PlantBricks

The iGEM team that I helped advise a couple years ago recently published a short paper about their project in the Journal of Biological Engineering (open access!). We were inspired to think about plant engineering in the context of iGEM and standardized genetic parts, in part thanks to an interesting passage in Stewart Brand?s book Whole Earth Discipline. In his chapter on genetic engineering, Brand writes:

One can imagine organic crops biotically engineered as Rachel Carson might do it. They would be designed in detail to protect and improve the soil they grow in, to foil the specific pets and weeds that threaten them, to blend well with other organic crops and with beneficial insects, to increase carbon fixation in the soil and reduce the release of methane and nitrous oxide, to be as nutritious and delicious as science can make them, and to invite further refinement by the growers.

Along with genetic BioBricks, let there be AgriBricks to finesse crop genomes for local ecological and economic fitness. (If Monsanto throws a fit, tell them that if they?re polite, you might license back to them the locally attuned tweaks you?ve made to their patented gene array. Pretty soon they?or some company that replaces them?will be providing you with lab equipment.)

Our project and the final paper were obviously of much much smaller scope, but we hope that other iGEM teams will be inspired to work with plants and to use our BioBricks to build something great. Here?s the abstract:

Background
Plant biotechnology can be leveraged to produce food, fuel, medicine, and materials. Standardized methods advocated by the synthetic biology community can accelerate the plant design cycle, ultimately making plant engineering more widely accessible to bioengineers who can contribute diverse creative input to the design process.

Results
This paper presents work done largely by undergraduate students participating in the 2010 International Genetically Engineered Machines (iGEM) competition. Described here is a framework for engineering the model plant Arabidopsis thaliana with standardized, BioBrick compatible vectors and parts available through the Registry of Standard Biological Parts (www.partsregistry.org). This system was used to engineer a proof-of-concept plant that exogenously expresses the taste-inverting protein miraculin.

Conclusions
Our work is intended to encourage future iGEM teams and other synthetic biologists to use plants as a genetic chassis. Our workflow simplifies the use of standardized parts in plant systems, allowing the construction and expression of heterologous genes in plants within the timeframe allotted for typical iGEM projects.

And you can download the paper (currently only a ?provisional PDF?) from the Journal:

• Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, DeWerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, and Silver PA. ?A BioBrick Compatible Strategy for Genetic Modification of Plants.? Journal of Biological Engineering, 2012, 6:8.

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Stockton, California's ratings fall ahead of bankruptcy

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Publishing flu research in context is better, UGA expert says

Tripp, associate director of the Influenza Pathogenesis and Immunology Research Center at the University of Georgia and Emory University, was one of the researchers into transmission of the H5N1 virus who agreed to a ?voluntary pause? on that work until the claims could be sorted out and the work presented in proper context.

?Everyone agreed to take a pause on the research until we had an understanding of what we really wanted to go out to the audience,? he said. ?At the end of the day, all of our research comes from funding made by the public. We need to properly educate them on why it is important to do this ? and what happens if we stop doing research like this.?

Public dissemination about work into flu transmission is important to advance scientific understanding, Tripp said.

?The features that contribute to transmission are poorly understood because of the fact that there?s not enough publication of the material,? he said.

In the current paper, for instance, four of the mutations that conferred greater transmission between ferrets were in the hemagglutinin gene, where it changed the preference from avian-like cells to cell receptors found in ferrets and humans.

?There?s a lot of thinking that that is sort of the barrier for (infecting a certain species),? Tripp said. ?This is what keeps those viruses from jumping.?

But even with these changes, it is still important to keep the relative risk in context, he said.

?The ability to do reverse genetics and actually make a virus that can be transmitted and replicate in man is unbelievably hard,? Tripp said. ?Nature has been trying to essentially do that for a long time with the H5N1s, and we still don?t have anything.?

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Greek coalition talks to enter 2nd day

Head of Greece's radical left-wing Syriza party Alexis Tsipras waves to his supporters in Athens, late Sunday, June 17, 2012. Alexis Tsipras and his party shot to prominence in the May 6 vote, where he came a surprise second and quadrupled his support since the 2009 election. Syriza party has vowed to rip up Greece's bailout agreements and repeal the austerity measures, which have included deep spending cuts on everything from health care to education and infrastructure, as well as tax hikes and reductions of salaries and pensions. (AP Photo/Petros Karadjias)

Head of Greece's radical left-wing Syriza party Alexis Tsipras waves to his supporters in Athens, late Sunday, June 17, 2012. Alexis Tsipras and his party shot to prominence in the May 6 vote, where he came a surprise second and quadrupled his support since the 2009 election. Syriza party has vowed to rip up Greece's bailout agreements and repeal the austerity measures, which have included deep spending cuts on everything from health care to education and infrastructure, as well as tax hikes and reductions of salaries and pensions. (AP Photo/Petros Karadjias)

