hostblog

Another adapted gadget I’m pretty pleased with - ‘the hostprods ™ pocket microscope light and image enhancer’.

For the Bioarama Hike I got hold of a bunch of these 60x to 100x pocket microscopes so that we can have a look at the bits and bobs and bugs we encounter as we go around. I took one out for a field trial when I tested the route the other day and wasn’t too impressed as they just don’t give enough light to penetrate any vaguely murky sample. So I’ve built a little light table to provide a strong a focussed light from below as well as above. In the test run I gave it I was able to see nematodes clearly in a few drops of water from the nematode extractor at 100x.

Its simple to make. You will need:

1 x pocket torch (the kind that comes on when you rotate the end with the bulb in it)
1 x CD case
1 x translucent plastic film for a diffuser ( I cut a circle from a plastic CD sleeve)
1 x plastic petri dish
super glue

remove the lid from the CD case and cut the plastic to fit snugly inside
carefully cut the petri dish lid in half
super glue its open side to the inside of the CD case lid
super glue the torch to the flat base of the cut petri dish so that there is room to turn the head to turn on the torch

you’re done.

And to think I nearly spent 25 quid on a light plate in Jessops.

Nematodes. Lots of them. Enough said.

My phone camera doesn’t dock well with the eyepeice of the microscope so you’ll have to take my word for it.

In the end it turns out that not only will I not be building the thiobacillus powered acid etching and datalogging device but I won’t be building the artists version muio-based fermenter either. After my misplaced optimism about it being affordable, having seen Ph probes for about 30 quid, I discovered that dissolved oxygen and conductivity probes cost more in the region of 200. Apparently laboratory equipment is habitually given a ludicrous price tag, and having scanned the Fisher life sciences catalogue I’m amazed at just how much. The plan is officially shelved until more funding comes in.

But, to prove lab gear doesn’t all have to cost the earth I’ve built this

behold

It’s a pretty simple device. A soil sample is wrapped up in kitchen paper like a teabag and placed in a small amount of water in the funnel. 24 hours later you draw of some water at the tap at the bottom and it should be rich with nematodes. The next post will probably say if it has worked or not…

The time is upon me when I need to start thinking about what sort of concrete results I can take from the time that’s left on this residency. I tend to think that the development of some sort of system, or a prototype of that system, that I can carry on working with would be a good idea. Maybe the apparatus I was imagining I could use to etch the landscape images whilst monitoring bacterial behaviours and states will be reworked as a general investigative fermenter.

A fermenter is a piece of laboratory equipment used for the intensive culture of microbes in quantities from a litre at smallest to many hundreds at biggest. The device is normally hooked up to a biocontroller to monitor and control the inputs and outputs and a PC to log the data over time. We have one hooked up at the moment in the lab where we’re trying to build up the quantities of our thiobacilli.

The logging computer is out of shot to the right but we can see the business end of the thing here. The machinery on the right is the biocontroller which is the primary interface receiving data from the sensors and controlling the stirrer and any necessary environmental conditioning devices.  On the left is the actual fermenter vessel which has a number of ports in the lid for the placement of air lines and sensor probes - in this one we have Ph, dissolved oxygen and temperature - as well as housing the stirrer motor. Inside the vessel are the air manifiold and the stirrer arm and blades. Its all very scientific and rigorous.

So I’m considering building one of these for artistic use. Apparently I can commandeer a flask from the science department, I’m ordering a couple of probes and a stirrer can be built using a cheap dc motor. The air supply and manifold is easy for someone with my experience of cobbling together apparatus from cheap aquarium gear and I can hook the whole thing up to the Muio board to read the sensors and control the motor. That would be enough to get a similar level of data out of the system and a basic level of environmental control in.

The addition of a couple of speakers,  a small LCD screen and some LED arrays should give me enough to begin testing the developing microbial colony’s reactions to information overload. A satellite hook up feature can be added at some point in the future alongside radio receivers and transmitters.

 

Here’s a tantalising quote from the 1914 edition of the Yearbook of the United States Department of Agriculture:

“If all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable, and if, as disembodied spirits, we could then investigate it, we should find its mountains, hills, vales, rivers, lakes and oceans represented by a thin film of nematodes. The location of towns would be decipherable, since for every massing of human beings there would be a corresponding massing of certain nematodes. Trees would still stand in ghostly rows representing our streets and highways. The location of the various plants and animals would still be decipherable, and, had we sufficient knowledge, in many cases even their species could be determined by an examination of their erstwhile nematode parasites.”

