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Friday, January 25, 2008

Scientist Making Artificial DNA

Now researchers are poised to cross a dramatic barrier: the creation of life forms driven by completely artificial DNA.

Scientists in Maryland have already built the world's first entirely handcrafted chromosome -- a large looping strand of DNA made from scratch in a laboratory, containing all the instructions a microbe needs to live and reproduce.

In the coming year, they hope to transplant it into a cell, where it is expected to "boot itself up," like software downloaded from the Internet, and cajole the waiting cell to do its bidding. And while the first synthetic chromosome is a plagiarized version of a natural one, others that code for life forms that have never existed before are already under construction.

Craig Venter, the iconoclast scientist who led part of the giant project to read the human genome, has not stopped there. Since the mid-1990s he's been on a quest to create nothing less than artificial life.

That's right, synthetic life--and today Venter and his team announce a major advance. They report, in the journal Science, that they have synthesized the genome -- the complete DNA -- of a bacterium called Mycoplasma genitalium.

"We consider this the second in significant steps of a three-step process in our attempts to make the first synthetic organism," Venter said this morning in a telephone briefing from Davos, Switzerland, where he's attending the World Economic Forum.

They picked the bacterium because it's relatively simple; while the DNA in human cells has three billion "base pairs" -- rungs, if you will, on that familiar spiral ladder you so often see -- M. genitalium has fewer than 600,000.

Venter talks of creating synthetic organisms that create energy to take the place of fossil fuels, or thrive by consuming toxic chemicals to allow easier cleanup. Perhaps, he says, some can be created that consume large amounts of carbon dioxide, helping to stave off climate change.

But, obviously, if he succeeds, Venter will raise all sorts of moral and ethical questions. He knows that, and, when he began, assembled a panel of bioethicists and others to consider the implications.

I spoke to Glenn McGee, who edits the American Journal of Bioethics, and was on the panel, and he urges caution. Will this project face the same political backlash as cloning? What if a bunch of people "with a bit of knowhow and a lot of anger" decided to create, say, synthetic anthrax?

Finally, he asks, isn't this playing God, with all that implies? Heavy stuff.

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scientists all over the world observed with surprise and awe a rare change in the atmosphere of Jupiter.

Mystery Of Jupiter's Jets Uncovered
At the end of March 2007, scientists all over the world observed with surprise and awe a rare change in the atmosphere of Jupiter. A giant perturbation occurred amongst its clouds and two extremely bright storms erupted in the middle latitudes of the northern hemisphere, where its most intense jet stream - reaching speeds of 600 kilometers per hour - resides. Research into these unusual storms (previous ones had been seen in 1975 and 1990) and the reaction of the jet to them, undertaken by an international team coordinated by Agustín Sánchez-Lavega, from the Higher Technical School of Engineering of the University of the Basque Country (UPV/EHU), gives a more precise idea about the origin of these current flows and likewise can help to gain a better understanding of terrestrial meteorology.

The team, made up of scientists from the UPV/EHU, researchers from the Fundación Observatorio Esteve Durán in Barcelona and from several North American centres: NASA, the Jet Propulsion Laboratory, the Universities of Berkeley and Arizona, as well as the University of Oxford in the United Kingdom, amongst others, monitored the event with a spatial and temporal resolution without precedent. On the one hand, they used the Hubble Space Telescope (HST) and, on the other, the NASA telescope at the mountain tops of Hawaii and the telescopes in the Canary Islands, due to the infra-red light of which, the highest clouds and temperature changes can be observed.

Moreover, also decisive was the help of a whole battery of smaller telescopes located around the Earth's southern hemisphere, from where planet Jupiter can currently be seen in better conditions. Fortunately, the beginning of the storm was observed by the HST as a backup of the observations that the New Horizons spaceship undertook in its overflight on its way to far off Pluto. They observed how the storm grew quickly from 400 km to 2,000 km in less than 24 hours, explained Mr Sánchez-Lavega.

According to the study, the very bright storms are formed amongst the deepest clouds of water on the planet, rising vigorously and injecting a mixture of ice ammonia and water up to 30 km above the visible clouds. The storms move with the maximum velocity of the jet, - more than 600 kilometers per hour, creating disturbances and generating a stele of turbulence of reddish clouds that circle the whole planet. The infrared images show the brilliant festoons that make up the storms abandoning the jet stream to leeward.

