Evolution is as complicated as 1-2-3

Public release date: 19-Sep-2012
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Contact: Layne Cameron
layne.cameron@cabs.msu.edu
517-353-8819
Michigan State University

EAST LANSING, Mich. A team of researchers at Michigan State University has documented the step-by-step process in which organisms evolve new functions.

The results, published in the current issue of Nature, are revealed through an in-depth, genomics-based analysis that decodes how E. coli bacteria figured out how to supplement a traditional diet of glucose with an extra course of citrate.

"It's pretty nifty to see a new biological function evolve," said Zachary Blount, postdoctoral researcher in MSU's BEACON Center for the Study of Evolution in Action. "The first citrate-eaters were just barely able to grow on the citrate, but they got much better over time. We wanted to understand the changes that allowed the bacteria to evolve this new ability. We were lucky to have a system that allowed us to do so."

Normal E. coli can't digest citrate when oxygen is present. In fact, it's a distinct hallmark of E. coli. They can't eat citrate because E. coli don't express the right protein to absorb citrate molecules.

To decipher the responsible mutations, Blount worked with Richard Lenski, MSU Hannah Distinguished Professor of Microbiology and Molecular Genetics. Lenski's long-term experiment, cultivating cultures of fast-growing E. coli, was launched in 1988 and has allowed him and his teammates to study more than more than 56,000 generations of bacterial evolution.

The experiment demonstrates natural selection at work. And because samples are frozen and available for later study, when something new emerges scientists can go back to earlier generations to look for the steps that happened along the way.

"We first saw the citrate-using bacteria around 33,000 generations," Lenski explained. "But Zack was able to show that some of the important mutations had already occurred before then by replaying evolution from different intermediate stages. He showed you could re-evolve the citrate-eaters, but only after some of the other pieces of the puzzle were in place."

In the Nature paper, Blount and his teammates analyzed 29 genomes from different generations to find the mutational pieces of the puzzle. They uncovered a three-step process in which the bacteria developed this new ability.

The first stage was potentiation, when the E. coli accumulated at least two mutations that set the stage for later events. The second step, actualization, is when the bacteria first began eating citrate, but only just barely nibbling at it. The final stage, refinement, involved mutations that greatly improved the initially weak function. This allowed the citrate eaters to wolf down their new food source and to become dominant in the population.

"We were particularly excited about the actualization stage," Blount said. "The actual mutation involved is quite complex. It re-arranged part of the bacteria's DNA, making a new regulatory module that had not existed before. This new module causes the production of a protein that allows the bacteria to bring citrate into the cell when oxygen is present. That is a new trick for E. coli."

The change was far from normal, Lenski said.

"It wasn't a typical mutation at all, where just one base-pair, one letter, in the genome is changed," he said. "Instead, part of the genome was copied so that two chunks of DNA were stitched together in a new way. One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed."

###

Additional co-authors include Jeff Barrick, University of Texas, and Carla Davidson, University of Calgary.

The research was funded in part by the National Science Foundation.

Michigan State University has been working to advance the common good in uncommon ways for more than 150 years. One of the top research universities in the world, MSU focuses its vast resources on creating solutions to some of the world's most pressing challenges, while providing life-changing opportunities to a diverse and inclusive academic community through more than 200 programs of study in 17 degree-granting colleges.

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Public release date: 19-Sep-2012
[ | E-mail | Share ]

Contact: Layne Cameron
layne.cameron@cabs.msu.edu
517-353-8819
Michigan State University

EAST LANSING, Mich. A team of researchers at Michigan State University has documented the step-by-step process in which organisms evolve new functions.

The results, published in the current issue of Nature, are revealed through an in-depth, genomics-based analysis that decodes how E. coli bacteria figured out how to supplement a traditional diet of glucose with an extra course of citrate.

"It's pretty nifty to see a new biological function evolve," said Zachary Blount, postdoctoral researcher in MSU's BEACON Center for the Study of Evolution in Action. "The first citrate-eaters were just barely able to grow on the citrate, but they got much better over time. We wanted to understand the changes that allowed the bacteria to evolve this new ability. We were lucky to have a system that allowed us to do so."

Normal E. coli can't digest citrate when oxygen is present. In fact, it's a distinct hallmark of E. coli. They can't eat citrate because E. coli don't express the right protein to absorb citrate molecules.

To decipher the responsible mutations, Blount worked with Richard Lenski, MSU Hannah Distinguished Professor of Microbiology and Molecular Genetics. Lenski's long-term experiment, cultivating cultures of fast-growing E. coli, was launched in 1988 and has allowed him and his teammates to study more than more than 56,000 generations of bacterial evolution.

