'Don't touch my junk DNA!' says gene signal sequence

Scientists at MIT say they have discovered a mechanism that prevents noncoding DNA from being copied, by pointing the copying in the right direction.?

By Eoin O'Carroll,?Staff / June 25, 2013

A computer illustration of the double-helix structure of DNA. Scientists say that they have uncovered a mechanism that prevents cells from copying so-called junk DNA.

The Wellcome Trust/Reuters

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Almost all of the human genome is made of noncoding, or "junk" DNA, that is, DNA that usually doesn't get copied and encoded into proteins.?

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So when copying DNA, how do cells tell the diference between actual genes and non-coding DNA??

Transcription begins at regions on the DNA molecule called promoters, sequences located at the beginning of genes that are to be copied. The enzyme that copies DNA, called RNA polymerase, latches on to the promoter and starts unzipping the DNA double helix, spooling out a chain of what will become messenger RNA ? mRNA for short ? that contains the information of the gene. [Editor's note: The original version of this paragraph used the term "replication" instead of "transcription." DNA replication is a different process. The Monitor regrets the error.] ?

But how does the RNA polymerase know which direction to go? Until now, scientists didn't know. But in research published in the current issue of the scientific journal Nature,?MIT biologists say they have discovered the mechanism that points transcription in the right direction.?

In all living things except bacteria, the RNA polymerase continues unzipping the DNA until it reaches a stop signal, at which point it stops copying and begins adding a chain of adenine bases to the pre-mRNA molecule, usually a couple hundred links long. This "poly-A" tail protects the mRNA as it exits the nucleus and travels to the ribosome, where the molecule's information is synthesized into proteins.

By sequencing mRNA of mouse embryonic stem cells, the researchers found that the signal sequences for creating poly-A tails ? a process known as polyadenylation ? are also prevalent "upstream" from the promoter. An RNA polymerase that encounters these sequences will chop up its pre-mRNA. Sequences of DNA that are to be coded into genes, by contrast, have a low density of?polyadenylation signal sequences.

The researchers also found that the?polyadenylation signal sequences are more likely to be?ignored when they appear within coding sequences, thanks to a tiny protein complex called U1 snRNP. When?U1 snRNP binds to an RNA polymerase,?polyadenylation is supressed. The researchers discovered that binding sites for?U1 snRNP are more prevalent in coding sequences than noncoding ones.

?Once you see some data like this, it raises many more questions to be investigated, which I?m hoping will lead us to deeper insights into how our cells carry out their normal functions and how they change in malignancy,? says?Phillip Sharp, a professor at MIT's Koch Institute for Integrative Cancer Research and a co-author of the study, in a statement.

Source: http://rss.csmonitor.com/~r/feeds/science/~3/yhaeIJ_jQoc/Don-t-touch-my-junk-DNA!-says-gene-signal-sequence

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What If the Superheroes from The Avengers Existed in Real Life?

Because we don't have any real life superheroes in this totally lame world of ours, we obsess over the lives of silly celebrities with beautiful cheekbones and photoshopped curves and cry over athletes wearing fresh laundry. It's what we call fun! But if superheroes existed on Earth, all those puny humans would never make the cover of magazines ever again. We'd obsess over superheroes all the time.

Prince William? Kate Middleton? Psh. LeBron James? Tom Brady? Who? There would be no Kardashian to fret about. Nobody counting how many chins on Honey Boo Boo's mother. All of the familiar faces that stare back at you in line of a grocery store and spur 30 second conversations about would be gone. Insert: make believe people who could actually do stuff. Because that's much better than real people who actually do make believe stuff!

MediAvengers created a lovely website that pretends those heroes actually do exist in a world where the paparazzi are permanently watching anyone famous. Kim, the woman behind MediAvengers, expertly parodies the Marvel universe on Earth to hilarious results. She explains:

Articles are written in the style of the publication?s real world counterpart (hence Cap?s great butt in the US Weekly spreads, and the trashy, repetitive, and apparently badly researched nature of the pieces in general).