Surprisingly, and despite the enormous amount of energy deposited by the storms and the mixture and whirlwinds generated thereby, the jet stream stayed practically still during all this perturbation and, when it was over, this stayed robust, despite the event suffered. The computer models simulating the progress of the phenomenon suggested that the jet stream goes deep into Jupiter's atmosphere, to more than 100 km below the visible cloud level and where solar energy cannot reach.

This confirms the results previously obtained by the Galileo probe when it penetrated Jupiter's atmosphere in December 1995. Although the regions studied are meteorologically different, everything points to Jupiter's jet streams going very deep and suggests that the internal energy source plays an important role in its generation, states Mr Sánchez-Lavega.

The comparison of the currently observed phenomenon with the previous cases of 1975 and 1990 show surprising similarities and coincidence, although without an explanation for the time being. The three eruptions have had a periodicity of between 15 to 17 years, strange for Jupiter as they do not bear any obvious relationship with the known natural periods of this planet. The storms arose at the peak of the jet, where the velocity is maximum, not to the North or to the South and there have always been two storms (not one or more or one less) and, finally, in all cases they move at the same speed. If, at some time in the future, we are able to crack this riddle, we will know the mysteries that lie beneath Jupiter's clouds, comments Mr Sánchez-Lavega.

The atmosphere of the giant gaseous planet of Jupiter, ten times the size of the Earth and where the day lasts only 10 hours, is in a permanent state of agitation. Atmospheric circulation is dominated by a system of jet streams, alternating in latitude and that distribute their clouds in bright and dark rings parallel to its equator - all these phenomena being unexplained. The changes in the cloud rings are sometimes violent ones circling the planet. Their origin and that of the energy source generating them as well as the jet streams are all matter for controversy amongst meteorologists and planet scientists. They might be generated by the deposition of solar radiation as on Earth or by the intense internal energy source emanating from Jupiter's interior or perhaps by a combination of both.

Knowing the mechanisms that operate in these phenomena is important for terrestrial meteorology - which is home to many storms and where jet streams also dominate atmospheric circulation. In this manner Jupiter represents a natural laboratory where scientists can study the nature of and the interrelation between jet streams, storms and violent atmospheric phenomena

The work, entitled "Depth of a strong Jovian jet from a planetary-scale disturbance driven by storms', is the cover of the 24 of January issue of the journal Nature.


Jupiter is the fifth planet from the Sun and is the largest one in the solar system. If Jupiter were hollow, more than one thousand Earths could fit inside. It also contains more matter than all of the other planets combined. It has a mass of 1.9 x 1027 kg and is 142,800 kilometers (88,736 miles) across the equator. Jupiter possesses 28 known satellites, four of which - Callisto, Europa, Ganymede and Io - were observed by Galileo as long ago as 1610. Another 12 satellites have been recently discovered and given provisional designators until they are officially confirmed and named. There is a ring system, but it is very faint and is totally invisible from the Earth. (The rings were discovered in 1979 by Voyager 1.) The atmosphere is very deep, perhaps comprising the whole planet, and is somewhat like the Sun. It is composed mainly of hydrogen and helium, with small amounts of methane, ammonia, water vapor and other compounds. At great depths within Jupiter, the pressure is so great that the hydrogen atoms are broken up and the electrons are freed so that the resulting atoms consist of bare protons. This produces a state in which the hydrogen becomes metallic.
Colorful latitudinal bands, atmospheric clouds and storms illustrate Jupiter's dynamic weather systems. The cloud patterns change within hours or days. The Great Red Spot is a complex storm moving in a counter-clockwise direction. At the outer edge, material appears to rotate in four to six days; near the center, motions are small and nearly random in direction. An array of other smaller storms and eddies can be found through out the banded clouds.

Auroral emissions, similar to Earth's northern lights, were observed in the polar regions of Jupiter. The auroral emissions appear to be related to material from Io that spirals along magnetic field lines to fall into Jupiter's atmosphere. Cloud-top lightning bolts, similar to superbolts in Earth's high atmosphere, were also observed.