The experiment demonstrates natural selection at work. And because samples are frozen and available for later study, when something new emerges scientists can go back to earlier generations to look for the steps that happened along the way.

"We first saw the citrate-using bacteria around 33,000 generations," Lenski explained. "But Zack was able to show that some of the important mutations had already occurred before then by replaying evolution from different intermediate stages. He showed you could re-evolve the citrate-eaters, but only after some of the other pieces of the puzzle were in place."

In the Nature paper, Blount and his teammates analyzed 29 genomes from different generations to find the mutational pieces of the puzzle. They uncovered a three-step process in which the bacteria developed this new ability.

The first stage was potentiation, when the E. coli accumulated at least two mutations that set the stage for later events. The second step, actualization, is when the bacteria first began eating citrate, but only just barely nibbling at it. The final stage, refinement, involved mutations that greatly improved the initially weak function. This allowed the citrate eaters to wolf down their new food source and to become dominant in the population.

"We were particularly excited about the actualization stage," Blount said. "The actual mutation involved is quite complex. It re-arranged part of the bacteria's DNA, making a new regulatory module that had not existed before. This new module causes the production of a protein that allows the bacteria to bring citrate into the cell when oxygen is present. That is a new trick for E. coli."

The change was far from normal, Lenski said.

"It wasn't a typical mutation at all, where just one base-pair, one letter, in the genome is changed," he said. "Instead, part of the genome was copied so that two chunks of DNA were stitched together in a new way. One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed."

###

Additional co-authors include Jeff Barrick, University of Texas, and Carla Davidson, University of Calgary.

The research was funded in part by the National Science Foundation.

Michigan State University has been working to advance the common good in uncommon ways for more than 150 years. One of the top research universities in the world, MSU focuses its vast resources on creating solutions to some of the world's most pressing challenges, while providing life-changing opportunities to a diverse and inclusive academic community through more than 200 programs of study in 17 degree-granting colleges.

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AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.

Source: http://www.eurekalert.org/pub_releases/2012-09/msu-eia091912.php

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AEG For Sale: Anschutz Co. To Sell Subsidiary That Owns LA Kings & Staples Center

LOS ANGELES ? Anschutz Entertainment Group, the owner of the Staples Center arena and the NHL's Los Angeles Kings, and the top contender to build a stadium and bring the NFL back to Los Angeles, is up for sale, its parent company said Tuesday.

The Denver-based Anschutz Co. said in a statement that it is "commencing a process" to sell the subsidiary known as AEG and had hired Blackstone Advisory Partners as an adviser.

It wasn't immediately clear how far along the company is in the sale process, or whether it has entertained any offers, but the price for AEG could be well into the billions.

The sale would mean a major ground shift in sports and entertainment in Los Angeles and around the world.

AEG's holdings also include pro soccer's Los Angeles Galaxy, part-ownership of the NBA's Los Angeles Lakers, and major entertainment and real estate holdings in downtown Los Angeles. Outside of L.A., AEG owns Major League Soccer's Houston Dynamo and New York's Barclay's Center, the new home of the NBA's Brooklyn Nets. It also owns arenas in Sweden, China and Australia.

The sale would also throw uncertainty into LA's nearly two-decade attempt to bring the NFL back to the city. The City Council is considering the approval of plans for Farmers Field, a downtown stadium proposed by AEG.

Los Angeles Mayor Antonio Villaraigosa said he has long known of the possibility of a sale, and both Denver billionaire Phillip Anschutz and AEG President Tim Leiweke have assured him the city's NFL hopes will remain the same.

"I have worked with both Phil Anschutz and Tim Leiweke for years to bring a football team to Los Angeles. I speak to both of them on a regular basis and I have known about this potential sale for some time," the mayor said in a statement Tuesday night. "I have the commitment from both of them that this won't affect plans for an NFL team to return to Los Angeles in the near future and so will not affect my support for moving ahead with Farmers Field."

Councilwoman Jan Perry, whose district includes the proposed stadium site, said she did not know about a pending sale but agreed that it wouldn't have adverse effects on courting an NFL team.

"The city has done a good job of protecting the taxpayer's interest in negotiating an agreement," Perry told The Associated Press, "so whoever steps into the shoes of Mr. Anschutz will have the same obligations."

Perry said the move "arguably is very positive" because she suspected it could lead to an enthusiastic new partner anxious to get in on the city's NFL prospects.

