All posts by bsirianni

There can be only one. The Highlander Bacteria.

I met Timo Diehl in Berlin, by the happy accident that he lived next door to a friend of mine. He is something of a “Jack of all sciences”, being a mathematician who’s worked in physics and now, microbiology. He also rose magnificently to the challenge of finding me peculiar figures of speech and unlikely translations into German. But when I found out last year that he was working in experimental evolution, I got shouty-excited had to know more!

Experimental evolution is exciting because, of course, evolution is something that typically happens over a mind-boggling length of time. To have a system that lets scientists see evolution happening over a readily observable period is, needless to say, a bit good. The other thing that had lasers shooting from my eyes with delight was the mention of an “evolution machine”. Of course, it’s not quite the chamber that first sprang to mind (resembling the teleporter in The Fly), but is still an impressive invention.

Experimental evolution is based on the ability of bacteria to mutate (relatively) quickly, and the fact that different micro-organisms have different environments in which they can live happily. That’s how fermentation preserves food: it creates an environment that favours belly-friendly microbes and is hostile to harmful types.

As I understand it, the evolution machine can function as a kind of gladiatorial arena in which different strains of bacteria compete (see Timo’s article below) or to test the ability of a strain of bacteria to adapt to changes in its environment. The latter is where it gets really interesting, because bacteria can’t just put on a woolly coat when it gets a bit chilly, for example: adaptation in this sort of situation requires mutation, with favourable mutations resulting in a new species that can survive in an environment that would have killed off its predecessor. The process of mutation is random, but the result is not, thanks to natural selection. It means that if a certain mutation allows the bacteria to survive better in the new conditions, these bacteria will grow faster and out-compete those without the handy mutation. The resulting adaptation may be slow by human standards (a couple of years), but is the blink of an eye relative to the evolution of the plants and animals we see around us.

That’s enough inexpert rambling from me. It’s over to Timo now to describe – in epic style – his own adventures in experimental biology.

There can be only one. The Highlander Bacteria.

Once upon a time in a microcosm far, far away, there was a field where, peaceful and without concern, bacteria dwelled – probably amongst other fellow bacteria, but in as much harmony as there is in a microcosm.

But lo! on the eve of a rainy day in March, a sterile tube was brought forth and dug deep into the very heart of the soil. Twelve grams of said soil were taken and carried away to a known institute of a town called Berlin. The soil and the bacteria within were put in an evolution machine to let them struggle, taxon against taxon, in mortal combat. The hypothesis was that after a while there would be only one left, and indeed, after two weeks of intense struggling amongst the bacteria, One was left.

Who is this One, the last of its kin, Duncan McBacteria, the stem that boldly went where no scientist ever expected?

Further tests must be conducted, more data must be gathered to dig deep and greedy into the essence of this phenomenon.

And indeed, tis a phenomenon of great curiosity, for the growth rate of Duncan McBacteria compared to its better investigated relative E. coli is hundredfold. Test after test was run, sweat was spoiled and Eppendorf tubes shattered before the final test was complete and the identity revealed. Behold! the One bacteria is Citerobacter diversus. For him the journey is over, but for us it has only just begun, for further places hold other stems and maybe there are other discoveries that lie in store for us beyond the bounds of human experience.

Timo Diehl
20 May 2012


Cosmology program has landed

Cosmology

Cosmology is a big word with deceptively simple meanings. On the surface, it is about the sky, stars, planets, dark matter and gravity; the duct tape that binds the universe together. Dig a little deeper and in cosmology hides philosophical thoughts about the universe and where humanity fits into the grand scheme of a thing that operates on such a scale that I can barely comprehend without hurting my head.

We’ve put together a full program of workshops to help you explore the realm of cosmology with us over the next four months. It will hurt your head in places (as it has ours during the creation process), but we’re looking forward to discovering more about our universe and hope you’ll find the time to join us.

Read all about it.


Skin in a jar!

It looks like it, anyway.

That’s why my fellow catalyst is calling this the “Hannibal Lecter Project” 🙂

The stuff that looks like skin is actually cellulose – the same stuff (more or less) that paper, cellophane, rayon and cotton are made from. Here it’s home to a colony of bacteria (mostly acetobacter) and yeast that live in happy harmony atop a brew of sweet and sour tea, with the bacteria pumping out strands of cellulose about a hundred-thousandth of a millimetre thick. And it’s reported that the bacteria can produce about their own length in this fibre every hour or two.

