Monday, April 1, 2013

DNA: How to unravel the tangle

Monday, April 1, 2013

A research coordinated by the scientists at SISSA of Trieste has now developed and studied a numeric model of the chromosome that supports the experimental data and provides a hypothesis on the bundle's function.

A chromosome spends most of its life "diluted" in the nuclear cytoplasm. To the untrained eye it may look like a randomly entangled thread, yet biologists claim the opposite: although a chaotic component does exist in the bundle, experimental measurements have identified regions that tend to contain specific genes. Thanks to such measurements, researchers have obtained maps of the chromosome in its diluted form, the one in which the DNA transcription processes occur.

Cristian Micheletti, a physicist of SISSA, the International School for Advanced Studies of Trieste, has coordinated an international research team - in which Marco Di Stefano and Angelo Rosa stand out - that has devised an ingenious method which, on one hand, has allowed to verify the already known experimental measures and, on the other, to find data in support of a theory which explains why the DNA bundle is arranged in regions. "Employing the vast amount of publicly available data on gene expression, we have identified families of genes co-regulated within a chromosome" explains Micheletti. The co-regulated genes codify "in accord", but how such synchronization occurs is a mystery, since often the genes are located very far from one another on the DNA filament. "Two main hypotheses may be considered: either 'messengers' exist that travel back and forth from one gene to the other and coordinate the activity, or the DNA filament folding up inside the tangle brings the genes belonging to the same family physically close."

On the basis of the second assumption Micheletti and his colleagues have used the computer to induce the DNA numeric model to bring the co-regulated genes closer. "The outcome of the simulation has provided a map of chromosome arrangement that is very close to the one obtained through experimentation," explains Micheletti. "Besides, the model has successfully brought closer the genes belonging to the same family, as we had asked for, in 80% of cases, that is without too much effort, which corroborates the validity of the hypothesis and the effectiveness of the simulation."

The article was chosen by PLOS Computational Biologyjournal as the cover story for the March issue.

###

International School of Advanced Studies (SISSA): http://www.sissa.it

Thanks to International School of Advanced Studies (SISSA) for this article.

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Source: http://www.labspaces.net/127533/DNA__How_to_unravel_the_tangle

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Nerds vs. Hipsters: Reddit Photo Explains It All

A lot of people describe themselves as nerds these days who really aren't. They're hipsters. But if you have a hard time differentiating, no one can blame you as there are plenty of similarities. Nevertheless, there are a few hipster tells.

Redditor moson posted this helpful image that clearly outlines the differences between nerds and hipsters. Fun fact: the original photo is of actual, honest-to-god scientist nerds from Poland. Hooray!

nerdsvshipsters

Via Reddit

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Source: http://www.huffingtonpost.com/2013/03/30/nerds-vs-hipsters-reddit_n_2985070.html

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2 in China first known deaths from H7N9 bird flu

BEIJING (AP) ? Two Shanghai men have died from a lesser-known type of bird flu in the first known human deaths from the strain, and Chinese authorities said Sunday that it wasn't clear how they were infected, but that there was no evidence of human-to-human transmission.

A third person, a woman in the nearby province of Anhui, also contracted the H7N9 strain of bird flu and was in critical condition, China's National Health and Family Planning Commission said in a report on its website.

There was no sign that any of the three, who were infected over the past two months, had contracted the disease from each other, and no sign of infection in the 88 people who had closest contact with them, the medical agency said.

H7N9 bird flu is considered a low pathogenic strain that cannot easily be contracted by humans. The overwhelming majority of human deaths from bird flu have been caused by the more virulent H5N1, which decimated poultry stocks across Asia in 2003.

The World Health Organization is "closely monitoring the situation" in China, regional agency spokesman Timothy O'Leary said in Manila.

"There is apparently no evidence of human-to-human transmission, and transmission of the virus appears to be inefficient, therefore the risk to public health would appear to be low," O'Leary said.

One of the two men from Shanghai, who was 87, became ill on Feb. 19 and died on Feb 27. The other man, 27, became ill on Feb. 27 and died on March 4, the Chinese health commission said. A 35-year-old woman in the Anhui city of Chuzhou became ill on March 9 and is being treated.