Every piece is carefully thought out, right down to what information would be ?allowed? into the public arena (say hello to Natalie Rushman), and incorporates quotes from the comics and other parts of the Marvel Multiverse to really give it a little more of an authenticity boost.

The fan made project is fantastic. Check it out here. [MediAvengers via Laughing Squid]

Source: http://gizmodo.com/what-if-the-superheroes-from-the-avengers-existed-in-re-580136072

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Report: Hernandez investigated for double murder

AP

With more than $5 million still arguably owed to Aaron Hernandez under the contract he signed last August, the Patriots likely will fight to avoid paying him another dime.? The two-front battle relates to the final $3.25 million installment of his $12.5 million signing bonus and guaranteed base salaries for 2013 and 2014.? The guaranteed base salaries total $2.5 million.

As to the signing bonus, the team?s decision to cut Hernandez makes it much more difficult to block the final payment or to recover any of the $8.75 million already issued to Hernandez.? As to the guaranteed salaries, multiple sources have indicated that Hernandez likely will not be entitled to any further payment.

Despite the absence of forfeiture language for the guaranteed salaries, the guarantee applies only to terminations made due to injury, skill (i.e., perceived lack of it), and the salary cap.? Because the Patriots cut Hernandez pursuant to paragraph 11 of the standard player contract, which permits termination of employment when the player ?has engaged in personal conduct reasonably judged by Club to adversely affect or reflect on Club,? the guarantee evaporates.

As we understand it, that?s not merely the team?s position.? The NFLPA, we?re told, agrees with the interpretation.

While this doesn?t prevent Hernandez from filing a grievance aimed at getting the money, it?s a steep uphill climb and, frankly, the least of his concerns.

The more intriguing fight will arise in connection with the unpaid $3.25 million installment of the signing bonus.? That money already has been earned by Hernandez.? But cutting him, the Patriots apparently surrendered any ability to recover the money that has been paid or to keep the portion that hasn?t been paid.

Still, it currently appears that the Patriots will at a minimum force Hernandez to sue for the rest ? and at most try to recover as much of the previously-paid signing bonus as they can.

The problem for Hernandez is that, even though the terms of the labor deal seem to be on his side, the facts can nudge the controversy toward a bad outcome.? The problem for other players is that, if Hernandez loses, a bad precedent will be created for them.

Either way, it appears that the Patriots have enhanced their ability to avoid the guaranteed salaries by cutting Hernandez, even if cutting him makes it harder to avoid paying the final $3.25 million.

Source: http://profootballtalk.nbcsports.com/2013/06/27/report-hernandez-is-being-investigated-for-july-2012-double-murder/related/

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Realistic robot carp created: First robot fish with autonomous 3-D movement in Asia

June 26, 2013 ? A team of researchers from the National University of Singapore's (NUS) Department of Electrical & Computer Engineering has developed a robot fish that mimics the movements of a carp. This robot which is essentially an autonomous underwater vehicle (AUV) is ready for applications, as it can be programmed to perform specific functions, for example, for underwater archaeology such as exploring nooks and corners of wreckage -- or sunken city which are difficult for divers or traditional AUVs to access. Other applications include military activities, pipeline leakage detection, and the laying of communication cable.

The team comprises Professor Xu Jianxin, Mr Fan Lupeng, graduating Electrical Engineering student and Research Fellow, Dr Ren Qinyuan. Mr Fan worked on the project for his final year which won the High Achievement Award at the Faculty's 27th Innovation and Research Award. It will also be featured at the IEEE/RSJ International Conference on Intelligent Robots and Systems, a top international conference on intelligent robots, in Tokyo on 3-7 November 2013.

Said Prof Xu, "Currently, robot fish capable of 2-D movements are common, meaning that these models are not able to dive into the water. Our model is capable of 3-D movements as it can dive and float, using its fins like a real fish. Compared to traditional AUVs, they are certainly more mobile, with greater manoeuvrability. If used for military purpose, fish robots would definitely be more difficult to detect by the enemy."