I’m delighted and excited by how quickly the pellicle (the cellulose-rich “skin”) has been growing, so here’s a little photo-diary of the project so far.

The "kombucha mother"

This is the established pellicle in a bit of a previous batch of kombucha, which provides the micro-organisms and acidity required to start the new culture. This pellicle is sometimes called the “kombucha mother”, from which a “baby” forms atop the new culture. I am chuffed with how fabulously organ-like it looks! You can see here how it’s made up of a number of thin sheets that stack together: some of this layering is due to successive “mothers” and “babies”, but formation also seems to happen in cycles in each culture, as you’ll see below.

Hearty thanks to our generous Culture Club contact for getting us underway with the source material!

And this is what getting underway looked like:

A very large tea-bag!

Transferring the "mother"

The "crew" on board!

And here’s the second of our cultures, bought from a supplier in Darwin:

Second "mother", day 2

Tendrils!

Self-assembled transient sculpture 🙂

Just a few days after starting the culture, a thin film of cellulose (and microbes) was beginning to appear atop the brew.

And a week or so later, it had grown to this!

Pellicle at ~2 weeks


At about the two-week mark, it had reached about 10mm thick. You can see here the layers I mentioned above – each about 1mm thick – suggesting it gets built in cycles. Cells are just like more complex organisms, in that they have a built-in “clock”; however, it could also be variations in temperature causing the different production rates.

The big bad 1st culture

The three cultures we have so far are each behaving a little differently, with the stuff we bought via mail order looking nice but growing more slowly. The rather splendid-looking “pancake” formed out of the litre or so of excess liquid I scooped out of the big 18 litre batch; this was a great surprise, because it had no “mother” in it, apart from whatever tiny things might have been swimming in the liquid at the time.

Two weeks ago, I decided it was time to try  “passaging” the culture (that’s what we call it in cell culture, when you take a portion of the culture and move it to a new home that has more room to move; splitting your culture from one flask into multiple flasks also lets you grow a lot more cells). We want to work up to large enough quantities to use the pellicle material as a kind of textile, so expanding the culture is a priority.

So I brewed up some fresh tea and performed a little surgery: a pellicular biopsy, if you like 🙂

The patient...

Preparing...

... the incision

... and the transplantation

And three days later, it was already starting to form an ever-so-slight film on top. This was a good sign of a robust process, because I deliberately made it difficult for the microbes by not giving them any of the “ripe” brew like one normally would. Instead, I just added vinegar to drop the pH to friendly levels, and relied on the tea, sugar and the microbes themselves to provide everything else. This one’s still growing more slowly than others, but it’s working nonetheless.

When playing with the cultures, I have been really impressed by how rigid the pellicle is – even the thin one shown at the top here is quite stiff. Although this surprised me, it actually fits with the microstructure shown by electron microscopy – an extremely fine meshwork of inter-weaving fibrils. Although the fibrils themselves are flexible, because there are so many and because they’re tangled over one another, they don’t easily move, and which makes the material stiff, strong and really difficult to cut!

It will be jolly interesting to see what it’s like once we get it out of the “vats”! I started one a few days ago, and it looks to be working nicely. More photos soon.

One last aside: another type of fermentation in which acetobacter make a cellulose-rich pellicle is in turning wine into vinegar. The pellicle in this case has been known as the “vinegar plant” or “mother of vinegar”. There’s a group at University of Western Australia who have recently started some similar textile-related experiments using this material.


Chic geeks at Science Fair

Chic geeks have not been forgotten at the Science Fair. Isobel Campbell, a swim and surf wear designer who specialises in digital print manipulation, will be taking care of fashionistas in the Microscopy for Fashion workshop.

Taking inspiration from a recent trend report by WSGN, an online trend-analysis and research service, Isobel is combining fashion with science.

WSGN’s advice for spring/summer 2013 was, “be inspired by the science laboratory and all it encompasses, from technical apparatus to diagrams and terminology.”

According to Isobel, “A big part of being a designer is trend research, and WGSN predictions cannot be ignored, so in honor of spring/ summer 2013 let’s make some mad scientist inspired prints!”

