Exploring The Invisible: microbiology and art workshop, University of Surrey

 

 

I ran the first microbiology and art workshop at the University of Surrey for over 30 participants last week. Here are the activities and outcomes.

Ehrlich Staining:  DIY histology and revealing the oral microbiome 

Paul Ehrlich made countless contributions to science  in fields as diverse as histology, haematology, immunology, oncology, microbiology and pharmacology. In the course of his investigations Ehrlich came across methylene blue, which he regarded as particularly suitable dye  for staining bacteria.

Here I have drawn upon Ehrlich’s early studies on staining bacteria and developed a simple off-the shelf/ DIYBio-staining procedure for bacteria and  human cells. It is based on methylene blue which is readily available as a “fish medicine”. The brand I used here is King British Methylene Blue. It works very well as it comes in the bottle, and without the need for any messy preparation. Here participants were asked to spit onto a microscope slide so that saliva could be examined for cheek cells, their nuclei, and the normal oral bacterial flora.

For comparison, below is an unstained saliva sample.

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Visualisation of saliva at 200x magnification using Differential Interference Contract Microscopy.

 

The stained saliva samples were initially observed at 200x magnification (below)

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Ehrlich staining of saliva, 200x magnification. If you look closely you can see cheek cells and the dark stained oval body inside is the nucleus of the cell.

 

When the stained saliva samples are observed at 1000x magnification far more detail is revealed (below).

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A saliva sample stained with methylene blue. Buccal epithelial cells are visible as large pale blue cells with a dark staining nucleus contained the genome/DNA. Numerous bacteria are visible either attached to the cells or in other parts of the stained sample. 1000x magnification

 

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A saliva sample stained with methylene blue. Buccal epithelial cells are visible as large pale blue cells with a dark staining nucleus contained the genome/DNA. Numerous bacteria are visible either attached to the cells or in other parts of the stained sample. 1000x magnification

 

Bacterial war-games: visualising bacterial motility, chemotaxis, quorum sensing, swarming and antibiotic production and resistance. 

“the microscope discovers, what motions, what tumult, what wars, what pursuits, what stratagems”  Samuel Taylor Coleridge

This process was inspired by  the boardgames of my childhood, Risk, Campaign and Diplomacy and the like,  and also by the inherent properties of bacteria.

Instead of coloured plastic counters, pigmented bacteria constitute the different armies  as billions of microscopic soldiers (bacteria) enter into battle.  Each colour is a different inoculum of living and pigmented bacteria, with each possessing a different characteristic/ability. The images here are of the initial inoculation (each differently coloured patch represents a seperate bacterial species), and the map after incubation, and after its nature has been changed dramatically as the bacteria became active, grew,  and interacted with each other. The red and purple pigmented bacteria are aggressive and swarm to infiltrate certain other species. Blue and yellow adopt a defensive strategies and produce powerful, and yet uncharacterized antibiotics, that kill red to protect their own territory. I can’t help but feel that this map is a metaphor for our own species and wonder, as bacteria predated us in evolutionary terms, whether the traits that we see here are hardwired into our own biology. The battles  take place on a layer of the fabric polycotton as  this facilitates the movement of the bacteria through its fibres.

The designs made by the participants before incubation.

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Before

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Before

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Before

 

The designs after incubation (below). During incubation the bacteria move and interact with each other,  and dramatically change the participants designs. The outcome reflects our modern understanding of bacteria how they interact and communicate with each other, collaboration, antagonism,   swarming, chemotaxis, modes of motility and much much more. I feel that the bacteria contribute to these designs, just as much as the human participants, and that the bacteria are very much coauthors in the works.

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After

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After

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After

 

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A smiley face. The yellow pigmented bacterium is producing an antibiotic which is preventing the red pigmented one from claiming its territory.

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The dried war-games. The cotton swatches with the bacterial designs ready for sewing together.

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The dried war-games. The cotton swatches with the bacterial designs ready for sewing together.

 

Toxic change: bioluminescent bacteria as bioreporters for toxic metals.

When we make physical cash transactions we exchange far more than just metal tokens with monetary value.  Carried invisibly at ever  transfer, are hundreds of invisible bacteria (see image below) , or the toxic residues of what the coins are made from.

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The bacteria on a coin revealed by imprinting onto bacteriological growth medium and after incubation.

 

Bioluminescent bacteria naturally produce an ethereal blue light. Healthy cells of these bacteria produce light, those that are damaged are dimmer, and those that are dead are completely  dark. Because of this, bioluminescent bacteria are commonly used in laboratories as sensitive and effective monitors of pollution, for testing environmental samples and drinking water for example. In the workshop participants placed coins onto a confluent layer of bioluminescent bacteria. After overnight incubation,  obvious zones of darkness are apparent  around the coins which means that chemical toxins have diffused from them into the media and killed the bacteria. Most likely this toxic effect is due to the presence of metals like copper and sliver in the coins (see below)

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Coins on a confluent layer of bioluminescent bacteria. Dark zones of inhibition, where toxic compounds from the coins have killed the bacteria, are clearly visible.

