Apple DNA code is cracked by geneticists


Golden Delicious apples The discovery could leader to better looking and tasting apples

A team of 86 global scientists have sequenced the genetic code of the Golden Delicious apple for the first time.

The DNA breakthrough could result in new and improved apple varieties which are more resistant to disease.

Scientists from 20 institutions took two years to unravel the code – the largest plant genome uncovered to date.

The findings are published in the leading journal Nature Genetics.

‘Competitive advantage’

Professor Riccardo Velasco at the Edmund Mach Foundation in Italy, who led the research team, said that sequencing the genome “would have huge implications for applied breeding”.

“This breakthrough will help us to develop high quality traits and bring new things to the apple market,” he told BBC News.

Kate Evans from Washington State University’s Tree Fruit Research and Extension Centre said the discovery would help the “long-term sustainable production” of apples.

Scientists hope improvements to the popular Golden Delicious variety – which originated in West Virginia, US, more than a century ago – could enhance the taste, look, and crunchiness of the fruit.

The researchers were also able to trace the apple’s ancestry, and found the domestic fruit’s wild ancestor Malus sieversii originally grew in the mountains of southern Kazakhstan. There are more than 7,500 varieties of apple known today.

The researchers also discovered that the huge size of the apple genome originated when it got accidentally duplicated far back in its evolutionary history.

A large number of genes can give plants a competitive advantage, providing more in-built defences against disease.

Will GM mosquitoes end dengue and malaria?


Anopheles-stephensi-mosquitoes-vg-glow-in-the-dark140_AnthonyJames.jpgA gene in the mosquitoes causes them to fluoresce under ultraviolet light

Anthony James

While great advances have been made in the lab, malaria-resistant mosquitoes are still a long way from being airborne, reports Katherine Nightingale.

When researchers first genetically modified an Anopheline mosquito — the type that spreads malaria — it was hailed as a major step towards creating armies of malaria-resistant mosquitoes that could take over populations, leaving them unable to transmit the disease.

But ten years since it was created, there are still no GM mosquitoes buzzing around the plains of Africa. Malaria-resistant mosquitoes have yet to even leave the laboratory.

Their production is taking much longer than first envisaged — and other ways of manipulating mosquitoes to stem disease transmission are overtaking them.

Survival of the fittest

After the 1998 genetic modification of Aedes aegypti, which transmits dengue virus, yellow fever and chikungunya virus, came the creation of the first GM anopheline mosquito in 2000. Two years later, scientists created the first malaria-resistant GM mosquito.

Marcelo Jacobs-Lorena leads the laboratory that produced this mosquito, which worked by producing an antimalarial substance when it fed on blood.

But GM mosquitoes are not necessarily fitter than their wild counterparts. Mechanisms are needed to ensure that the antimalarial genes are ‘driven’ through populations instead of dying out. This has proved to be a major challenge.

“Up to now — almost ten years later — no one has really found out how to do that,” saysJacobs-Lorena, a professor at the Johns Hopkins Malaria Institute, United States.

One approach has been the ‘selfish genes’ — or ‘Medea’ — approach. These genes have been shown, in fruit flies, to ensure their carriers’ survival.

But scientists have not yet managed to combine Medea genes with malaria resistance genes in fruit flies, which they use as models. Nor have they successfully transferred the Medea effect into mosquitoes. This should be possible within 2–3 years, says Anthony James, a professor of microbiology and molecular genetics at the University of California at Irvine, United States.

GM bacteria: a new way forward?

Instead of waiting for genetic drive systems to be perfected, Jacobs-Lorena has switched to genetically modifying a different organism: bacteria that live in mosquitoes.

His team has shown that when the bug Escherichia coli is modified so that it produces the same malaria-inhibiting molecule that first made mosquitoes resistant, the mosquito itself displays a lower level of malaria infection.

“The question is similar to the one we had with the transgenic mosquitoes — how do you introduce a GM bacteria into mosquitoes in the field? That is a challenge which we think we have a handle on.”

Jacobs-Lorena’s team is collaborating with an Italian laboratory to work with types of bacteria called Asaia that occur naturally in mosquitoes. Asaia is passed from female mosquitoes to their offspring.