Using microscopes as cameras, Isobel’s workshop will teach you the step-by-step processes that designers undergo when creating textiles. She’ll then be taking those images to create unique digital print designs in Photoshop.

Although new to the world of microscope photography, Isobel is excited about her collaboration with QUT science and The Edge’s Catalyst Cameron Wilson to explore this trend more and see what kind new designs she can come up with.

“Print design and sublimation is a technique that results in entirely original designs.”

“A designer’s personalised print is unique to their brand and can act as a strong point of difference in the market. This differentiating factor is what inspired me to focus on print development in my graduate collection.”

Isobel feels the possibilities are endless when it comes to fashion and science, pointing to the innovative work of Hussein Chalayan and our other fashion-themed workshop as sources of inspiration.

“There is no limit to fashion when in collaboration with science and technology.”

“I am super excited about the DIY Organic Textile workshop and growing your own textile from bacteria and yeast. I have only read about this process in textile journals and could easily become the way of the future for sustainable textile development.”

Read more about the science behind this project in Cameron’s post.

Science Fair is at The Edge on Saturday, 23 May. Isobel’s Microscopy for Fashion workshops starts at 1pm and 3pm and run for 1.5 hours. No bookings are required. Get involved in your own science experiments and enter your creations in the Science Fair Awards to win a bunch of great prizes.


More Microbial Cellulose

You might by now have seen some of the fashion and artistic applications of the “fabric from a vat” technology I mentioned yesterday. Now I’d like to show you some of the medical applications, because although a bit less DIY-friendly, it’s where some pretty magnificent research is happening. And at least one of the pictures looks like The Future if ever I’ve seen it; you’ll know which one I’m talking about when you see it, especially if you ever saw Terry Gilliam’s film, Brazil. Have a look; it’s exciting stuff! I’d love to hear from any dermatologists in Australia who use cellulose dressings like CelMat (Poland) or Dermafill (USA) for treating burns and other large wounds.

And to further update on yesterday’s post, I’ve just been informed by our Creative Production Manager that it’s the structure of paper that matters for writing on it – the ability for the ink to catch on the chunks of fibre. It’s the effective smoothness of bacterial cellulose sheets that might pose a problem for such applications, then. But there are always ways around problems like that. If anyone knows of people already making paper from microbial cellulose, please link away!


Growing fabrics?! (A call to collaboration)

One of my splendid Edgy colleagues spotted this presentation on TED. It got me rather excited. Suzanne Lee is using sheets of (mostly) cellulose manufactured by millions of microbes to make clothing! The project is called BioCouture (follow the blog link from the bottom of the BioCouture page for most up-to-date info).

There is so much to love about this, but as someone who loves a nice cup of Sri Lanka’s finest infusion, I am particularly delighted by the fact that the culture is grown in tea. The brew is called kombucha (which literally translates as “seaweed tea”), and has long been used as a kind of tonic drink, although having seen the stuff, I am curious as to how anyone thought to try drinking it! As you’ll see in Suzanne Lee’s videos, a couple of weeks of the microbes working away in a tub produces a thick mat on top of the tea, which looks to me rather like a big slab of pig skin.

The microbes that do the work are a collection of bacteria and yeasts: each helps keep conditions friendly for the other, which we call a symbiotic relationship (such a culture is sometimes known as a SCOBY – Symbiotic Culture Of Bacteria and Yeast). If my basic understanding is sensible, the yeast help keep the environment acidic, which makes the acetobacter cells happy to pump out cellulose fibrils; over time, these form a network that becomes great big floating home to all those tiny microbes.

Although kombucha has remained mostly in the culinary domain, Ms Lee isn’t the first to see the potential of cellulose-based materials made by microscopic things instead of plants (cellulose is the stuff we get from plants to make paper, cellophane, Rayon/viscose, and is the main component of textiles like cotton; it’s the main structural material plants make and are made from). Nöle Giulini used kombucha to make some rather fleshy-looking sculptures, and, as outlined in this jolly convenient article, microbe-produced cellulose has already found uses in food, medical and paper-making.

