Discovery in Synthetic Biology Takes Us a Step Closer to New 'Industrial Revolution'

Scientists report that they have developed a method that cuts down the time it takes to make new 'parts' for microscopic biological factories from 2 days to only 6 hours.

The scientists, from Imperial College London, say their research brings them another step closer to a new kind of industrial revolution, where parts for these biological factories could be mass-produced. These factories have a wealth of applications including better drug delivery treatments for patients, enhancements in the way that minerals are mined from deep underground and advances in the production of befouls, according to Science Daily.

Professor Paul Freemont, Co- Director of the Centre for Synthetic Biology and Innovation at Imperial College London and principle co-investigator of the study, which is published February 1 in the journal Nucleic Acids Research, says: "Before the industrial revolution most items were made by hand, which meant that they were slower to manufacture, more expensive to produce and limited in number. We are at a similar juncture in synthetic biology, having to test and build each part from scratch, which is a long and slow process. We demonstrate in our study a new method that could help to rapidly scale up the production and testing of biological parts."

Parts made up of DNA are re-engineered by scientists and put into cells to make biological factories. However, a major bottleneck in synthetic biology is the lack of parts from which to build new types of factories. To build parts using the current time-consuming method, scientists have to re-engineer DNA in a cell and observe how it works. If it functions according to their specifications, then the scientists store the part specifications in a catalogue.

Now, scientists from Imperial College London have devised a much quicker method that does away with the need for them to re-engineer a cell every time they want to make a new part. The team say their work could lead to vast new libraries of off-the-shelf components that could be used to build more sophisticated biological factories.

James Chappell, co-author of the study from the Centre for Synthetic Biology and Innovation at Imperial College London, says: "One of the major goals in synthetic biology is to find a way to industrialise our processes so that we can mass produce these biological factories much in the same way that industries such as car manufacturers mass produce vehicles in a factory line. This could unlock the potential of this field of science and enable us to develop much more sophisticated devices that could be used to improve many facets of society. Excitingly, our research takes us one step closer to this reality, providing a rapid way of developing new parts."

In the study, the Imperial researchers demonstrate for the first time that the same method can be achieved in a test tube outside of a cell. This involves extracting from cells the machinery that produces mRNA and proteins and providing the energy and building blocks to help them survive in test tubes. The team then add their re-programmed DNA to the solution and observe how it functions.

The advantage of this method is that scientists can develop litres of this cell-like environment so that multiple re-programmed DNA can be tested simultaneously, which speeds up the production process of parts.

The next stage of the research is to expand the types of parts and devices that can be developed using this method. They also are aiming to develop a method using robots to speed up and make the whole process automated.

Professor Richard Kitney, co- Director of the Centre for Synthetic Biology and Innovation at Imperial College London says: "Synthetic biology is seen by the British Government as having the potential to create new industries and jobs for the benefit of the UK economy. This work is part of a wider, major research programme within the Centre to develop technology that can be used across a range of industrial applications."

M.Wassouf

Aztec Conquest Altered Genetics Among Early Mexico Inhabitants, New DNA Study Shows

For centuries, the fate of the original Otomí inhabitants of Xaltocan, the capital of a pre-Aztec Mexican city-state, has remained unknown. Researchers have long wondered whether they assimilated with the Aztecs or abandoned the town altogether.

According to new anthropological research from The University of Texas at Austin, Wichita State University and Washington State University, the answers may lie in DNA. Following this line of evidence, the researchers theorize that some original Otomies, possibly elite rulers, may have fled the town. Their exodus may have led to the reorganization of the original residents within Xaltocan, or to the influx of new residents, who may have intermarried with the Otomí  population, according to Science Daily.

Using ancient DNA (aDNA) sampling, Jaime Mata-Míguez, an anthropology graduate student and lead author of the study, tracked the biological comings and goings of the Otomí people following the incorporation of Xaltocan into the Aztec empire. The study, published in American Journal of Physical Anthropology, is the first to provide genetic evidence for the anthropological cold case.

Learning more about changes in the size, composition, and structure of past populations helps anthropologists understand the impact of historical events, including imperial conquest, colonization, and migration, Mata-Míguez says. The case of Xaltocan is extremely valuable because it provides insight into the effects of Aztec imperialism on Mesoamerican populations.

Historical documents suggest that residents fled Xaltocan in 1395 AD, and that the Aztec ruler sent taxpayers to resettle the site in 1435 AD. Yet archaeological evidence indicates some degree of population stability across the imperial transition, deepening the mystery. Recently unearthed human remains from before and after the Aztec conquest at Xaltocan provide the rare opportunity to examine this genetic transition.

As part of the study, Mata-Míguez and his colleagues sampled mitochondrial aDNA from 25 bodies recovered from patios outside excavated houses in Xaltocan. They found that the pre-conquest maternal aDNA did not match those of the post-conquest era. These results are consistent with the idea that the Aztec conquest of Xaltocan had a significant genetic impact on the town.

Mata-Míguez suggests that long-distance trade, population movement and the reorganization of many conquered populations caused by Aztec imperialism could have caused similar genetic shifts in other regions of Mexico as well.

In focusing on mitochondrial DNA, this study only traced the history of maternal genetic lines at Xaltocan. Future aDNA analyses will be needed to clarify the extent and underlying causes of the genetic shift, but this study suggests that Aztec imperialism may have significantly altered at least some Xaltocan households.

R.Sawas

Cats killing billions of animals in the US

Cats are one of the top threats to US wildlife, killing billions of animals each year, a study suggests.

The authors estimate they are responsible for the deaths of between 1.4 and 3.7 billion birds and 6.9-20.7 billion mammals annually.

Writing in Nature Communications, the scientists said stray and feral cats were the worst offenders.