Leader of the New Democracy conservative party Antonis Samaras, center, speaks during a press conference in Athens, Sunday, June 17, 2012. The pro-bailout New Democracy party came in first Sunday in Greece's national election, and its leader has proposed forming a pro-euro coalition government.(AP Photo/Petros Giannakouris)

Leader of the New Democracy conservative party Antonis Samaras, speaks to supporters at an election kiosk at Syntagma square in Athens, Sunday, June 17, 2012. The pro-bailout New Democracy party came in first Sunday in Greece's national election, and its leader has proposed forming a pro-euro coalition government.(AP Photo/Kostas Tsironis)

Supporters of the far right party of Golden Dawn celebrate the results of the elections outside their headquarters office in Thessaloniki, Greece Sunday, June 17, 2012. Official projections showed the Golden Dawn party returning to the 300-member parliament with 18 seats, just three fewer than it had won in an inconclusive election on May 6, when no party won enough votes to form a government amid a deep financial crisis that threatens Greece's place in the Eurozone and could hurt the global economy. The pro-bailout New Democracy party came in first Sunday in Greece's national election, and its leader has proposed forming a pro-euro coalition government. (AP Photo/Dimitri Messinis)

Leader of the New Democracy conservative party Antonis Samaras leaves an elections kiosk after speaking to his supporters at Syntagma square in Athens, Sunday, June 17, 2012. The pro-bailout New Democracy party came in first Sunday in Greece's national election, and its leader has proposed forming a pro-euro coalition government. (AP Photo/Petros Karadjias)

ATHENS, Greece (AP) ? Negotiations to form a government in crisis-struck Greece look set to enter a second day, after the head of the country's socialist party insisted on a broad coalition and said negotiations must wrap up by the end of Tuesday.

Monday's political wrangling came a day after the second national election in six weeks again left no party with enough votes to form a government on its own. The conservative New Democracy party won Sunday's ballot, but without enough votes to form a government on its own.

The socialist PASOK came third. Both have said they will stick to Greece's international bailout commitments, although they want to renegotiate some of the harsh austerity terms taken in return for the international rescue loans.

Sunday's results eased concern that Greece faced an imminent exit from Europe's joint currency. A Greek exit from the 17-nation eurozone would have potentially catastrophic consequences for other ailing European nations and hurt the United States and the entire global economy.

PASOK head Evangelos Venizelos, a former finance minister, finished in the election behind the radical left-wing anti-bailout Syriza party. But his 33 seats in the 300-member Parliament mean he could form a government with New Democracy, which gained 129 seats.

Syriza has refused to join the other two parties in a government, saying it will not cooperate with any group that insists on implementing the harsh austerity measures taken in return for Greece's two international bailout agreements.

Venizelos, however, insisted on a broad coalition.

"The most crucial thing for us right now is to achieve the greatest possible range of consensus, and this must happen by tomorrow night at the latest," he said after meeting with New Democracy head Antonis Samaras, who as election winner has the first go at trying to form a government.

Venizelos criticized Syriza chief Alexis Tsipras for his refusal to join in governing Greece, which has been wracked by a financial crisis that has left it dependent on international loans since May 2010.

"You can't have some people choosing the easy position of being in opposition and lying in wait for the government to fail ? or rather trying to create the conditions for the government, that is the country, to fail," Venizelos said.

On the streets of Athens, the mood was mixed, with many saying party leaders must get their act together.

"The election result isn't strong enough to put people's minds at ease," said sandwich shop owner Mary Moutafidis, 57. "They still have to agree to form a government."

Associated Press

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Tropical Lakes on Saturn Moon Could Expand Options for Life

News | Space

A subsurface source of liquid methane may be replenishing equatorial lakes on Titan, which might be a crucible for life

By Maggie McKee and Nature magazine ?| June 14, 2012?|

Saturn's moon Titan (orange, in background) seems to have lakes of methane near the equator, as well as at the poles. Image: NASA/JPL/Space Science Institute

From Nature magazine

Nestling among the dunes in the dry equatorial region of Saturn's moon Titan is what appears to be a hydrocarbon lake. The observation, by the Cassini spacecraft, suggests that oases of liquid methane ? which might be a crucible for life ? lie beneath the moon's surface. The work is published today in Nature.

Besides Earth, Titan is the only solid object in the Solar System to circulate liquids in a cycle of rain and evaporation, although on Titan the process is driven by methane rather than water.

