microbelog

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Archive for the ‘Technology’ Category

See-through soil

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ResearchBlogging.orgImaging technologies have come a long way since the invention of the microscope 400 or so years ago. Now we can look at the circulatory system in a developing chicken embryo or the hair cells on a terrapin’s inner ear, but there’s one very familiar place that remains a mystery: the inside of a plant pot.

There’s a good reason why it would be great to have a peek into the peat – to learn what’s going on between the plant roots and soil-dwelling microbes in situ (something we’ve written about before). These interactions are environmentally and economically important, and many have been intensely studied. The symbiosis between rhizobia and plant roots allows nitrogen fixing, and many pathogens, such as fungi of the genus Phytophthora, use roots as a route into a plant.

So what’s stopping us looking at the roots? The answer’s fairly obvious: you can’t see through soil.  You can overcome this hurdle by using non-optical imaging techniques such as MRI to look at root structures, much as you can use them to see inside your head – but they can’t pick up light emitted by fluorescent proteins, for example.

I read a short paper this week that is making early inroads into another option: make soil see-through. Well, not soil precisely, but lumps of Nafion – a polymer invented in the 1960s that’s used in fuel cells. By grinding the Nafion down, researchers in Scotland have made it into particles similar to those found in soil.

Nafion isn’t normally see-through, but it has a refractive index very close to that of water. What that means in practice is that when you add water, the polymer disappears (this video shows something similar).

The Nafion particles that have been produced aren’t totally identical to soil, but they’ve been altered to have similar water and nutrient availability. It seems to work: plant growth in the transparent soil is comparable to growth in the real thing.

The researchers have already visualised GFP-labelled E. coli O157:H7 colonising the roots of lettuce seedlings. This bacterium, which is an important human pathogen, can grow quite happily on salad vegetables. The above picture is from the paper, showing the fluorescent E. coli on the lettuce roots.

This demonstrates how useful this technology could become. Although the authors concede that it’s not perfect for every type of plant–microbe interaction, there’s so much we don’t know about life in the loam that any insights we can get should advance both plant science and microbiology significantly.

Benjamin Thompson

Downie H, Holden N, Otten W, Spiers AJ, Valentine TA, & Dupuy LX (2012). Transparent soil for imaging the rhizosphere. PloS one, 7 (9) PMID: 22984484

Image Credit: PLOS ONE

Written by Benjamin Thompson

22/10/2012 at 10:00 am

Posted in Technology

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Getting out of a sticky situation

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ResearchBlogging.orgBiofilms get a pretty bad rep, and rightly so. Colloquially known as ‘slime’, these sticky scaffolds of polysaccharides, proteins and DNA are produced by colonies of bacteria and let them cling to wet surfaces, whether those are crustacean shells, water pipes or artificial cardiac valves.

Bacteria within biofilms are difficult to kill, which makes them a real problem in hospitals. The bacterial colonies are often more resistant to antibiotics than their free-living relatives, perhaps because the biofilm cocoons the bacteria in the centre and prevents drugs from reaching them. Biofilms are also tricky to remove by cleaning and are impervious to many detergents. Once they’re there, you’re kind of stuck with them, if you’ll excuse the pun.

But what if we could harness the adhesive power of biofilms for good? Could we use them to deliver useful molecules or drugs? A group of researchers is working on that very problem, right now.

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Written by Benjamin Thompson

06/09/2012 at 9:00 am

Future gazing: growing your own battery.

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Today I had a meeting with my boss, who told me about a great talk he’d been to by Professor Angela Belcher, from Massachusetts Institute of Technology. In it, she decribed using viruses to make energy generating devices, such as solar panels. Luckily, she gave the same talk at a TEDx event, which I’ve posted here. It gets interesting (from a microbiologist’s perspective) around six minutes in. At the very end are some working examples of what she’s talking about. Although it’s still very early days, I really do think this is rather exciting!

Benjamin Thompson

Written by Benjamin Thompson

20/02/2012 at 7:33 pm

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Guest Post: Sequencing for the microbiological masses

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Despite being in its relative infancy, genome sequencing (and the technologies that drive it) have become central to much of the molecular biology that we take for granted. In this guest post, Nick Tucker takes a closer look at the past, present and potential future of DNA sequencing as it becomes cheaper and more readily available.

Mining databases of microbial genomes has rapidly become a routine part of experimental work for microbiologists the world over. It must be impossible for this year’s new intake of PhD students to imagine a world without them. But let’s reminisce for a moment, just to see how far we’ve come.

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Written by microbelog

18/10/2011 at 11:58 am

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Bacterial spam mail

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ResearchBlogging.org

History dictates that Alexander Fleming will be best remembered for his discovery of penicillin, what with him winning the Nobel Prize and all. Perhaps what he should be remembered for, however, are the paintings he made on agar using different coloured bacteria. Quite why this culturally important art form never caught on is anybody’s guess.

It may have been Fleming’s strange hobby that inspired a group of scientists to go one stage further and develop an encrypted messaging system (obviously), which uses printed patterns, known as arrays, of different coloured bacteria. These bugs are coloured by the expression of genetically engineered fluorescent proteins, and the scientists in question have called the system ‘steganography by printed arrays of microbes’, or (ahem) SPAM for short… Read the rest of this entry »

Written by microbelog

11/10/2011 at 6:13 pm