Jacobs-Lorena hopes to one day produce a ‘cocktail’ of bacteria, each secreting a different antimalarial molecule, to ward off resistance in a way similar to combining antimalarial drugs. Creating the bacteria and testing their spread through populations should take about 8–10 years, he says.

Dengue hope

That he sees 8–10 years as a shortcut gives an indication of just how far from the field disease-resistant GM mosquitoes are. Another GM strategy, however, is much closer to fruition.

Instead of using genetic engineering to create resistance, researchers at biotech company Oxitec a spin-off from Oxford University, United Kingdom are using GM to reduce A. aegypti mosquito populations.

The method targets dengue fever, a disease which infects up to 100 million people each year and for which there is no treatment or vaccine.

The Oxitec team uses a system known as RIDL (release of insects carrying a dominant lethal) to genetically sterilise mosquitoes. Their strategy is based on releasing male GM mosquitoes that can’t produce viable offspring.

One benefit of using Wolbachia is the bacteria’s ability to spread through mosquito populations

Flickr/AJC1

In one example, offspring all die at the larval or pupal stage and, in the other, female offspring cannot fly or feed and therefore cannot mate.

“It’s a self-limiting system, you release sterile males, they mate with wild females and the progeny die before they can bite and transmit disease. If you release them for long enough the wild population will decline and collapse,” says Luke Alphey, research director of Oxitec.

The first strategy was tested in successful contained trials in a purpose-built house in Malaysia during 2007–2008. The second strategy, developed by a large consortium funded by the Gates Foundation’s Grand Challenges in Global Health programme, is being tested in outdoor cages in Mexico. Open field trials of both strategies are being planned.

Oxitec is concentrating on this kind of ‘population suppression’ strategy rather than disease resistance because it should have an impact sooner, says Alphey.

But whether the technique is sustainable in the long term is doubtful, says James, who is principal investigator of the Gates-funded consortium. The very property that could make these mosquitoes more acceptable to regulators and the public — that the transgene dies out with the mosquito — means that the mosquitoes have to be released continually.

“You have to have the political will … It’s a public health paradox: if you spend a whole lot of money releasing mosquitoes you don’t have a problem, but if you stop doing it, then you do,” says James.

Amongst the objections to using GM mosquitoes is the issue of the ’empty niche’, in which other — perhaps more dangerous — insects might move into the ecological niche vacated by the mosquitoes.

But Alphey says the issue is not unique to GM mosquitoes and he is confident that there are few insects that would replace A. aegypti, particularly given that it isn’t a native species in most of the areas where it spreads dengue fever.

“We’ve done extensive environmental analysis and it’s very hard to see any significant, tangible risk from releasing these insects.”

Non-GM solutions

Closer still to field trials is a non-GM approach. A team of researchers led by Scott O’Neill from the University of Queensland, Australia, will start field trials of its dengue-resistant mosquitoes — which contain a bacterium called Wolbachia — in about six months, he says.

The researchers originally found that a strain of Wolbachia cuts the lifespan of mosquitoes so much that they cannot pass on the dengue virus.

But more recently they have discovered that many Wolbachia strains also make the mosquitoes resistant to the virus — though they do not yet know how.

The researchers have tested the mosquitoes in a large ‘greenhouse’ in Australia complete with mock-ups of houses — and volunteers for the mosquitoes to feed on.

“When we introduce Wolbachia mosquitoes into a wild population, they quickly invade,” says O’Neill.

Initial field trials in Australia — for which the team is awaiting government approval after an extensive risk analysis — will check safety, followed by larger trials assessing whether the method cuts dengue transmission in Vietnam next year. The whole process should take around three years, says O’Neill.

One benefit of using Wolbachia is the bacterium’s ability to spread through populations. It is transmitted only by the female mosquito, via its eggs, to its offspring. Unusually, if a male infected with Wolbachia mates with a female that is not, her eggs die.

“That makes it interesting from a bio-control perspective because [the bacterium] can spread very effectively yet is quite specific so we don’t have to worry so much about secondary environmental effects,” says O’Neill.