Fish robots are also quieter and consume less energy, compared to traditional AUVs. Said Mr Fan who studied the movements of real life carps for three months, in order to develop their robot, "We chose to study carps because most fish swim like them. There is no literature at all on designing a mathematical model on the locomotion of fish and so we had to start from scratch. We used a camera to capture all the possible movements of a carp and then converted the data mathematically so that we could transfer the locomotion of real carp to our robot using different actuators."

This has been most challenging as fish use a lot of different muscles to move, and many actuators are required to enable the robot to move in the same manner.

Added Dr Ren, "Some fish can achieve almost 180 degree turning in a small turning radius through bending their body while traditional underwater vehicles have a much larger turning radius. Hence it is quite a feat for us to achieve this movement in our robot fish."

Other challenges included waterproofing the fish body, the motor and the control box. The fins and tails also need to be flexible and the team decided to use very fine (1mm) acrylic board for these. Buoyancy and balance for the robot is maintained by using plastic foams attached to both sides. For the diving mechanism, their robot fish is equipped with an internal ballast system to change density. The system is sophisticated enough to enable the fish to dive suddenly, as well as to the precise depth intended.

The team has constructed two fish robots. The larger prototype is about one and half metres in length, weighing about 10kg and it can dive to a depth of 1.8 metres. The smaller robot is about 60 centimetres long and weighs a mere 1.5kg. It is developed for investigation on 2D motion control and motion planning in a small place, and it can only swim at water surface.

"To my knowledge, the world's smallest fish robot is one about 12.7 centimetres (5 inches) in length. It was designed by MIT for specific military purpose and could go to a depth of 1.5 metres," said Dr Ren.

Moving forward

Underwater vehicles have long gone past the days of the submarines, said Mr Fan. Fish robots, besides being a micro submarine, can also be fully autonomous and can be programmed to perform many difficult and dangerous tasks.

The team hopes to make their robot fish even smaller and more realistic. Said Mr Fan, "We intend to equip it with more sensors like GPS and video camera to improve autonomous 3-D movement. We also intend to test out our fish with more challenging tasks such as object detection."

Source: http://feeds.sciencedaily.com/~r/sciencedaily/strange_science/~3/Hexvc4gQL0o/130626113027.htm

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Snowden not on flight to Cuba, whereabouts unclear

MOSCOW (AP) ? A plane took off from Moscow on Monday headed for Cuba, but the seat booked by National Security Agency leaker Edward Snowden was empty, and there was no sign of him elsewhere on board. His whereabouts were unknown.

An Aeroflot representative who wouldn't give her name told The Associated Press that Snowden wasn't on flight SU150 to Havana. AP reporters on the flight couldn't see him.

Security around the aircraft was heavy prior to boarding and guards tried to prevent photographers and cameramen from taking pictures of the plane, heightening the speculation that he might have been secretly escorted on board.

The Interfax news agency, which has extensive contacts with Russian security agencies, cited a source as saying that Snowden could have flown out in a different plane unseen by journalists. Others speculated that Russian security agencies might want to keep Snowden in Russia for a more thorough debriefing.

Aeroflot said earlier that Snowden had registered for the flight using his American passport, which the United States recently annulled.

Snowden has not been seen since he arrived in Moscow on Sunday from Hong Kong, where he had been hiding for several weeks to evade U.S. justice. Ecuador is considering Snowden's asylum application.

After spending a night in Moscow's Sheremetyevo Airport, the former National Security Agency contractor ? and admitted leaker of state secrets ? had been expected to fly to Cuba and Venezuela en route to possible asylum in Ecuador.

Snowden, also a former CIA technician, fled Hong Kong to dodge U.S. efforts to extradite him on espionage charges. Ecuador's Foreign Minister Ricardo Patino said his government had received an asylum request, adding Monday that the decision "has to do with freedom of expression and with the security of citizens around the world." The anti-secrecy group WikiLeaks also said it would help Snowden.

