Protein origami: Quick folders are the best

Jan. 31, 2013 ? The evolutionary history of proteins shows that protein folding is an important factor. Especially the speed of protein folding plays a key role. This was the result of a computer analysis carried out by researchers at the Heidelberg Institute for Theoretical Studies (HITS) and the University of Illinois at Urbana Champaign. For almost four billions of years, there has been a trend towards faster folding. "The reason might be that this makes proteins less susceptible to clumping, and that they can carry out their tasks faster," says Dr. Frauke Gr?ter (HITS) who led the analysis.

The results were now published in PLoS Computational Biology.

Proteins are elementary building blocks of life. They often perform vital functions. In order to become active, proteins have to fold into three-dimensional structures. Misfolding of proteins leads to diseases such as Alzheimer's or Creutzfeld-Jakob. So which strategies did nature develop over the course of evolution to improve protein folding?

To examine this question, the chemist Dr. Frauke Gr?ter (Heidelberg Institute for Theoretical Studies) looked far back into the history of Earth. Together with her colleague Prof. Gustavo Caetano-Anolles at the University of Illinois at Urbana-Champaign, she used computer analyses to examine the folding speed of all currently known proteins. The researchers have seen the following trend: For most of protein evolution, the folding speed increased, from archaea to multicellular organisms. However, 1.5 billion years ago, more complex structures emerged and caused a biological 'Big Bang'. This has led to the development of slower-folding protein structures. Remarkably, the tendency towards higher speed in protein origami overall dominated, regardless of the length of amino acid chains constituting the proteins. "The reason for higher folding speed might be that this makes proteins less susceptible to aggregation, so that they can carry out their tasks faster," says Dr. Frauke Gr?ter, head of the Molecular Biomechanics research group at HITS.

Genetics and biophysics for large volumes of data

In their work, the researchers used an interdisciplinary approach combining genetics and biophysics. "It is the first analysis to combine all known protein structures and genomes with folding rates as a physical parameter," says Dr. Gr?ter. The analysis of 92,000 proteins and 989 genomes can only be tackled with computational methods. The group of Gustavo Caetano-Anolles, head of the Evolutionary Bioinformatics Laboratory at Urbana-Champaign, had originally classified most structurally known proteins from the Protein Database (PDB) according to age. For this study, Minglei Wang in his laboratory identified protein sequences in the genomes, which had the same folding structure as the known proteins. He then applied an algorithm to compare them to each other on a time scale. In this way, it is possible to determine which proteins became part of which organism and when.

After that, Cedric Debes, a member of Dr. Gr?ter's group, applied a mathematical model to predict the folding rate of proteins. The individual folding steps differ in speed and can take from nanoseconds to minutes. No microscope or laser would be able to capture these different time scales for so many proteins. A computer simulation calculating all folding structures in all proteins would take centuries to run on a mainframe computer. This is why the researchers worked with a less data-intensive method. They calculated the folding speed of the single proteins using structures that have been previously determined in experiments: A protein always folds at the same points. If these points are far apart from each other, it takes longer to fold than if they lie close to each other. With the so-called Size-Modified Contact Order (SMCO), it is possible to predict how fast these points will meet and thus how fast the protein will fold, regardless of its length. "Our results show that in the beginning there were proteins which could not fold very well," Dr. Gr?ter summarizes. "Over time, nature improved protein folding so that eventually, more complex structures such as the many specialized proteins of humans were able to develop."

Shorter and faster for evolution

Amino acid chains, which make up proteins, also became shorter over the course of evolution. This was another factor contributing to the increase in folding speed, as has been shown in the study. "Since eukaryotes, i.e. organisms with a cell nucleus, emerged, protein folding became somewhat less crucial," says Frauke Gr?ter. Since then, nature has developed a complex machinery to prevent and repair misfolded proteins. One example are the so-called chaperones. "It seems as if nature would accept a certain level of disorder in order to develop structures which could not have evolved otherwise."

The number of known genomes and protein structures is continually increasing, thus expanding the data bases for further computer analyses of protein evolution. Frauke Gr?ter says "With future analyses of protein evolution, it might be possible for us to answer the related question whether proteins became more stable or more flexible over their billion-year-long history of evolution." The study was supported by the Klaus Tschira Foundation and the National Science Foundation of the US.