I’m beginning to get interested (again) in nematodes for a number of reasons. Firstly I remember the excitement when I first saw one when I first started to use my biological microscope (which I am missing a lot), secondly I love this idea of their super abundance as an indicator of all sorts of other biological systems (nematode tricorder?), thirdly they are one of the model organisms, a group of organisms of which the most symbolic must be the E Coli bacterium and the fruit fly Drosophila that are used as experimental ‘work horses’, fourthly because C Elegans was the first multicellular organism to  have its genome comletely sequenced and fifthly because they survived the STS-107 mission disaster aboard the Columbia space shuttle.

I have vague ideas about subjecting nematodes out on the moors to amplified signals from GPS satellites…

 

Had a bit of a reality check today when Paul informed me that what I was trying to develop was actually a tricorder and was pretty much impossible with current technological and microbiological techniques. I don’t know why but my idea of building a device that would consist of a microcontroller and a few well selected lab probes to plug into any organic system to record meaningful data didn’t seem to way out at first. As it turns out the reality is that a slow, laborious process in the lab will yield very specific information and that the fuller picture is built piecemeal with further experiments and measurements. Now I have the problem of discovering ways of creatively using very specific and non spontaneous data from the stuff I’m doing. I’m still going to build the device and thanks to Steve Symons I have a Muio board on which to base it, next week I should have a couple of probes - most probably Ph and dissolved oxygen - and I’ll be able to do something. But I guess I’m still some way away from finding the way to tap into that pervasive netwroked information system that is out there.

There is hope, however. In 1996 Vital Technologies Corporation sold a portable device which they called the “Official Star-Trek Tricorder Mark 1″. The device featured an electromagnetic field meter, a weather station with thermometer and barometer, a colorimeter, a light meter, and a clock and timer. They claimed it was a serious scientific instrumentand sold 10,000 of them before going out of business.

Currently under development is a device known as “lab on a chip” (LOC) or Micro Total Analysis Systems. LOCs combine multiple laboratory processes on a single chip and are capable of  a number of experiments and processes simultaneously.

Obviously NASA are seriously investigating this technology. If I can just get my hands on one I should be able to do many of the things I was hoping to do - I’m off to check eBay…

So here it is:

On the left, a big fat glass flask containing Bristol’s medium for green algae and a sample of Water4.

Green algae are autotrophic (self feeders) in that they use the energy of sunlight to to assemble carbon dioxide and water into the macromolecules they need. They also need sources of nitrogen, sulfur, and phosphorus in order to synthesize proteins and nucleic acids; substantial amounts of magnesium, calcium, and potassium and small amounts of Fe, Mo, Zn, B, and Cu. Most of these micronutrients or trace elements are used in enzymes. Trace amounts of copper, for example, are incorporated in one of the enzymes used in photosynthesis.

Ironically, Copper sulfate (CuSO₄) is a widely used and potent algaecide - an agent that kills unwanted algae in municipal water supplies, swimming pools, but trace amounts provide an element essential to their life.

Hopefully within a few days this flask will be full of green algae which will supply oxygen for the etching process.

On the right is an enricher which does a similar job to the flasks of soil samples and suplhur that were put on the shaker about 4 weeks ago. A large amount of soil from Soil4 has been placed in the basket and is continuously soaked with a stream of water via a small pump and a heath robinson style array of spray bars and tubes. The sample was fed a couple of spoon fulls of suplhur and left for the thiobacilli to do their thing. I’m going to be hooking up my DIY lab datalogger (more on this soon - as I keep saying) to this enricher and monitoring Ph levels, dissolved oxygen and any other meaningful data I can measure with a few cheap probes from eBay.

I’m not getting anywhere near as much time as I’d like in the lab at the moment but I spent a couple of hours again today looking for the calcite producing bacilli from my soil samples. There were two petri dishes that had looked promising showing some nice translucent creamy streaks without any of the hairiness you would normally associate with moulds or fungi. I made a couple of slides form these and gram stained them to make them easier to check for bacteria. Gram staining is a process whereby you flood the slide with Methyl Violet, Iodine, Alcohol and Fuschin to see whether you have gram positive or gram negative bacteria in your sample. Basically the gram positives will show up violet on the slide while the gram negatives will show up as a softer pinky colour. Its all to do with the biology of the cell walls of the different types and how they hold the stain or not.  There is more info on gram staining here for anyone that wants it.

So, slides heat sealed - 30 seconds soak with Methyl Violet then rinsed, 30 seconds soak with Iodine then rinsed, 15 second soak with alcohol then rinsed, 30 seconds soak with Fuschin then rinsed, blotted around the edges and put on the microscope.