Jupiter's Ring
Unlike Saturn's intricate and complex ring patterns, Jupiter has a simple ring system that is composed of an inner halo, a main ring and a Gossamer ring. To the Voyager spacecraft, the Gossamer ring appeared to be a single ring, but Galileo imagery provided the unexpected discovery that Gossamer is really two rings. One ring is embedded within the other. The rings are very tenuous and are composed of dust particles kicked up as interplanetary meteoroids smash into Jupiter's four small inner moons Metis, Adrastea, Thebe, and Amalthea. Many of the particles are microscopic in size.

The innermost halo ring is toroidal in shape and extends radially from about 92,000 kilometers (57,000 miles) to about 122,500 kilometers (76,000 miles) from Jupiter's center. It is formed as fine particles of dust from the main ring's inner boundary 'bloom' outward as they fall toward the planet. The main and brightest ring extends from the halo boundary out to about 128,940 kilometers (80,000 miles) or just inside the orbit of Adrastea. Close to the orbit of Metis, the main ring's brightness decreases.

The two faint Gossamer rings are fairly uniform in nature. The innermost Amalthea Gossamer ring extends from the orbit of Adrastea out to the orbit of Amalthea at 181,000 kilometers (112,000 miles) from Jupiter's center. The fainter Thebe Gossamer ring extends from Amalthea's orbit out to about Thebe's orbit at 221,000 kilometers (136,000 miles).

Jupiter's rings and moons exist within an intense radiation belt of electrons and ions trapped in the planet's magnetic field. These particles and fields comprise the jovian magnetosphere or magnetic environment, which extends 3 to 7 million kilometers (1.9 to 4.3 million miles) toward the Sun, and stretches in a windsock shape at least as far as Saturn's orbit - a distance of 750 million kilometers (466 million miles). : , , , ,
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carbon nanotubes to diagnose and treat brain tumors

Benham Badie, M.D., director of the Department of Neurosurgery and the Brain Tumor program at City of Hope, performs a minimally invasive procedure to surgically remove a pituitary tumor. Nanotube technology may help in the development of new treatments that would require only minimally invasive procedures no matter the location of the brain tumor.

Nanotubes Help Advance Brain Tumor Research

The potential of carbon nanotubes to diagnose and treat brain tumors is being explored through a partnership between NASA's Jet Propulsion Laboratory, Pasadena, Calif., and City of Hope, a leading cancer research and treatment center in Duarte, Calif.

Nanotechnology may help revolutionize medicine in the future with its promise to play a role in selective cancer therapy. City of Hope researchers hope to boost the brain's own immune response against tumors by delivering cancer-fighting agents via nanotubes. A nanotube is about 50,000 times narrower than a human hair, but it length can extend up to several centimeters.

If nanotube technology can be effectively applied to brain tumors, it might also be used to treat stroke, trauma, neurodegenerative disorders and other disease processes in the brain, said Dr. Behnam Badie, City of Hope's director of neurosurgery and of its brain tumor program.

"I'm very optimistic of how this nanotechnology will work out," he said. "We are hoping to begin testing in humans in about five years, and we have ideas about where to go next."

The Nano and Micro Systems Group at JPL, which has been researching nanotubes since about 2000, creates these tiny, cylindrical multi-walled carbon tubes for City of Hope.

City of Hope researchers, who began their quest in 2006, found good results: The nanotubes, which they used on mice, were non-toxic in brain cells, did not change cell reproduction and were capable of carrying DNA and siRNA, two types of molecules that encode genetic information.

JPL's Nano and Micro Systems Group grows the nanotubes on silicon strips a few square millimeters in area. The growth process forms them into hollow tubes as if by rolling sheets of graphite-like carbon.

Carbon nanotubes are extremely strong, flexible, heat-resistant, and have very sharp tips. Consequently, JPL uses nanotubes as field-emission cathodes -- vehicles that help produce electrons -- for various space applications such as x-ray and mass spectroscopy instruments, vacuum microelectronics and high-frequency communications.

"Nanotubes are important for miniaturizing spectroscopic instruments for space applications, developing extreme environment electronics, as well as for remote sensing," said Harish Manohara, the technical group supervisor for JPL's Nano and Micro Systems Group.