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Story Source:

The above story is reprinted from materials provided by Heidelberg Institute for Theoretical Studies.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

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Journal Reference:

1. C?dric Deb?s, Minglei Wang, Gustavo Caetano-Anoll?s, Frauke Gr?ter. Evolutionary Optimization of Protein Folding. PLoS Computational Biology, 2013; 9 (1): e1002861 DOI: 10.1371/journal.pcbi.1002861

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

Source: http://feeds.sciencedaily.com/~r/sciencedaily/computers_math/information_technology/~3/4WPLz0EByD4/130131084421.htm

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Sports Scoreboard 1-26

Sports Scoreboard 1-26

?Boy?s basketball

?Tamaqua?71 Palmerton 34

?North Schuylkill 64 Marian Catholic 36

?Athens 56 Notre Dame of Elmira 55

?Pittston Area 56 Berwick 36

?#8 St. John Neumann 73 Millville 56

?#1 Williamsport 67 White Plains NY 58

?Sullivan County 44 Muncy 41

?Hughesville 62 Prep Charter 46

?Girl?s basketball

?Minersville 80 Jim Thorpe 32

?Riverside 41 West Scranton 37

?Wrestling

?Wyoming Valley West 50 Berwick 27

?Bald Eagle Area 43 Shikellamy 24

?Women?s College basketball

?Keystone 67 Valley Forge Christian 66

?California of Pa 71 Lock Haven 60

?Delaware Valley 63 Wilkes 53

?Desales 63 King?s 48

?FDU-Florham 64 Misericordia 35

?Marywood 75 Notre Dame of Maryland 27

?Bucknell 62 Holy Cross 59

?Widener 80 Lycoming 59

?Drew 67 Susquehanna 48

?Shippensburg 74 ESU 55

?West Chester 65 Bloomsburg 59

?Lackawanna 72 CC of Philadelphia 60

?Scranton 65 Juniata 58

?Men?s College basketball

?#14 Ohio State 65 Penn State 51

?DeSales 73 King?s 61

?Delaware Valley 67 Wilkes 54

?Lycoming 88 Widener 71

?Misericordia 71 FDU-Florham 57

?California of Pa. 81 Lock Haven 67

?West Chester 88 Bloomsburg 82 OT

?ESU 99 Shippensburg 56

?Cabrini 95 Keystone 79

?Marywood 84 Cairn 70

?Immaculata?57 Baptist Bitle 56

?Susquehanna 74 Drew 66

?Bucknell 65 Holy Cross 58

?American Hockey League

?WBS Penguins 3 Toronto 1

Source: http://columbiacounty.wnep.com/news/news/143616-sports-scoreboard-1-26

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From pets to 'recess': High school stress relief

In this Jan. 14, 2013 photo, a student pets Junie, the school's "therapy dog," at Prospect High School in Mt. Prospect, Ill. Stress, anxiety and panic attacks are on the rise at many U.S. high schools, due to heightened academic expectations and troubles at home made worse by the shaky economy. So some schools are trying unconventional methods, such as therapy dogs, to help students cope. (AP Photo/Martha Irvine)

In this Jan. 14, 2013 photo, a student pets Junie, the school's "therapy dog," at Prospect High School in Mt. Prospect, Ill. Stress, anxiety and panic attacks are on the rise at many U.S. high schools, due to heightened academic expectations and troubles at home made worse by the shaky economy. So some schools are trying unconventional methods, such as therapy dogs, to help students cope. (AP Photo/Martha Irvine)

In this Jan. 14, 2013 photo, Junie, a "therapy dog" at Prospect High School, sits in a classroom at the school in Mt. Prospect, Ill. The 18-month-old golden retriever is one way this school is trying to help students cope with a rise in stress, anxiety and panic attacks. Many say these issues are a problem in schools across the country. (AP Photo/Martha Irvine)

In this Jan. 14, 2013 photo, Junie, a "therapy dog" at Prospect High School, lies on the floor in a classroom in Mt. Prospect, Ill. The 18-month-old golden retriever is one way this school is trying to help students cope with a rise in stress, anxiety and panic attacks. Many say these issues are a problem in schools across the country. (AP Photo/Martha Irvine)