The potential sale was first reported by the Wall Street Journal.

AEG transformed the Los Angeles landscape with the building of Staples Center and the later addition of the LA Live entertainment complex, helping to revitalize the city's long-neglected downtown and bring new energy and several championships to its sports teams.

Opening in 1999, the Staples Center is among the world's busiest arenas. It hosted six playoff games in four days for its main tenants ? the NBA's Lakers and Clippers, and the NHL's Kings, who won their first Stanley Cup in June.

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Source: http://www.huffingtonpost.com/2012/09/19/aeg-for-sale-anschutz-co-_n_1895548.html

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Free speech, religion clash over anti-Muslim film

A Muslim youth pauses near a poster during a protest against an anti-Islam film in Jakarta, Indonesia, Monday, Sept. 17, 2012. Indonesians enraged over an anti-Islam film hurled rocks and Molotov cocktails at the U.S. Embassy in Jakarta on Monday, marking the first violence in the world's most populous Muslim country since outrage exploded last week in the Middle East and beyond. (AP Photo/Dita Alangkara)

A Muslim youth pauses near a poster during a protest against an anti-Islam film in Jakarta, Indonesia, Monday, Sept. 17, 2012. Indonesians enraged over an anti-Islam film hurled rocks and Molotov cocktails at the U.S. Embassy in Jakarta on Monday, marking the first violence in the world's most populous Muslim country since outrage exploded last week in the Middle East and beyond. (AP Photo/Dita Alangkara)

Kashmiri Muslim protesters burn an effigy representing the United States as they shout slogans during a protest in Srinagar, India, Tuesday, Sept. 18, 2012. The protest was held against an anti-Islam film called "Innocence of Muslims" that ridicules Islam's Prophet Muhammad. (AP Photo/Mukhtar Khan)

Indonesian Muslims burn an American flag during a protest against an American-made film that ridicules Prophet Muhammad outside the U.S. Consulate in Medan, North Sumatra, Indonesia, Tuesday, Sept. 18, 2012. Indonesians continue to protest the anti-Islam film "Innocence of Muslims," torching the flag and tires outside the consulate in the country's third largest city of Medan. (AP Photo/Binsar Bakkara)

An Indonesian Muslim holds up a poster as a tire burns during a protest against an American film that ridicules Prophet Muhammad outside the U.S. Consulate in Medan, North Sumatra, Indonesia, Tuesday, Sept. 18, 2012. Indonesians continue to protest the anti-Islam film "Innocence of Muslims," torching the flag and tires outside the consulate in the country's third largest city of Medan. The poster reads: "Muslims are ready for war."(AP Photo/Binsar Bakkara)

CERRITOS, Calif. (AP) ? While the man behind an anti-Islam movie that ignited violence across the Middle East would likely face swift punishment in his native Egypt for making the film, in America the government is in the thorny position of protecting his free speech rights and looking out for his safety even while condemning his message.

It's a paradox that makes little sense to those protesting and calling for blood. To them, the movie dialogue denigrating the Prophet Muhammad is all the evidence needed to pursue justice ? vigilante or otherwise ? against Nakoula Bassely Nakoula, an American citizen originally from Egypt.

In America, there's nothing illegal about making a movie that disparages a religious figure. And that has the Obama administration walking a diplomatic tight rope less than two months before the election ? how to express outrage over the movie's treatment of Islam without compromising the most basic American freedom.

"The thing that makes this particularly difficult for the United States is that ... we treat what most of us would refer to as hate speech as constitutionally protected speech and Americans don't appreciate, I think, how unusual this position seems in the rest of the world," said Lawrence Rosenthal, a professor at Chapman University's School of Law in Orange, Calif.

The situation also raises vexing questions about how far the government can and should go to protect someone who exercises their First Amendment right. In the past, for example, police have stood guard to ensure Nazis and the Ku Klux Klan could march without being attacked for their views.

But Nakoula's case invites scrutiny because the free speech he exercised with the film "Innocence of Muslims" has had such far-reaching and violent implications.

If the government were to overtly protect Nakoula, it could be seen by some as tacit approval of the film, and further enflame protests. Leaving him to fend for himself could have deadly consequences. There are examples of violence against others who have written or spoken against Muhammad.

So far, the government has acknowledged offering very limited assistance. Los Angeles County sheriff's deputies escorted Nakoula to an interview with federal probation officials. They did so in the dead of night and allowed Nakoula to cover his face. And early Monday, deputies answered his family's request for help leaving the house where they'd been holed up for five days so they could reunite with the 55-year-old filmmaker. All remain in hiding.

