Posts Tagged ‘Australia’

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.

Call out to Aussies! Watch transit of Venus on the tall ship Endeavour

// February 3rd, 2012 // Comments Off on Call out to Aussies! Watch transit of Venus on the tall ship Endeavour // Science at Home, Science Communication

HMB Endeavour in full sail

True blue replica of Captain Cook’s tall ship HMB Endeavour is circumnavigating Australia and dropping into me home town Adelaide for a spell. Australians can sail the tall ship replica Endeavour in June 2012 to watch the rare transit of Venus from Lord Howe Island, Cook’s real reason for mapping the east coast of Australia and claiming it for England. Read on, Macduff…

You know how they say when one door closes, a window opens? For me it’s the opposite. I closed all the windows to open the door, and an opportunity has flown SMACK into the glass. I can’t go on the HMB Endeavour, ‘cos I’m leaving Australia soon! Bummed out doesn’t begin to describe it.

For you peeps still in Aus, here’s the lowdown.

Cook’s Endeavour is currently sailing with a full, hammock-napping, rigging-climbing, star-gazing crew about Australia.

Over halfway through its yearlong trek, it’s docking in Adelaide from 16-23 February 2012 to open to those of the public keen to run their hands across the varnished wood and polished brass and marvel at the many ropes. Swoon. Details here.

If you, like me, want a closer inspection of the vessel and to get in those hammocks yourself, here’s your chance.

From end of May to mid June, the Endeavour is sailing from Sydney to Lord Howe Island to observe the transit of Venus on June 6. It’s a prime viewing location, and one of the first spots in Australia to see the rarest of eclipses.

Cook travelled to Tahiti in 1769 to view the transit, part of a global movement to find out the size of the solar system (specifically, how far Earth is from the Sun, an astronomical unit) by watching the transit in different locations around the world. Worked pretty well, too!

All Australia is in a good spot to see the transit, when Venus moves between Earth and the Sun and looks like a small black dot on our bright sun disk.

Don’t actually look at the Sun, will you, ‘cos you’ll damage your eyes. Use eclipse glasses or shadows. Though I do find eye patches rather fetching…

Transit of Venus, credit NASA/LMSAL

Transits of Venus happen in pairs eight years apart, but each pair is separated by over a hundred years. This is the last one in the pair, so if you miss this transit – that’s it until 2117 when we’ll probably be dead or robots.

This is another opportunity that has faceplanted into my closed window. I’m going to be in South America during the transit, one of the few places where you get to see zip, zilch, zero. Bummer…

So I’ll be living vicariously through you, dear Australian readers, so make the most of it! See it at home, or hit up the Endeavour and make a trip from it. The voyage in June is $4000, so quite pricey but a trip of a lifetime! Crew will be selected by ballot, and you need to enter here before 10 February 2012 – which is really soon. Do it now. Are you doing it? Go, right now, click here, live my dream. Take a pirate hat!

I travelled on the Young Endeavour back in me younger days, another replica tall ship used as a training sail vessel, it’s one of those memories that just sticks with you. Like seeing Stonehenge or being in a circus. Ballots for that are open too, but only available to people 16-23 years old. If that’s you, check it out and apply now!

Looks like I’m missing out on the sailing action in Australia this year, but I’ve got some pretty sweet plans myself. I’m heading out that door and leaving in just over a week for Vancouver, Canada, where I’m hitting the AAAS annual meeting. I’ll tell you all about it!

Science behind the headlines – beyond seven billion people

// December 9th, 2011 // 1 Comment » // Science Communication

We reached a big milestone last month as the world’s population exceeded seven billion people for the first time. Looking behind the headlines was Paul Willis at the RiAus and a panellist of scientists and journalists on Tuesday (event details here.)

In the 20th century we added five billion people to the Earth. Before that, we had only added two billion in total. Part of the reason is a decreased death rate, due to better medical facilities, coupled with an increase of food made possible by the Haber process that produces nitrogen fertiliser from nitrogen in the air. The chemistry makes it possible to, on some level, make food from air.

But population increase is not exponential. The UN expects the population to level off at 10 billion in the next fifty years, after a dramatic decrease in fertility, which no one anticipated.

“It is unconscionable to have a policy to increase mortality!” says Graeme Hugo, Director of the Australian Population and Migration Research Centre at the University of Adelaide. “The only way forward is to decrease fertility, that’s the only thing on the table.”