In this Jan. 14, 2013 photo, Douglas Berg, a social worker at Prospect High School, watches as a student pets Junie, the school's "therapy dog," at the Mt. Prospect, Ill. school. Stress, anxiety and panic attacks are on the rise at many U.S. high schools, due to heightened academic expectations and troubles at home made worse by the shaky economy. So some schools are trying unconventional methods, such as therapy dogs, to help students cope. (AP Photo/Martha Irvine)

In this Jan. 14, 2013 photo, Douglas Berg, a social worker at Prospect High School, left, and guidance counselor Lynn Thornton stand in the school's office with Junie, a "therapy dog," at the school in Mt. Prospect, Ill. Stress, anxiety and panic attacks are on the rise at many U.S. high schools, due to heightened academic expectations and troubles at home made worse by the shaky economy. So some schools are trying unconventional methods, such as therapy dogs, to help students cope. (AP Photo/Martha Irvine)

MT. PROSPECT, Ill. (AP) ? The four-legged member of the counseling team at the high school in suburban Chicago waits patiently, as a crush of students fills the hallways. Her tail wags with the first pat on the head, then another and another.

"Puppy! Ohhh, puppy dog!" one teenager croons, as he affectionately tousles the ears of the 18-month-old golden retriever. Junie began her role as a "therapy dog" at Prospect High School less than four months ago.

It's just one of a number of ways high schools across the country are trying to address what some call an epidemic of stressed-out, overwhelmed students.

Some schools now offer yoga classes or teach relaxation techniques in the classroom. Others, from California to Minnesota and New Jersey, are instituting homework-free nights or are offering a bit of free time between classes ? the equivalent of recess for teenagers.

In Maine, at least two high schools have converted classrooms into "wellness rooms" staffed by volunteer professionals who offer massage therapy and other stress-reducing treatments for students, with parental permission.

The idea is to help them slow down and cope with their problems in an overpacked, 24-7 world, where many students stay up late to finish homework and fall asleep with their cellphones in their hands.

"Things cycle for them so quickly. So it's hard for them to be able to develop the patience, or the ability to think something through and to realize that it may take some time for it to get resolved," says Douglas Berg, a social worker at Prospect High, where he and other staff are seeing more students hospitalized with anxiety and panic attacks related to stress.

Some might question whether a dog in the school corridors, or a 20-minute break, addresses the deeper issues at hand. But many school officials say they have to do what they can to alleviate the growing pressure to achieve. That pressure, they say, has only been heightened by the commonly held belief that it's tougher than ever for a young person to make it in this economy.

More than ever, a college degree is seen as a must. So more students are taking college courses in high school, and even more are enrolling in rigorous "advanced placement," or AP classes to try to earn college credit. Add year-round sports and after-school jobs and volunteering, as a way to bolster the college application, and many students say they have little time for anything else.

"There's just too much," says Lexi Botts, a senior at Prospect High who sought comfort from Junie and, ultimately, school counselors after her grandfather's death last fall.

The intensity of school has become so great, says one mom in Paoli, Pa., that she and her family have dubbed the senior year of high school "the crying year."

"When does a child get to be a child anymore?" said Carol Meerschaert. "I fear how they will burn out when the pressure has been on them since elementary school."

Abbie Kaplan, a junior at the Boston Latin School ? a public high school that requires students to take an exam for entry ? knows what she means.

On a scale of 1 to 10, she places her stress level at a pretty steady 9. She regularly has four hours of homework a night, some done before swim practice. She eats dinner around 9:30 p.m., then finishes the rest of her homework and generally goes to bed at 11:30. Then she's up at 6 a.m. so she can be at school by 7:45.

She calls her hectic schedule "the new normal."

"You keep telling yourself that it will prepare you for the future," Kaplan says. "It's just sort of how it is."

She, too, has had anxiety attacks related to her workload, she says. And some parents say school shootings, including the recent massacre in Newtown, Conn., only worsen the stress.

"My son came home from school and said, 'I'm really worried this could happen at our school,'" says Jane Robertson, a mother of a 16-year-old in Belfast, Maine. She's also a chiropractor, who helped start one of the wellness rooms in her area. The first one opened in Camden, Maine, after a spate of suicides more than 10 years ago, she said.