Lo and behold there were huge amounts of violet coloured egg shaped blobs all over the slide… but far too big to be bacteria and probably yeast cells. Apparently they may do the job themselves but I’m a little vague on that and weirdly attached to using bacteria. A scraping was taken from the petri dish and plated out again a few times on a general soya medium to encourage any bacteria that are there to come out and show themselves…

preparing the slides

gram staining

Saturday 9th June
Before our Time - a 10 mile guided walk to look at the prehistory of the Marsden Moor area.
10 miles : 5.5 hours

I’d been looking forward to this walk for a while thinking it would give me a lot of useful information about the history of trade routes and networks across the Pennines whilst exploring some areas I hadn’t been to before. In the end it did a little of both but not as much as I hoped. I learned that the area across the moor around Pule and March hills is the narrowest point of the Pennines and thus provided a good crossing and strategic point - there had been people using it as a gathering place for since 6 or 7000 BC. I learned that the trees disappeared around 6000 years ago and that the peat layer is 15m thick in places and that 8000 years ago it all looked very different.

The route was similar to the one I did in my first walk but nudged upwards a little, going the other side of Haigh Clough to the reservoir, climbing to the top of March hill, dropping down to the Pennine way along millside edge (again), then cutting across the moor to the old tunnel workings engine house before climbing Pule hill and dropping back down to Marsden. There were a few new sights such as 5000 year old tree remains, the crash site of a WW2 plane and the remains of the old packhorse route built on top of a roman road - and not forgetting the new sight of all this in sunshine. And the new sight of my arms and neck getting redder and redder as I burnt myself to a crisp.

5000 year old tree stumps with Pule hill in the background

packhorse route and roman road remains

the tunnel works engine house. This place is actually sited near as damn it to where the line from Rock Stones to Holme Moss masts crosses the tunnel route - which means I’ll probably try and do something with the site at some point.

Monday 11th June
A quick circuit to March Haigh and back.
5 miles : 2.5 hours

I was out in Standedge having a meeting with the waterways board people so I decided to take the opportunity to go out and grab some more samples from crossing points. Taking along a big water bottle, a plastic tub and an improvised scooping device I set off along the same route as the first part of Saturday’s walk to March Haigh. My initial plan was to take a soil sample from the crossing point at 53°36′39.70″N, 1°57′46.89″W but I got my physical location and GPS coordinates mixed up and abandoned it deciding instead to head for the crossing on the other side at  53°36′32.72″N,   1°58′18.18″W. On the way I stopped to grab some water from a gorgeous little waterfall and pool which I marked as Water4 and will serve to provide algae cultures back in the lab. The other crossing was found easily enough and Soil4 was duly collcted - it was just next to a tempting mini-bog with loads of interesting green slime - couldn’t resist adding some to Water4 thinking that it should guarantee algal growth of some sort.

Soil 4 has now been placed in the enricher in the studio and will be connected to the eco-probe device as it evolves (more on this device to come).

water4 location

view to Pule hill from Soil4 (and Water4b)

cultures of thiobacillus:

The soil samples have been in the flasks mixed with sulphur on the shaker for about 2 weeks now. Ph readings were taken on Friday and surprisingly it had dropped considerably, this wasn’t entirely expected as the Ph was fairly low to begin with. Sample 1 from half way across Berry Greave had dropped from about 4.5 to 3.3, sample 2 from the cairn on the Pennine way was down from about 5.1 to 3.6 and sample 3 from the old turnpike at Warcock Hill was at 2.8 from 5.2. Considering that the Ph scale is logarithmic this is quite a drop. Apparently this is still not a solid proof that sample 3 is the lowest Ph because it has the highest concentration of Thiobacillus - there are all sorts of mineral gradients and relationships with sulphates that can skew the readings. More media, platings, shakings, pipettings and readings are going to be necessary before we now we can etch with the best of the bunch.

the other bacilli:

The 12 petri dishes were removed from the incubator where they’d been happily resting at 25º for a few days and instead of seeing a few nice slimy white dots there was a collection of veritable fungal forests.

This could be down to a couple of things. Firstly and quite probably my aseptic technique isn’t what it ought to be and the plates got contaminated as soon as they were prepared. Secondly, there is probably a very high concentration of spores in the soil anyway and the medium may have not been specific enough to discourage their growth. The solution - do it all again on a slightly different media and a bit more carefully.

However, there is a ray of light. One of the 12 plates had a vaguely promising pair of small dots on it. I scraped a bit off and prepared and stained a couple of slides (30 seconds crystal violet, 30 seconds gram’s iodine, rinse with distilled water) and had a look at 1000x magnification. Amongst the many many fungal spores are one or two tiny rod like shapes which could just be bacteria. A sample from these blobs has been streaked out on a couple more petri dishes and we await to see what grows. Otherwise its start again time…. again.

its a little tedious but it has to be done…