Tuesday, December 8, 2009

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

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