Posts Tagged ‘Research’

Shape-shifting devices, gadgets for the future

// April 29th, 2013 // 1 Comment » // Recent Research

I’ve always wanted a computer that would fold up like a newspaper. I could sit on a bench and open it to read, then close it up and cram into a bag. It wouldn’t be backlit like a computer screen, just a soothing paper-like display. There’s something lacking in e-readers today that look terribly phoney. As in, they look like giant phones or tablets. I want one like a book, an extremely lightweight paperback.

That’s been the dream since before iPhone’s were released, and it looks like it’s a step closer now. New prototypes for shape-shifting mobile devices were unveiled today at the Computer-Human Interaction Conference CHI2013 in Paris. They transform on demand, bending up to hide personal information or curving around to make a console for playing games. The press release says they can even curl into a stress ball, which doesn’t sound very healthy for a smart phone, though I can imagine it might come in handy.

Here’s a nifty video of the “Morphees” in action.

There are a few different ways the researcher’s achieved this kind of movement. Some prototypes used wires attached to motors that pulled and pushed them. Others used memory wire, which reverts to its original shape when heated by running a current through the wire.

The research was led by Dr Anne Roudaut and Professor Sriram Subramanian from the University of Bristol. They have also introduced a new metric to help guide the developing industry – “shape resolution.” Like screen resolution, shape resolution allows different devices to be compared easily, measuring the ability to stretch, bend, curve and so on.

On a related note, researcher Roel Vertegaal from Queen’s University is working on thinfilm phones, called the world’s first paper computer. The work was presented at the same conference, CHI, in 2011. Here’s a quick video. Looks incredible.

Pretty keen to head over to the next CHI conference, which is in Toronto on April 26, 2014. Though it might be easier to get to the 2015 one in Asia, as it’s a bit closer to Australia. For more info on the conferences, check out the Special Interest Group on Computer-Human Interaction.

Toothbrushes and breath testers for tuberculosis

// January 15th, 2013 // Comments Off on Toothbrushes and breath testers for tuberculosis // Recent Research

Far-advanced tuberculosis diagnosed by x-ray. Image from the CDC, accessed on Wikipedia.

Tuberculosis is a major health issue, with around a third of the world’s population infected with the bacteria mycobacterium tuberculosis. Not all these people actually have signs of illness, only 10% will go on to have any symptoms during their life. For the rest it remains latent, the bacteria is present but not causing any problems.

As tuberculosis is only contagious and dangerous when it’s active, that’s usually what people test for. Chest x-rays can check whether TB has affected the lungs, and are required for people travelling from high-TB countries to low-TB countries including Australia and the United Kingdom. The other avenue for diagnoses is the slightly grosser method of analysing the gunk people cough up, to see if there’s bacteria in it. For  mycobacterium tuberculosis, growing a sample in agar takes weeks.

A breath test would be a much safer and faster way to see if bacteria are present in the lungs, and that’s what our first paper is looking at. Researchers from the University of Vermont are finding out whether bacteria can be identified by their “chemical fingerprint,” a cocktail of chemicals that makes its way from the lungs to the breath. Their research is published in the Journal of Breath Research.

Now, it’s some time before police can pull you over for a quick TB test when you’ve been swerving off the road from a coughing fit. “Honestly, it’s just the flu!” But it’s got to be a cheaper option for many countries with low health care budgets.

TB poster, image from Wikipedia.

It is early research. They studied the tiny puffs from mice, rather than humans, and looked at two different bacteria that cause lung infections Pseudomonas aeruginosa and Staphylococcus aureus (Golden staph), neither of which are the TB bacteria. Clearly there is more research to be done, but it’s a promising start.

Read more about it here.

TB can be cured with a course of antibiotics, or more specifically a combination of several antibiotics that have to be taken for six months. Like Golden Staph, the bacteria that causes tuberculosis is becoming increasingly drug resistant. Drug resistant strains need different antibiotics and take 18 months or more to cure.