Department spokesman Steve Whitmore stressed the agency is not providing protective custody. He referred questions to federal authorities, who have declined to comment.

Jody Armour, a professor at the University of Southern California's Gould School of Law, said it's "not unusual at all for the government to step in and give a citizen in distress or danger special protection, but it can't unlimited. They're going to have to strike a balance."

A 14-minute trailer for the film posted on YouTube sparked violence in the Middle East, including an attack in Libya in which a U.S. ambassador was killed. Nakoula, a Coptic Christian and American citizen who served federal prison time for check fraud, told The Associated Press in a short interview last week that he was involved in management and logistics for the anti-Islamic film. Federal officials, however, told the AP they have concluded he was behind the movie.

Furor over the film has been widespread. Bahrain protesters used Twitter to organize demonstrations that included burning American flags in the nation that hosts the U.S. Navy's 5th Fleet. Pakistan's conservative Islamist parties sent out text messages, mosque announcements and made phone calls to bring out protest crowds, including about 1,000 people in the northwestern city of Peshawar on Sunday and hundreds who rushed the U.S. consulate in Karachi, sparking clashes with police in which one demonstrator was killed.

"Yes, we understand the First Amendment and all of this stuff," wrote Khalid Amayreh, a prominent Islamist commentator and blogger in Hebron on the West Bank. "But you must also understand that the Prophet (for us) is a million times more sacred than the American Constitution."

Were he in his native Egypt, Nakoula could be charged with "insulting religion," a crime punishable by up to three years in prison or could face the more serious charge of "upsetting national security," which carries a life sentence.

In America, the government can't even order that the video be removed from YouTube. All it can do is ask. And so far, parent company Google has declined, saying the video was within its guidelines for content. The company did restrict access to the video in certain countries, including Egypt, Libya and Indonesia, the world's most populous Muslim nation.

"This can be a challenge because what's OK in one country can be offensive elsewhere," the company said in a statement.

That's precisely the point about the First Amendment, Armour said.

"The reason it is a constitutionally protected interest is precisely because it may prove unpopular," he said. "Words and images don't just convey information, they are attached to consequences. That's when we really have to ask ourselves, 'What price are we willing to pay for that First Amendment interest?' And these are the times that really test our convictions."

In 1975, former CIA agent Philip Agee published a book detailing agency operations and disclosing the names of a number of CIA agents working undercover overseas, Rosenthal said. Even in that instance, the U.S. government didn't press criminal charges but instead revoked Agee's passport and sued him for the book's profits.

"It's not clear that there is, on the books today, a law that makes what (Nakoula) did a crime," Rosenthal said. "This is an extremely difficult problem."

Indeed, federal officials have said they are looking at Nakoula only in the context of whether he violated his probation for the fraud conviction. Under terms of his sentence, he was banned from using computers or the Internet as part of his sentence.

The probation issue "gives the government a relatively low visibility way of prosecuting him but not technically for what he said and how inflammatory it was," Armour said. "It may be a way of splitting the baby."

___

Associated Press writer Brian Murphy in Dubai, United Arab Emirates, contributed to this report.

Associated Press

Source: http://hosted2.ap.org/APDEFAULT/386c25518f464186bf7a2ac026580ce7/Article_2012-09-18-Egypt%20Filmmaker-Free%20Speech/id-17e00efa7f3a40719859323a84a3ff53

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Threshold Pharma cancer drug fails to meet study secondary goal

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Goldman Sachs' Schwartz to replace Viniar as CFO

NEW YORK (AP) ? Goldman Sachs Group Inc.'s chief financial officer is retiring, and his replacement is a longtime executive at the investment bank.

David Viniar, 57, is stepping down after 32 years with Goldman, the last 12 as CFO. Harvey M. Schwartz, 48, will replace him at the end of January, the bank said Tuesday

After Viniar leaves the post, he will join Goldman's board as a non-independent director.

Schwartz served most recently as the global co-head of Goldman' securities division. He joined the firm as a vice president in 1997, became a managing director in 1999, and was named partner in 2002.

In his new role, Schwartz will have oversight of operations, technology and finance at the bank. He will also serve as co-head of the Firmwide Risk Committee.

Schwartz "has deep experience in credit, liquidity, market and operational risk," Goldman Sachs Chairman and CEO Lloyd C. Blankfein said. "Harvey's risk management judgment and broad understanding of our business and our clients have defined his career, and will be the basis of his strengths as an effective CFO."