Ecuador has rejected the United States' previous efforts at cooperation, and has been helping WikiLeaks founder Julian Assange avoid prosecution by allowing him to stay at its embassy in London.

Snowden gave documents to The Guardian and The Washington Post newspapers disclosing U.S. surveillance programs that collect vast amounts of phone records and online data in the name of foreign intelligence, often sweeping up information on American citizens. Officials have the ability to collect phone and Internet information broadly but need a warrant to examine specific cases where they believe terrorism is involved.

Snowden had been in hiding for several weeks in Hong Kong, a former British colony with a high degree of autonomy from mainland China. The United States formally sought Snowden's extradition from Hong Kong to face espionage charges but was rebuffed; Hong Kong officials said the U.S. request did not fully comply with their laws.

The Justice Department rejected that claim, saying its request met all of the requirements of the extradition treaty between the U.S. and Hong Kong. During conversations last week, including a phone call Wednesday between Attorney General Eric Holder and Hong Kong Secretary for Justice Rimsky Yuen, Hong Kong officials never raised any issues regarding sufficiency of the U.S. request, a Justice representative said.

The United States was in touch through diplomatic and law enforcement channels with countries that Snowden could travel through or to, reminding them that Snowden is wanted on criminal charges and reiterating Washington's position that Snowden should only be permitted to travel back to the U.S., a State Department official said.

U.S. officials spoke on condition of anonymity because they were not authorized to publicly discuss the case.

Caitlin Hayden, a spokeswoman for the National Security Council, said, "Given our intensified cooperation after the Boston marathon bombings and our history of working with Russia on law enforcement matters ? including returning numerous high-level criminals back to Russia at the request of the Russian government ? we expect the Russian government to look at all options available to expel Mr. Snowden back to the U.S. to face justice for the crimes with which he is charged."

Still, the United States is likely to have problems interrupting Snowden's passage. The United States does not have an extradition treaty with Russia, but does with Cuba, Venezuela and Ecuador. Even with an extradition agreement though, any country could give Snowden a political exemption.

The likelihood that any of these countries would stop Snowden from traveling on to Ecuador seemed remote. While diplomatic tensions have thawed in recent years, Cuba and the United States are hardly allies after a half-century of distrust.

Another country that could see Snowden pass through, Venezuela, could prove difficult, as well. Former President Hugo Chavez was a sworn enemy of the United States and his successor, Nicolas Maduro, earlier this year called President Barack Obama "grand chief of devils." The two countries do not exchange ambassadors.

It also wasn't clear Snowden was finished disclosing highly classified information.

Snowden has perhaps more than 200 sensitive documents, Sen. Dianne Feinstein, chairwoman of the Senate Intelligence Committee, said on CBS' "Face the Nation."

___

Associated Press White House Correspondent Julie Pace and Associated Press writers Philip Elliott, Matthew Lee and Frederic J. Frommer in Washington, Lynn Berry in Moscow, Kevin Chan in Hong Kong and Sylvia Hui in London contributed to this report.

___

Follow Philip Elliott on Twitter: http://www.twitter.com/philip_elliott

Source: http://news.yahoo.com/snowden-not-flight-cuba-whereabouts-unclear-141749907.html

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Syria says rebels will take years to match army's strength

BEIRUT (Reuters) - A decision by Western and Arab countries to arm rebels fighting to topple Syria's President Bashar al-Assad poses a danger to peace talks, the Syrian foreign minister said on Monday.

Walid al-Moualem told a news conference in Damascus that the opposition had little hope of matching the Syrian army's strength despite a pledge by the states that make up the "Friends of Syria" to increase military support to the rebels.

"If they expect or fantasize that they can create a balance of power, I think they will need to wait years for that to happen," he said during the televised news conference.

Western and Arab countries as well as Turkey, who have thrown their weight behind the opposition, said their decision to arm the rebels was to rebalance the conflict in which more than 93,000 people have been killed, most of them civilians.

Assad is seen as having gained momentum, seizing a strategic town near the Lebanese border which helps him cement control between the capital Damascus and his stronghold on the Mediterranean coast.