The Chinese Center for Disease Control and Prevention conducted tests and confirmed Saturday that all three cases were H7N9, the health commission said.

Scientists have been closely monitoring the H5N1 strain of the virus, fearing that it could mutate into a form that spreads easily among people, potentially sparking a pandemic. So far, most human cases have been connected to contact with infected birds.

Source: http://news.yahoo.com/2-china-first-known-deaths-h7n9-bird-flu-092118642.html

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Kobe passes Wilt for 4th on NBA scoring list

SACRAMENTO, Calif. (AP) ? Kobe Bryant has passed fellow Los Angeles Lakers great Wilt Chamberlain for fourth place on the NBA's career scoring list.

Bryant made a pull-up jumper from the free throw line with 7:54 remaining in the second quarter to eclipse Chamberlain's mark of 31,419 points. He tied Chamberlain 22 seconds earlier with a layup.

Bryant entered the game four points behind Chamberlain.

Kareem Abdul-Jabbar tops the NBA's career scoring list with 38,387 points, Karl Malone is second with 36,928 and Michael Jordan is third with 32,292.

The 34-year-old Bryant is in his 17th season ? all with the Lakers.

Source: http://news.yahoo.com/kobe-passes-wilt-4th-nba-scoring-list-030255554--spt.html

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Patients of Okla. doctor line up for tests

TULSA, Okla. (AP) ? Hundreds of patients of an Oklahoma oral surgeon accused of unsanitary practices showed up at a health clinic Saturday, looking to find out whether they were exposed to hepatitis or the virus that causes AIDS.

Letters began going out Friday to 7,000 patients who had seen Dr. W. Scott Harrington during the past six years, warning them that poor hygiene at his clinics created a public health hazard. The one-page letter said how and where to seek treatment but couldn't explain why Harrington's allegedly unsafe practices went on for so long.

Testing for hepatitis B, hepatitis C and the virus that causes AIDS began at 10 a.m. Saturday, but many arrived early and stood through torrential downpours. The Tulsa Health Department said 420 people were tested Saturday at its North Regional Health and Wellness Center. Screenings resume Monday morning.

Kari Childress, 38, showed up at 8:30 a.m., mainly because she was nervous.

"I just hope I don't have anything," said Childress, who had a tooth extracted at one of Harrington's two clinics five months ago. "You trust and believe in doctors to follow the rules, and that's the scariest part."

Inspectors found a number of problems at the doctor's clinics in Tulsa and suburban Owasso, according to the state Dentistry Board, which filed a 17-count complaint against Harrington pending an April 19 license revocation hearing. According to the complaint, needles were reinserted into drug vials after being used on patients, expired drugs were found in a medicine cabinet and dental assistants, not the doctor, administered sedatives to patients.

One patient, Orville Marshall, said he didn't meet Harrington until after he had two wisdom teeth pulled about five years ago at the Owasso clinic. A nurse inserted the IV for his anesthesia; Harrington was there when Marshall came to.

"It's just really scary. It makes you doubt the whole system, especially with how good his place looked," said Marshall, 37.

An instrument set reserved for use on patients with infectious diseases was rusty, preventing its effective sterilization, and the office autoclave ? a pressurized cleaner ? was used improperly and hadn't been certified as effective in at least six years, according to the complaint.

Dr. Matt Messina, a Cleveland dentist and a consumer adviser for the American Dental Association, said creating a safe and hygienic environment is "one of the fundamental requirements" before any dental procedure can be performed.

"It's not hard. It just takes effort," he said.

Weekly autoclave testing can be performed for less than $400 annually, according to the website of the Autoclave Testing Services of Pearl River, New York.

Autoclaves typically can be purchased for $1,000 to $8,000, depending on their size and features. And an average dental practice can expect to pay more than $40,000 a year in equipment, tools and supplies alone, according to several dental organizations.