In Papua New Guinea, extensively drug resistant TB is a problem. A recent outbreak there and movement of patients to better health facilities in Queensland and the Torres Strait Islands has triggered alarm and, frankly, scaremongering media reports and political backlash. You can read about it on the Conversation, because I’ve been out of Aus too long to be in on the goss (but I’m back in a month, yay!)

The next weapon against drug resistant TB may come in the unlikely form of a traditional toothbrush. The South African toothbrush tree contains a compound called diospyrin, which inactivates an enzyme critical for bacteria reproduction (but does not affect the similar enzyme found in human cells.) The enzyme is a DNA gyrase… would you care to know how it works?

When DNA is replicated, the two strands normally joined in a double helix are broken apart, and you can imagine it’s like putting your fingers into a rope and pulling apart the strands. If this imaginary rope is a circle (as DNA in bacteria is) then it can’t just unwind itself at the ends. Instead, things will get messy, and the DNA will coil and twist up on itself. These “positive supercoils” are a bit like like twisting a shoelace until it bunches up, and is bad for the DNA. Gyrases relax the positive supercoils by cutting the DNA and moving one strand to the other side, then joining them up again.

Circular DNA supercoiling. Image by Richard Wheeler.

Circular DNA supercoiling. Image by Richard Wheeler.[/caption]

By stopping gyrase activity, the bacteria can’t replicate its DNA. The research by a team from the UK and South Africa described how this compound from the toothbrush tree interferes with gyrase, and importantly, that it acts in a different way to existing antibiotics. This will hopefully be a chink to exploit in the armour of drug resistant bacteria.

Here’s the paper from the Journal of Biological Chemistry and the press release.

Brains compensate for a stuffy nose

// August 13th, 2012 // Comments Off on Brains compensate for a stuffy nose // Recent Research

Image by Miguel Angel Pasalodos, licensed on Creative Commons CC BY-SA 2.5

Nothing like a stuffy nose to ruin your day. You sound like a ponce, food tastes like cardboard and you have to sleep with your mouth open for spiders to crawl in. No joke. It happened to a friend of a friend of mine.

But have you ever noticed how quickly your sense of smell returns? Almost as soon as the sniffles are gone, you’re back to sniffing roses, and new research is finding out how our brain can adjust so fast to changes in sensory input.

What I love about this study is how they did it.

For a whole week, 14 people had their noses completely blocked during the day. At night, they slept sans-nose-blockers in a special low-odour hospital room.

A low odour hospital room? All the ones I’ve been to smell weirdly like custard. I wonder if all 14 shared the same room, or if they were spread out… I mean, even if you do have a spesh no-custard hospital dorm, if 14 people spending the night there it won’t be low odour for long.

Brain activity in response to odours changed after a week of smell deprivation in two regions. Activity increased in the orbital frontal cortex, but decreased in the piriform cortex, both are related to our sense of smell.

“These changes in the brain are instrumental in maintaining the way we smell things even after seven days of no smell,” said lead author Keng Nei Wu, Northwestern University Feinburg School of Medicine, in the press release.

“When your nostrils are blocked up, your brain tries to adjust to the lack of information so the system doesn’t break down. The brain compensates for the lack of information so when you get your sense of smell back, it will be in good working order.”

Once the 14 participants were released to sniff wildly, their brains soon returned to normal, showing pre-experimental levels of excitement when offered something smelly.

This rapid reversal in the realm of smell is quite different to sight, where deprivation usually has longer-lasting effects. Wu suggests this could be because smell deprivation is pretty common, given our penchant for catching colds and having allergies. Perhaps it has evolved to be more agile, or perhaps the endless sniffles we get in primary school gave our brains ample chance to practice.

Either way, it seems the quick adjustments by our brains protect our sense of smell, so it can rebound quicker than you can say “the one who smelt it dealt it.”

Wu ends by saying “more knowledge about how the system reacts to short-term deprivation may provide new insights into how to deal with this problem in a chronic context.”

Chronic loss of smell is nothing to be sniffed at (lol.) It really takes the fun out of life. This column, 20 years of living without a sense of smell, was clearly written from the pits of despair for want of a whiff of fabric softener.