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Coins on a confluent layer of bioluminescent bacteria. Dark zones of inhibition, where toxic compounds from the coins have killed the bacteria, are clearly visible.

 

Memories of Failure Externalised: visualising slime mould memories and intelligence 

One of the microbes we explored in the workshop was and old favourite, the yellow coloured slime mould Physarum polycephalum. This is a remarkable microorganism that can solve the shortest root through a maze and that also possesses a spatial memory. In essence, as it moves it lays down a layer of slime in a complex 2-dimensional network. When it has explored a region of its environment where there is no food or opportunity, it retracts from this area, but leaves its traces of slime behind. If it encounters these abandoned threads of slime again, it will not re-explore this region, as it knows that it has visited this area before and that there is no reward here. Here participants, like Hansel laid a trail of white pebble, set out a trail of slime mould food (porridge oats) for the organisms to seek out and follow.

I explored a number of  ways to represent the participants work and am most pleased with this process that uses  a discarded Overhead Projector (OHP) for this. The role of the yellow pigment,  that is characteristic of Physarum, is probably to absorb light and to protect the organism from its damaging impact. The images here (below) are of the slime mould as projected via the OHP, and thus after the microorganism has modified and interacted with the light passing through it. I have a strong sense that this process inverts usual microscopic practice, so that instead of a single observer peering down at microscopic worlds through complex series of lenses, the worlds themselves are projected directly into our own macroscopic reality where we can touch and interact with them.

 

Above the OHP projecting the trail made by the slime mould.

 

Below are projections of the slime mould, each over a metre in diameter

 

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Park’s Kitchen Agar (PKA): DIY bacteriological growth media

Plate Count Agar (PCA) is a widely used general media for isolated bacteria from many different environments. Park’s Kitchen Agar (PKA) is a novel modification of Plate Count Agar. It can be used for obtaining microbial counts from any environment, and is specifically designed for use in facilities where the availability of chemicals may be restricted by Health and Safety issues or by problems with supply. Unlike any other microbiological agar, it is edible, but consumption is not recommended once it has been inoculated.

The principles of the medium are as follows.  The casein present in dried skimmed milk powder provides amino acids and other complex nitrogenous substances that are necessary to support bacterial growth. Marmite, is a form of yeast extract, and primarily supplies the B-complex vitamins need as co-factors. Honey is a natural source of carbohydrates (fructose and glucose) and provides the energy source for growth. The medium can be supplemented with various natural chromogenic compounds that will change colour depending on microbial activity (extract of red cabbage and turmeric are recommended).

This medium wasn’t used for the current workshop but has been widely  and successfully used used in many microbiology workshops.

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Park’s Kitchen Agar. Uninoculated.

 

 

“Bacterial War-Games”: before and after

 

I ran the first science and art workshop at the University of Surrey last week. These are “Bacterial War-games” from it. The participants make designs using pigmented bacteria and we then incubate these to allow the bacteria to move and interact. Before and after. Bacteria as co-authors in the designs. Reflects quorum sensing, swarming, chemotaxis, modes of motility and much much more.

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Memories of Failure Externalised

 

This week I ran a microbiology and art workshop with 30 participants  at the University of Surrey for the first time.

One of the microbes we explored was and old favourite, the Yellow coloured slime mould Physarum polycephalum. This is a remarkable microorganism that can solve the shortest root through a maze and that also possesses a spatial memory. In essence, as it moves it lays down a layer of slime in a complex 2-dimensional network. When it has explored a region of its environment where there is no food or opportunity, it retracts from this area, but leaves its traces of slime behind. If it encounters these abandoned threads of slime again, it will not re-explore this region, as it knows that it has visited this area before and that there is no reward here.

I’ve been exploring ways to represent the participants work and an am exploring the use of a discarded Overhead Projector (OHP) for this. The role of the yellow pigment,  that is characteristic of Physarum, is probably to absorb light and to protect the organism from its damaging impact. The images here are of the slime mould as projected via the OHP, and thus after the microorganism has modified and interacted with  the light passing through it. I have a strong sense that this process inverts usual microscopic practice, so that that instead of a single observer peering down at microscopic worlds through complex series of lenses, the worlds themselves are projected directly into our own macroscopic reality.

 

Prokaryotic Psychoactives?