Attempts to reach Harrington have been unsuccessful. No one answered the door Thursday at his Oklahoma home, which property records show is worth more than $1 million. His practice a few miles away, in a tony section of Tulsa where plastic surgeons operate and locals congregate at bistros and stores such as Saks Fifth Avenue, has a fair-market value of around $851,000.

Property and tax records show Harrington owns another residence in Carefree, Ariz., in an area of upscale homes tucked into in the boulder-strewn mountains north of Phoenix.

Nobody was at home Saturday at the low-slung, 1950s-style vacation home, across from the Boulders Resort. Neighbors said they had seen a lot of activity at the home in recent weeks.

Harrington's malpractice lawyer, Jim Secrest II, did not respond to phone messages left Thursday or Friday. A message at Harrington's Tulsa office said it was closed and an answering service referred callers to the Tulsa Health Department.

Suzy Horton, an old friend of Harrington's, said she can't believe the allegations about the man who removed two of her teeth in the early '90s. Horton's ex-husband sold Harrington his home in Carefree ? a home where she once lived.

"I've been to dentists my whole life, so I know what a professional office looks like," Horton, who now lives in Phoenix, said in a telephone interview. "His was just as professional as anybody."

Horton hasn't seen Harrington in years, but she said he has sent her a Christmas card and wreath every year since her 1999 divorce.

"It was a long time ago, so I suppose anything can change, but the kind of person they're portraying in the news is not the kind of person who sends you a Christmas" card, she said.

___

Associated Press writers Traci Carl in Carefree, Ariz., and Jeannie Nuss in Little Rock, Ark., contributed to this report.

Source: http://news.yahoo.com/patients-oklahoma-doctor-line-tests-204306341.html

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New models predict drastically greener Arctic in coming decades

Mar. 31, 2013 ? New research predicts that rising temperatures will lead to a massive "greening," or increase in plant cover, in the Arctic. In a paper published on March 31 in Nature Climate Change, scientists reveal new models projecting that wooded areas in the Arctic could increase by as much as 50 percent over the next few decades. The researchers also show that this dramatic greening will accelerate climate warming at a rate greater than previously expected.

"Such widespread redistribution of Arctic vegetation would have impacts that reverberate through the global ecosystem," said Richard Pearson, lead author on the paper and a research scientist at the American Museum of Natural History's Center for Biodiversity and Conservation.

Plant growth in Arctic ecosystems has increased over the past few decades, a trend that coincides with increases in temperatures, which are rising at about twice the global rate. The research team -- which includes scientists from the Museum, AT&T Labs-Research, Woods Hole Research Center, Colgate University, Cornell University, and the University of York -- used climate scenarios for the 2050s to explore how this trend is likely to continue in the future. The scientists developed models that statistically predict the types of plants that could grow under certain temperatures and precipitation. Although it comes with some uncertainty, this type of modeling is a robust way to study the Arctic because the harsh climate limits the range of plants that can grow, making this system simpler to model compared to other regions such as the tropics.

The models reveal the potential for massive redistribution of vegetation across the Arctic under future climate, with about half of all vegetation switching to a different class and a massive increase in tree cover. What might this look like? In Siberia, for instance, trees could grow hundreds of miles north of the present tree line.

"These impacts would extend far beyond the Arctic region," Pearson said. "For example, some species of birds seasonally migrate from lower latitudes and rely on finding particular polar habitats, such as open space for ground-nesting."

In addition, the researchers investigated the multiple climate change feedbacks that greening would produce. They found that a phenomenon called the albedo effect, based on the reflectivity of Earth's surface, would have the greatest impact on the Arctic's climate. When the sun hits snow, most of the radiation is reflected back to space. But when it hits an area that's "dark," or covered in trees or shrubs, more sunlight is absorbed in the area and temperature increases. This has a positive feedback to climate warming: the more vegetation there is, the more warming will occur.

"By incorporating observed relationships between plants and albedo, we show that vegetation distribution shifts will result in an overall positive feedback to climate that is likely to cause greater warming than has previously been predicted," said co-author Scott Goetz, of the Woods Hole Research Center.