Nanotubes are a fairly new innovation, so they are not yet routinely used in current NASA missions, he added. However, they may be used in gas-analysis or mineralogical instruments for future missions to Mars, Venus and the Jupiter system.

JPL's collaboration with City of Hope began last year, after Manohara, Badie and Dr. Babak Kateb, City of Hope's former director of research and development in the brain tumor program, discussed using nanostructures to better diagnose and treat brain cancer. Badie said his team's nanomedical research continues, and the next goal will be to functionalize and attach inhibitory RNA to the nanotubes and deliver it to specific areas of the brain.

The JPL and City of Hope teams published the results of the study earlier this year in the journal NeuroImage.

Badie says that JPL's contribution to City of Hope's nanomedicine research has been invaluable.

"The fact that we can get pristine and really clean nanotubes from Manohara's department is unique," he said. "The fact that we are both collaborating for biological purposes is also really unique."

The collaboration between JPL and City of Hope is conducted under NASA's Innovative Partnership Program, designed to bring benefits of the space program to the public.


Carbon nanotube
Carbon nanotubes (CNTs) are allotropes of carbon. A single-walled carbon nanotube (SWNT) is a one-atom thick sheet of graphite (called graphene) rolled up into a seamless cylinder with diameter on the order of a nanometer. This results in a nanostructure where the length-to-diameter ratio exceeds 1,000,000. Such cylindrical carbon molecules have novel properties that make them potentially useful in many applications in nanotechnology, electronics, optics and other fields of materials science. They exhibit extraordinary strength and unique electrical properties, and are efficient conductors of heat. Inorganic nanotubes have also been synthesized.

Nanotubes are members of the fullerene structural family, which also includes buckyballs. Whereas buckyballs are spherical in shape, a nanotube is cylindrical, with at least one end typically capped with a hemisphere of the buckyball structure. Their name is derived from their size, since the diameter of a nanotube is in the order of a few nanometers (approximately 1/50,000th of the width of a human hair), while they can be up to several millimeters in length. Nanotubes are categorized as single-walled nanotubes (SWNTs) and multi-walled nanotubes (MWNTs).

The nature of the bonding of a nanotube is described by applied quantum chemistry, specifically, orbital hybridization. The chemical bonding of nanotubes are composed entirely of sp2 bonds, similar to those of graphite. This bonding structure, which is stronger than the sp3 bonds found in diamond, provides the molecules with their unique strength. Nanotubes naturally align themselves into "ropes" held together by Van der Waals forces. Under high pressure, nanotubes can merge together, trading some sp² bonds for sp³ bonds, giving great possibility for producing strong, unlimited-length wires through high-pressure nanotube linking

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79 percent quarterly leap -Xbox key to strong quarter for Microsoft
(24hoursnews) Jan. 24 Microsoft Corp. Thursday reported a 79 percent jump in quarterly net income from a year ago after figuring deferred sales of Windows Vista and Office.Quarterly revenue by the world's largest software company jumped 30 percent amid a surge in sales for the Windows operating system and holiday sales of the Xbox 360 videogame console, the Wall Street Journal said.Microsoft shares climbed 4.4 percent in after-hours trading to $34.70 after rising 4.1 percent in regular trading Thursday.The company reported net income of $4.71 billion, or 50 cents a share, for the quarter ended Dec. 31, compared with $2.63 billion, or 26 cents a share, a year earlier.


Microsoft Corp.'s X-factor is the Xbox 360.
The software giant rode strong sales of its video game console over the holiday season and growing demand for the Windows Vista operating system to record quarterly results, bucking the recent trend of disappointing forecasts by U.S.-based technology companies such as Intel Corp. and Apple Inc.
On Thursday, Microsoft announced it was raising its forecast for fiscal 2008, and the company's upbeat outlook should ease concerns of slower consumer technology spending in a weakening U.S. economy.
“Results for the quarter were outstanding,” Microsoft chief financial officer Chris Liddell said.