Moualem said that a move towards openly giving military support to the rebels would encourage terrorism and that radical Islamist groups linked to al Qaeda would benefit the most.

"The decision in Doha is dangerous...because it aims to prolong the crisis, to extend the violence and the killing, and to encourage the terrorists to carry out their crimes," he said.

The United States and Russia are planning a peace conference in Geneva between the opposition and Assad's government.

"Arming the opposition will obstruct Geneva. Arming the opposition will kill more of our people," Moualem said. "We head to Geneva not to hand over power to another side.

"Whoever on the other side imagines this, I advise them not to go to Geneva."

The government was willing to discuss forming a broad-based government of national unity in Geneva, he added.

The Syrian conflict began as peaceful protests against four decades of Assad family rule, but descended into a civil war that has drawn in foreign fighters to both sides of the fight, increasing regional ethnic and sectarian tensions.

Syria's opposition, led mostly by the Sunni Muslim majority, has attracted foreign Islamist fighters. Shi'ites from Iraq and Lebanon have joined the fight on the side of Assad, who is from the minority Alawite sect, an offshoot of Shi'ite Islam.

Moualem said Syria wanted a ceasefire in order to hold talks at Geneva.

"We are insistent that if Geneva is held there must be a ceasefire, and we are ready to study mechanisms for observing it on the basis that neighboring states abide, by halting training, arming and financing and sending them to Syrian territory," he said.

In Brussels, a European Union report said the bloc should support a political settlement but also ease sanctions to help people in rebel-held areas, following steps to exempt the rebels from oil and banking sanctions.

The report from the EU's executive Commission and foreign policy chief Catherine Ashton also said the two-year-old Syrian conflict and a refugee exodus were putting severe strain on Syria's neighbors, threatening the internal stability of Lebanon and Jordan,

Having taken in more than half a million refugees, Lebanon authorities were unable to cope alone, the report said.

"It is imperative to shield the country from the efforts of some of the local and regional actors to wage the Syrian struggle on Lebanese soil," it said.

Lebanon has suffered growing violence at home as the conflict turns into a proxy war along sectarian lines. Lebanon's Hezbollah Shi'ite militia has joined the war on Assad's side.

(Reporting by Erika Solomon; Editing by Angus MacSwan)

Source: http://news.yahoo.com/syria-says-rebels-years-match-armys-strength-123228650.html

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Kerry: Syria urgently needs a political solution

DOHA, Qatar (AP) ? Unless the bloodshed in Syria stops, the region could descend into a chaotic sectarian conflict, U.S. Secretary of State John Kerry said Saturday, as he called for an urgent political resolution to the war that has dragged on for two years and claimed 93,000 lives.

The top U.S. diplomat and his counterparts from 10 Arab and European nations agreed at a daylong meeting in Qatar to step up military and other assistance to the Syrian rebels. But Kerry would not disclose details of the aid, saying only that it would re-balance the fight between the rebels and President Bashar Assad's better-equipped forces that are increasingly backed by Iranian and Hezbollah fighters.

"The continued bloodshed at the hands of the Assad regime and the increasing involvement of Iran and its proxy, Hezbollah, threaten the very prospects of a political settlement and of peace," Kerry said, adding that the U.S. and other nations are not backing the rebels to seek a military victory in Syria.

"We do so to ... find a political settlement," he said. "Reliable civilian governance and a stronger and more effective armed opposition will better enable the opposition to be able to provide the counterweight to the initiative of Assad to reach out across borders ... to bring Iranians and to bring Hezbollah - again, a terrorist organization - to the table."

Rebels say they have already received new weapons from allied countries? but not the U.S. ? that they claim will help them to shift the balance of power on the ground where regime forces have scored recent military victories. Experts and activists said the new weapons include anti-tank missiles and small quantities of anti-aircraft missiles.