This work was funded by the National Science Foundation, grants IPY 0732948, IPY 0732954, and Expeditions 0832782. Other authors involved in this study include Steven Phillips (AT&T Labs-Research), Michael Loranty (Woods Hole Research Center and Colgate University), Pieter Beck (Woods Hole Research Center), Theodoros Damoulas (Cornell University), and Sarah Knight (American Museum of Natural History and University of York).

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The above story is reprinted from materials provided by American Museum of Natural History, via EurekAlert!, a service of AAAS.

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


Journal Reference:

  1. Richard G. Pearson, Steven J. Phillips, Michael M. Loranty, Pieter S. A. Beck, Theodoros Damoulas, Sarah J. Knight, Scott J. Goetz. Shifts in Arctic vegetation and associated feedbacks under climate change. Nature Climate Change, 2013; DOI: 10.1038/nclimate1858

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/top_news/~3/_-wyLznOOuE/130331165603.htm

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Pope makes Easter pleas for Mideast peace

Pope Francis holds a San Lorenzo's soccer team jersey after celebrating his first Easter Mass in St. Peter's Square at the Vatican, Sunday, March 31, 2013. Pope Francis celebrated his first Easter Sunday Mass as pontiff in St. Peter's Square, packed by joyous pilgrims, tourists and Romans and bedecked by spring flowers.Wearing cream-colored vestments, Francis strode onto the esplanade in front of St. Peter's Basilica and took his place at an altar set up under a white canopy. (AP Photo/Alessandra Tarantino)

Pope Francis holds a San Lorenzo's soccer team jersey after celebrating his first Easter Mass in St. Peter's Square at the Vatican, Sunday, March 31, 2013. Pope Francis celebrated his first Easter Sunday Mass as pontiff in St. Peter's Square, packed by joyous pilgrims, tourists and Romans and bedecked by spring flowers.Wearing cream-colored vestments, Francis strode onto the esplanade in front of St. Peter's Basilica and took his place at an altar set up under a white canopy. (AP Photo/Alessandra Tarantino)

Pope Francis hugs a child after celebrating his first Easter Mass in St. Peter's Square at the Vatican, Sunday, March 31, 2013. Pope Francis celebrated his first Easter Sunday Mass as pontiff in St. Peter's Square, packed by joyous pilgrims, tourists and Romans and bedecked by spring flowers.Wearing cream-colored vestments, Francis strode onto the esplanade in front of St. Peter's Basilica and took his place at an altar set up under a white canopy. (AP Photo/Gregorio Borgia)

Pope Francis, holding the pastoral staff, celebrates the Easter mass in St. Peter's Square at the Vatican, Sunday, March 31, 2013. "Our daily problems and worries can wrap us up in ourselves, in sadness and bitterness, and that is where death is," he said. "Let the risen Jesus enter your life, welcome him as a friend, with trust: he is life!" said Pope Francis during the Easter vigil. (AP Photo/Gregorio Borgia)

Pope Francis, holding the pastoral staff, walks past the closed icon of Jesus as he celebrates the Easter mass in St. Peter's Square at the Vatican, Sunday, March 31, 2013. "Our daily problems and worries can wrap us up in ourselves, in sadness and bitterness, and that is where death is," he said. "Let the risen Jesus enter your life, welcome him as a friend, with trust: he is life!" said Pope Francis during the Easter vigil. (AP Photo/Gregorio Borgia)

Pope Francis, holding the pastoral staff, celebrates the Easter mass in St. Peter's Square at the Vatican, Sunday, March 31, 2013. "Our daily problems and worries can wrap us up in ourselves, in sadness and bitterness, and that is where death is," he said. "Let the risen Jesus enter your life, welcome him as a friend, with trust: he is life!" said Pope Francis during the Easter vigil.(AP Photo/Gregorio Borgia)

(AP) ? Pope Francis delivered a plea for peace in his first Easter Sunday message to the world, decrying the seemingly endless conflicts in the Middle East and on the Korean peninsula after celebrating Mass at an outdoor altar before more than 250,000 people in flower-bedecked St. Peter's Square.