This cycle is expected to form liquid bodies near the moon's poles, but not at its dune-covered equator, where Cassini measurements show that humidity levels are low and little rain falls to the surface. "The equatorial belt is like a desert on Earth, where evaporation trumps precipitation," says astrobiologist Jonathan Lunine of Cornell University in Ithaca, New York.

Any surface liquid there should evaporate and be transported to the cooler poles, where it should condense as rain. "Lakes at the poles are easy to explain, but lakes in the tropics are not," says Caitlin Griffith, a planetary scientist at the University of Arizona in Tucson. Indeed, Cassini has spotted hundreds of lakes and three seas in Titan's polar regions.

Now Griffith and her colleagues think they have found a tropical lake ? some 60 kilometres long and 40 kilometres wide, and at least 1 metre deep ? in Cassini observations made between 2004 and 2008. It appears as a black splotch at seven near-infrared wavelengths that can travel relatively unimpeded through the moon's thick atmosphere, which blocks visible light.

Caverns measureless to man
The team also found four smaller, brighter splotches, which Griffith says may be "shallower ponds similar to marshes on Earth, with knee-to-ankle-level depths". Because tropical lakes on Titan should evaporate over a period of just a few thousand years, the researchers argue that these ponds and lakes are being replenished by subsurface oases of liquid methane.

That would expand the number of places on the moon where life could potentially originate. Methane, which is made up of one carbon and four hydrogen atoms, is the source of more complicated organic molecules found on Titan. "There may be organic chemical processes that occur in liquid hydrocarbons that could lead to compounds analogous to proteins and information-carrying molecules," says Lunine, who was not involved in the work. "There might be a kind of life that works in liquid hydrocarbons."

Lunine and Griffith are members of a proposed NASA mission to look for such complex chemistry, called the Titan Mare Explorer (TiME). The TiME probe would spend three months bobbing around Ligeia Mare, a sea near Titan's north polar region, measuring its chemistry with a mass spectrometer.

But should that mission, the fate of which will soon be decided by NASA, land on a tropical lake instead? No, says Lunine. He points out that a number of lines of evidence ? including telltale radar signatures ? show that the polar regions are filled with liquid hydrocarbon lakes and seas. So far there is less evidence for the tropical features. "Something else that just happens to be dark at those wavelengths", such as a solid organic compound, might mimic a lake, he says.

Only 17% of the equatorial region's surface area has been analysed at the high resolutions required to spot these small features, but Lunine says that lower-resolution observations suggest tropical lakes are relatively few and far between. Still, the idea of oases on Titan appeals to him. "There's a place on Titan named Xanadu, and if you go back to the Coleridge poem on Xanadu, he talks about 'caverns measureless to man',? Lunine says. He adds that he would love to find such caverns filled with methane on Titan.

This article is reproduced with permission from the magazine Nature. The article was first published on June 14, 2012.

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Former Yemen president hospitalized

SANAA, Yemen (AP) ? The party of Yemen's former president says the 69-year old Ali Abdullah Saleh has been admitted to a hospital for regular checkups and minor procedures.

The Sunday statement by the General People's Congress didn't provide further details or say to which hospital was Saleh admitted.

Saleh had spent time in Saudi Arabia and the U.S. earlier this year for medical treatment for wounds sustained in a June assassination attempt that left much of his body burnt. Saleh stepped down in February and was replaced by his deputy, current President Abed Rabbo Mansour Hadi.

But Hadi and other political groups in Yemen have complained that Saleh, the country's ruler for 33 years, has continued to play a behind-the-scenes role in local affairs, impeding Hadi's efforts to implement a reform program.

THIS IS A BREAKING NEWS UPDATE. Check back soon for further information. AP's earlier story is below.

SANAA, Yemen (AP) ? Fresh clashes between al-Qaida fighters and government forces in Yemen left 17 dead on Sunday, military officials said, as the army pushed on with an offensive to regain a key town in the county's south that fell to the militants more than a year ago.

Officials said eight al-Qaida fighters, four soldiers and five civilian volunteers fighting alongside the military were killed since the early hours of Sunday.

The army started a two-pronged attack on the town of Jaar on Friday. It is part of a broader assault to take back Zinjibar, the provincial capital of Abyan, which has been also under al-Qaida control for more than a year.

Al-Qaida-linked fighters took advantage of Yemen's 2011 uprising to overrun a swath of territory and several towns in the south, pushing out government forces and establishing their own rule. In recent weeks, the army has launched a concerted effort to uproot the militants from their strongholds ? and is closely coordinating with a small contingent of U.S. troops who are helping guide the operations from inside Yemen.

Officials say U.S. drones have been providing information to their forces.