Overall, a recent national survey of adolescent mental health found that about 8 to 10 percent of teens ages 13 to 18 have an anxiety disorder. And of those teens, only 18 percent received mental health care, according to the National Institute of Mental Health.

School officials across the country, meanwhile, say they're seeing a steady uptick in mental health referrals, often stress-related. Timothy Dorway, a principal at a high school in Chanhassen, Minn., just outside Minneapolis, is among them. He says such referrals have doubled since his school opened in 2009.

"We're asking these kids to do things that we don't even ask adults to do," Dorway says, noting sports and academic requirements that often leave them sleep-deprived.

Besides the mental health issues, he noted that students from his school have been in car accidents after falling asleep at the wheel ? one of them on the way to school, at 7:45 a.m.

All of it led him and his school community to come up with a motto ? "Balance, Perspective, Growth" ? and to look for ways to put it into practice.

Now, Chanhassen High is among a small but growing number of schools that has homework-free nights scattered throughout the school year. Two days a week, students at Chanhassen also get a 20-minute "recess" break in the morning. Some play hackie sack or grab a snack. They chat in the hallways, catch up on homework or rest.

The break is a time "to let all the information of the day settle in my mind," says Zach Anderson, a junior at the school. "We need time to think."

The changes at the school have not come without controversy. A few parents see the break as a waste of time that could be better used at the beginning of the school day.

"Let them sleep in, or get a better breakfast, or come to school at the usual time to talk to a teacher if they need to," says Karrie Shroyer, a mom of a sophomore at Chanhassen High.

When it comes to homework, she says the school would better serve students by cutting back on what some view as an inordinate amount of "busy work," repetitive work that students who've mastered the concepts may not need to do.

"Are we trying to hide the real problem with a simple fix?" Shroyer asks.

Raychelle Lohmann, a professional counselor and author based in South Carolina, says any step schools take to reduce stress for students is a "step in the right direction."

But she says parents, too, need to keep their own expectations in check, even for young children.

"We're seeing parents who are putting their preschoolers in tutoring programs," she says. "The intentions are good. But we're missing the important point, to let them develop and play" ? even in high school.

She says parents also have to model the behavior for their children.

"I'll be honest. I'm guilty. I don't take a day off," she says. "But at some point, we just have to stop ? and prioritize ? and teach our children to do the same.

"We have to give up this 'go, go, go' mentality."

Lisa Lawrence, a mom in Austin, Texas, said she realized this when her daughter, now a sixth-grader, told her she felt like "nothing she did was ever good enough" for her mom.

"It sent chills down my spine," Lawrence says. "I think I felt that way growing up."

So she's backed off. And so has Dorway, the principal in Minnesota who's also a dad.

After his son's seventh-grade band concert last year, he recalls watching three kids "running down the hall, literally stripping out of their band uniforms with basketball uniforms underneath."

"This is insane," he says. So once the homework issue is further examined, he's vowing to take on the "holy grail" of issues at his school ? the packed practice and game schedules of student athletes.

Back at Prospect High in suburban Chicago, counselor Lynn Thornton ponders the question of expectations, as she pets Junie, who is sitting next to her in a school counseling office.

Educators are feeling the pressure to perform, too, she says. And while raising standards can be good thing, she wonders if we've taken things too far by making "high school the new college."

"I really don't see it changing," Thornton says, "until maybe colleges would really step up and say, 'Hey, you know what? You guys teach high school and we'll teach college."

Until then, students will find Junie at their beck and call, often on the counseling office couches.

___

Martha Irvine is an AP national writer. She can be reached at mirvine(at)ap.org or at http://twitter.com/irvineap

___

AP reporter Jeff Baenen in Minneapolis contributed to this report.

Associated Press

Source: http://hosted2.ap.org/APDEFAULT/386c25518f464186bf7a2ac026580ce7/Article_2013-01-31-Stressed%20Students/id-4b2010592ccb438eada9236fb1845603

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USCCB, in Supreme Court briefs, defends marriage as union of man ...

CWN - January 30, 2013

As the Supreme Court considers the constitutionality of the Defense of Marriage Act and Proposition 8, the United States Conference of Catholic Bishops (USCCB) has filed briefs in their defense.