Francis shared in his flock's exuberance as they celebrated Christianity's core belief that Jesus Christ rose from the dead following crucifixion. After Mass, he stepped aboard an open-topped white popemobile for a cheerful spin through the joyous crowd, kissing babies and patting children on the head.

One admirer of both the pope and of the pope's favorite soccer team, Argentina's Saints of San Lorenzo, insisted that Francis take a team jersey he was waving at the pontiff. A delighted Francis obliged, briefly holding up the shirt, and the crowd roared in approval.

Francis has repeatedly put concern for the poor and suffering at the center of his messages, and he pursued his promotion of the causes of peace and social justice in the Easter speech he delivered from the central balcony of St. Peter's Basilica, the same vantage point above the square where he was introduced to the world as the first Latin American pope on March 13.

The Roman Catholic leader aimed his Easter greetings at "every house and every family, especially where the suffering is greatest, in hospitals, in prisons." Francis prayed that Jesus would inspire people to "change hatred into love, vengeance into forgiveness, war into peace."

As popes before him have, he urged Israelis and Palestinians to resume peace talks and end a conflict that "has lasted all too long." And, in reflecting on the two-year-old Syrian crisis, Francis asked, "How much suffering must there still be before a political solution" can be found?

The pope also expressed desire for a "spirit of reconciliation" on the Korean peninsula, where North Korea says it has entered "a state of war" with South Korea. He also decried warfare and terrorism in Africa, as well as what he called the 21st century's most extensive form of slavery: human trafficking.

The first pontiff to come from the Jesuits, an order with special concern for the poor, and the first pope to name himself after St. Francis, a medieval figure who renounced wealth to preach to the down-and-out, Francis lamented that the world is "still divided by greed looking for easy gain."

Earlier, wearing cream-colored vestments, Francis celebrated Mass on the esplanade in front of the basilica at an altar set up under a white canopy. He frequently bowed his head as if in silent reflection.

The sun competed with clouds in the sky Sunday, but the square was a riot of floral color in Rome, where chilly winter has postponed the blossoming of many flowers. Yellow forsythia and white lilies shone, along with bursts of lavender and pink, from potted azalea, rhododendron, wisteria and other plants.

Francis thanked florists from the Netherlands for donating the flowers. He also advised people to let love transform their lives, or as he put it, "let those desert places in our hearts bloom."

The Vatican had prepared a list of brief Easter greetings in 65 languages, but Francis didn't read them. The Vatican didn't say why not, but has said that the new pope, at least for now, feels at ease using Italian, the everyday language of the Holy See. Francis also has stressed his role as a pastor to his flock, and, as Bishop of Rome, Italian would be his language.

The pontiff improvised his parting words to the crowd. He repeated his Easter greeting to those "who have come from all over the world to this square at the heart of Christianity" as well as to those "linked by modern technology," a reference to TV and radio coverage as well as social media.

Francis added that he was especially remembering "the weakest and the neediest" and praying that all of humanity be guided along "the paths of justice, love and peace."

In another departure from Easter tradition, Francis won't be heading for some post-holiday relaxation at the Vatican's summer palace in Castel Gandolfo, in the hills southeast of Rome. That retreat is already occupied by his predecessor, Benedict XVI, who went there in the last hours of his papacy on Feb. 28. Benedict became the first pope in 600 years to resign from the position, and eventually is to move back to the Vatican, after a convent there is readied for him.

Francis so far has declined to move into Benedict's former apartment in the Apostolic Palace, into the rooms whose studio overlooks St. Peter's Square. He is still in the Vatican hotel where earlier this month he was staying along with other cardinals participating in the secret conclave to choose Benedict's successor.

While Francis has just begun to make his mark on the church, it is plain he has little desire to embrace much of the pomp customarily associated with the office.

Associated Press

Source: http://hosted2.ap.org/APDEFAULT/cae69a7523db45408eeb2b3a98c0c9c5/Article_2013-03-31-Vatican-Easter/id-c2101bf8bd25477caff866d640526422

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