km perhaps. That's 10,000 times the surface area of the original 100cm2 detector concept.
Then you would only have to drift for 100m to detect one cfu!

Of course there may be organisms that are hard to culture but which can still be detected by RT-PCR for instance. But these calculations certainly set an upper pessimistic boundary of what effort is needed to biodetect at altitude.

How big a cavity is 10 million litres? Could you perhaps sample this big a volume using the interior of the balloon?
10 million litres is 10,000 cubic metres
4/3 pi (r)cubed
So 30000 = 4 pi (rA)cubed
So 7500 = pi (r)cubed
So 24000 = (r)cubed
So the cube root or 24000 = r in metres
This is a radius of about 29m
So, a balloon 58m across has a volume of 10 million litres
Is this too big? How much does the canopy weigh? I have no idea.
One could in theory fly the canopy with helium to altitude, then rapidly deflate it and fill it with ambient air. If it was fully sealed, the canopy would then rapidly descend and collapse upon itself since the exterior air would be getting much denser. You would be left with a crumpled canopy with a volume, at ground level, of about 100,000l - a precious sample of high-altitude air of a sufficient amount to possibly replicate the U2 experiments.

Please feel free to pick this apart/add references! I can just about believe the U2 results from this (so much air sampled along the transect) but now have doubts about any bioprospecting results claimed from high altitude balloons so far, unless they drifted for long distances (1000s km) before recovery. Both of these types of experiments involved culturing on the ground, so as always ground contamination, or contamination of the balloon before flight or by aerophiles in the troposphere, remains a possibility.
Our efforts to carry out experiments at altitude negate this BUT how do we sample enough air? Must we fly on a long duration balloon now?
One cfu literally means one single bacterium landed on the detector and was able to divide and grow into a visible colony. In turn this would literally mean only single copies of key genes to be detected by us by RT-PCR etc. In short, it doesn't matter how sensitive your assay is if the odd bacteria you are chasing in millions of litres doesn't happen upon your detector - otherwise there is nothing to detect!

Long duration? MAIDs? (Microfluidic?) Collapsed canopies? Any thoughts gratefully received!

Ol
------------------

Wednesday, November 18, 2009

'Wild' micro-organisms



At the end of October, I went out to a secluded area of campus and sampled the micro-organisms in the air on settle plates (agar plates) for 5min. I used two types of plates, just plain LB agar and this with some magnets in, as I was interested to see if the magnets would have any affect on the growing bugs. (Later I may use the magnets to hold down the plates.) I used 4 plates per experiment but exposed them all at the same time, then incubated them at 4, 24 or 37°C. After 24h nothing had happened but after 48h small fluffy white colonies were found on the 24°C plate, then after 2weeks colonies were found on both the 4 and 24°C plates but not on the 37°C plates. At the time of sampling I also used the homemade impinger and will use the DNA in this for detection in the RPA reaction. I can now use this reaction to amplify sequences from DNA derived from archaea and yeasts too.

Tuesday, October 27, 2009

Pscyhrophines, hypobariophiles and radiophile

In researching how we’re going to detect microbes in the stratosphere I have been looking into what they might have to deal with – the cold (psychrophiles), low pressure (hypobariophiles) and radiation (radiophiles). There’s quite a bit of research out there reporting on psychrophiles – many organisms are surviving in the ice in the Arctic and the Antarctic, from bacteria or fungi. A whole conference has been held on them! There’re also reports on radiophiles, such as Deinococcus radiodurans, which is being exploited by NASA. But of hypobariophiles there is little (actually none that I can find) information of their existence. We should also think that these organisms will be xerophiles, meaning they can tolerate and grow in low water conditions, these can also be halophiles eg the fungus Trichosporonoides nigrescen, or endoliths, that live inside rocks, which would help with radiation protection too. The latter tend to be autotrophs too, making essential chemicals by themselves. Some many requirements......can there be such an organism?

Wednesday, October 7, 2009

Recombinase Polymerase Amplification

Just a quick update to say that the first run of the recombinase polymerase amplification (RPA) has been successful. This is a great technique, that is over shadowed by the popular PCR reaction, that amplifies DNA sequences, the massive advantage here is that no specialist cyclers are required and it may even work at below room temperature....lots of things to try! For more info try the Twist DX website.

Tuesday, October 6, 2009

NURBS rubber duck!


Not to be outdone.... I have successfully created a fully NURBS rubber duck floating on a funky textured ocean, being regarded by a giant floating eyeball.

Seriously though... this is my first Rhino structure - a powerful 3D design and imaging suite.


I have now completed preliminary training and can proceed to designing the High Altitude Bioprospector as a 3D model - which we can then actually produce as finished parts using a 3D Printer.

In many ways this might actually be simpler than that duck - all straight edges! It took bloody ages to get those eyes right and even then it has a rather menacing myopia to it...

Set up 1



I had a mini glass impinger made by the glass blower at the university and then bought myself a small battery driven fish tank pump. With a few modifications to the pump I now have a system for pulling air through the impinger, perhaps a little wildly, but its a start.

video

Saturday, September 19, 2009

Fw: [high altitude bioprospecting] New comment on Your humblesmartphone for balloon communications?....

To Alexander whom suggested APRS instead of using a mobile phone:
YES, I would love to get into this. This is what our colleagues at NASA use on their balloons for instance.
Can you give us further details?
Do we need a ham license?
I was thinking of using a 'phone because our PC104 supplier does combined GPRS and GPS cards etc., and also because we could link into Google Latitude etc easily. But APRS is the proven ballooning solution... No APRS PC104 card compatible with the rest of my components though...
Again, any suggestions?
An APRS with a serial modem perhaps?

------------------


From: ALexander Kent <noreply-comment@blogger.com>
Date: Fri, 18 Sep 2009 22:48:28 -0700 (PDT)
To: <go.vertitech@googlemail.com>
Subject: [high altitude bioprospecting] New comment on Your humble smartphone for balloon communications?....

ALexander Kent has left a new comment on your post "Your humble smartphone for balloon communications?...":

What about APRS?



Posted by ALexander Kent to high altitude bioprospecting at September 19, 2009 6:48 AM

Friday, September 4, 2009

Glassblower



I've been thinking on the glass impingers and went to see Steve the glassblower over in Chemistry. He is going to make a little tiny one, just 5cm and we'll see what we can get with that!

Tuesday, August 18, 2009

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?

Thursday, August 13, 2009

first tranche of funding now here!

Wednesday, August 5, 2009

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?

Tuesday, June 23, 2009

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.

Thursday, May 28, 2009

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.

------------------

Tuesday, May 26, 2009

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?

Friday, May 8, 2009

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.

------------------

Thursday, May 7, 2009

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.

------------------

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.


------------------

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?...


------------------

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)
------------------

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!!!
------------------

Saturday, May 2, 2009

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?

------------------

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!
------------------

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...
------------------

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?

------------------

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


------------------

I'll never hear another bad word against Gmail

Just one more:
Look what my Googlemail gave me as a directed advert!:
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):
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...

Friday, May 1, 2009

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?
------------------

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!)
------------------

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.
------------------

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! :-(
------------------