 

Streptomyces/Actinomyces are a species of bacteria commonly found in soil. Being metabolically diverse they are able to utilize many different types of compounds and are thus vitally important for the ecology of soil, and indeed, much of the characteristic earthy smell of healthy soils arises from chemicals emitted by this species. Beyond this, these bacteria  are the largest group of antibiotic producing bacteria in the microbial world, producing the majority of antibiotics used in human medicine, and with some of their compounds also  giving rise to cancer therapies. Despite this, the number of new antimicrobial compounds reported to have been isolated from this group has declined in recent years and is predicted to fall to zero in the next 1-2 decades. The Streptomyces, as a group, are predicted to be capable of producing at least 100,000 antibiotics, and only a minute fraction of this therapeutic diversity has been unearthed so far. The reduction in reports describing new antibiotics arising from these bacteria is due then to a decline in screening efforts rather than due an exhaustion of their compounds.

These are a collection of Streptomyces/Actinomyces strains that I foraged from Old Down Wood (a local woodland in Hampshire) in order to identify novel antimicrobial compounds.

One of the other remarkable properties of these bacteria is their potent and effecting smell. They smell divine, and each one slightly different, but all distinctively of the earth and of forests. In the laboratory, each inhalation gives me an incredible and almost visceral sense of wellbeing and connection to the natural world. It’s almost a psychoactive experience, and very addictive, and I have a very strong sense that my mood is being manipulated by these apparently simple lifeforms, for the better, and I am content with this.

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Die Urpflanze: speculations on the origin of plants

 

Shortly before Johann Wolfgang von Goethe published Die Metamorphose der Pflanzen in 1790, he was exploring the concept of the Urpflanze, which he speculated was an archetypal prototypical plant, that contained within it, all the plants of the past, present and future. Whilst there is no reference to this speculative Ur-Plant in his book, it is described (as below) in his letters to Charlotte von Stein which were sent by Goethe during his stay in Palermo, Italy.

“Seeing such a variety of new and renewed forms, my old fancy suddenly came back to mind: among this multitude might I not discover the Primal Plant (Urpflanze)?”

If we extend Goethe’s concept of the primordial botanical entity, to our current understanding of evolution and contemporary science, then a type of microbiological life, the Cyanobacteria,  seem close to what he initially envisaged in many respects. In this context, the process of photosynthesis evolved in this group of bacteria, as did the ability to make the important plant structural polysaccharide cellulose. Indeed, the chloroplast, the organelle within plant cells which carries out photosynthesis, actually derives from a process called endosymbiosis, where in the distant biological past, a cyanobacterium would have gained access to the cytoplasm of a primordial plant cell, and conferred upon instantly, the ability to make energy and assimilate carbon from sunlight and carbon dioxide. In a sense, this life form would contain, the latent instructions for the rich diversity of plant life that we see today, and can easily be imagined as Die Urpflanze.

The works here explore Goethe’s imagined Urpflanze and show the growth forms of various cyanobacteria when grown autotrophically  in sunlight which allows the bacteria  to autogenically generate complex, multicellular and prototypical plant forms  on sold agar surfaces.

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Invisible Worlds

Taken with NightCap Pro. Light Trails mode, 29.73 second exposure.

Invisible World. 29.73 second exposure, 100x magnification

I was in my garden today. I could hear a Song Thrush and Blackbird singing close by. A handful of House Martins flew overhead, and scores of bees and insects buzzed backwards and forwards. Life seemed abundant.

I’ve developed a novel process that rather than recording micro-videos in real-time, records instead the paths taken by microscopic creatures under the microscope. The images generated, result from the accumulation of the activity tracks of these usually invisible life forms and reveal the hugely complicated dynamic of their manifold activities and interactions. The process generates images that are in some sense similar to those of radioactive decay, or atomic particle collisions, as they are seen using cloud chambers.  The process is transformative, in that it converts the mundane and disregarded, into something remarkable, not by changing it, but by revealing another level of reality that is usually withheld from us. Each sample generates a unique signature of accumulated biological wavelengths and frequencies.

As all of the macroscopic activity above was taking place , I used this process to exam a small bucket of of collected rainwater for normally unseen and overlooked  microbial activity. The bucket is below:

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Macroscopic View

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The unpromising bucket of rainwater

The process revealed an invisible world whose activity dwarfed that of the macroscopic life around it. All of the activity below,  was happening in a minute slice of collected rainwater just a few microns in diameter.

Taken with NightCap Pro. Light Trails mode, 29.73 second exposure.

29.73 second exposure, 100x magnification

Taken with NightCap Pro. Light Trails mode, 45.76 second exposure.

45.76 second exposure, 100x magnification

Taken with NightCap Pro. Light Trails mode, 79.29 second exposure.

79.29 second exposure, 100x magnification

Taken with NightCap Pro. Light Trails mode, 129.47 second exposure.

129.47 second exposure. 400x magnification

Taken with NightCap Pro. Light Trails mode, 61.56 second exposure.

61.56 second exposure, 400x magnification

Taken with NightCap Pro. Light Trails mode, 81.30 second exposure.

81.30 second exposure, 400x magnification

Taken with NightCap Pro. Light Trails mode, 52.75 second exposure.

52.75 second exposure, 400x magnification