Microsoft forecasted earnings per share of $1.85 (U.S.) to $1.88 for the year ending June 30, topping Wall Street expectations of between $1.78 and $1.81. The Redmond, Wash.-based company said revenue is expected to be in the range of $59.9-billion to $60.5-billion and operating income of $24.2-billion to $24.4-billion.
Investors on Wall Street drove shares of the world's largest software company up more than 5 per cent on the Nasdaq Stock Market in after-hours trading yesterday, after hearing the news that Microsoft's forecasts followed the lead of other technology firms with international reach, such as IBM Corp. With 60 per cent of sales now coming from outside the United States, Mr. Liddell said Microsoft expects to weather any storms caused by U.S. economic woes.
PC sales were better than Microsoft had expected for the quarter, which helped to push sales of the company's software, specifically Windows Vista and Office. Client division sales – which includes Vista – rose 67 per cent to $4.34-billion for the quarter, while sales in the business division – which oversees Office software – jumped 37 per cent. More than 100 million licences have been sold for Windows Vista so far.
For the second consecutive quarter, Microsoft's entertainment and devices division finished in the black, after holiday shoppers snapped up Xbox 360 consoles at a record pace. Microsoft has said the division, which oversees the company's Xbox, Zune music player and Windows Mobile brands, is expected to turn an annual profit for the first time this fiscal year.
So far, things are on track, with division revenue rising 25 per cent over the same period last year to $4.9-billion, and topping $524-million in profit in the first six months of the financial year.
More than 17.7 million Xbox 360 consoles were sold worldwide by the end of 2007. In Canada, the Xbox 360 outsold both Sony's Playstation 3 and Nintendo's Wii in December, the first time the console has beaten both its rivals since September when the wildly popular game Halo 3 shattered records upon its release.
However, the Wii outsold Microsoft's console 567,200 to 385,200 for the year, and is catching up in overall sales despite the Xbox 360's 12-month head start in this current generation battle of the console wars.
In addition to strong console sales, the division also had four video game titles which sold more than one million copies, signed its 10-millionth Xbox Live member six months ahead of schedule and watched the number of songs downloaded from the Zune Marketplace double over the same period last year.
For the quarter ending Dec. 31, Microsoft reported profit of $4.71-billion or 50 cents, compared with $2.63-billion or 26 cents in the year-earlier period. Revenue rose 31 per cent to $16.37-billion from $12.54-billion.