The world has done very well to reduce fertility, halving it since the 1970’s.

However, in some areas of Africa and isolated pockets in Asia it is not dropping as fast as expected. Two years ago East Timor each woman was having around eight children. The continued high fertility may be because we’ve taken our foot off the pedal when it comes to efforts like increasing contraceptives, women’s education and emancipation.

Beyond numbers

But it’s not all about the numbers, and that was the key point the scientists spoke about on Tuesday. Population is a complex issue, and has to be considered in connection to age and spatial distribution and consumption of goods.

The cost of looking after an aging semi-majority (the baby boomers) is a worry for some political movements. Balanced age groups are important to ensure the number of dependents and the number of workers is stable.

Migration may not change the global numbers, but it’s important for people are spread out in the right way. That means considering how many people a local environment can sustain in terms of food and water.

Consumption is also critical. One baby born in the United States consumes the equivalent of 30 babies born in Africa according to Udoy Saikia, School of the Environment, Flinders University (here’s a relevant link.) “People in developed countries should limit their consumption,” says Hugo. “In many developing countries, consumption needs to go up because they’re not consuming enough to be healthy.”

One way for more developed countries to limit consumption is to go vego. A more vegetarian diet is able to support more people for the same number of resources. Bring on the lentils!

This Tedx talk on the topic, I can’t recommend it enough.

Magic bullets

Scientists agreed that coverage of the seven billion people story has been pretty good overall, far better than stories about migration.

One issue they mentioned was the trend to look for a magic bullet, fixing just one thing to solve the whole population problem. It’s also hard for journalists with limited inches to talk about all the factors in a complex issue like population science.

Stopping population growth won’t work unless you take consumption into account, as well as the other factors. There needs to be a holistic approach. That doesn’t end (or even start) with policy – everyone needs to make a decision to change their consumption.

Australia

How many Australians should there be? There is no magic number where everything will fall into place. There are definite demographic problems regarding aging populations and dispersion (or lack thereof).

The scientists agreed we need a policy that allows for sustainable growth. They said it would devastate Australia if we stopped population growth tomorrow, but it would be also devastating to have uncontrolled growth.

“Every day we waste about 40% of the food (in Australia),” says Saikia. “There is some hope that the 10 billion population can survive very well, depending on distribution and consumption.”

Paul Willis summed up by asking whether Australian’s should “be concerned, not alarmed.” It’s not the end of the world, but we do need major changes and responses to population dynamics, says Hugo. “Be concerned, AND alarmed – about consumption,” says Saikia.

This post was also featured on the RiAus website.

Future floating laboratory, prospectus of the HMS Beagle Project

// December 2nd, 2011 // 1 Comment » // Science Communication

Yesterday afternoon I went to a prospectus to the HMS Beagle Project while founder David Lort Phillips is in Adelaide.

It’s a CRAZY exciting project which plans to build a modern version of Darwin and FitzRoy’s tall ship the HMS Beagle, kitted out as a floating laboratory.

Marine biologists could benefit from getting much-needed ship time. As it’s a tall ship, it can get closer to land than large cruise vessels, giving it an extra bonus to people studying tidal areas. Groups into DNA barcoding might find it useful too, as it can be tricky to get high quality samples for DNA testing – most are set in formalin which ruins the info. More on DNA barcoding soon.

Climate research can be done from the boat, the connection between biodiversity and climate change could be exploited in the project. There’s a collaboration of the HMS Beagle with NASA, combining observations from space with water samples in the ocean.

Space shuttle before docking with space station. Image by NASA

In 2009 the Brazilian tall ship Tocorime with the International Space Station, and they ran live hook-ups between scientists on the boat, an astronaut above, and school children in Paraty. Looks like Keven Zelnio from Deep Sea News was there! The students had questions written in English on paper which they screwed into a sweaty ball with excitement, according to Karen James, involved with the HMS Beagle Project.

Most interesting for me is the prospect of science communication on the high seas. We can take high-tech science to ports around the world, including remote areas that often miss out on science engagement events.

I’d like to see the online aspect of the beagle able to webcast and tweet from the deck, setting up chat sessions with classrooms and the public. Maybe people could watch the Beagle’s progress through the ocean, and be updated with the science we on the way. Oh, I gots ideas!