"Our information from Doha says that five countries have decided to start arming us immediately, and four other countries will give us logistical and technical support and, at a later stage, arm the Free Syrian Army," a spokesman for the opposition fighters, Loay AlMikdad, said in an interview with Qatar's Al-Jazeera TV. He said the nations were both Arab and non-Arab, but he would not elaborate.

It was Kerry's first meeting with his counterparts about aid to the Syrian rebels since President Barack Obama announced that the U.S. would send lethal aid to the opposition despite concern that the weapons could fall into the hands of Islamic extremists in Syria. That decision was partly based on a U.S. intelligence assessment that Assad had used chemical weapons, but Kerry expressed deeper concern about how Iran and Hezbollah fighters had joined the fight.

"That is a very, very dangerous development," Kerry said. "Hezbollah is a proxy for Iran. ... Hezbollah in addition to that is a terrorist organization."

Kerry blamed Hezbollah and Assad with undermining efforts to negotiate a settlement and set up a transitional government.

"We're looking at a very dangerous situation," that has transformed "into a much more volatile, potentially explosive situation that could involve the entire region," Kerry said.

The war already has spilled into neighboring countries and is increasingly being fought along sectarian lines, pitting Sunni against Shiite Muslims and threatening the stability of Syria's neighbors.

Kerry said top U.S. diplomats are ready to go to Geneva to meet with U.N.-Arab League envoy Lakhdar Brahimi and other officials next week to advance the political process.

Doha was the first stop on Kerry's two-week trip through the Mideast and Asia. He is to discuss a wide range of bilateral issues on Sunday and Monday with Indian officials in New Delhi ? just one stop on a seven-nation tour where he will tackle prickly U.S. foreign policy issues ? from finding peace between the Israelis and Palestinians to trying to gain traction on U.S. talks with the Taliban to end the Afghanistan war.

James Dobbins, U.S. special envoy to Afghanistan and Pakistan, arrived in Doha on Saturday, but talks with the Taliban, which were supposed to take place in coming days, have not been scheduled. They are to be held at a controversial new political office the Taliban just opened in Doha.

Kerry said the Americans and Qataris were on board to help negotiate a political resolution to the war, but it was up to the Taliban to come to the table. "We are waiting to find out whether the Taliban will respond, Kerry said, lowering expectations about the prospects for negotiation.

"We will see if we can get back on track. I don't know whether that's possible or not," Kerry said. "If there is not a decision made by the Taliban to move forward in short order, then we may have to consider whether the office has to be closed."

At the close of the meeting, the eleven nations ? the U.S., Qatar, Saudi Arabia, United Arab Emirates, Jordan, Egypt, Turkey, Britain, Germany, France and Italy ? expressed concern about the growing sectarian nature of the Syrian conflict, renewed their call on the regime to let U.N. investigators probe the reported use of chemical weapons and condemned the intervention of Hezbollah militias and fighters from Iran and Iraq.

In a joint press conference in Tehran, Iran Foreign Minister Ali Akbar Salehi and his Lebanese counterpart Adnan Mansour lambasted Western powers that arm and support Syrian opposition fighters.

"I am shocked to see how Western powers speak of human rights and act otherwise when it comes to Syria ? where they arm cannibals who fought in Syria so that they (opposition fighters) continue their atrocities more than before," Salehi said.

In their communique, the ministers expressed support for a transitional governing body that would take charge of military and other government institutions. But they added that "Bashar Assad has no role in the transitional governing body or thereafter."

That is a sticking point with Russia, a key Assad ally that has resisted calls for his removal.

Russia may have worked to assure Assad government's attendance at any future peace conference, but Moscow also has been undermining peace efforts by sending more weapons to help the Syrian government's counteroffensive against the rebels.

Russian leaders warn that if Assad steps aside, the resulting power vacuum could be quickly filled by al-Qaida connected rebels, who are well-armed and aggressive.

___

Associated Press writers Amir Vahdat in Tehran and Sarah El Deeb in Beirut contributed to this report.

Source: http://news.yahoo.com/kerry-syria-urgently-needs-political-solution-192130086.html

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