ResearchBlogging.orgKeng Nei Wu, Bruce K Tan, James D Howard, David B Conley & Jay A Gottfried (2012). Olfactory input is critical for sustaining odor quality codes in human orbitofrontal cortex
Nature Neuroscience : 10.1038/nn.3186

The brewer’s yoke, the domestication of microbes

// July 15th, 2012 // Comments Off on The brewer’s yoke, the domestication of microbes // Recent Research

Something happened when I was spliced, something wrong. Some random event in my chromosomes, I suppose it was. In any event, I wound up lacking. My sister took all the toxin genes, and I was left with nothing.

It’s a scary world out there for a fungus without a toxin. How would I strike fear into the hearts of all animals who dared to eat the plants I was eating? How, without my precious aflatoxin to attack the liver, causing acute sickness or eventual cancer?

Quite simply, I’m surprised I lasted as long as I did before they found me.

Indeed, I’m not sure how they did find me. I had a pretty good disguise, growing colonies of blue along the endless islands of white rice grains, just like my toxic cousins always had. Safe from munching animals by my don’t-eat-me mimicry, the promise of sickness is the discoloured rice.

For some reason, these sake brewers saw past it all. I thought I was a goner when they lifted me up from the wild and plonked me into a house of wood.

Then I saw the food.

A. oryzae in heaven. Image by Forrest O.

It’s hard for mould like me to see, lacking in the eye department, but I knew it was there. An endless carpet of steamed rice. With my filamentous fronds I could touch it. Drill down into it and grow cottony soft, sprout fruiting bodies on the surface and spread on and on.

Call me legion, for we are many. Better yet, call me qū meí jūn in Pinwin, kōji-kin in Japanese, nulook-gyun in Korean or the grandiose Aspergillus oryzae in scientific circles. Back then, some 2000 years ago, I didn’t know who I was, or that I would one day be the National Fungus of Japan.

That’s when the changes happened.

I didn’t notice at first, I don’t know that there was ever a master plan. It felt… natural. Human hands, bristling with microbes and pitted with pores, dropped me into heaven. And when I had eaten the heaven for a time, they picked me up and dropped me once more into fresh heaven.

Incomprehensible! These hands must have spent hours polishing the rice to remove all the husks, then steamed it to perfection, cooled it so I didn’t burn my filaments, then spread it out – just for me! It was like being a king! King Kōji-kin!

I'm a national icon, and pretty cute too. Image by Ryoku Kasinn

As they fed me and I ate, we gradually adapted to please one another. Heaven grew ever more heavenly, until the temperature and humidity was just so.

For my part, I started growing much faster, hell, I had brilliant conditions for it and not a doubt in the world that I could grow as fast as I pleased. Fearlessly fast.

Over generations, they selected only the best for their purposes, which at that stage I knew nothing about. They selected the sons and daughters (hell, we’re all of one gender here) that could best turn rice starch to sugar. They also preferred fungi of least colour, but most smell and flavour. Each generation, the best of me would be plucked and propagated.

Turning starch to sugar is a tricky thing. I suppose the point of starch is to tie up the sugar molecules into a big, complex network so the plant can use them later. For me, kōji-kin I secrete the amylase enzymes, biological machine that chops starch into pieces of sweet. From a couple of recently-licked hands, I’ve learned humans make the same enzyme in their saliva. My amylases, however, not only make glucose, but a few other sugars that produce a wonderful flavour.

But why, pray tell? Have you worked it out yet?

Winemakers use yeast to turn the natural sugars in grapes into alcohol. Beer brewers must malt their barley, partially growing the seed to convert starch to sugar, to ferment it with yeast into alcohol.

And I, the humble fungus, plucked from the wild a millennia ago for a deficit in character. My non-toxic self excels, above all other moulds, in turning rice starch into sugars.

From the beds of heaven, me and my alchemical rice is transferred to the fermenting tank. Mixed with yeast, water and more rice, then left to stew in our own juices for a month.