At the moment they have blueprints and some collaborations sorted out, but are still looking for funding to get it built and in the water. The first five years it would retrace the first voyage of the Beagle, including along the South American coast.

Chile are planning to build their own ship in connection to the project, possibly named after the Beagle support ship, the Adventure.

Darwin was 22 when he signed on with the Beagle, an amateur with an interest in science – mainly geology. What he saw from the ship and at port, particularly in the Galapagos Islands, lead him to a world-changing hypothesis.

Maybe the new Beagle will have the same effect on some young scientists. Good heavens, I just really hope they build this tall ship, and when they do, that I’m on it helping to share their discoveries online, in ports, worldwide.

Exploring the blurry line between colony and individual

// August 3rd, 2011 // 1 Comment » // The Realm of Bizzare

I found this great post on the Portuguese man-o-war, known as the bluebottle in Australia, over at Deep Sea News the other day. It’s eating a fish!

The post also said:

Remember this species is colonial and made of four different polyps or zooids, working in unison and dividing labor. The bladder is a single polyp called a pneumatophore. The long tentacles are dactylzooids used for fishing. The dactylzooids bring the fish up to another set of zooids, gastrozooids, responsible for digestion. Last, there is set of zooids, gonozooids, in charge of reproduction.

So it looks like a jellyfish, but it ain’t. It’s a colony of four specialists working together, each with their own nervous system but incapable of living by themselves.

Bluebottle on Woolongong Beach, NSW. Image by Fiona Wilkinson

As I was doing a bit of research about bluebottles and how they sting even when dead and dried up, I came across an interesting question. How do they reproduce? If the gonozooids are responsible for getting jiggy with it, don’t they just make more gonozooids? Where do the rest of the polyps come from?

Well, no one really is a hundred percent sure. I guess that’s fair enough, studying a swarm (a navy) of man-o-wars during mating season doesn’t sound too good. But here’s what they think.

A gonozooid from one man-o-war will make sperm which combines with an egg from another man-o-war gonozooid. Hey presto, you’ve got fertilisation and one embryo – which will become the bladder polyp at the top. That embryo divides several times, then reproduces asexually to make more zooids, which bud out of it. The budding polyps will become either tentacle, digestion or reproduction individuals.

That’s where I got confused. Does this mean that each of the zooids actually come from a single polyp? Are they just differentiated forms of the original polyp, specialised for their particular role? How is this different to a human embryo producing heart cells?

One explanation uses phylogenetics – comparing organisms to see how similar and different they are. Each zooid is similar to solitary Cnidaria (the phylum that includes jellyfish, coral and bluebottles), so can be considered an individual in its own right and a bluebottle as a colony.

But if we define an individual as something with similarity to other individuals, then all the cells of a multicellular organism would be individuals. Are individual humans really colonies of individual human cells? Really, the microbes on and in you outnumber your human cells 10 to one, so you’re more like a walking microbial factory anyway.

White poplars, a kind of aspen, form clonal colonies. Image by Jacob Halun

I think we have a very human-centric model for defining individuals, which is not surprising really. But most species on the planet don’t reproduce like we do, the boundaries between individual and colony are much less clear.

Take aspen trees, which can grow by seeds (sexually) or by underground runners which sprout a tree-clone (asexually.) Over time the runners can decay separating the trees. How can we tell if the trees are individuals or clones, and if we can’t, how do we study adaptation and natural selection?

Tasmania has these Huon pines that are the oldest genetically identical stand of trees which has lasted 10,000 years. Each tree lives about 2,000 years, but the original tree renews itself through genetic clones. Tassie also has the oldest genetically identical plants, clones of King’s lomatia estimated to be at least 43,000 years old.

Strawberries do it too, as do fungus. A single specimen of Armillaria solidepes was found in Oregon the size of 1,220 football pitches and estimated at 2,400 years old. It’s one of the largest organisms in the world.

Where does the individual end and a colony begin? Looking at all the bizarre stuff out there, I can’t help but wonder if we’re the weird ones.

ResearchBlogging.org

Clarke, E. (2010). The Problem of Biological Individuality Biological Theory, 5 (4), 312-325 DOI: 10.1162/BIOT_a_00068

Read it at the homepage of Ellen Clarke






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