However, they added that pet cats also played a role and that owners should do more to reduce their impact.

The authors concluded that more animals are dying at the claws of cats in the United States than in road accidents, collisions with buildings or poisonings.

The domestic cat's killer instinct of has been well documented on many islands around the world.

Felines accompanying their human companions have gone on to decimate local wildlife, and they have been blamed for the global extinction of 33 species.

But their impact on mainland areas has been harder to chart.

To find out more, researchers from the Smithsonian Conservation Biology Institute (SCBI) and the US Fish and Wildlife Service carried out a review of studies that had previously looked at the predatory prowess of cats.

Their analysis revealed that the cat killings were much higher than previous studies had suggested: they found that they had killed more than four times as many birds as has been previously estimated.

Birds native to the US, such as the American Robin, were most at risk, and mice, shrews, voles, squirrels and rabbits were the mammals most likely to be killed.

Dr Pete Marra from the SCBI said: "Our study suggests that they are the top threat to US wildlife."

The team said that "un-owned" cats, which they classified as strays, feral cats and farm cats, were killing about three times as many animals as pet cats, but that their owners could do more to limit the impact.

Dr Marra said: "We hope that the large amount of wildlife mortality indicated by our research convinces some cat owners to keep their cats indoors and that it alerts policymakers, wildlife managers and scientists to the large magnitude of wildlife mortality caused by cat predation."

A spokeswoman for the UK's animal welfare charity the RSPCA said that a properly fitted collar and bell could reduce a cat's success when hunting by at least a third.

R.S

Brazil to survey Amazon rainforest

The Brazilian government has announced that it plans to undertake the huge task of recording an inventory of the trees in the Amazon rainforest.

The Forestry Ministry said the census would take four years to complete, and would provide detailed data on tree species, soils and biodiversity in the world's largest rainforest.

 The last exhaustive survey was carried out more than 30 years ago.

In that time the rainforest has become increasingly threatened by logging.

The Brazilian government made a commitment in 2009 to reduce deforestation in the Amazon by 80% by the year 2020,according to BBC.

According to the government, in 2012 the destruction of the Amazon rainforest reached its lowest level since monitoring began more than two decades ago.

But ministers said they would be able to act more effectively if they had more accurate data.

"We are going to come to know the rainforest from within," Forestry Minister Antonio Carlos Hummel said announcing the inventory.

Environment Minister Izabella Teixeira said it would help the government to formulate environmental policies.

"In international debates about climate change, for example, we will know how much forest we have and what state it is in (...), we'll discover species, and gain knowledge about species becoming extinct, as well as information about the distribution of the forest and its potential economic use", Ms Teixeira said.

Brazil's national development bank said it would contribute $33m to the project.

The last detailed survey of the Brazilian Amazon was carried out in the 1970s, and its results published in 1983.

Forestry Minister Hummel said partial results would be published yearly, as it progressed.

M.Wassouf

 

New clock revolves around an atom's mass

It’s part clock, part scale: A newly developed atomic clock measures time based on the mass of a single atom. The research, published online January 10 in Science, is controversial but could provide scientists with more precise methods of measuring both time and mass.

“This is the first clock based on a single particle,” says Holger Müller, a physicist at the University of California, Berkeley. “Its ticking rate is determined only by the particle’s mass.”

The idea for the clock stemmed from the quantum principle that particles also behave as waves, and vice versa. In particular, Müller and his colleagues wanted to determine how frequently the wave form of a single atom oscillates, a quantity that in quantum mechanics is inherently linked to the atom’s mass. Then the researchers could use those oscillations like swings of a pendulum to create a clock,according to Science News Magazine.

The snag in Müller’s plan was that it’s impossible to directly measure the oscillation frequency of waves of matter. The frequency of these waves is about 1025 hertz, 10 orders of magnitude higher than that of visible light waves. So Müller and his colleagues came up with an apparatus that creates two sets of waves — one based on a cesium atom at rest and another on the atom in motion. The researchers measured the frequency difference between the waves and then used that number, a manageable 100,000 hertz or so, to calculate the much larger oscillation frequency of cesium at rest.

With this approach, Müller was able to use the wave frequency of the cesium atom to create a clock that would gain or lose a second after eight years. That’s better than a wristwatch but about a hundred millionth as precise as today’s best atomic clocks, which count the frequency of light emissions from an atom as its electrons release small bursts of energy.

Physicists not involved with Müller’s research are impressed with his clever technique but are skeptical about its potential for precise timekeeping. “I think the paper is slightly oversold,” says Vladan Vuletić, a quantum physicist at MIT.

Other researchers have a more conceptual objection: Because there is nothing at this frequency actually oscillating within the atom, they say it is not a clock at all. “It may be a clock numerically, but it’s not a physical clock,” says Christian Bordé, a physicist at the Paris Observatory. Müller counters that the clock’s simplicity is its greatest trait: He is measuring an intrinsic quantum property of an atom, one that depends only on the atom’s mass.

In fact, this relationship between frequency and mass means Müller’s technique may prove most useful as a scale for measuring mass. Scientists define the kilogram, the base unit of mass, with a lump of metal stored in a French vault — a lump that is likely gaining heft from contamination (SN: 11/20/10, p. 12). The international General Conference on Weights and Measures, led by Bordé, wants to replace this artifact with a kilogram standard based on fundamental physical constants.

Müller says he can do just that by measuring the frequency of matter waves to accurately determine an atom’s mass. Once he finds the mass of one atom, he says, it is straightforward to relate it to the masses of other atoms. He will have a lot of convincing to do, but Müller plans to let the scientific process play out to test his ideas. “This is a concept that physicists never thought about,” he says. “This frequency wasn’t measurable until now."

M.W