Wolbachia already lives in around two-thirds of insects, including some mosquitoes that bite humans, so the risk to human health is tiny, says O’Neill. And because the bacteria are spread only from female to offspring there is little chance of them infecting other insects.

But it’s unlikely to be a permanent solution. Resistance could emerge eventually, says O’Neill, so he is working on different Wolbachia strains that could be deployed one after another to prolong effectiveness — like changing from one insecticide to another.

Political hurdles

Despite progress in O’Neill’s non-GM approach, he acknowledges that it is likely to be the elusive, disease-resistant mosquito that has the most potential in the long term.

James, who works on both resistant and sterile GM mosquitoes, agrees. “[Disease-resistant mosquitoes] are envisioned to be able to achieve not only control and elimination but also target the more ambitious goal of eradication,” says James.

There is strong support for O’Neill’s non-GM approach from Australia and Vietnam

O’Neill/McGraw Lab, University of Queensland

But public attitudes and regulatory processes may prove to be the biggest barrier.

O’Neill’s field trials are going ahead because of strong community support for the idea in both Australia and Vietnam. But GM technology is controversial in many countries and campaigning groups such as Greenpeace are against GM science, whatever its aims.

“The political/social side of GM is a major hurdle,” says Andrew Read, professor of biology and entomology at Penn State University in the United States.

“The first GM vector product will be critical it needs to work really well and alleviate suffering right away.”

Jacobs-Lorena says that the public might be more accepting of GM insects and bacteria than of crops because the insects have the potential to save lives, rather than produce cheaper food.

But a 2001 Zogby International poll found that just 39 per cent of Americans surveyed agreed with genetically modifying insects to fight disease.

The insects may prove more popular in developing countries where people see first-hand the devastation of malaria and dengue fever.

The WHO is developing guidelines for countries to use as the basis for developing their own regulations for the field testing and release of GM insects. Draft guidelines should be ready by October this year, Yeya Touré, leader of the Innovative Vector Control Interventions programme at the WHO, told SciDev.Net.

He is confident that GM mosquitoes will have a role to play in future malaria and dengue control and says that the Cayman Islands, Malaysia and Mexico are interested in using GM sterile mosquitoes to tackle dengue.

As for the armies of disease-resistant GM mosquitoes, they may not be a pie in the sky anymore, but they’re not airborne either — and seem unlikely to be anytime soon.

Quantum Physicists Dream Up Smallest Possible Refrigerator


ou may have a $10,000 Sub-Zero fridge in your kitchen, but this is cooler. Theoretical physicists have dreamed up a scheme to make a refrigerator out of a pair of quantum particles such as ions or atoms, or even a single particle. The fridges may be the smallest ones possible. “It’s very elegant and innovative,” says Nicolas Gisin, a theorist at the University of Geneva in Switzerland. Theo Nieuwenhuizen, a theorist at the University of Amsterdam, says “I don’t see any error, so probably this would work.”

The challenge is to make a few quantum particles act like a so-called thermal machine, the theory of which was set out by French engineer Sadi Carnot in 1824. Carnot imagined a piston filled with gas that could be compressed or expanded. The piston could make contact with either of two large bodies (say, massive steel blocks) at different temperatures, which could serve as the “hot bath” and the “cold bath.”

Carnot put the imaginary piston through a cycle of motions, including one in which the gas expands while in contact with the hot bath and another in which it is compressed while in contact with the cold bath. During the cycle, the piston does work while absorbing heat from the hot bath and releasing heat into the cold one, making it a “heat engine.” Reverse the cycle and, in response to work done on it, the piston acts as a refrigerator, absorbing heat from the cold bath and releasing it into the hot one.

Now, Noah Linden, Sandu Popescu, and Paul Skrzypczyk of the University of Bristol in the United Kingdom report that, at least in principle, they can make a refrigerator out of a few quantum particles called “qubits.” Each qubit has only two possible quantum states: a zero-energy ground state and a fixed-energy excited state. The theorists have found a way to siphon energy out of one qubit by making it interact with just two others.