Despite the excitement and potential, there are always a bunch of intimidating technical challenges in projects like these. Suzanne Lee’s scientific collaborators are working on how to make the kombucha-derived material more water-resistant and durable (it currently absorbs water readily and breaks down quite quickly), as well as working on ways to optimise the bacteria’s productivity. This video touches on a few of the challenges and approaches. You may also note from Professor Brown’s summary that people don’t seem to be making paper purely from bacterial cellulose; I presume this is because you big sturdy fibres to make paper, and the bacteria (being tiny and single-celled) make tiny fine meshes. Or maybe it’s to do with the other material present that helps to bind the layers in wood-derived paper. Please comment if you know!

Clearly there is still much to learn and much to try, and one of the things I find exciting about this is that it’s science you can experiment with at home (or, say, at The Edge)! We are eager to see what we can do in this area, and would love to get more clever and enthusiastic people aboard. We’ll be teaming up with some university-based fashion innovators, and I would be delighted to hear from any kombucha enthusiasts, microbiologists, biochemists, polymer chemists, paper- and/or textile-makers, and anyone else who’s interested! So, if you want to get all mad sciency and try growing clothing, fabrics, fibres, paper or something entirely new in a vat, please leave a comment below or just drop in at The Edge: I’m usually about on Mondays, Tuesdays and Fridays, and will also be at the Mad Scientist Tea Party on 12 June and the Science Fair on 23 June.

Let’s get something brewing!


Window Farm: some thoughts on current version

I thought it time for a WindowFarm update. The lettuce we planted a couple of months ago have grown to towers with flowers at their tips. I do note that going to seed is generally a sign that (a) the lettuce isn’t being picked (true) and/or (b) is under stress. The latter would likely be because the current pumping system seems to waste quite a bit of water, and the reservoir typically needs topping up with a litre or two of nutrient twice a week, in order to maintain enough depth for the pumping to keep working. Nonetheless, the plants have been resilient and are currently flourishing, and since the reservoir has been kept in the dark, we’ve had no more algae problems. Please feel free to come by and pluck a few leaves!

The pumping system I’m using at present isn’t the “air lift” described in the WindowFarms version 2 instructions.  I was hoping to get away from the fluid depth sensitivity of that system, so tried a setup to draw water into the tube by the Venturi effect: when you have a small hole in a pipe, a quick flow through the pipe will suck air or liquid in through the hole. This turned out not to avoid the need for the intake to be submerged at a substantial depth, but it did make it easier to keep it on the base of the reservoir (I previously had problems with the hose curling up, and because we had algae problems at the time, I didn’t want to put in more parts to use as bracing). The problem with the Venturi setup is that the water comes out as a fairly fine spray, and I suspect this is how we’re losing quite a lot of liquid. In contrast, the WindowFarms model has the liquid come out in a slow drip. So I’ll probably revert to that (or something else entirely) when I get time to make another…


Getting bigger without the BANG!

Life survives by being adaptable. When you blow up a balloon, it’ll stretch to a certain point, then give out with a bang. Thankfully, our tissues have a rather less devastating way to respond as we grow up and/or out.

In a previous post, I asked how my skin would keep up with my increasing waistline if I put myself on DrRiviera’s “window to weight-gain” diet. The details are something scientists and engineers are still working on, but the general answer is that skin grows when it’s stretched beyond a certain comfortable limit. Just as we feel pain if our arms are pulled too hard in opposite directions, the cells in skin also release a kind of alarm signal when over-loaded, but this signal shouts “grow!” And it keeps growing until it feels suitably relaxed again.

So what does “grow” mean in this case?

To answer this, let’s have a quick look at what tissues are and what they’re made of. Tissues are the materials that organs are made from, and include stuff like skin, bone, muscle and even blood. The main things that make up a tissue are cells and what we call extracellular matrix.

You can think of a cell as the basic living unit of a body. That is, they can survive and reproduce on their own if you give them the right conditions (note: this won’t produce a whole human body J). Different cells act as builders, repairers, sensors, controllers and communications teams: in short, they do the work. In some cases, they’re also part of the structure: your skin keeps out the rest of the world, and your blood vessels keep your blood inside, by cells holding tightly onto one another.

The extracellular matrix (ECM) is the stuff in between the cells. If cells were spiders, the ECM would be the web. When a palaeontologist digs up an ancient bone, the cells that built, maintained and lived in that bone have long gone, but the matrix remains. It’s a mix of proteins, fats and sugars (and tiny plates of mineral, in the case of bones and teeth) that are produced and organised by the cells. If this all seems a bit abstract, think of a bowl of jelly: that’s pretty much the stuff I’m talking about (the jelly more so than the bowl).