This mash is pressed and filtered, and the sweet, alcoholic liquid that pours forth is bottled as sake.

Not to ring my own bell filaments, but I make soy sauce and miso too. That’s a whole meal – appetizer, main, and a drink.

Domesticated A oryzae (left) and wild A flavus (right). Image by John Gibbons, Vanderbilt University

These days I hardly recognise myself! So much of me has changed by growing with the sake brewers. Though I still share some 95% of my genome with my wild and toxic cousin A. flavus (and you, human reader, share 99% of yours with a chimpanzee), I am given all I could ever want to eat and praised world-over for my skill in sake making. While A. flavus, the wild thing, is targeted daily for a war against fungi with resistant crops and competitive yeasts.

What must the wolf think of the dog? Or the auroch of the cow? Well, to their accusations I say this: We may change our genes and appearance for protection and care, but, in doing so, we also mould the humans who cooperate with us. Through their attentions and skills, they, too, are domesticated.

This story was inspired by this recent research by Vanderbilt University into the domestication of microbes. “Although people don’t often think about it, we haven’t only domesticated animals and plants, but we have also domesticated dozens of different microbes.” – Assistant Professor of Biological Sciences Antonis Rokas in the press release. You can find more information on brewing sake here, and a beautiful description of koji pampering by interns at a sake house in Japan who blogged their experiences.

ResearchBlogging.orgGibbons, J. et. al. (2012). The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae Current Biology

Good God Particle, is that the Higgs boson?

// July 5th, 2012 // Comments Off on Good God Particle, is that the Higgs boson? // Recent Research

higgs boson

Simulated model of Higgs boson decaying into four muons (shown in yellow). Image by CERN.

The world of science is abuzz with the news! CERN have discovered a new particle, and it looks like the elusive Higgs boson. That large hadron collider has really come in handy!

It was announced today at CERN as a ‘curtain raiser’ for the International Conference of High Energy Physics – ICHEP2012 – currently on in Melbourne, Australia. And what a curtain raiser it is.

The Higgs boson is a subatomic particle that, theoretically, gives mass to everything. It interacts with the Higgs field which permeates the Universe, kicking up a drag as it moves. That drag, or attraction, gives protons and electrons their mass as they zoom through the Higgs field. In the model, the Higgs boson is absent in photons of light, which is why they have no mass.

It’s been a long, hard road to find it – taking 45 years. Why? Partly because, after the collisions, they decay very fast, and partly because the way in which they decay doesn’t stand out. It seems to vanish into very normal smoke, that is, quarks, antiquarks and muons the same as those made by run-of-the-mill activity from other LHC collisions. It’s like trying to spot stars in daylight, according to this neat article by Matt Strassler.

The physicists are being cautious with their discovery, describing it as a Higgs-like particle. There’s more data analysis and experiments to be done. But if it looks and smells like a Higgs boson…

Peter Higgs

Will Peter Higgs, theoretical physicist, be winning a Nobel Prize for this? Image by CERN and Claudia Marcelloni.

What it looks and smells like, to be precise, is a ‘bump’ in the data with a mass of 125.3 gigaelectronvolts, about as heavy as 125 protons.

Analysing the data, so far, has put it at a confidence level of 5 sigma. That means there’s less than a one-in-three million chance of receiving the same result completely by chance, without a Higgs boson. Put another way, that means they can feel over 99.999 percent sure this is it – a boson that acts like a Higgs.

“The results are preliminary but the 5 sigma signal at around 125 GeV we’re seeing is dramatic. This is indeed a new particle. We know it must be a boson and it’s the heaviest boson ever found,” said CMS experiment spokesperson Joe Incandela in the press release. “The implications are very significant and it is precisely for this reason that we must be extremely diligent in all of our studies and cross-checks.”

“It’s hard not to get excited by these results,” said CERN Research Director Sergio Bertolucci in the same release.

It is exciting! Even though it’s still a preliminary result – guys, it could be the God particle! How cool is that?






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