The theorists arrange things so that each qubit has a different excited-state energy but the trio of qubits has two configurations with the same total energy. One is the configuration in which only the first and third qubits are in their excited states—denoted (101). The other is the configuration in which only the second qubit is in its excited state—denoted (010). If all three qubits were at the same temperature, then the system would flip with equal probability back and forth between these two configurations.

But the researchers skew that flipping, as they explain in a paper in press at Physical Review Letters. The trick is to put the first two qubits in contact with a cold bath and the third one in contact with a hot bath. The higher temperature makes it more likely that the third qubit will be in its excited state—and thus that the trio will be in the (101) state instead of the (010) state. But that means the system is more likely to flip out of (101) and into (010) than the other way around. So on average the flipping takes the first qubit from its excited state to its ground state and draws energy out of the first qubit. After a flip, the qubits essentially reset by interacting with the baths, allowing the cycle to start again.

The theorists measure the fridge’s size in terms of the number of its quantum states, and the three qubits have a total of eight possible states. That number can be clipped to six, if they replace the second and third qubits with a single “qutrit,” a particle with a ground state and two excited states—although those two states have to be in contact with different baths. “We believe that’s probably the smallest number of states you can get away with,” Linden says.

In theory, such a fridge can get arbitrarily close to absolute zero, and Popescu says that it might be possible to make one using trapped ions for the qubits and streams of laser light as the baths. Some researchers hope to use such qubits as the guts for a quantum computer, and Popescu says the refrigerator scheme might allow researchers to cool some set of qubits with a few others. David Wineland, an experimental physicist with the U.S. National Institute of Standards and Technology in Boulder, Colorado, says he believes such schemes can indeed be implemented in trapped ions.

Others suggest that such tiny quantum refrigerators might already be humming along in nature. It’s possible that one part of a biomolecule might work to cool another in such a fashion, says Hans Briegel, a theorist at the University of Innsbruck in Austria. “I don’t expect that you will have a mechanism exactly like this,” Briegel says, “but it gives you a framework valuable for telling what to search for.”

No word yet on when physicists might unveil the smallest possible beer.

calcuim supplementaion and CVD


OBJECTIVE: To investigate whether calcium supplements increase the risk of cardiovascular events. DESIGN: Patient level and trial level meta-analyses.
DATA SOURCES: Medline, Embase, and Cochrane Central Register of Controlled Trials (1966-March 2010), reference lists of meta-analyses of calcium supplements, and two clinical trial registries. Initial searches were carried out in November 2007, with electronic database searches repeated in March 2010.
STUDY SELECTION: Eligible studies were randomised, placebo controlled trials of calcium supplements (>or=500 mg/day), with 100 or more participants of mean age more than 40 years and study duration more than one year. The lead authors of eligible trials supplied data. Cardiovascular outcomes were obtained from self reports, hospital admissions, and death certificates.
RESULTS: 15 trials were eligible for inclusion, five with patient level data (8151 participants, median follow-up 3.6 years, interquartile range 2.7-4.3 years) and 11 with trial level data (11 921 participants, mean duration 4.0 years). In the five studies contributing patient level data, 143 people allocated to calcium had a myocardial infarction compared with 111 allocated to placebo (hazard ratio 1.31, 95% confidence interval 1.02 to 1.67, P=0.035). Non-significant increases occurred in the incidence of stroke (1.20, 0.96 to 1.50, P=0.11), the composite end point of myocardial infarction, stroke, or sudden death (1.18, 1.00 to 1.39, P=0.057), and death (1.09, 0.96 to 1.23, P=0.18). The meta-analysis of trial level data showed similar results: 296 people had a myocardial infarction (166 allocated to calcium, 130 to placebo), with an increased incidence of myocardial infarction in those allocated to calcium (pooled relative risk 1.27, 95% confidence interval 1.01 to 1.59, P=0.038).
CONCLUSIONS: Calcium supplements (without coadministered vitamin D) are associated with an increased risk of myocardial infarction. As calcium supplements are widely used these modest increases in risk of cardiovascular disease might translate into a large burden of disease in the population. A reassessment of the role of calcium supplements in the management of osteoporosis is warranted.