So when we talk about skin growing, we’re talking about more cells and more matrix. Cells divide and spit out a bunch more matrix such as collagen. The tricky bit is that they have to do this while still doing their job of holding together a tight seal against the outside world. Can you imagine how hard it would be to make a bridge longer while there are cars driving over it?

We still have a lot to learn about how this works, but surgeons have been putting the idea of mechanically-driven growth to work for a few decades now. Lengthening a bone was first attempted (as far as we know) in 1905 by Italian surgeon, Alessandro Codavilla, and the current method, known as distraction osteogenesis (used, for example, to replace large amounts of bone smashed by an accident), was pioneered in theUSSR by Gavriil Ilizarov in the 1940s or ’50s. Distraction osteogenesis involves letting the fracture (or cut) begin healing, but before it gets too far, to slowly move the two bone fragments apart – a rate somewhere around 1mm a day, if I remember rightly. The current procedure is reportedly painful enough, but I read that Codavilla tried to do the expansion all in one hit! Bone has not been the only target tissue. Also in the 1950s, Charles Neuman implanted a balloon beneath the skin to cause expansion as it was gradually inflated. Both of these methods have become widely used since the 1980s.

The great thing about skin expansion is that it lets the surgeon use the patient’s own skin to cover up defects, so you get the right amount of skin, it’s alive and fully functional already and won’t be rejected by the immune system. It’s challenging, though, for both clinician and patient: it’s hard to know exactly what size and shape of expander you need and how much to inflate it (because the elasticity of skin means it will shrink once the extra tension is removed), and the patient has to put up with having a huge bubble under their skin for a few weeks. But it works beautifully.

Getting back to how… Both the matrix and the cells of skin are under constant tension, like the rubber of an inflated balloon. Skin has to be pretty flexible to let us move, but once it’s stretched past this normal range of movement, the cells have to get busy to avoid the skin breaking.

There are a few different ways by which cells detect stretch, and that’s probably getting a bit too technical. But the effects on the cell are basically these: the cell gets set to divide (the process is called mitosis, and results in one cell becoming two of the same), it produces more extracellular matrix like collagen, and it gives out signals to encourage other cells around it to do the same. Not all of this goes on in any one cell at one time, but the end effect is, as mentioned above, more cells and more matrix. In the outer layer (the epidermis), we need more cells to cover the increasing surface area. Beneath this (in the dermis), we need more cells to build and maintain the tissue, and they need more matrix to hang on to and to carry the load.

To divide, a cell has to first detach from its surroundings and shrink back into a ball. So when a tissue grows, only a small proportion of its cells can divide, while the others go on holding everything in place. Likewise, when new matrix is produced, the existing structure needs to be disrupted somewhat to jostle it into place. It’s these processes that particularly fascinate me at present. I hope to have a lot more to tell you about them in the coming months!

 

An interesting aside: cells divide along the line of maximum tension. This is handy for skin growth, because it means a cell doubles in the direction of stretch. But the cartilage of growing bones is under a compressive load – that is, it’s being pushed rather than pulled. When you squeeze something elastic, you’ll notice it spreads out to the sides. So when the cartilage in the growth plate gets compressed, the cells are stretched sideways, which means they also divide sideways. For the bone to get longer, then, the newly divided cells have to do a little tumble so they’re both lined up with the axis of the bone (and load).


Window Farm Update: Victory Against Algae!

I’m pleased to report that we’ve now gone a week without any green slimy stuff showing up in our nutrient reservoir, so I think I can safely declare that keeping the reservoir in the dark is the solution.

I am less convinced about my alternative pumping system, using the venturi effect instead of lifting water with bubbles. It works, but takes a lot of tuning to get the right flow rate, and at present, isn’t working very efficiently. Still, the plants are surviving, so it’ll do for now…

More pictures to come…


Alex Becomes a Welcome Part of The Edge Family

Alex busy at work in The Edge foyer space

Local artist Alex Jack is a familiar face here at The Edge, whether she is doing a workshop or refining her skills in Photoshop.

I caught up with her on a sunny Easter Saturday in Brisbane as she relaxed in The Edge’s foyer space to find out what is it about The Edge that has her coming back.