Bacterial Chromosome Take Step Toward Synthetic Life

(24hoursnews)From scratch an entire microbial chromosome, a loop of synthetic DNA carrying all the instructions that a simple cell needs to live and reproduce.
The feat marks the first time that anyone has made such a large strand of hereditary material from off-the-shelf chemical ingredients. Previous efforts had yielded DNA strands less than one-twentieth the size, and those pieces lacked many of the key biological programs that tell a cell how to stay alive.
On the basis of earlier experiments, the researchers believe the new, full-length loop would spontaneously "boot up" inside a cell, just as a downloaded operating system can awaken a computer -- a potentially historic event that would amount to the creation of the first truly artificial life form. Taking a significant step toward the creation of synthetic forms of life,
researchers reported Thursday that they had manufactured the entire genome of a bacterium by stitching together its chemical components.
Scientists had previously constructed the complete DNA of viruses, but this is the first time it has been done for bacteria, which are far more complex. The genome is more than 10 times as long as the longest piece of DNA ever synthesized.
The feat is a watershed for the emerging field called synthetic biology, which involves the design of organisms to perform particular tasks, like making biofuels. Synthetic biologists envision being able to design an organism on a computer, press the “print” button to have the necessary DNA made and then put that DNA into a cell to produce a custom-made creature.
“What we are doing with the synthetic chromosome is going to be the design process of the future,” said J. Craig Venter, the boundary-pushing gene scientist.
Dr. Venter assembled the team that made the bacterial genome as part of his well-publicized quest to create the first synthetic organism. The work was published online Thursday by the journal Science.
But there are concerns that synthetic biology could be used to make pathogens, or that errors by well-intended scientists could produce organisms that run amok. The genome of the smallpox virus can in theory now be synthesized using the techniques reported on Thursday since it is only about one-third the size of the genome manufactured by Dr. Venter’s group.
In any case, there are many hurdles to overcome before Dr. Venter’s vision of “life by design” is realized. The synthetic genome made by Dr. Venter’s team was not designed from scratch, but rather was a copy, with only a few changes, of the genetic sequence of a natural bacterium called Mycoplasma genitalium.
Moreover, Dr. Venter’s team, led by a Nobel laureate, Hamilton O. Smith, has yet to accomplish the next — and biggest — step. That would be to insert the synthetic chromosome into a living microbe and have it “boot up” and take control of the organism’s functions.
If that happened, it would be considered by some to be the creation of the first synthetic organism. The failure to achieve that tempered the reaction of some outside scientists to the announced achievement.
“Right now, all they’ve done is shown they can buy a bunch of DNA and put it together,” said George M. Church, a professor of genetics at Harvard Medical School.
Dr. Venter’s team last year reported successfully doing such a chromosome transplant, but it was with the natural genome of one type of Mycoplasma transplanted into another species of that bacterium.
Dr. Venter said in a telephone news conference Thursday that each pair of donor genome and recipient cell presented unique problems. The scientists also think they interrupted the functioning of one crucial gene, a correctable problem.
“It’s not a slam dunk or we would be announcing it today,” Dr. Venter told reporters. Still, he said, “I will be equally surprised and disappointed if we can’t do it in 2008.”
The bacterial genome that was synthesized consisted of 582,970 base pairs, the chemical units of the genetic code represented by the letters A, C, G and T. The longest stretch of synthetic DNA reported in a scientific paper was about 32,000 bases long, though some companies say they have made ones with about 50,000.
The machines that string bases together make many errors, so it is impractical to make a string of more than 50 to 100 bases at once. But some companies — the foundries of the biotechnology era — now make genes thousands of bases long by splicing the shorter strings.
The Venter team ordered 101 such sequences, each 5,000 to 7,000 bases long, from these companies. It then joined them into ever-bigger pieces. Finally, four big pieces were put into yeast, which hooked them together using a natural gene repair mechanism.
The process was started in late 2002, Dr. Venter said, and cost millions of dollars. That led some scientists to question why someone would want to synthesize an entire organism when existing organisms can be modified through genetic engineering.
“To some extent, it’s something that was driven by ‘I want to be the first person to do it,’ ” surmised Jeremy Minshull, chief executive of DNA 2.0, a company that supplied some of the DNA stretches to the Venter team.
Dr. Minshull said that scientists did not yet know enough about how living things work to design an entire genome. “Our synthetic capability way outpaces our understanding of what we want to do,” he said.
For now, that is the case, Dr. Venter concedes. He runs a company, Synthetic Genomics, that is using genetic engineering to produce biofuels. But he and other scientists say that DNA synthesis is following the path of computer chips, with capability rising rapidly and costs — now about $1 per base — falling swiftly. At some point, they say, it will become faster and cheaper for scientists to synthesize an organism from scratch rather than cut and paste genes from one organism to another.
The ability to synthesize genomes would allow for more scientific experimentation. Dr. Venter said he would now be able to create organisms missing dozens of genes to answer the initial question that inspired the research in 1995: What is the minimum set of genes needed for life?
Dr. Venter, who runs the nonprofit J. Craig Venter Institute in Rockville, Md., is most known for sequencing the human genome in a race with the publicly financed Human Genome Project.
Some activist groups say that Dr. Venter is going too far, too fast, this time, and that synthetic biology needs outside regulation to prevent the introduction of dangerous organisms, created by evil intent or by innocent error.
“The fact that he’s pushing ahead with this without any societal oversight is very worrying,” said Jim Thomas, a program manager at the ETC Group, a technology watchdog group based in Canada. He also said it was worrisome that Dr. Venter was applying for very broad patents in synthetic biology.
Dr. Venter said that the field had discussed ethics and safety since it started and that his work had been reviewed by ethicists.
In the new genome, he said, one gene was changed to make any resulting organism noninfective. (Mycoplasma genitalium, which can be transmitted sexually, is associated with inflammation.)
The team also added some DNA segments to serve as “watermarks,” allowing scientists to distinguish the synthetic genome from the natural one.
These watermarks, Dr. Venter noted, contain coded messages. Sleuths would have to determine the amino acid sequence coded for by the watermarks to decipher the message.
“It’s a fun thing that has a practical application,” he said.

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