Arguing in defense of the federal Defense of Marriage Act, the USCCB brief noted that

there is no fundamental right to marry a person of the same sex. Such a claim must be rejected because it does not satisfy the test to which this Court adheres in determining whether an asserted right is fundamental. Specifically, civil recognition of same-sex relationships is not deeply rooted in the Nation?s history and tradition?quite the opposite is true. Nor can the treatment of such relationships as marriages be said to be implicit in the concept of ordered liberty, such that neither liberty nor justice would exist if they were sacrificed ? This Court?s decisions describing marriage as a fundamental right plainly contemplate the union of one man and one woman.

The USCCB brief also argued that ??sexual orientation? is not a classification that should trigger heightened scrutiny,? as discrimination on the basis of sex or race would. Homosexual behavior ?is not a trait attributable from conception or birth,? the brief states, adding:

Elevation of sexual orientation to a quasi-suspect class would immerse federal courts into a quagmire of family law issues reserved to the states, issues for which the Judicial Branch is not institutionally suited ? Application of heightened scrutiny would hinder the ability of legislatures to create accommodations for those with religious or moral objections to homosexual conduct.

?The claim that homosexual persons today have ?no ability to attract the attention of the lawmakers? is frivolous,? the brief added.

The brief concluded:

If this Court were to conclude that the Constitution requires a redefinition of marriage to include persons in same-sex relationships?a requirement that we believe cannot reasonably be inferred from the Constitution?it is unclear where the logical stopping point would be. This Court will ultimately be asked why other interpersonal relationships are not entitled to similar inclusion, and why other ?barriers? to marriage (such as those posed by youth, kinship, or multiplicity of parties) should not also have to be struck down as inconsistent with this redefinition.

In its defense of Proposition 8 ? the 2008 California ballot initiative defining marriage as the union of a man and a woman ? the USCCB argued that

first, as a matter of simple biology, the union of one man and one woman is the only union capable of creating new life. Second, the People of California could reasonably conclude that a home with a mother and a father is the optimal environment for raising children, an ideal that Proposition 8 encourages and promotes. Given both the unique capacity for reproduction and unique value of homes with a mother and father, it is reasonable for a State to treat the union of one man and one woman as having a public value that is absent from other intimate interpersonal relationships.

?Proposition 8 is not rendered invalid because some of its supporters were informed by religious or moral considerations,? the brief continued. ?Many, if not most, of the significant social and political movements in our Nation?s history were based on precisely such considerations.?

?The current debate specifically concerns the meaning of marriage and the proposal to redefine marriage, not the phenomenon of same-sex attraction and the persons who experience such attraction,? the brief added. ?For this reason, the suggestion that opposition to the redefinition of marriage is equivalent to an animus against people who experience same-sex attraction is particularly offensive and plainly wrong ? The further suggestion that opposition to homosexual conduct is simply animus against persons who engage in such conduct is also erroneous and offensive.?

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Source: http://www.catholicculture.org/news/headlines/index.cfm?storyid=16943

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Just Moved? Get to Know Your New City : Ardor New York Real ...

By Rehna on January 30th, 2013

Moving is tough. Even with all the excitement it usually brings (you?re relocating for a new job, you?re closer to family, you moved in with your girlfriend) a new city can be pretty intimidating. But as soon as you unpack most of your belongings and find a few seconds to explore, here are a few things you want to do:

1.) Pick up a local newspaper or magazine. Local newspapers and magazines are your source for all your local news. Sure the national papers will have more information about what?s going on in the world, but these little tidbits will contain information about new community developments like that brand new dog park that opened last week or a list of concerts going on this weekend. They might have an article about a local eatery that?s been around forever or one that?s just opening.

2.) Take a class. Now is the time for a clean slate! So many people avoid taking classes about things they?re interested in because they feel embarrassed about who they might see there. Always wanted to learn how to dance? Take a class! You?ll not only meet plenty of like-minded people but will also develop a new skill. That?s the best of both worlds!

3.) Pick up where you left off in your old city. Were you in a book club every Sunday? Hit the gym a few times a week? Do the same in your new city. Find a local book club or a gym or whatever it is and dive right into your old schedule. Besides meeting new people you?ll probably start to feel a little more relaxed and at home in your old habits.