Viniar made "extraordinary contributions" to Goldman Sachs and "represents the very best of Goldman Sachs and its culture," Blankfein said.

The announcement was made after shares of Goldman slipped 2 cents to close at $119.88. The stock lost another 3 cents, to $119.85, in after-hours trading.

Goldman, which is based in New York, said Viniar is the longest-serving chief financial officer of a major Wall Street financial institution.

He joined Goldman in 1980 in the Investment Banking Division. He assumed responsibility for the firm's financing activities in the Treasury Department in 1992 and for the Controllers Department in 1994. From 1998 until 1999, Viniar was deputy CFO.

Before becoming global co-head of Goldman's securities division, Schwartz was global head of the division's sales operations. Before that, he was co-head of the Americas Financing Group within Goldman's investment banking business, which centralizes financing-related advice, origination and execution for clients.

With Viniar set to join the company's board as a non-independent member, Goldman said it expects to appoint additional independent directors "in the near term."

Associated Press

Source: http://hosted2.ap.org/APDEFAULT/f70471f764144b2fab526d39972d37b3/Article_2012-09-18-Goldman%20Sachs-Chief%20Financial%20Officer/id-6e658bb84cb04ab2a38265f6d4009f88

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A Day at the National College of Leadership | Country Education ...

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Source: http://cep.org.au/2012/09/17/a-day-at-the-national-college-of-leadership/

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Music professor inspires success through commitment, passion ...

When Virginia Novine-Whittaker was choosing an instrument to pursue, her reason for choosing the saxophone was a bit unorthodox.

?When I first had to choose an instrument, I thought, ?What can I play that?s involved in the most groups so I could be in everything??? Whittaker said. ??What would be kind of cool?? And (the saxophone) is it.?

Now, Whittaker ? an adjunct instructor of music at Elon University ? is passing on her love for the saxophone through private instruction with students of all levels of expertise. Outside of her lessons with music majors, Whittaker said she is happy to take on students who have never played an instrument before.

?There?s a lot of opportunities for students on campus to get involved in the music department if they?re not majors,? Whittaker said. ?I had a student last semester [who] just always thought saxophone was cool and she wanted to take something that was different.?I taught her how to read music. In one semester, we went from her not ever blowing a note on an instrument or reading music, to being able to play some intermediate jazz lines that sounded really good.?

Of course, Whittaker also offers private instruction to advanced music majors, and many of her students have gone on to procure jobs in the professional industry. A number of Elon graduates are now working as band directors and studio musicians. One particular alumnus is now teaching saxophone students in the military, she said.

You have to live a life that has meaning. You have to live life large, and then you just play it large.
?Virginia Novine-Whittaker, adjunct instructor of music

For Whittaker, though, the study of music has never been about career success. Rather, it is about the passion and the expression.

?Musicians have a means of expression that goes beyond words, and people who don?t have that wish for it,? she said. ?That?s what grabs me.?And I love all the different emotions you can play, and all the colors and all the different roles you can take on.?

Whittaker said many students are not used to wearing their hearts on their sleeves, which is practically required of musicians. But with some instruction, she said she believes anyone can learn how to express themselves.

?You have to live a life that has meaning,? Whittaker said. ?You have to live life large, and then you just play it large. I want to be able to share that and teach students how they can get in touch with that part of themselves.?

Whittaker?s most sincere example of student transformation comes from several years ago, when a down-and-out high school student, who had run away from home, was still attending her saxophone lessons despite living on the streets.

?I just hung in there with her, I kept teaching her,? Whittaker said. ?It was the one thread that held her from falling off. For some [students], this is what they do. We?ve got to let them do it. It?s so important.?

Whittaker said the importance of arts education is what drives her to keep teaching.

?It is important on so many levels for someone to study this,? she said. ?It?s one of the few things that we do that has delayed gratification.?It teaches the concept of how wonderful it is to achieve something after you?ve worked so hard and so long for it.?

Department of Music, Elon University Saxophone Studio, featured, saxophone, Virginia Novine-Whittaker

About Rebecca Iannucci

Rebecca Iannucci is the Arts & Entertainment Editor for The Pendulum. She is a print and online journalism major from Nutley, N.J. She has previously worked with the organization as a Copy Editor and reporter. View all posts by Rebecca Iannucci ?

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Source: http://elonpendulum.com/2012/09/music-professor-inspires-success-through-commitment-passion/

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