Interesting

Virtual germ created on computer for first time. By Paul Marks

C0134775-Mycoplasma_genitalium_bacteria,_SEM.jpg

(Image: Thomas Deernick, NCMIR/Science Photo Library)

In a move that promises to bring the advantages of computer aided design (CAD) to genetic engineers, the first computer model of a complete bacterium has been produced in the US. It means researchers will soon be able to modify models of an organism’s genome on a computer screen - or create artificial lifeforms - without the risks of undertaking wet biology in secure biosafety labs.

The pathogen is called Mycoplasma genitalium, a bacterium implicated in a number of urethral and vaginal infections. The bug was ripe for modelling say researchers at Stanford University in California, because it has the smallest genome of any free-living organism, with just 525 genes. By contrast, the popular lab pathogen E. coli has 4288 genes.

The modelling was undertaken by bioengineer Markus Covert and colleagues. To get the raw data for their model, they undertook an exhaustive literature review - spanning 900 research papers - to allow them to program into their model some 1900 experimentally observed behaviours and molecular interactions that M. genitalium can take part in during its life cycle.

In software terms, they found the behaviours of the 525 genes could be described by 28 algorithms, each governing the behaviour of a software module modelling a different biological process. “These modules then communicated with each other after every time step, making for a unified whole that closely matched M. genitalium’s real-world behaviour,” claims the Stanford team in a statement. Their research appears in the journal Cell (doi: 10.1016/j.cell.2012.05.044).

Such models will ultimately give biologists the freedom to undertake “what if” scenarios common in regular engineering - changing parameters in a genome design, say, like a civil engineer adjusts the width of a bridge deck on a computer to see what happens. As well as being experimentally useful, allowing artificial organisms and synthetic lifeforms to be created virtually (harming no-one), they could also boost biosafety by preventing accidental creations of lethal pathogens. In 2001, for instance, researchers in Australia accidentally created a lethal strain of mousepox.

In a commentary article in Cell, systems biologists Peter Freddolino and Saeed Tavazoie of Columbia University say they hope the work will soon be extended to more commonly used lab bugs like E. coli - but also warn that the technique’s accuracy has yet to be demonstrated. It is unclear, they say, “how well overall behaviors will be predicted from a collection of separately obtained parameters” gleaned from hundreds of research papers.

But the US National Institutes of Health, which funded the modelling work, is excited. It believes the model a major step towards finding “new approaches for the diagnosis and treatment of disease”, says James Anderson, an NIH program director.t

Morflora bio-based generic and non-transgenic trait introduction solution

TraitUP™ is a revolutionary, fast, non-transgenic platform for trait introduction into seeds enabling immediate expression of traits in plants. This patent-pending method can easily be implemented as part of universal commercial seed treatment procedures. This pioneering technology enables seed companies and breeders for the first time to quickly provide protection against threats to crops, and at a later stage, introduce improved traits into seeds

The TraitUP™ components and the introduced gene(s) do not integrate into the plant’s genome and as of current knowledge are not heritable. Expression or silencing of genes of interest occurs within a few days in all herbaceous plants tested, including tomatoes and wheat, and in up to a month as tested in woody trees. Expression is durable and persists throughout the life span of the plant (read more in the science section).

Until today, introduction of genes to a given plant, by breeders relied on classical methods which can take up anytime between three to seven years to develop and express the desired trait in particular plant species, or by genetic engineering which is time and capital consuming.

Morflora’s TraitUP™ offers for the first time an innovative, fast and non-transgenic alternative for protecting and enhancing crops, easily by a simple seed treatment and expressed within days. Employing TraitUP™ reduces the dependency on chemical control, resulting in reduced pollution, healthier crops and increased yield.

The capability of adding desired traits into seeds for both protection and enhancement purposes, in a scaled-up commercial fashion which takes only a few days, constitutes a paradigm shift in the seed industry worldwide.

Swarm troopers: Mutant armies waging war in the wild. By Henry Nicholls

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We can now genetically modify animals to kill off their own kind, while leaving other species unharmed

Editorial: ”Give geo- and genetic engineering a fair trial”

IN THE urban jungle of Juazeiro in Brazil, an army is being unleashed. It is an army like no other: the soldiers’ mission is to copulate rather than fight. But they are harbingers of death, not love. Their children appear healthy at first but die just before they reach adulthood, struck down by the killer genes their fathers passed on to them.

These soldiers are the first of a new kind of creature - “autocidal” maniacs genetically modified to wipe out their own kind without harming other creatures. The first animals being targeted with these “living pesticides” are disease-carrying mosquitoes and crop-munching caterpillars, but the approach should work with just about any animal - from invasive fish and frogs to rats and rabbits. If it is successful, it could transform the way we think about genetically engineered animals.

In essence, much the same method has already been successfully employed for more than half a century. In the so-called “sterile male technique”, large numbers of the target pest are bred, sterilised and the males let loose. When they mate with wild females, the resulting eggs are not viable, so releasing enough sterile males can eventually exterminate wild populations.

Infographic: Compare the sterile insect and autocidal techniques

This method is widely used and has notched up many successes. For instance, it helped to eliminate the screwworm fly from the US and other areas - the fly’s larvae burrow into the flesh of livestock and even people. It also helped clear the tsetse fly from Zanzibar.

And it is not limited to insects: a similar approach is being used to try to control an invasive parasitic fish in the American Great Lakes. Male lampreys are being trapped, chemically sterilised and released.

The sterile male technique has the huge benefit of being incredibly focused, homing in only on the species you want to control. Pesticides, by contrast,harm a wide range of other species, including us.

So why isn’t the method more widely used? The main problem is that it is very difficult to sterilise animals without harming them in other ways. The usual way of sterilising insects is to zap them with radiation, for instance, which leaves the males weakened. Establishing the optimal dose of radiation for a species is thus crucial - too little and fertile insects will be released, too much and the males will be too feeble to compete for females. Working out the optimal dose is best done in the field, but the task is laborious without an easy way to distinguish sterilised insects from wild ones.

Enter Oxitec, a biotechnology company based just outside Oxford in the UK. It has created a pink bollworm - a moth caterpillar - with a built-in fluorescent marker called DsRed. The bollworm is a major pest in cotton fields, and in 2002 an eradication campaign was launched in the US, part of which includes releasing sterilised bollworms. In 2006, Oxitec’s fluorescent bollworm became the first genetically engineered animal to be deliberately released into the environment. Over three years of successful trials, more than 20 million mothshave been released in the US so far.

These modified moths are just the start. When the founder of Oxitec, Luke Alphey, first learned about the sterile insect technique from a colleague in the 1990s, he realised that the molecular tools he was using in his everyday research might provide a better alternative. Within a matter of years, he had created fruit flies with genes that kill their offspring (Science, vol 287, p 2474).

In theory, unlike zapping animals with radiation or chemosterilisation, the genetic approach should work well with just about any species. Besides the pink bollworm, Oxitec is targeting the mosquito Aedes aegypti, the single most important carrier of dengue, a viral disease that affects 50 to 100 million people in tropical regions every year, including a few in Florida andQueensland, Australia. Usually the symptoms are mild, but around 1 in 20 people become seriously ill. There is no vaccine and no treatment, so the only way to combat the disease is to kill the mosquitoes that carry it - and they are becoming resistant to pesticides.

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