The military officials said Yemeni warplanes pounded targets some five kilometers (three miles) outside Jaar. Up to 70 percent of Jaar's residents have fled the town over the past months to escape the fighting.

The officials, who spoke on condition of anonymity in line with military regulations, said the militants used suicide car bombing against military checkpoints and vehicles to hinder the army's advance and had called for reinforcements from neighboring towns.

Yemen's new president, Abed Rabbo Mansour Hadi, took office in February as part of a U.S.- and Saudi-backed deal aimed at ending the unrest. He has made fighting al-Qaida one of his top priorities.

The official news agency SABA said Maj. Gen. Ken Tovo, a U.S. commanding general of special operations, met Saturday with Yemen's chief of staff Maj. Gen. Ahmed Ali al-Ashwal and discussed U.S. aid to Yemen in combating terrorism and the fight against al-Qaida.

Meanwhile Yemen's Defense Minister Major General Mohammed Nasser Ahmed, who is directly supervising the operations in the south, paid a 24-hour visit to Saudi Arabia and returned to the Yemeni capital Sanaa Sunday.

A government official said Yemen was seeking military hardware aid from Saudi Arabia to enable it to keep up the momentum of the operations against al-Qaida. The official spoke on condition of anonymity because he was not authorized to brief the media.

Associated Press

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Issues Remain In Greek Debt Talks

BRUSSELS -- Talks between Greece and its private creditors on cutting the country's massive debt load have made some progress, but disagreements remain on key parts of the deal, a person close to the negotiations said Thursday. Big banks and investment firms have been asked to forgive Greece some 50 percent of its debts so that the country can concentrate on getting its economy back in shape and eventually raise money on financial markets again. Athens has been kept afloat by a ?110 billion ($144 billion) bailout from the eurozone and the International Monetary Fund since May 2010 and has been promised an extra ?130 billion in aid if investors agree to share part of the burden. The idea is that by forgiving Greece part of its debt, private creditors avoid the much bigger losses they would face in a tumultuous default. While the eurozone and bank representatives reached a tentative deal on a debt restructuring in late October - which would see Greece debt cut by some ?100 billion - discussions on the details of the agreement have dragged on. The plan was to agree on the terms of a bond swap by the end of the year, so that private investors could exchange their old bonds for ones with a lower value in January or February, ahead of a ?14.4 billion repayment deadline Athens faces in March. In recent days, the Greek government and private investors agreed on some structural aspects of the package, but are still divided on central financial questions, which will determine the level of losses private creditors have to accept, said the person, who has been briefed in the talks. The person was speaking on condition of anonymity because talks are still ongoing. Investors won concessions from the government negotiators, who agreed to provide legal certainty that private creditors won't face more losses if Athens runs into trouble again in the future. For instance, the swapped bonds will be treated in the same way as loans from the eurozone in case of a future default by Greece. On top of that, the new bonds will be issued under U.K. rather than Greek law, giving investors extra security that the parliament in Athens won't be able to change their terms in the years to come. But the person said that there was still no deal on when Greece will have to repay the new bonds and at what interest rate. A high interest rate could add billions of euros to Greece's financial burden. Greek Finance Minister Evangelos Venizelos said Tuesday that he expected to reach an agreement with the private sector by early January, but the person close to the negotiations declined to commit to a deadline. He said informal discussions would continue in the coming days. All participants in the negotiations - Greece, the IMF and the eurozone on the one side and the bank representatives on the other - are under enormous pressure to reach a deal that can convince enough bondholders to participate. The IMF said in a report earlier this month that "near-universal participation" in the bond swap was necessary for Greece's debt to become sustainable again. How difficult that may be became clear earlier this month, when hedge fund Vega Asset Management resigned from the committee that has been leading the negotiations for the private investors. In a letter dated Dec. 7, Vega threatened legal action against Greece if it was forced to take steep losses as part of the restructuring. The person close to the talks said that letter was friendly in tone, and that some holdouts were to be expected, since different bond holders have different interests at stake. For example, a hedge fund, which may have bought its bonds when they were already trading at a steep discount, may be more willing to bet on getting bigger payments through a law suit than a bank or insurance fund more focused on cutting its risks. Separately, Greece's Finance Ministry said it exceeded its deficit-cutting targets in the first eleven months of the year, despite a revenue shortfall. A ministry statement on state budget execution Thursday showed the deficit was ?20.6 billion ($26.7 billion), a little bit lower than the ?21.1 billion target. The figures exclude certain categories of spending. ____ Nicholas Paphitis in Athens contributed.

Copyright 2011 by The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

Source: http://www.wpxi.com/money/30054795/detail.html

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