4) Get out and about. One of the most frustrating things about moving to a new city (at least for me, anyway) is not knowing where everything is. In general, no one looks for a hardware store until you need one, and searching for 30 minutes just adds added stress onto whatever project you were in the middle of in the first place. So take some time and drive/walk/bike around town to find a few staples. Grocery stores, the police station and hospital, the hardware store, a decent autoshop, a few parks, the gym, your church, where you?ll be going to work and other places you might need to know.

5.) Hit the tourist spots. It sounds silly, but you live here now! It?s as insane to live in New York City and never see the Statue of Liberty as it is to live in Montana and never see Glacier National Park. Whatever city you?re in is sure to have some tourist spots or at least a few nearby, so take a day or a weekend and check them out! Plus, it really gives you something to do when people come to visit and you don?t quite know your way around yet.

Source: http://www.ardorny.com/blog/index.php/2013/01/just-moved-get-to-know-your-new-city/

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White House blames Sandy, cuts for shrinking economy

President Barack Obama speaks about immigration reform Tuesday, Jan. 29, 2013, at Del Sol High School in Las Vegas.??It?s not our fault! The White House on Wednesday blamed the devastation from superstorm Sandy and disruptions from deep scheduled spending cuts as the economy shrank in the fourth quarter of 2012. The surprise 0.1-percent drop in gross domestic product (GDP) was the first such contraction since early 2009 when the country was in the grips of the Great Recession.

The chairman of President Barack Obama?s Council of Economic Advisers, Alan Krueger, said in a post on the official White House blog that the bad news came ?amid signs that Hurricane Sandy disrupted economic activity and Federal defense spending declined precipitously, likely due to uncertainty stemming from the sequester.?

That law will slash some $1.2 trillion in spending over ten years by targeting domestic and defense programs with across-the-board cuts. Obama and Republicans in Congress have been starkly at odds over how bets to replace the sequester with less disruptive debt-battling measures. The president has said spending cuts must be paired with tax revenue increases, something Republicans oppose.

Republican Senate Minority Leader Mitch McConnell renewed the GOP?s calls for spending cuts, urging a look into ?the dark corners that often evade real scrutiny? on a mission to make government programs more efficient and scrap those that don?t work.

?We need to root out waste, which will serve as the first real test of Democrats? seriousness in this debate,? he said.

?Why is the federal government funding Chinese studies on pig manure, and research into the smoking habits of Jordanian college students, and reality TV shows in India? Are Democrats prepared to cut this kind of waste?,? he said on the Senate floor.

Krueger took pains to defend Obama?s first-term economic record, stressing that ?over the last fourteen quarters, the economy has expanded 7.5 percent overall,? and touting private sector growth, investment, and consumption. Over all of 2012, the economy grew 2.2 percent. And economists largely agreed with the White House's take on the impact of Sandy and spending cuts.

?Federal defense purchases declined at an annual rate of 22.2 percent in the fourth quarter of 2012, the largest quarterly decline in 40 years,? Krueger said. ?The decline in government spending across all levels reduced real GDP by 1.33 percentage points in the quarter.?

Sandy also played a role, Krueger said, notably by disrupting trade, ?although a precise estimate of the effect of the hurricane on GDP is not available.?

Krueger also warned Congress against dealing the economy any ?self-inflicted wounds.?

Source: http://news.yahoo.com/blogs/ticket/white-house-blames-sandy-spending-cuts-economy-shrinks-152505590--politics.html

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McCain: Immigration reform failure would cost GOP

WASHINGTON (AP) ? Sen. John McCain is warning fellow Republicans that failure to pass comprehensive immigration legislation could mean continued election losses for the GOP, as Republican-friendly states like Arizona fall to the Democrats.

The Arizona Republican, one of eight senators to sign onto a bipartisan immigration reform framework this week, says failure to act means the trend of Hispanic defections from the GOP would continue.

Latino voters supported President Barack Obama in large numbers in November, helping to ensure his victory.

McCain said that the demographics of states like Arizona with growing Hispanic populations "means that we will go from Republican to Democrat over time."

McCain spoke alongside Democratic Sen. Charles Schumer of New York at a breakfast hosted by Politico on Wednesday.

Source: http://news.yahoo.com/mccain-immigration-reform-failure-cost-gop-140826315--politics.html

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